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Articles in press have been peer-reviewed and accepted, which are not yet assigned to volumes/issues, but are citable by Digital Object Identifier (DOI).
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Label-free detection of microRNA by polymerization and isomerization cyclic amplification coupled with G/Hemin DNAzyme
Xinlan Zhu, Ziyan Zhang, Ruiyang Ma, Huachu Chen, Yi Zheng, Su Zeng, Zheyong Li, Sheng Cai
, Available online  , doi: 10.1016/j.jpha.2025.101536
Abstract:
A label-free detection technique for microRNA (miRNA) was developed based on target replacement cycling, polymerization and isomerization cyclic amplification (PICA), and G/Hemin DNAzyme signal output. The designed hairpin probe undergoes cyclic alternation of polymerization and isomerization catalyzed by Bst DNA polymerase, enabling target replacement cycling and continuous self-extension of single-stranded DNA (ssDNA) strands. This process generates abundant G-quadruplex sequences that bind to Hemin, achieving label-free detection of miRNA through catalytic reactions. Its key advantages include a specific primer self-extension mechanism that avoids spurious amplification, one step isothermal design simplifies workflow and enhances system robustness, adapting to diverse detection scenarios, and label-free detection strategy that substantially reduces cost. Therefore, it is poised to become a reliable tool for clinical miRNA analysis, offering potential guidance for the early diagnosis, treatment, and prognosis of tumor biomarkers.
Natural product-based strategies targeting inflammation in Alzheimer's disease: Mechanisms, drug delivery, and clinical trials
Gaoshuang Fu, Mingmin Pan, Qingling Sun, Guangxin Yue, Tong Lei
, Available online  , doi: 10.1016/j.jpha.2025.101535
Abstract:
Recent studies have shown that neuroinflammation plays a critical role in the pathogenesis of Alzheimer's disease (AD), exacerbating disease progression. Due to their multi-target mechanisms and favorable safety profiles, natural products have gradually emerged as a potential therapeutic strategy for modulating neuroinflammation and improving the symptoms in AD. This study aims to review the pharmacological mechanism and clinical application of natural products in the treatment of AD, and explore the drug delivery forms of natural products, such as self-assembly and nanoparticle loading. The natural products targeting neuroinflammation were summarized, such as Ginkgo biloba leaf extract, curcumin and resveratrol, and their mechanisms in ameliorating AD-related cognitive impairment. Additionally, it was highlighted the progress of clinical trials involving natural products for AD treatment, analyzing their potential in improving cognitive function, psychiatric symptoms, and slowing disease progression in AD patients. Finally, the challenges and future directions of natural products in AD therapy were discussed, emphasizing the importance of enhancing their bioavailability and developing novel drug delivery systems. This review may provide a theoretical foundation and practical reference for research on natural products targeting neuroinflammation to improve cognitive impairment and mental symptom in AD.
Development of A Novel NanoBRET High-Throughput Drug Screening Assay for Human GnRH Receptor Using Sulfo-cyanine 5 Fluorophore
Li Shen, Xiaozhe Du, Yakai Yang, Ming Su, Rong Rong, Jia Meng, Lee Wei Lim, David G. Fernig, Zhi-Liang Lu
, Available online  , doi: 10.1016/j.jpha.2025.101532
Abstract:
G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors and targets for over 30% of current clinical drugs, remain crucial for future therapeutic development. This study introduces a novel NanoLuciferase (NanoLuc, Nluc) bioluminescence resonance energy transfer (NanoBRET)-based ligand binding assay, utilizing the gonadotrophin-releasing hormone (GnRH) receptor as a model system. Our study demonstrates that sulfo-cyanine 5 (sCy5) is an ideal fluorophore compatible with NanoBRET, enabling sensitive measurement of ligand binding on living cell membranes. A novel GnRH analogue, sCy5-D-Lys6-GnRH, was synthesised by conjugating sCy5 on the substituted D-Lys6 of the native GnRH I. Substitution of Gly6 of GnRH I with sCy5-D-Lys6 stabilises the βII’ turn configuration of the decapeptide that exhibits high affinity and specificity for GnRH receptors while maintaining agonist activity. To address the characteristically low expression of the human GnRH receptor (hGnRHR), we engineered a modified receptor by fusing NanoLuc with an interleukin-6 secretory signal peptide (secNluc) to the N-terminus of the hGnRHR and deleting Lys191 (K191Δ) within the 2nd extracellular loop. This modification (N-secNluc-hGnRHR-K191Δ) significantly enhances receptor expression without altering ligand binding affinity, resulting in a robust BRET signal detection (Z' ≥ 0.5) between sCy5-D-Lys6-GnRH and the modified receptor. Our innovative approach using sCy5 to conjugate ligands offers several key advantages: high sensitivity and specificity, remarkably low non-specific binding (NSB), compatibility with live-cell assays, and suitability for high-throughput drug screening, which may accelerate the discovery of new therapeutics for GnRH receptor signal-selective drugs and potentially for other GPCRs.
Unveiling the Multifaceted Potential of Artemisia: Cutting-Edge Insights into Nutritional Benefits and Emerging Therapeutic Applications
Samy Selim, Mohammad Harun-Ur-Rashid, Soad K. Al Jaouni
, Available online  , doi: 10.1016/j.jpha.2025.101531
Abstract:
The Artemisia genus, comprising over 500 species, is a cornerstone of traditional and modern medicine due to its extensive phytochemical diversity and remarkable therapeutic properties. As highlighted in this review, Artemisia demonstrates exceptional potential across nutritional, therapeutic, and industrial domains. The genus is rich in bioactive compounds, including flavonoids, sesquiterpene lactones, and terpenoids, which exhibit potent antioxidant, anti-inflammatory, and antimicrobial effects. Its nutritional benefits are equally notable, with species like Artemisia annua and Artemisia absinthium providing macronutrients, essential minerals, and vitamins critical for metabolic health and immune support. This review systematically explores Artemisia's role in addressing chronic diseases, including its neuroprotective potential against Alzheimer's and Parkinson's disease through oxidative stress reduction and inflammatory pathway modulation. Furthermore, Artemisia's contributions to sustainable agriculture, functional foods, and cosmeceuticals underline its adaptability and economic significance. However, gaps in clinical validation, sustainable cultivation, and regulatory frameworks remain barriers to fully harnessing its potential. Future multidisciplinary research and ethical policies are essential to integrate Artemisia more effectively into global health and industry. The insights provided here aim to inspire innovation in the utilization of Artemisia as a transformative botanical resource for health, industry, and sustainability.
β-Caryophyllene confers protection against type 2 diabetic osteoporosis by blocking ferroptosis via the AMPK/Nrf2 pathway
Lai-lai Fan, Chun-hui Chen, Wen-hao Zheng, Li-jiang Han, Yi-tian Yu, Yi-yun Lv, Wen-lai Fang, Ling-ling Lin
, Available online  , doi: 10.1016/j.jpha.2025.101522
Abstract:
Type 2 diabetic osteoporosis (T2DOP) is a chronic bone disorder marked by increased fracture risk and osteonecrosis, exacerbated by a persistent high-glucose and high-fat (HGHF) environment, distinguishing it from postmenopausal osteoporosis. Ferroptosis, an iron-dependent form of programmed cell death caused by lipid peroxidation, plays a crucial role in the death of bone marrow mesenchymal stem cells (BMSCs) due to glucolipotoxicity. β-Caryophyllene (BCP), a natural bicyclic sesquiterpene found in essential oils, shows extensive pharmacological promise for various diseases. This study investigated BCP’s role and mechanisms in mitigating HGHF-induced ferroptosis. A murine T2DOP model was established via HGHF diet and streptozotocin injection, while BMSCs were cultured under HGHF conditions to mimic diabetic pathology in vitro. Our findings indicated that BCP mitigated HGHF-induced ferroptosis and bone loss, as shown by decreased mitochondrial reactive oxygen species, lipid peroxidation, and malondialdehyde levels, along with increased glutathione in vitro. BCP enhanced bone mass and increased levels of p-AMPK, GPX4, and osteogenic markers in distal femurs. Mechanistically, BCP activated the AMPK/Nrf2 pathway, and AMPK knockdown via siRNA abolished its protective effects in HGHF-exposed BMSCs. Collectively, BCP ameliorates T2DOP by inhibiting ferroptosis via AMPK/Nrf2 signaling activation and may have potential clinical applications.
Discovery and optimization of a novel non-nitrocatechol COMT inhibitor for modulating levodopa metabolism
Rong Zhu, Pu Wang, Sheng-Lan Qi, Yu Zhang, Chun-Lan Xie, Ya Yang, Cong Hu, Zi-Qiong Zhou, Dong-Fang Zhao, Chao Yang, Jie Sun, Xian-Wen Yang, Guang-Bo Ge, Ping Wang
, Available online  , doi: 10.1016/j.jpha.2025.101520
Abstract:
Human catechol-O-methyltransferase (COMT) is a key target for neuropsychiatric disorders. Inhibiting COMT to prevent levodopa metabolism is a crucial strategy for Parkinson’s disease treatment. While clinically used COMT inhibitors are primarily nitrocatechol-based, they often cause adverse effects, prompting efforts to develop safer non-nitrocatechol alternatives. In this study, baicalein ( BA ) was identified as a potent lead compound for COMT inhibition after screening a series of natural flavonoids using a fluorescence-based visualization inhibitor screening method. Subsequent multi-dimensional structural optimizations addressed the druggable deficiencies of BA , resulting in compound BA24 , which demonstrated a 26-fold increase in cellular COMT inhibition and approximately 10-fold improvements in metabolic stability, membrane permeability and oral bioavailability, respectively, compared to BA . Mechanistically, BA24 competitively inhibited COMT by binding to the catechol pocket with a Ki of 89.28 nM. Furthermore, BA24 exhibited favorable safety profiles and significantly modulated levodopa metabolism in rats. Additionally, the relationships between the structural properties, inhibitory activity and metabolic stability of flavonoids as COMT inhibitors were comprehensively investigated. Collectively, this work not only presents a novel non-nitrocatechol COMT inhibitor with favorable safety profiles and potent anti-COMT effects both in vitro and in vivo, but also provides valuable insights into optimizing the druggability of flavonoids as lead compounds.
Recent advances in proteomic strategies for target identification of traditional Chinese medicine
Xueyan Zhen, Jingwen Liu, Yan Ren
, Available online  , doi: 10.1016/j.jpha.2025.101516
Abstract:
Traditional Chinese medicine (TCM) has played an indispensable role in health intervention and disease treatment. Identifying the target proteins of TCM is crucial to clarifying therapeutic mechanisms. One approach taken to enhance the breadth, depth, and precision of studies on the active cellular pathways induced by TCM has been to use proteomics to reveal potential drug targets with direct interactions. Proteomic strategies facilitate identifying and characterizing target binding proteins relevant metabolism pathways, which involves enriching the complex of small molecule and their targets based on the affinity, as well as utilizing the changes in physicochemical properties of target proteins that occur due to drug binding for proteomic identification and quantification. Probe labeling and enrichment technologies have accelerated the field of chemical proteomics. Technologies focused on measuring the changes in target proteins have been widely extended into several different approaches, and these now drive the establishment of further strategies. This review summarizes the advances in proteomics strategies mainly based on mass spectrometry (MS) for the identification of TCM targets to the present. Enhancing the application of proteomics would provide a new viewpoint on TCM treatment, while underscores the potential of TCM as biological probes and sources of novel drug candidates.
Gut-Brain Axis Dysregulation in Parkinson’s Disease: Mechanisms Linking Microbiota to Neuroinflammation and α-Synuclein Pathology
Zhenxiong ZHAO, Mengdie DONG, Zhen MU, Zhencang ZHENG, Zhengwei ZHANG
, Available online  , doi: 10.1016/j.jpha.2025.101521
Abstract:
Parkinson’s disease (PD) is increasingly understood as a multisystem disorder originating not only in the central nervous system (CNS) but also involving the gut-brain axis (GBA). A key driver of PD pathogenesis is gut microbiota dysbiosis, which contributes to disease progression by inducing intestinal inflammation, altered microbial metabolite production, and compromised gut barrier integrity. These alterations can initiate the misfolding and aggregation of α-synuclein in the enteric nervous system (ENS), facilitating its spread to the CNS via vagal pathways. Furthermore, microbiota-derived molecules, including short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS), are implicated in triggering systemic and neuroinflammatory cascades that exacerbate the degeneration of dopaminergic neurons. This review consolidates current evidence on the mechanistic connections between gut microbiota dysregulation, neuroinflammation, and α-synuclein pathology in PD. We also discuss the translational potential of microbiota-focused biomarkers and innovative therapeutic strategies, providing new perspectives for early diagnosis and disease modification. Elucidating the GBA in PD paves the way for personalized medicine and microbiome-targeted therapies.
ERBB2 mutations promote recurrence and metastasis in non-muscle-invasive bladder cancer via HIF-1 phosphorylation: insights from whole exome sequencing
Xu Wang, Long Jin, Xinlin Zou, Ankang Zhu, Mingyu Li, Haitao Fan
, Available online  , doi: 10.1016/j.jpha.2025.101519
Abstract:
This study investigates the role of ERBB2 mutations in promoting recurrence and metastasis of non-muscle-invasive bladder cancer (NMIBC). Analysis of whole exome sequencing (WES) data from the The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases revealed a significant association between ERBB2 mutations and immune cell infiltration. To validate these findings, formalin-fixed, paraffin-embedded tumor tissues from patients with recurrent NMIBC were analyzed, with a focus on ERBB2 mutations. In addition, bladder cancer cell lines carrying wild type or mutant ERBB2 were established using clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) technology. Functional experiments, including Western blotting, protein stability assays, and ubiquitination analyses, demonstrated that ERBB2 mutations promote hypoxia-inducible factor-1 (HIF-1) phosphorylation, leading to its stabilization and enhancing the proliferative, migratory, and invasive capacities of tumor cells. Furthermore, flow cytometry, 5-ethynyl-2'-deoxyuridine (EdU), Cell Counting Kit-8 (CCK-8), and Transwell assays confirmed the impact of these mutations on cellular behavior, while drug sensitivity assays indicated increased susceptibility of ERBB2-mutant cells to therapeutic agents. In vivo studies using mouse models further supported these findings, showing that ERBB2 mutations promote tumor growth, metastasis, and macrophage infiltration. Collectively, these results suggest that ERBB2 mutations drive NMIBC progression by stabilizing HIF-1 through phosphorylation, thereby facilitating tumor development and immune modulation, and underscore the potential of ERBB2 as a therapeutic target for preventing NMIBC recurrence and metastasis.
SERS detection of osteoarthritis-linked microRNA-204 via a DNAzyme-catalyzed self-amplifying circuit
Zhe Ni, Xingshi Yuan, Zhengliang Luo, Xiaoqi Zhang, Min Chen, Lee Jia, Jie Wang, Xifu Shang
, Available online  , doi: 10.1016/j.jpha.2025.101518
Abstract:
Sensitive detection of microRNA-204 (miR-204) is critical for the early diagnosis and management of osteoarthritis (OA). This work presents a novel surface-enhanced Raman scattering (SERS) biosensor for the ultrasensitive and specific detection of OA-associated miR-204. The platform integrates a self-amplifying nucleic acid circuit with DNAzyme-catalyzed etching of a plasmonic nanoprobe. At its core is a single, rationally designed overhang-containing hairpin probe (O-HP) that functions as both the recognition element and amplification initiator. Upon binding to miR-204, the O-HP triggers polymerase-mediated extension, generating G-quadruplex structures. These structures bind hemin to form DNAzymes that catalyze the localized production of reactive oxygen species (ROS), which subsequently etch the silver shell of the AuNS/Ag@4-ATP SERS nanoprobe. This etching causes the desorption of Raman reporters and a quantifiable 'signal-off' response. This biosensor achieves a remarkably low detection limit of 8.13 fM with a broad dynamic range from 10 fM to 150 nM, and exhibits high specificity, capable of discriminating single-nucleotide variants. Furthermore, it successfully quantified miR-204 in clinical cartilage samples, showing a strong correlation with real-time quantitative polymerase chain reaction results. The modular design of the O-HP also facilitated the adaptation of the platform for detecting miR-21, demonstrating its generalizability. This work provides a robust and versatile biosensing strategy with significant potential for clinical miRNA diagnostics.
Iontophoresis-assisted transdermal drug delivery for the treatment of inflammatory dermatoses: A review
Zhixiong Wang, Xiumei Jiang, Changzhao Jiang, Xiaohua Tao, Jincui Ye
, Available online  , doi: 10.1016/j.jpha.2025.101512
Abstract:
Inflammatory dermatoses, including psoriasis, atopic dermatitis (AD), and acne vulgaris, pose significant challenges in dermatological treatment due to the skin’s natural barrier, the stratum corneum(SC), which limits the efficacy of topical formulations. Iontophoresis, a non-invasive technique that applies low-level electrical currents to enhance transdermal drug delivery, has emerged as a promising solution to overcome these barriers. This review explores the application of iontophoresis-assisted drug delivery for treating inflammatory skin conditions, focusing on its mechanisms, benefits, and potential for combination with existing topical formulations. Iontophoresis enhances the penetration of both small molecules, such as corticosteroids, and biological macromolecules, including monoclonal antibodies and nucleic acid-based therapies, into deeper skin layers. This optimized therapeutic delivery maximizes localized efficacy while minimizing systemic exposure and potential adverse effects. Furthermore, when combined with other transdermal enhancement techniques such as microneedles and sonophoresis, iontophoresis demonstrates synergistic effects, facilitating the delivery of challenging drug molecules and enabling controlled, targeted release. Recent advances in wearable iontophoresis devices present new opportunities for continuous and patient-friendly drug administration, particularly for chronic conditions requiring long-term management. Despite these advantages, challenges such as variability in skin response, potential irritation, and device costs remain. Further research and technological advancements are needed to optimize iontophoresis systems for broader clinical applications. Overall, this review highlights the versatility and prospects of iontophoresis as an innovative therapeutic approach in managing inflammatory dermatoses.
A novel proteolysis-targeting chimera strategy targeting multiple immune checkpoints containing ITIMs enhances antitumor immunity
Yue-Yuan Qiu, Zhao-Wei Wang, Lei He, Ge-Ge Shi, Zhao-Zhao Li, Shuang-Xin Ma, Duo Yu, Hai-Chen Du, Fei Xie, Cun Zhang, Ying-Qi Zhang, Meng Li, Wei-Na Li
, Available online  , doi: 10.1016/j.jpha.2025.101511
Abstract:
Immune checkpoint inhibitors (ICIs) have significantly advanced and revolutionized cancer treatment over the past decade; however, their clinical benefits have been limited to a subset of cancer patients. While ICI-based combinations have emerged as promising strategies, they risk broader toxicities and significant cost burdens. This highlights the critical need for the development of inhibitors that target multiple immune checkpoints. In this study, we developed a peptide that emulates the conserved sequence of the phosphatase-2 (SHP2) C-SH2 domain, which is capable of binding to immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in the cytoplasmic tails of multiple immune inhibitory receptors. By utilizing this peptide as the protein of interest (POI) ligand and coupling it with the von hippel‒lindau (VHL) ligand via a peptide linker, a proteolytic targeting chimera (PROTAC) named PROTAC of ITIM-targeting inhibitory peptide (PITIP) was constructed. PITIP effectively induced the degradation of multiple immune inhibitory receptors in a proteasome-dependent manner, thereby attenuating immunosuppressive signaling within T cells, natural killer (NK) cells, and macrophages. In vivo investigations demonstrated that PITIP elicited a robust antitumor immune response in xenograft and allograft tumor model mice, including those resistant to anti-PD-1 therapy. Moreover, the encapsulation of PITIP within liposomes conjugated with anti-CD45 antibodies enhanced the targeting of immune cells by PITIP, thereby improving the therapeutic efficacy of the antibodies. This study reports, for the first time, a universal strategy targeting the common structural motifs of immunosuppressive receptors, which facilitates broader and more extensive immune activation through the ubiquitination-mediated degradation of multiple immune checkpoints.
Designing lysate-based hydrogels for on-demand therapy
Yang Lv, Siteng TIENG, Xiaoling Xu, Wei Chen
, Available online  , doi: 10.1016/j.jpha.2025.101514
Abstract:
Hydrogels are three-dimensional hydrophilic networks formed via physical or chemical crosslinking. Owing to their structural mimicry of native extracellular matrices and tunable capacity for therapeutic cargo delivery, they have garnered substantial attention in biomedical engineering. Traditional hydrogels primarily function as passive scaffolds for drug encapsulation; however, recent advances have shifted toward integrating bioactive lysates that extract derived from cells or tissues are rich in growth factors, cytokines, and antigenic components to construct dynamic, multifunctional platforms. Lysate-based hydrogels combine the intrinsic bioactivity of lysate-derived factors (e.g., tumor-specific neoantigens or bacteria-derived pathogen-associated molecular patterns) with the spatiotemporal control afforded by hydrogel matrices. This synergy enables precise modulation of the tumor microenvironment, immune priming, and tissue regeneration. In this review, we highlight the emergence of lysate-based hydrogels, which hold significant guiding value for the entire field of bioengineering. This technology represents an innovation in both design concepts and therapeutic strategies, with potential applications across multiple related disciplines. By proposing strategies to exploit underexplored lysate sources (e.g., microbiota-derived components) and integrate stimuli-responsive materials, this work aims to advance lysate-based hydrogels as next-generation platforms for precision oncology, while balancing biological complexity with engineering reproducibility. Key challenges in the development of lysate-based hydrogels include determining the optimal dosage and composition of lysate-derived factors, as well as coordinating their interactions. The presence of multiple factors endows these hydrogels with pluripotent therapeutic effects, but potential crosstalk between factors may limit their efficacy. This area requires further in-depth exploration in future research.
Synergistic cell membrane-coated ECL-DNA biosensor for specificity-enhanced drug lead evaluation
Dan Wu, Qi Hu, Qianhui Wu, Guoxi Xia, Jiabo Wang, Yusi Bu, Xiaoyu Xie, Sicen Wang
, Available online  , doi: 10.1016/j.jpha.2025.101515
Abstract:
Cell membrane coating technology has recently emerged as a promising platform for drug activity assessment due to its unique biointerfacing capabilities. Nevertheless, its integration with conventional detection methods such as high performance liquid chromatography (HPLC) and fluorescence probe analysis remains limited by poor specificity and low accuracy, primarily resulting from non-specific adsorption of non-target membrane receptors and interference from background signals. In this study, we presented a collaborative strategy that integrates aptamers with cell membrane coating technology to establish a novel electrochemiluminescence (ECL)-DNA biosensor platform for specifically detecting drug-target receptor interactions. High specificity was achieved through competitive binding between aptamers and drug candidates for membrane receptors, while high accuracy was ensured by employing an ECL detection system incorporating signal cascade amplification and three-dimensional (3D) DNA walkers, enabling reliable performance even with complex biological samples. Using this approach, we demonstrated a linear dynamic range of 1 nmol/L to 2 μmol/L for the detection of desloratadine activity, with a limit of detection (LOD) of 0.16 nmol/L. Furthermore, the platform was successfully applied to evaluate the binding activity of eight drugs to angiotensin-converting enzyme 2 (ACE2), and their pharmacological activities were further characterized. Overall, this aptamer-cell membrane coating synergistic strategy offered excellent specificity and ultra-high sensitivity, making it a valuable tool for elucidating drug-receptor mechanisms of action and providing a robust reference for preclinical drug activity evaluation.
Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China
Caihong Wu, Limin Zhang, Zhong Chen, Wencui Ma, Yanhua Fu, Ke Yang, Mei Liu, Yanjun Li, Xiaohong Chen, Mingjie Hou, Min Liu, Aihua Deng, Qingxia Zhao, Lukun Zhang, Quan Wang, Jun Peng, Yongli Li, Keji Deng, Jingsong Bai, Hai Long, Yaokai Chen, Hui Wang, Yun He, Jin Li, Jiahui Guo, Bianchuan Cao, Yizhi Cui, Min Wang, Tuofu Zhu, Jun Yao, Tong Wang
, Available online  , doi: 10.1016/j.jpha.2025.101513
Abstract:
Human immunodeficiency virus type 1 (HIV-1) drug resistance remains a major challenge in HIV/AIDS management, particularly in individuals with low-level viremia (LLV) where RNA-based drug resistance testing (DRT) often fails. Although HIV-1 DNA DRT represents a promising alternative, its clinical utility has been constrained by insufficient evidence. This nationwide study in China enrolled 9,428 people living with HIV (PLWH), analyzing 10,903 samples spanning a wide viral load (VL) spectrum. To improve RNA detection, an optimized primer design combined with an extracellular particle (EP)-HIV co-isolation technique was developed. We then evaluated the reproducibility of drug resistance mutation (DRM) profiles between paired RNA and DNA DRTs using Sanger sequencing (SS), with single-molecule sequencing employed to establish a dominant sequence threshold. Our findings demonstrated that primer optimization and EP-co-isolation significantly enhanced RNA amplification success. DRMs were prevalent across all VL strata. The combined concordance and degeneracy rates (C/D rates) (where multiple DNA DRMs included all RNA-derived DRMs) between RNA and DNA DRTs ranged from 90.4% to 100% in different gene regions, with higher discordance observed in the nucleoside reverse transcriptase inhibitor (NRTI) and non-NRTI (NNRTI) regions. Based on Stanford penalty scores across 25 antiretroviral drugs, the degeneracy group showed a 98.3% ± 1.7% interpretation agreement. Even within the discordance group, mean agreement remained high (89.5% ± 5.0%), with only four NNRTIs exhibiting agreement below 85%. The dominant sequence proportion threshold for HIV-1 DNA was determined to be 24.6%. This study provides strong evidence supporting the integration of HIV-1 DNA DRT into clinical practice for reliable drug resistance surveillance and treatment monitoring.
Therapeutic repurposing of old drugs to modulate the tumor immune microenvironment and enhance immunotherapy efficacy
Yakai Song, Nannan Zheng, Xu Yang, Zhaofan Tao, Qinghui Wang, Zhiyue Cao, Yi Zhang, Mengmeng Li, Ruixin Mao, Yuhao Chen, Chen Zhao, Huanjie Yang, Bin Yang, Qiuyue Ma, Liangcan He, Shaoqin Liu, Kai Li
, Available online  , doi: 10.1016/j.jpha.2025.101510
Abstract:
Although immunotherapy has demonstrated remarkable progress in cancer treatment, its clinical benefits remain restricted to a subset of patients and specific cancer types, primarily due to the immunosuppressive nature of the tumor microenvironment (TME) in solid tumors. Therefore, many strategies have focused on targeting the immunosuppressive TME to enhance immune-mediated tumor eradication. In parallel, the repositioning of old drugs represents an attractive discovery approach compared with the traditional de novo drug discovery process, which is time-consuming and costly. Thus, repurposing U.S. Food and Drug Administration (FDA)-approved old drugs to modulate the tumor immune microenvironment represents a promising strategy to augment the effectiveness of cancer immunotherapy. Indeed, emerging evidence indicates that several approved drugs can reprogram the tumor immune landscape, thereby enhancing responses to immunotherapy. This review provides a comprehensive overview of FDA-approved old drugs with immunomodulatory properties in the tumor context. We discuss their mechanisms in reversing immunosuppression, summarize key findings from preclinical studies and clinical trials involving their combination with immunotherapies, and outline future perspectives for their clinical translation. Collectively, this work highlights the translational potential of drug repurposing as a strategy to expand the therapeutic reach of cancer immunotherapy.
Synovial Microenvironment and Fluorescence Imaging for Early Rheumatoid Arthritis Diagnosis
Hua Wang, Pan Zhou, Huixiang Chen, Jiachen Zheng, Linlin Wei, Jiabin Chen, Yu Lei
, Available online  , doi: 10.1016/j.jpha.2025.101509
Abstract:
Rheumatoid arthritis (RA) is a chronic, systemic autoimmune inflammatory disease that primarily affects the joints and surrounding soft tissues. Early diagnosis is crucial for preventing joint damage and improving the prognosis and quality of life in RA patients. Therefore, this article reviews conventional diagnostic methods, such as serologic tests (including rheumatoid factor (RF), anti-cyclic citrullinated peptide antibody (ACPA), and anti-carbamylated protein (anti-CarP)) and imaging tests and also focuses on innovations in AI-driven diagnostic and therapeutic technologies. Additionally, we provide insights into new biomarkers (including macrophages, neutrophils, and synovial fibroblasts) in the synovial microenvironment that correlate with RA disease activity and severity at the molecular level. Importantly, we are optimistic about fluorescence imaging (FOI) techniques (including visible light imaging and near-infrared (NIR)-FOI), which can accurately quantify abnormal levels of molecular markers using fluorescent probes. This provides detailed information about pathological changes in RA, opening new horizons for early diagnosis and treatment.
Intelligence on the Graph: Graph Neural Networks for Mechanistic Drug Target Discovery
Jing Chen, Nini Fan, Yuqing Lu, Jianhua Yang, Wenchao Song, Haiyang Sheng, Yinfeng Yang, Shengxi Chen, Jinghui Wang
, Available online  , doi: 10.1016/j.jpha.2025.101508
Abstract:
Drug discovery is increasingly challenged by rising costs, long development cycles and high attrition rates, with accurate target identification remaining a critical bottleneck. Although artificial intelligence (AI) has demonstrated transformative potential, the systematic application of graph neural networks (GNNs) to drug target discovery remains underexplored. To address this gap, this paper provides a comprehensive and structured analysis of recent advances in GNN-based methods for drug-target interaction (DTI) and drug-target affinity (DTA) prediction. We dissect the methodological foundations of representative architectures including graph convolutional networks (GCNs), graph attention networks (GATs) and graph autoencoders (GAEs), and compare their mechanisms, advantages and applicable scenarios in modeling complex molecular and biological systems. Also, we synthesize frontier paradigms such as multimodal data fusion, high-order graph reasoning and dynamic GNNs, which enable the capture of atom-residue interactions, multi-target coordination mechanisms and cross-scale biological features. By systematically mapping methodological innovations to biological applications, this paper offers both theoretical guidance and translational insights. The key contributions of this paper include: (1) establishing a comparative framework that clarifies when and how different GNNs architectures can be applied in drug target discovery; (2) integrating cutting-edge paradigms rarely addressed in prior reviews, such as multimodal fusion and high-order graph modeling; and (3) highlighting representative case studies that bridge algorithmic innovation with practical drug discovery outcomes. Collectively, this work provides an authoritative and forward-looking reference, promoting the development of AI-driven, efficient and interpretable drug discovery pipelines.
Cuproptosis tracker: Visualizing organelle dynamics with a dual-targeted fluorescent probe
Furao Li, Chunyan Liang, Xifeng Mo, Xiaohuan Xu, Yongbiao Wei, Chunyan Zhou, Ting Meng, Hui Zhang, Fan Yang
, Available online  , doi: 10.1016/j.jpha.2025.101500
Abstract:
Cuproptosis often interacts with mitochondrial (Mito) dysfunction and lipid droplets (LDs) metabolism disturbances, thus resulting in programmed cell death, whereas their dynamic interaction lacks a rational analyzing tool. Herein, we show a Mito-LDs dual-targeted fluorescent reporter (MLR) for tracking the Mito-LDs interaction during cuproptosis by dynamic monitoring of intracellular sulfur dioxide (SO2) dynamics. MLR integrates a coumarin-derived SO2-responsive core linked via piperazine to a benzopyronium Mitol anchor, enabling one-step synthesis with exceptional sensitivity (0.34 μM) and rapid response (<10 s). Live-cell imaging demonstrated MLR’s SO2-triggered translocation from Mito to LDs during cuproptosis, directly visualizing inter-organelle communication. Dual fluorescence channel imaging associated SO2 fluctuations with Mito-LDs targeting, revealing the interaction between LDs-Mito during Cu2+ and elesclomol induced apoptosis. In addition to imaging, MLR-based test strips and hydrogels can achieve rapid (< 1 min) on-site SO2 detection. As a dual-organelle tracer for cuproptosis, MLR overcomes single-target probe limitations, offering a transformative platform to analyze spatiotemporal organelle dynamics for advancing diagnostic tools development.
Techniques for the determination of dipeptidyl peptidase IV and screening of its inhibitors
Hong-Hong Ma, Xiao-Dong Li, Xing-Kai Qian, Li-Wei Zou
, Available online  , doi: 10.1016/j.jpha.2025.101499
Abstract:

Dipeptidyl peptidase IV (DPP-IV), an important member of the serine hydrolase family, plays a core regulatory role in various physiological and pathological processes because of its unique broad-spectrum substrate specificity. DPP-IV-mediated proteolytic processing of endogenous peptide substrates serves as a fundamental regulatory mechanism governing physiological processes. An in-depth exploration of the enzymatic characteristics and mechanisms regulating DPP-IV activity will not only provide a theoretical basis for revealing the molecular pathogenesis of related diseases but also contribute to the construction of a complete disease regulatory network map. Furthermore, the development of specific DPP-IV inhibitors constitutes a key strategy for innovative therapy, holding significant promise for clinical translation. This review provides a comprehensive comparison of the applications, merits, and limitations of DPP-IV detection at the messenger RNA (mRNA), protein, and functional levels, along with an in-depth analysis of how DPP-IV enzymatic activity assessment profoundly impacts disease pathogenesis, progression, and therapeutic interventions. Particular emphasis is placed on the superior performance of probes based on drugs and optical substrates (e.g., for fluorescence and bioluminescence) in the functional determination of DPP-IV. Through metabolic phenotyping, we further summarize drug screening systems that target DPP-IV across multiple biological levels, including recombinant proteins (e.g., proteins derived from humans, animals, and gut bacteria), tissues, cells, human organ-on-a-chip models, and whole-animal studies. Furthermore, this review comprehensively evaluates both synthetic and natural DPP-IV inhibitors. Additionally, systematic investigations of their structure‒activity relationships (SARs) provide a rational foundation for developing novel inhibitors with enhanced efficacy and safety.

Enhancing ginsenoside isomers annotation by integrated analysis of electron-activated dissociation and collision-induced dissociation tandem mass spectrometry
Wenxiang Fan, Ziwei Li, Longchan Liu, Rufeng Wang, ChenChun Zhong, Kaixian Chen, Zhengtao Wang, Li Yang
, Available online  , doi: 10.1016/j.jpha.2025.101495
Abstract:
Natural products, with their diverse structures and biological activities, are a critical source for new drug development. Advances in mass spectrometry have significantly enhanced the accurate and rapid identification of natural products. However, differentiating isomers remains a challenge. This study establishes a complementary approach combining collision-induced dissociation (CID) and electron-activated dissociation (EAD) to effectively distinguish isomers, exemplified by ginsenoside isomers. The CID mode clearly distinguishes the structural types of ginsenosides, while EAD mode identifies the substitution sites (e.g., C-3, C-6, C-20) of the glycosyl groups. Mass spectrometry molecular network (MN) analysis showed that, compared to CID-MN, the EAD-MN demonstrated more robust clustering of ginsenosides and more accurately reflected structural similarities of ginsenosides. The developed method enables precise characterization of unknown ginsenoside isomers in Panax species including Panax ginseng, Panax notoginseng, and Panax quinquefolius, and reveals species-specific features, thereby facilitating improved quality control. The proposed strategy effectively addresses the challenge of distinguishing ginsenoside isomers by integrated analysis of CID and EAD tandem mass spectrometry to identify diagnostic ions specific to each isomer. This approach enhances the accuracy of natural product annotation.
Metabolic heterogeneity, networks, and biomarkers of drug-induced liver injury
Xian Ding, Hongchuan Liu, Qingrong Qiu, Kongcai Zhu, Xiaohong Zhu, Rui Zhao, Ting Hu, Yuan Sun, Zhuoling An
, Available online  , doi: 10.1016/j.jpha.2025.101496
Abstract:
Drug-induced liver injury (DILI) represents a major adverse drug reaction with significant clinical implications. The diversity of causative drug agents, incomplete understanding of pathogenic mechanisms, and absence of specific diagnostic biomarkers pose substantial challenges for DILI diagnosis and clinical management. This study aimed to characterize the metabolic heterogeneity across different types of DILI and identify high-specificity metabolic biomarkers for DILI classification. A multicenter targeted metabolomics study was conducted on 516 serum samples collected from 200 patients with DILI and 221 healthy controls. We characterized the metabolic dynamics throughout DILI progression, with significant disruptions presented in glutathione, fatty acid, and carnitine metabolism. By characterizing and comparing the metabolic profiles among antibiotics-, herbs-, non-steroidal anti-inflammatory drugs-, and statins-DILI patients, we constructed four drug-specific metabolic networks of DILI based on the metabolic coordination between metabolites. Notably, the elevated long-chain acylcarnitines (such as C18:1 Car and C16:2 Car) distinctively underlie herb-DILI's pathological progression. In monocrotaline-induced liver injury mouse models, hepatic carnitine acyltransferase II (Cpt2) mRNA expression was suppressed. Further, two-sample Mendelian randomization supported a causal relationship between C18:1 Car and total bilirubin levels. Finally, we developed a 10-metabolite classifier to distinguish between different DILI subtypes using machine learning algorithms, yielding accuracies of 0.915 and 0.904 on two independent test sets. These findings enhance the understanding of the metabolic heterogeneity in DILI and provide evidence supporting the use of responsive metabolic traits for the clinical diagnosis and treatment of DILI.
HIF-1α in CD4+ T cells drives gout pathogenesis via metabolic reprogramming and Th17 differentiation
Siyue Song, Jiatao Li, Fusen Chen, Kaiyue Shi, Yu Lou, Anyi Xu, Yun Zhang, Chengping Wen, Tiejuan Shao
, Available online  , doi: 10.1016/j.jpha.2025.101494
Abstract:
Hypoxia-inducible factor 1-alpha (HIF-1α), a central regulator of immunometabolic reprogramming, has been associated with multiple inflammatory conditions. However, its function in CD4+ T cell-mediated glycolytic dysregulation during gout pathogenesis remains unclear. Herein, we demonstrated that HIF-1α expression was elevated in CD4+ T cells derived from patients with gout and urate oxidase (Uox)-knockout (KO) mice. Both pharmacological inhibition (PX-478) and CD4+ T cell-specific genetic ablation of HIF-1α alleviated gout symptoms, including reduced serum uric acid, diminished T helper 17 cells (Th17) polarization, and mitigated renal injury. RNA sequencing (RNA-seq) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that HIF-1α disruption impaired Th17 differentiation, which was further validated using flow cytometry. Seahorse metabolic profiling and 2-deoxy-D-glucose (2-DG) treatment confirmed that HIF-1α promotes gout pathogenesis by driving glycolysis-dependent Th17 expansion and interleukin-17 (IL-17) production. Importantly, the natural compound dioscin was found to directly bind HIF-1α, suppress its expression, and reverse disease phenotypes in vitro and in vivo. Conversely, HIF-1α activation using 1,1-dimethylethyl ester 6-[2,5-dihydro-5-oxo-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl]-3-pyridinecarboxylic acid (IOX4) exacerbated gout features, which were effectively counteracted by dioscin. Collectively, these findings identify CD4+ T cell-derived HIF-1α as a key glycolytic regulator in gout and highlight dioscin as a promising candidate for HIF-1α-targeted therapeutic intervention.
M1-NP1 interfering-peptide inhibits cancer cell proliferation and migration by targeting the transcription factor FOXM1
Chaozhu Pei, Ziwu Xu, Min Ouyang, Huitong Bu, Zhenyu Zou, Yuting Ma, Zhengqing Zhu, Yan Chen, Li Yu, Mingmin Huang, Yongjun Tan
, Available online  , doi: 10.1016/j.jpha.2025.101493
Abstract:
Multiple cancers overexpress forkhead (FOX) box M1 (FOXM1), a transcription factor (TF) that holds great promise for developing cancer drugs. Herein, through yeast-two-hybrid (Y2H) screening, we obtained a novel FOXM1-targeting peptide M1-NP1, which significantly inhibited the cell cycle and migration of cancer cells. Mechanistically, M1-NP1 bound to the C-terminal region of FOXM1 and disrupted its interactions with the cell cycle-related kinase polo-like kinase 1 (PLK1) and the transcriptional co-activator cyclic AMP response element-binding protein (CREB) binding protein (CBP), thus inhibiting FOXM1 transcriptional activities. Additionally, M1-NP1 affected FOXM1 distribution in cells, preventing FOXM1 from infiltrating the nucleus to exert its effects. Furthermore, M1-NP1 treatment in cancer cells downregulated the gene sets of cell cycle phase transition and upregulated the gene sets of cell adhesion. Moreover, M1-NP1’s anti-cancer effects were confirmed in wild-type (WT) mice, without any notable toxic or side effects. In addition to its good safety indications, such as the low levels of immunogenicity and hemolysis, M1-NP1 also exhibited a favorable profile regarding stability and distribution in mice. Overall, M1-NP1 targets FOXM1 for cancer therapy.
Hyaluronic acid-modified polymeric nanoplatform delivering 131I-Hyp suppresses post-ablation residual lesions in colorectal cancer metastases via necrosis-targeted radiotherapy
Han Bao, Ning Wang, Xiaowen Zhu, Song Chen, Yang Wang, Xiangjun Han, Hongshan Zhong
, Available online  , doi: 10.1016/j.jpha.2025.101488
Abstract:
Despite serving as a radical alternative to surgery for inoperable colorectal hepatic metastases patients, thermal ablation faces local tumor progression rates up to 25% from residual tumors, seriously compromising treatment efficacy and survival of patients. We constructed hyaluronic acid (HA)-modified nanoparticles as carriers for the hydrophobic necrosis-avid agent 131I-hypericin (131I-Hyp), enabling tumor necrosis-targeted radiotherapy. 131I-Hyp was synthesized via iodogen-catalyzed electrophilic substitution and loaded into amphiphilic block copolymer hyaluronan-b-poly(ε-caprolactone) (HA-PCL) using dialysis, yielding HA-PCL@(131I-Hyp) nanoparticles (HP-NPs). HP-NPs were characterized in terms of size, stability, and drug release. Biodistribution and antitumor efficacy in vivo were evaluated in rodent models (nude mice and SRG rats bearing HT-29 subcutaneous tumors) with residual tumors induced by incomplete microwave ablation. HP-NPs showed 84.32% encapsulation efficiency, a uniform spherical shape with a hydrodynamic diameter of 75.66 nm, and rapid cytosolic degradation, enabling the release of 131I-Hyp in necrotic regions. After intravenous injection into animals with residual tumors, HP-NPs accumulated in tumor tissue through the enhanced permeability and retention (EPR) effect and CD44/HA receptor-ligand interactions. The released 131I-Hyp remained selectively in necrotic areas, delivering localized β-radiation to the surrounding residual tumor tissue and significantly inhibiting tumor growth via induction of apoptosis. In conclusion, HP-NPs enable targeted radiotherapy to residual tumor tissue after ablation for colorectal metastases by leveraging necrosis avidity and CD44-mediated HA endocytosis, effectively reducing post-ablation tumor progression. This nanoplatform shows potential for clinical translation in colorectal metastasis treatment.
AIE-active dual-channel fluorescent probe for simultaneous viscosity and HClO detection in ferroptosis, acute liver injury and hepatocellular carcinoma models
Jiakang Sun, Lidong Cao, Yumeng Liu, Yun Wang, Yong Zhan
, Available online  , doi: 10.1016/j.jpha.2025.101489
Abstract:
This study addresses the technical challenge of simultaneously detecting viscosity and hypochlorous acid (HClO) within the liver disease microenvironment by developing a novel near-infrared (NIR) dual-channel fluorescence probe, BCz-DCN-TPA, based on the aggregation-induced emission (AIE) mechanism. The probe exhibits pronounced fluorescence enhancement at 675 nm (viscosity-responsive) and 465 nm (HClO-responsive), attributed to the restriction of intramolecular motion (RIM) effect and HClO-specific oxidation reactions, respectively. It also possesses high sensitivity, excellent selectivity (toward 15 types of interferents), superior photostability (for more than 300 min), and a low limit of detection (LOD) as low as 0.233 nM for HClO. Theoretical calculations revealed the ground state and excited state reaction pathways underlying the reaction between HClO and BCz-DCN-TPA. In vitro experiments validated its ability to monitor real-time changes in viscosity and oxidative stress levels during ferroptosis, which auds in elucidating ferroptosis mechanisms. In acetaminophen (APAP)-induced acute liver injury (ALI) and hepatocellular carcinoma models, the probe tracked dual parameters abnormal viscosity and HClO levels in liver injury regions and tumor microenvironments in vivo, with live imaging clearly delineating lesion areas. Notably, BCz-DCN-TPA enabled deep tissue photoacoustic imaging (PAI) in a hepatocellular carcinoma model. This multimodal probe provides a versatile platform for studying liver disease pathology and advancing precision diagnosis and treatment strategies.
Immunocyte senescence: A new perspective on the remodeling of the ovarian cancer microenvironment and therapeutic intervention
Xiang Li, Xian Li, Sha Ni, Xiaohui Zhang, Bingnan Liu
, Available online  , doi: 10.1016/j.jpha.2025.101492
Abstract:
Immune cell senescence in ovarian cancer manifests as distinct phenotypic alterations in T cells, natural killer (NK) cells, macrophages, and dendritic cells (DCs), alongside dynamic crosstalk with the tumor microenvironment (TME). This senescence contributes substantially to the high mortality and therapeutic resistance characteristic of ovarian carcinoma. Senescent immune cells develop a senescence-associated secretory phenotype (SASP), secreting pro-tumorigenic cytokines and chemokines that drive regulatory T cell expansion, extracellular matrix (ECM) remodeling, and the establishment of an immunosuppressive niche. Key drivers of immunocyte senescence include telomere erosion, epigenetic dysregulation, metabolic stress, DNA damage from chemotherapy, and chronic inflammatory signals. Emerging interventions, such as senolytic agents to selectively eliminate senescent immune cells, senomorphic compounds to attenuate SASP factors, and strategies to reprogram immune effectors, hold promise for restoring antitumor immunity and overcoming resistance to conventional therapies. A deeper understanding of the molecular mechanisms governing immunosenescence will be critical for the rational design of combination regimens and the development of next-generation immunotherapies in ovarian cancer.
Recent advances in the analysis of unsaturated fatty acids in biological samples based on chemical derivatization and mass spectrometry techniques
Yuanyuan Lin, Ningbo Chen, Wenda Chen, Fan Yin, Ling Yang, Xuan Chen, Jian-Liang Zhou, Tian Xie
, Available online  , doi: 10.1016/j.jpha.2025.101491
Abstract:
Fatty acids (FAs) play a vital role in various physiological processes in the human body, and the analysis of FA isomers is of utmost importance in the research of various diseases and FA metabolic pathways. Over the last few years, the use of chemical derivatization methods to alter the composition of FAs has been found to be highly effective in overcoming the drawback of poor sensitivity in mass spectrometry analysis due to the poor ionizability of functional groups in FA molecules. Furthermore, certain chemical derivatization methods have enabled detection of C=C and differentiation of cis-trans isomers. As a result, the development and use of chemical derivatization-based mass spectrometry to analyze FAs has gained significant interest. This review highlights technological innovations in the development of mass spectrometry detection methods for unsaturated FAs (UFAs) based on chemical derivatization. Special emphasis is placed on two significant strategies: carboxyl group derivatization and C=C derivatization. In addition, it focuses on applications in various fields, discusses persistent challenges, and explores potential future directions. This review aims to provide a better perspective on the advanced design and development of mass spectrometry detection methods of FAs based on chemical derivatization.
Protein S-palmitoylation: Potential strategy for inflammation-related diseases
Sunan Li, Xinyue Dou, Jiamei Sun, Yongyuan Xiao, Tianyang Wang, Qiyuan Shan, Xin Han, Gang Cao
, Available online  , doi: 10.1016/j.jpha.2025.101490
Abstract:
S-palmitoylation represents a dynamic and reversible modification wherein palmitate forms covalent bonds with cysteine residues in proteins, thereby modifying their localization, stability, signaling pathways, and protein-protein interactions. Aberrations in S-palmitoylation are associated with the progression of various diseases, particularly inflammatory conditions. This association can be attributed to its regulation of pattern recognition receptors (PRRs) and its influence on immune cell functions, including macrophages, T cells, neutrophils, and natural killer cells (NK cells). This review synthesizes current knowledge regarding the impact of S-palmitoylation on inflammation-related diseases through examination of its regulatory roles in PRRs and immune cell functions. The objective is to illuminate the underlying mechanisms and regulatory networks involved in inflammation-related diseases.
High-Throughput Screening of EGFR/Ca2+ Signaling Modulators in Cardiac Hypertrophy Using a Tetrahedral DNA Nanostructure-Based hESC Platform
Ke-Jia Wu, Yan-Fa Dai, Zhi-Qiang Wang, Wen Sun, Ya-Nan Zhu, Fan Chen, Ling Shao, Yao-Ye Huang, Qi Chen, Xin Liu, Yan Li, Hui-Min David Wang, Ning Sun
, Available online  , doi: 10.1016/j.jpha.2025.101479
Abstract:
Cardiac hypertrophy, a precursor to heart failure, involves intricate signaling networks characterized by epidermal growth factor receptor (EGFR) activation and calcium (Ca2+) dysregulation. Therapeutic inhibition of EGFR has emerged as a promising approach to attenuate maladaptive hypertrophic remodeling, particularly by restoring Ca2+ homeostasis, a critical factor in maintaining myocardial function. However, drug discovery targeting EGFR/Ca2+ pathways remains constrained by the limited proliferative capacity of human cardiomyocytes and the lack of real-time probes capable of concurrently monitoring EGFR and Ca2+ signaling in living cells. To address these limitations, we developed a tetrahedral DNA nanostructure-based probe (TDN-EA) integrated with human embryonic stem cell-derived cardiomyocytes (hESC-CMs) for real-time, concurrent detection of EGFR and Ca2+ dynamics via FRET-ON mechanism. The TDN-EA probe demonstrated high specificity, stability, and biocompatibility in hESC-CMs. Leveraging TDN-EA, we established a high-throughput screening platform that identified paromomycin (PM) as a novel therapeutic candidate from a library of 420 natural compounds. PM attenuated cardiac hypertrophy effectively in vitro and in vivo by inhibiting EGFR/Ca2+ signaling pathway. This study underscores the potential of TDN-EA as a transformative tool for high-throughput drug discovery, enabling the identification of therapeutics that simultaneously target EGFR and Ca2+ signaling pathways in cardiac hypertrophy.
Targeting angiogenesis in diabetic wound healing: New insight from chemical architecture to functional outcomes
Junren Chen, Siqi Qin, Ziwei Xing, Cheng Peng, Dan Li
, Available online  , doi: 10.1016/j.jpha.2025.101475
Abstract:
Diabetic wound healing (DWH) is a multifaceted process hindered by impaired angiogenesis that usually leads to increased risks of infection and amputation. Targeting impeded angiogenic signals to restore the microenvironment favoring vascular network re-establishment is a promising therapeutic strategy for diabetic wound. Natural products have emerged as potential therapeutic agents for diabetic wounds by regulating endotheliocytes functions and their cross-talks with immune cells and fibroblasts, while the similarities and differences of the chemical structures greatly determine their distinct efficient and underlying mechanisms in diabetic wound angiogenesis. In this review, relevant literature was retrieved from PubMed, Google Scholar, and Web of Science databases, covering publications from 2020 to 2025. This paper reviews the role of angiogenesis in DWH and the action of natural products in DWH by targeting angiogenesis, particularly highlighting their chemical architecture driven specific biological activity on angiogenesis, with the aim of providing references for angiogenesis-based therapeutic strategies for diabetic ulcers and promoting the development of angiogenesis-targeting agents.
The correlation between characteristics and pharmacological effects of Monoterpene glycosides and Tannins in Radix Paeoniae Alba
Qitong Zheng, Mengyao Chen, Jialiang Ying, Zhichao Wang, Qiyuan Shan, Xia-Nan Sang, Gang Cao
, Available online  , doi: 10.1016/j.jpha.2025.101471
Abstract:
The pharmacodynamic material basis constitutes the central element of traditional Chinese medicine (TCM) in disease treatment. By summarizing the active compounds' characteristics, bioavailability, pharmacological effects, and molecular mechanisms, we can explain the complex interactions between TCMs and diseases. Previous studies have demonstrated that monoterpene glycosides and tannins are related to the pharmacological activity of Radix Paeoniae Alba (RPA). However, research on RPA has primarily focused on monoterpene glycosides, and the functional role of tannins in RPA has received little attention. Observations from animal studies indicate that monoterpene glycosides and tannins exhibit poor bioavailability. Carboxylesterase, produced by gut microbiota, is crucial for metabolizing these compounds in the intestine. Monoterpene glycosides and their gut metabolites can be absorbed into the bloodstream, exerting various pharmacological effects, including anti-inflammatory, immunomodulatory, and neuromodulator activities. In contrast, tannins consist of highly hydrophobic polyphenols that form insoluble protein-tannin complexes. Due to their inability to cross the intestinal barrier, tannins primarily exert localized pharmacological effects within the digestive system. This study systematically reviews the pharmacological activities and mechanisms of monoterpene glycosides and tannins in RPA, while establishing their therapeutic contributions to the herb's pharmacological effects.
UGP system: A deep learning-driven platform for automated identification of ultrafine granular powders using chromatographic fingerprinting
Fei Huang, Ya-ling An, Li-jie Zhang, Jia-wei Wang, Ming-jin Zhang, Zhen-wei Li, Xiao-kang Liu, Dai-di Zhang, Qian-liang Zhang, Li-hua Peng, Wei-lin Qiao, De-an Guo
, Available online  , doi: 10.1016/j.jpha.2025.101474
Abstract:
This study developed an intelligent identification system for ultrafine granular powder (UGP) by integrating high performance liquid chromatography (HPLC) fingerprinting with deep learning algorithms. A comprehensive HPLC fingerprint database encompassing 530 batches from 53 UGP varieties across 29 botanical families was established using a standardized 60-min, six-wavelength detection protocol (210, 230, 254, 280, 327, and 380 nm). Chromatographic reproducibility was ensured with quality control sample retention time relative standard deviations (RSDs) below 2%. A three-layer one-dimensional convolutional neural network (1D-CNN) was designed with 32, 64, and 128 filters in successive layers for species classification. Data augmentation techniques including noise interference, baseline drift, and retention time shifts (3.5–60 min) expanded the dataset sixfold and enhanced model generalization capabilities. The optimized model achieved excellent performance on test data with 97.62% accuracy, 97.97% precision, and 97.16% recall, demonstrating consistent reproducibility with mean accuracy of 97.2% ± 0.65% across ten independent training runs. External validation using 63 commercial samples yielded 95.24% identification accuracy, confirming practical applicability. The Flask-based web system enables automated workflows from data upload to species identification and is accessible to users without specialized expertise. This work establishes a standardized approach for intelligent authentication of food-medicine homologous Chinese medicinal UGPs, addressing regulatory and consumer requirements for product authenticity and safety in pharmaceutical and functional food industries.
Extraction and determination of Sartans: Recent advances and analytical perspectives
Peng-li Wei, Yuan Zhang, Cheng Du, Xue-song Feng, Xiao-dan Liu
, Available online  , doi: 10.1016/j.jpha.2025.101472
Abstract:
Sartans are essential antihypertensive drugs requiring reliable analytical methods for quality and efficacy monitoring. This review provides a comprehensive overview of recent analytical advances for sartans, focusing on pretreatment and detection methods. For sample preparation, conventional methods like protein precipitation, liquid-liquid extraction and solid-phase extraction (SPE) have been optimized through the adoption of green solvents and automation. Emerging novel microextraction techniques including liquid phase microextraction and solid phase microextraction, in combination with advanced materials improve selectivity, especially for complex biological matrices. In the realm of detection, liquid chromatography-mass spectrometry (LC-MS) remains dominant, with high-resolution mass spectrometry (HRMS) (time-of-flight, orbitrap) enabling trace-level quantification and structural identification, outperforming traditional low-resolution mass spectrometry. Emerging sensors offer rapid screening but lack MS-level multiplexing capability. The choice of methods should be based on sample complexity and analytical needs: biological samples benefit from microextraction-HRMS combinations, whereas pharmaceutical analysis may use simpler SPE-LC/MS workflows. Future directions should emphasize miniaturized, automated, and eco-friendly approaches to enhance throughput while reducing environmental impact. This review serves as a practical guide for selecting suitable strategies for the analysis of sartans across diverse analytical scenarios.
Sweat as a diagnostic biofluid: analytical advances and future directions
Dayanne Mozaner Bordin, Janice Irene McCauley, Eduardo G. de Campos, David P. Bishop, Bruno Spinosa De Martinis
, Available online  , doi: 10.1016/j.jpha.2025.101473
Abstract:
The use of sweat as an alternative specimen for biological analyses is well recognised and has been successfully applied in forensic toxicology and clinical health assessments. Compared to conventional matrices such as urine and blood, sweat samples are easy to obtain, are less invasive and present a reduced number of endogenous interferents. Advanced analytical techniques in sweat analysis have considerably expanded capabilities in the isolation of drugs, detection of complex metabolites and identification of biomarkers. The ability to detect a broader range of substances with greater sensitivity and accuracy, improved speed and efficiency and enhanced reliability present opportunities for non-invasive chemical sensing in sweat for a much broader scope of metabolites than traditionally recognised. The year 2023 was marked by an evolutionary step in artificial intelligence (AI), opening the door for improved pattern analysis and classification algorithms to improve diagnostic precision and therapeutic accuracy. It is anticipated that when combined with advances in the performance and miniaturization of integrated circuits, stretchable electronics, wireless connectivity and longer battery life, a substantial impact is expected on the development of wearable biosensor devices to provide meaningful information to the physiology of end-users, expanding its role in personalised medicine and health monitoring. Therefore, the aim of this review is to provide an integrative overview of sweat as a diagnostic and monitoring biofluid by first discussing traditional methods in clinical and forensic applications. Recent advancements in sweat biomarker detection are then highlighted, followed by an evaluation of sweat's potential for real-time physiological monitoring.
ACAA1 mediates arachidonic acid dysregulation and membrane phospholipid remodeling to promote crystal-cell adhesion and ferroptosis susceptibility in calcium oxalate kidney stone
Qinhong Jiang, Yanqi Xie, Chao Song, Caitao Dong, Wenbiao Liao, Qianlin Song, Xiaozhe Su, Heng Xiang, Yunhan Wang, Bobo Cheng, Ziqi He, Sixing Yang
, Available online  , doi: 10.1016/j.jpha.2025.101470
Abstract:
Crystal adhesion is a key process in the formation of kidney stones, playing a synergistic role at every crystallization stage. Damage to the renal tubular epithelial cell (RTEC) membrane provides essential sites for crystal adhesion. During the terminal phase of ferroptosis, accumulated polyunsaturated phospholipids integrate into the cell membrane, leading to membrane damage and deformation, which may be an important mechanism in calcium oxalate (CaOx) crystallization. In this study, targeted peroxidomics analysis revealed a significant increase in arachidonic acid (AA) levels in a CaOx kidney stone model. Meanwhile, transcriptomic analysis indicated that the key enzyme in fatty acid metabolism, acetyl-coenzyme A (CoA) acyltransferase 1 (ACAA1), was significantly downregulated in the CaOx kidney stone model. Besides, overexpression of ACAA1 (OE-ACAA1) alleviated AA accumulation and reduced oxalate (Ox)-induced RTEC ferroptosis. Notably, the OE-ACAA1 alleviated the accumulation of AA-containing polyunsaturated phospholipids without regulating acyl-CoA synthetase long-chain family member 4 (ACSL4) expression, thereby reducing membrane peroxidative damage and crystal adhesion. Furthermore, transcription factor array analysis identified the downregulation of activating transcription factor 1 (ATF1), an upstream transcriptional regulator of ACAA1, which might be involved in the transcriptional repression of ACAA1. Finally, OE-ATF1 partially alleviated Ox-induced RTEC membrane peroxidative damage and crystal adhesion. These findings demonstrated that ferroptosis participates in the early crystallization process by mediating RTEC membrane peroxidative damage and provided a novel approach to influencing downstream lipid peroxidation by regulating fatty acid activation substrates rather than ACSL4. Therefore, this study offers potential therapeutic targets for the prevention and treatment of CaOx kidney stones.
Raman spectroscopy combined with multiple technologies for label-free identification of immune cells: An overview
Chengshun Jiang, Jie Deng, Wanwan Gan, Jiaqi Zou, Tongkai Cai, Hao Yin, Yongbing Cao
, Available online  , doi: 10.1016/j.jpha.2025.101468
Abstract:
Traditional immune cell identification and sorting methods rely on antibodies and fluorophores, which may compromise cell viability and functionality. Raman spectroscopy, a label-free and highly sensitive technique, enables precise differentiation of immune cell subtypes based on their intrinsic biochemical composition. When integrated with chemometrics, microfluidics, and machine learning (ML)/deep learning (DL) approaches, Raman spectroscopy significantly enhances the accuracy, throughput, and efficiency of immune cell sorting. This review systematically analyzes the principles and advantages of these integrated strategies and explores their potential applications in immunological research, clinical diagnostics, and precision medicine, paving the way for non-invasive and high-efficiency immune cell analysis.
19F-{1H} NMR spectroscopy in weakly orienting solvents for the enantiomeric resolution of fluorinated chiral drugs: The case of fluoxetine
Vincent Chiapolino, François-Marie Moussallieh, Philippe Lesot, Boris Gouilleux
, Available online  , doi: 10.1016/j.jpha.2025.101469
Abstract:
A rapid and simple method combining 19F-{1H} nuclear magnetic resonance (NMR) and weakly orienting chiral solvents is proposed for the spectral discrimination and accurate quantitation of fluoxetine enantiomers. Fluoxetine (FLX) is a well-known bioactive chiral drug in pharmacology with well-established anti-depressant properties (Prozac or Sarafem) and currently used as a racemate. Since 1991, it has been established that the (S)-form of FLX shows different pharmacokinetic and pharmacodynamic profiles in comparison to the (R)-form, hence the development of novel enantioresolved NMR methods for analyzing FLX is of interest. The reported approach, relying on a commercial polymer: poly-γ-benzyl-L-glutamate (PBLG) as chiral selector, addresses the enantiomeric analysis of FLX hydrochloride solutions with a high level of accuracy in a short time. The influence of experimental parameters, such as solute concentration and temperature on the enantiomeric resolution is investigated and discussed in depth. In particular, the uniformity and stability of PBLG-based lyotropic liquid crystals (LLCs) in presence of a hydrochloride analyte is assessed for the first time by 19F NMR imaging. All the outcomes obtained highlight the analytical potential of this NMR approach for the enantiomeric analysis of fluorinated chiral drugs while the spectral data recorded at various conditions in temperature and mesophase composition provide new valuable insights toward a better understanding of chiral recognition processes in polypeptide orienting media.
Covalent modification of Keap1 Cys489 by NU6300 activates Nrf2 signaling and suppresses NLRP3 inflammasome-mediated pyroptosis
Xueqin Jiang, Hongyu Zheng, Xinlu Zhang, Minghai Tang, Jing Peng, Xiaoying Cai, Kaiyue Su, Ruijia Zhang, Neng Ye, Lei Lin, Rupei Ma, Caiyun Shen, Wenshuang Wu, Haoyu Ye
, Available online  , doi: 10.1016/j.jpha.2025.101458
Abstract:
Nuclear factor erythroid 2-related factor 2 (Nrf2), a master regulator of oxidative stress and inflammasome, plays a critical role in modulating pyroptosis. In this study, we identified NU6300 as a novel small-molecule activator of Nrf2 that restores mitochondrial function, alleviates oxidative stress, and suppresses inflammasome activation and pyroptosis. Mechanistically, NU6300 covalently modified Kelch-like ECH-associated protein 1 (Keap1) at cysteine-489, disrupting the Keap1-Nrf2 interaction, thereby promoting Nrf2 nuclear translocation and transcription of antioxidant genes. Notably, NU6300 inhibits NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome activation and gasdermin D (GSDMD)-mediated pyroptosis through redox-dependent mechanisms, representing the first evidence that covalent modification of Keap1 at cysteine-489 by NU6300 bridges Nrf2 activation and inflammasome suppression. In vivo, NU6300 exhibits potent antioxidant and anti-inflammatory protection against acetaminophen-induced acute liver injury in mice. Collectively, these findings demonstrate that NU6300 is a novel Nrf2 activator and offers a promising therapeutic strategy for pyroptosis-driven inflammatory diseases.
Metabolic difference of potentially toxic components from Psoraleae Fructus and Euodiae Fructus in Sishen formula by different compatibilities and physiologies
Lili Hong, Yijin Yang, Lianxing Wang, Yiqing Yao, Yadan Zou, Hongda Wang, Xue Li, Yuan Li, Lingli Ma, Xiaoying Wang, Xiumei Gao, Wenzhi Yang
, Available online  , doi: 10.1016/j.jpha.2025.101467
Abstract:
Compatibility attenuation is an effective strategy to ensure the safety of traditional Chinese medicine (TCM). Mechanistic elucidation is essential, however, no consensus reaches on the scientific connotation of compatibility attenuation in Sishen formula (SSF). Given TCM metabolism is closely associated with its toxicological consequences, this study was designed to systematically decipher and compare the holistic metabolic differences of potential toxicants derived from Psoraleae Fructus (PF) and Euodiae Fructus (EF) within SSF. In total, 23 potential toxicants from PF and EF were identified through a comprehensive literature review. Using ultra-high performance liquid chromatography/ion-mobility quadrupole time-of-flight mass spectrometry and ultra-high performance liquid chromatography/triple quadrupole-linear ion trap mass spectrometry, the metabolic difference of target components among differentiated compatibility and physiological state was elucidated by integrating serum metabolomics and poly-pharmacokinetics analyses. Holistically, the compatibility could suppress the transformation of potential toxicants, whereas irritable bowel syndrome (IBS) state exhibited a promoting effect. Myristicae Semen (MyS) or Schisandrae Chinensis Fructus (SCF) increased the exposure of toxicants from PF, while EF demonstrated an opposing effect. SCF promoted the exposure of toxicants from EF, which could be mitigated by Ershen formula. The IBS mice exhibited greater exposure to potential toxicants and their metabolites from PF (compared to the sham operation group), yet SSF alleviated this effect. Furthermore, potential toxicants in the SSF group tended to exhibit reduced metabolic transformation, decreased exposure, enhanced tissue distribution, and facilitated excretion. Collectively, these findings provide novel insights into the metabolic mechanisms underlying SSF detoxification and offer valuable safety recommendation in clinical use.
Unveiling the ‘Eating Poison’ of Polygala tenuifolia xylem: Mood changes and myocardial injury
Fusheng Zhang, Lijun Zhang, Wei Mao, Yunzhi Ma, Yingxin Lou, Xiaoying Li, Huan Liu, Lin Zhao, Dingding Guo, Zhenyu Li
, Available online  , doi: 10.1016/j.jpha.2025.101466
Abstract:
The precise processing methods of traditional Chinese herbal medicines are paramount to ensuring their safety and efficacy. Leigong PaoZhi Lun, the seminal work on the processing of Chinese herbal medicine, documents that the ingestion of Polygala tenuifolia Xylem (PTX) induces a state referred to as "MEN". However, the biological phenotypic effects of PTX-induced "MEN" and its underlying mechanisms remain largely unexplored. This study employs a comprehensive approach, integrating behavioral observations related to the central nervous system (CNS) and cardiovascular system (CVS), electrocardiogram analysis, myocardial enzyme detection, Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q/TOF-MS)-based metabolomics, plasma exosomal microRNA (miRNA) sequencing, intracerebral cannulation of the lateral habenula (LHb) with administration of the N-Methyl-D-Aspartate receptor (NMDAR) antagonist 2-amino-5-phosphonopentanoic acid (AP5), molecular docking, and a combination of in silico and wet lab experiments. This multifaceted methodology unveiled the chemical phenotype of PTX, identifying 245 chemical constituents, including 7 specific metabolites. Two key findings emerged: PTX disrupts the glutamate (Glu)-gamma-aminobutyric acid (GABA) balance within the LHb, leading to CNS-related depressive-like mood alterations. Additionally, tenuifolin and sibiricose A5 in PTX mediate aldehyde dehydrogenase 2 (ALDH2) inactivation, resulting in CVS-related myocardial cell damage, subsequently causing increased heart rate and hypoxia. These findings provide a novel research perspective on the "safety" quality control and evaluation of P. tenuifolia. Additionally, they offer new evidence to elucidate the modern scientific implications of the theories of "same origin with different effects" and "co-existence of opposite properties" in traditional Chinese medicine.
Lactate metabolism and lactylation: Therapeutic and pre-clinical implications in neovascularization in peripheral artery disease
Sheng-Quan Chen, Shu-Jing Zhang, Pei-Jun Liu, Yi Wu, Si-Xuan Li, Jian-Cang Ma, Wu-Jun Li, Shao-Ying Lu, Ji-Chang Wang
, Available online  , doi: 10.1016/j.jpha.2025.101457
Abstract:
Peripheral artery disease (PAD) is a progressive ischemic condition with limited therapeutic options at advanced stages. Current treatments predominantly target revascularization, often neglecting the metabolic dysregulation underlying this condition. Emerging evidence positions lactate not merely as a glycolytic byproduct but as a critical signaling metabolite that orchestrates neovascularization, vascular remodeling, and immune modulation. Furthermore, lactate-induced histone and nonhistone lactylation dynamically regulate gene expression in ischemic tissues, exerting stage- and cell type-specific effects that may be protective or deleterious. This duality underscores the complexity of lactate signaling and its context-dependent influence on PAD progression. Importantly, lactate and lactylation profoundly affect key vascular cell functions, including endothelial cells (ECs), vascular smooth muscle cells (VSMCs), and macrophages, modulating neovascularization and remodeling. This review summarizes recent advances in the understanding of lactate and lactylation, focusing on their regulatory roles in PAD-associated neovascularization and therapeutic potential for PAD.
Role of oxidative stress in sepsis: Mechanisms, pathways, and therapeutic strategies
Xin-Ru Yang, Ri Wen, Ni Yang, Yang Gao, Tie-Ning Zhang
, Available online  , doi: 10.1016/j.jpha.2025.101452
Abstract:
Sepsis, a life-threatening condition caused by dysregulated host response to infection, leads to high morbidity and mortality, primarily due to sepsis-induced organ dysfunction. Oxidative stress, driven by excessive reactive oxygen species (ROS), plays a central role in sepsis pathophysiology, exacerbating inflammation, mitochondrial dysfunction, and cellular damage in multiple organs, including the heart, kidneys, liver, lungs, brain, and skeletal muscles. This review provides a comprehensive analysis of mechanisms by which oxidative stress contributes to sepsis-induced organ injury. Most current research examining the interplay between ROS, inflammation, mitochondrial dysfunction, and cell death pathways such as apoptosis, ferroptosis, and pyroptosis, are animal- or cell-based. Key signaling pathways, including nuclear factor κB (NF-κB), NLR family pyrin domain-containing 3 inflammasome (NLRP3), nuclear factor erythroid 2-related factor 2 /heme oxygenase-1 (Nrf-2/HO-1), and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), are explored as potential therapeutic targets. This review also highlights the roles of mitochondrial quality control, autophagy, and noncoding RNAs in mitigating oxidative damage.
Principles and strategies in cold/hot property studies of traditional Chinese medicine: an evolution from traditional theory to modern elucidation
Min Zhang, Xin Zhang, Rui Wei, Yi-nuo Li, Ying Hu, Ya-dan Zou, Xue Li, Yue-fei Wang, Wen-zhi Yang, De-an Guo
, Available online  , doi: 10.1016/j.jpha.2025.101455
Abstract:
Property of traditional Chinese medicine (TCM) is the core of the basic theories of TCM. Especially, the cold and hot properties are considered as closely related to the clinical medication and have the guiding significance. Driven by the ongoing advances of modern analytical technology, studies on the ancient theory of TCM cold and hot properties are flourishing recently, however, the review focusing on the applied research methods is insufficient. This review, by the bibliometric analysis of 996 associated publications, discloses the methodological evolution in researching the cold and hot properties of TCM from the traditional temperature-based methods (e.g. cold/hot plate differentiating and infrared thermography technologies) to modern elucidation that relies on the material basis-oriented strategies (multi-omics and gut microbiomics). The analytical techniques that are appliable to the in vitro/in vivo characterization of TCM decoction, analysis of effects on endogenous substances, and use of machine learning models for predicting properties, are systematically summarized. In addition, a review on the principles, characteristics, and applications of these analytical methods is conducted, to highlight the important research ideas and key results. It is thus expected to provide valuable reference for the in-depth analysis and better understanding of the theory of TCM properties.
A novel high-entropy TiVCrMoC3Tx assisted LDI MS for serum metabolic fingerprint in rheumatoid arthritis
Zhilong Chu, Xi Yu, Xiao Wang, Wenqiang Zhang, Yuming Li, Xinfeng Yan, Weining Yan, Hongzheng Meng, Lingyu Li, Guanhua Zhang, Ruya Wang, Miaomiao Li, Jun Li, Weiqiang Liang, Chunxia Ma
, Available online  , doi: 10.1016/j.jpha.2025.101456
Abstract:
Worldwide, rheumatoid diseases account for approximately 37.57/100,000 disability-adjusted life years (DALYs). Early diagnosis of rheumatoid arthritis (RA) can effectively reduce associated risks and improve quality of life. To achieve this, accurate and rapid advanced tools are required. Herein, TiVCrMoC3, a novel high-entropy two-dimensional (2D) carbide MXene that exhibits excellent electrical conductivity, is prepared and applied to surface-assisted laser desorption ionization mass spectrometry (SALDI-MS) analysis for the first time. TiVCrMoC3 demonstrates superior performance in small-molecule detection compared with typical inorganic and organic substrates. Moreover, its exhibits ultrahigh sensitivity (limit of detection (LOD) at the 10 pg/mL level), excellent repeatability (coefficient of variation (CV) <4%), excellent quantitative detection capability (coefficient of determination = 0.99987), clean background, and broad analyte coverage. Results showed that TiVCrMoC3-assisted laser desorption ionization mass spectrometry (LDI-MS) is efficient in screening RA diseases, with the advantages of high throughput and low cost. It enables accurate and quantitative analysis of various low-concentration metabolites in 1 μL of biological fluid within seconds. Combined with machine learning, TiVCrMoC3-assisted LDI-MS is used to accurately diagnose multiple RA samples. A total of 8 potential different small-molecule metabolites between individuals with osteoarthritis (OA) and RA were identified based on relative quantification methods, and their associated metabolic changes were discussed. TiVCrMoC3-assisted LDI-MS provides a potential tool for the rapid diagnosis of RA and may pave the way for precision medicine.
Tranilast ameliorates experimental abdominal aortic aneurysm by inhibiting the NLRP3 inflammasome pathway
Haole Liu, Kangli Tian, Weilai Fu, Longlong Qin, Ruipu Tian, Panpan Wei, Jiawei Zou, Naqash Alam, Fizza Malik, Kexin Li, Meng Li, Boyu Xu, Jia Guo, Congcong Xia, Rong Wang, Weirong Wang, Liang Bai, Enqi Liu, Baohui Xu, Yankui Li, Sihai Zhao
, Available online  , doi: 10.1016/j.jpha.2025.101453
Abstract:
An abnormal inflammatory response is one of the main pathogenic mechanisms of abdominal aortic aneurysms (AAAs), and tranilast, an antiallergic drug, has anti-inflammatory properties. The effect and mechanism of action of tranilast on AAAs remain incompletely defined. To evaluate the preventive and therapeutic effects on experimental AAAs induced by intra-aortic elastase infusion in mice, tranilast was administered either before or after elastase infusion and continued until the experimental endpoint. Bioinformatics analysis and corresponding validation experiments were used to explore the possible mechanisms by which tranilast affects AAA progression. Compared with vehicle treatment, both tranilast pre-treatment and post-treatment therapies markedly inhibited aneurysmal aortic expansion. Treatment with tranilast attenuated the degradation of aneurysmal medial elastin and the depletion of smooth muscle cells. Aortic leukocyte accumulation was significantly lower in aneurysmal aortas from tranilast-treated mice than in those from vehicle-treated mice. Mural abnormal angiogenesis and aortic matrix metalloproteinase (MMP) 2 and 9 expression levels were also reduced after tranilast treatment. Bioinformatics analysis revealed that nucleotide-binding oligomerization domain-like receptor family protein 3 (NLRP3) may be a hub target through which tranilast affects AAAs. NLRP3 expression levels were lower in the aneurysmal aortas of tranilast-treated mice than in those of vehicle-treated elastase-infused mice. Both Nlrp3 deficiency and treatment with the NLRP3 inhibitor MCC950 attenuated experimental AAAs. However, cotreatment with tranilast had no additive or synergistic influence on AAA suppression. Additionally, tranilast treatment reduced caspase 1 cleavage by the NLRP3 inflammasome and consequently interleukin-1β secretion in peritoneal macrophages in vitro. These findings indicate that the protective effect of tranilast on AAA may be partially mediated by the inhibition of the NLRP3 inflammasome pathway and may represent a potential drug for the treatment of AAA in the clinic.
Pharmacological effects, classification, genetic and molecular studies of different chemotypes essential oil of Perilla frutescens (L.) Britt.: A review
Wei Wei, Zhaoyuan Li, Bin Wang, Yang Liu, Yuxuan Sun, Dong Wen, Mei Rong, Pengcheng Huang, Yuwei Guo, Qiuling Wang, Zhihui Gao, Jianhe Wei
, Available online  , doi: 10.1016/j.jpha.2025.101454
Abstract:
Perilla frutescens (L.) Britton (P. frutescens) is a highly valuable medicinal plant known for a wide variety of chemotypes based on the components of its essential oils. The appropriate and secure medicinal use of P. frutescens has been severely limited due to the lack of chemotype classification standards and pharmacological studies. In this paper, a classification standard for essential oils in P. frutescens was proposed. The pharmacological activities of different chemotypes or their main components were summarized. Genetic and molecular studies related to the formation of different chemotypes were also reviewed. The molecular mechanism underlying the formation of P. frutescens chemotypes is also discussed to pave the way for the innovation of P. frutescens germplasms for medicinal use.
Integrating High-resolution Bioassay Profiling with Affinity-based Ligand Fishing for Unveiling Galloylated Derivatives as Novel Catechol-O-methyltransferase Inhibitors in Paeonia lactiflora Pall.
Jiaming YUAN, Zhuoping ZHENG, Zhongkang WANG, Hao TIAN, Lingling XI, Jacques CROMMEN, Tingting ZHANG, Jincai WANG, Zhengjin JIANG
, Available online  , doi: 10.1016/j.jpha.2025.101449
Abstract:
Catechol-O-methyltransferase (COMT) inhibition is a critical therapeutic strategy for Parkinson’s disease (PD), yet clinical inhibitors face limitations in bioavailability and hepatotoxicity, driving demand for novel natural scaffolds. In this study, we developed an integrated analytical platform by coupling high-resolution bioassay profiling (HRBP) and affinity-based ligand fishing system to effectively characterize bioactive compounds targeting COMT in Paeonia lactiflora Pall. (the most frequently used core herb in tradition Chinese medicine prescriptions for PD treatment). Parallel High-performance liquid chromatography with diode-array detection and tandem mass spectrometry (HPLC-DAD-MS/MS) coupled with nanofractionation enabled real-time bioactivity mapping via 384-well COMT inhibition assays, while semi-preparative liquid chromatography was employed to further identify co-eluted components. HRBP and immobilized COMT ligand fishing identified 16 and 21 candidates, respectively, with 5 overlapping bioactive markers. Notably, the potent inhibitors galloylpaeoniflorin (IC50 = 16.2 ± 3.4 μM) and 1,2,3,4,6-O-pentagalloylglucose (IC50 = 3.1 ± 0.5 μM) exhibited comparable potency to the positive control morin (IC50 = 10.1 ± 0.7 μM). Molecular docking results further revealed the critical interactions and binding sites between the active compounds and COMT. The validated platform demonstrates significant potential for rapid discovery of plant-derived enzyme inhibitors, bridging advanced separation, bioactivity screening, and mechanistic validation in neurodegenerative therapeutic development.
Polydatin for Treating Spinal Cord Injury: Multiple Mechanisms and Challenges
Zhishuo Wang, Jiaming Zhang, Longyu Li, Yuhao Zhang, Haoyu Shen, Chunfeng Shang, Zikuan Leng, Guowei Shang, Hongwei Kou, Keya Mao, Hao Han, Songfeng Chen, Hongjian Liu
, Available online  , doi: 10.1016/j.jpha.2025.101451
Abstract:
Spinal cord injury (SCI) is a serious neurological system disease. After SCI, a series of cascade reactions can cause irreversible damage, with a high disability rate and mortality rate. The complexity of the pathological mechanism of SCI limits the efficacy of various traditional therapies, and it is urgent to find new therapeutic means. In recent years, the method of extracting effective components from natural Chinese herbs for treating diseases has attracted widespread attention. Polydatin (PD) is an active ingredient extracted from Polygonum cuspidatum and its structure is similar to the traditional drug resveratrol. Sufficient studies have proved that PD plays anti-inflammatory, antioxidant, anti-apoptotic and neuroprotective roles in the treatment of multisystem diseases. These effects are also significant in the treatment of SCI. Based on the structural differences between PD and resveratrol, this paper illustrates the feasibility of PD in the treatment of SCI, and systematically expounds the pathophysiological process of SCI and the molecular mechanism of PD in the treatment of SCI. Furthermore, this article discusses feasible measures to improve the bioavailability of PD, summarizes the application of new drug delivery systems in PD, and analyzes the challenges and prospects of PD in SCI treatment.
PFKM promotes chemoresistance in lung adenocarcinoma by regulating RAB8B mediated exosome release
Qiang Wang, Qiyao Nong, Junguo Zang, Meiyu Gao, Ying Zhang, Xinyuan Hao, Yuan Tian, Fengguo Xu, Pei Zhang
, Available online  , doi: 10.1016/j.jpha.2025.101450
Abstract:
Lung adenocarcinoma (LUAD), the most widely existing subtype of non-small cell lung cancer (NSCLC), is a leading cause of cancer-related mortality, characterized by challenging early diagnosis, high rates of recurrence and metastasis, and poor prognosis. Chemotherapy remains the primary treatment for advanced LUAD, but its effectiveness is often hindered by the development of chemoresistance. In this study, a targeted metabolomics method unveiled a marked up-regulation of glycolysis in chemotherapy-resistant LUAD cells. Particularly, the ratio of fructose 1,6-bisphosphate (FBP) to fructose 6-phosphate (F6P) reflected the activity of the rate-limiting enzyme Phosphofructokinase muscle isoform (PFKM) was significantly elevated. We further observed a significant increase in exosome release in chemotherapy-resistant cells. More importantly, it was found that the interaction between PFKM and exosomes plays a role in regulating chemoresistance in LUAD. Mechanistically, PFKM influences exosomes release by modulating Ras-related protein Rab-8B (RAB8B) expression, impacting apoptosis and glycolytic metabolism, thereby promoting chemoresistance. Furthermore, drug-resistant cells enhance chemoresistance in sensitive cells by releasing exosomes with heightened glycolytic activity. These findings highlight the crucial role of the PFKM-RAB8B axis in promoting chemoresistance, suggesting it as a potential therapeutic target for countering LUAD chemoresistance.
Novel Bioactive Peptides Targeting Keap1-Nrf2 Interaction for Combating UVA-Induced Skin Aging: Computational Discovery and Experimental Validation
Haiqiong Guo, Yueting Sun, Wenyu Shi, Rui Huang, Xiaobei Zhi, Qingsong Liu, Ping Zhao, Qingyou Xia
, Available online  , doi: 10.1016/j.jpha.2025.101446
Abstract:
Ultraviolet A (UVA)-induced skin aging poses a significant threat to skin health and aesthetics, yet effective and biosafe therapeutic interventions remain scarce. This study focused on identifying bioactive peptide inhibitors targeting the Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) protein-protein interaction (PPI) to counteract UVA-induced skin aging. Using computational virtual screening, we identified two high-affinity, low-toxicity peptides, Seq1 and Seq3, which effectively activated the Nrf2-antioxidant response element (ARE) pathway. This activation led to the upregulation of antioxidant genes and significantly reduced oxidative stress. Additionally, these peptides inhibited the mitogen-activated protein kinase (MAPK) and nuclear factor kappa-B (NF-κB) signaling pathways, thereby reducing inflammation and suppressing the expression of matrix metalloproteinases (MMPs), key contributors to skin aging. In vivo studies demonstrated that Seq1 and Seq3 effectively prevented UVA-induced epidermal thickening, collagen degradation, and the upregulation of pro-inflammatory cytokines in mouse models. Our results underscore the therapeutic potential of Seq1 and Seq3, particularly Seq3, as novel bioactive peptides targeting the Keap1-Nrf2 PPI for combating UVA-induced skin aging, offering promising avenues for skincare and healthcare applications.
Polysaccharides self-healing hydrogel for skin regeneration
Nan Xu, Fanhe Meng, Binglun Zhang, Xing Yang, Haibo Wang, Fan Yang
, Available online  , doi: 10.1016/j.jpha.2025.101447
Abstract:
Damaged skin is prone to infection and impaired healing, making efficient wound care materials critical. Polysaccharide-based self-healing hydrogels have demonstrated significant potential in skin regeneration due to their biocompatibility, biodegradability, and ability to mimic the extracellular matrix (ECM). This review summarizes the fabrication techniques, core polysaccharide materials, and challenges of these hydrogels. Hydrogel preparation primarily involves chemical cross-linking, physical cross-linking, and three-dimensional (3D) bioprinting. Chemical cross-linking confers high mechanical strength but limited self-healing capacity, while physical cross-linking enables rapid self-healing via dynamic non-covalent interactions, responsive to stimuli like pH and temperature. 3D bioprinting allows customizable tissue-like structures with precise control over cell distribution and bioactive molecule release. Key polysaccharides include alginate, chitosan, hyaluronic acid (HA), cellulose, and dextran. Alginate forms reversible networks via calcium ion cross-linking, suitable for wound dressings and tissue engineering. Chitosan, with amino and hydroxyl groups, exhibits antibacterial activity and promotes cell proliferation, widely used in infected wounds. HA achieves self-healing through dynamic covalent bonds, accelerating collagen deposition and angiogenesis. Cellulose derivatives employ boronic ester or Schiff base linkages for self-healing systems in injectable formulations. Dextran utilizes Diels-Alder reactions for self-healing under physiological conditions, ideal for drug delivery. Commercial products like HyStem® and Chitogel® have entered clinical use, integrating growth factors or antimicrobials to enhance wound healing. However, challenges persist, including insufficient mechanical strength, mismatched degradation rates with healing processes, long-term safety concerns, and scalability. Future directions focus on "smart" hydrogels, combined with clustered regularly interspaced short palindromic repeats (CRISPR) gene editing or artificial intelligence (AI)-optimized design, to enhance functionality and clinical translation.
Comparative analysis for optimal LSD1 inhibitors evaluation techniques:pros and cons
Qiange Yin, Congcong Ma, Xiaoying Zhao, Panjie Wang, Dandan Shen, Chenchen Ren, Baojin Wang, Feiyan Li, Yan Yang, Hui-Min Liu, Li Yang, Yi-Chao Zheng
, Available online  , doi: 10.1016/j.jpha.2025.101430
Abstract:
Aberrant expression of lysine-specific demethylase 1 (LSD1) has been consistently implicated in a broad spectrum of malignancies, underscoring its relevance as a therapeutic target. Despite growing interest, the development of LSD1 inhibitors continues to face significant challenges, in part due to the enzyme’s dual role in catalysis and as a scaffolding protein within chromatin-remodeling complexes. Recent insights into the non-enzymatic functions of LSD1 have shifted the focus toward disrupting its protein–protein interactions, particularly with chromatin-modifying enzymes, as a complementary or alternative therapeutic strategy. In light of the limited systematic evaluation of available technologies, this work provides a critical overview and comparative analysis of current screening platforms and binding affinity assays, with particular attention to approaches capable of identifying LSD1 scaffold inhibitors. These efforts aim to accelerate the discovery of next-generation LSD1-targeted therapies with improved translational potential in oncology.
Drug delivery system of curcumin to the lungs based on poly(3-alloxyloxy-1,2-propylene succinate)-sebacic acid copolymers
Karolina Knap, Konrad Kwiecień, Jonasz Czajkowski, Rafał Szostecki, Daria Niewolik, Katarzyna Jaszcz, Peter Olinga, Katarzyna Reczyńska-Kolman, Elżbieta Pamuła
, Available online  , doi: 10.1016/j.jpha.2025.101434
Abstract:
Polyanhydrides are attractive materials for drug delivery matrices as a result of their cytocompatibility and fast degradation rate. Here, we synthesized and characterized copolymers of poly(3-allyloxy-1,2-propylene succinate) (PSAGE) and sebacic acid (SBA). The successful polymerization was confirmed by proton nuclear magnetic resonance (1H NMR) and Fourier transform infrared (FTIR) spectroscopy analyses. The material with 40% PSAGE (PSAGE-SBA60) was more hydrophilic than the material with 20% PSAGE (PSAGE-SBA80) (water contact angle 82.2 ± 11.6° vs. 98.6 ± 8.9°, respectively). PSAGE-SBA60 also had a lower molecular weight than PSAGE-SBA80 (Mn = 6,400 Da vs. 9,800 Da). Both polyanhydrides were used to encapsulate curcumin (CUR) as a potential anti-inflammatory, antimicrobial and anticancer agent. The unloaded microparticles (MPs) and CUR-loaded MPs were produced using the emulsification/solvent evaporation method. The CUR was uniformly distributed within the MPs, as confirmed by fluorescence microscopy. All MPs had a geometric diameter < 5 μm and their surface charge was negative. MPs_PSAGE-SBA80 + CUR had the best aerodynamic properties, as shown by laser diffraction measurements and flowability parameters, i.e. Carr index and Hausner ratio. The MPs obtained from PSAGE-SBA60 degraded faster than those of PSAGE-SBA80. All MPs were noncytotoxic at a concentration of up to 100 μg/ml in the in vitro model (BEAS-2B lung epithelial cells) and ex vivo precision-cut tissue slices (PCTSs) rat model. The developed MPs are promising CUR carriers for pulmonary delivery in a dry powder formulation.
Legacy effects of lifestyle intervention on circulating metabolites in people with impaired glucose tolerance: a cross-sectional analysis of the Da Qing Diabetes Prevention Study
Meng Yu, Xin Qian, Hongmei Jia, Jinping Wang, Siyao He, Xinxing Feng, Yali An, Qiuhong Gong, Hongzhao You, Guangwei Li, Yanyan Chen, Zhongmei Zou
, Available online  , doi: 10.1016/j.jpha.2025.101433
Abstract:
Lifestyle intervention is considered a global consensus for preventing and delaying the development of type 2 diabetes (T2D). This study aims to investigate the differences in metabolites associated with the long-term effect of lifestyle intervention in people with impaired glucose tolerance (IGT). The study enrolled 60 and 57 people with IGT who were originally assigned to the intervention and control (non-intervention) groups in a lifestyle intervention 6-year trial (1986-1992), respectively, as part of the Da Qing Diabetes Prevention Study. In 2006, 14 years after completion of the intervention trial, blood samples were collected for metabolomics analyses and T2D outcomes were assessed. Metabolomics outcomes were not analyzed at baseline. The untargeted metabolomics revealed that 14 plasma metabolites were significantly different between lifestyle intervention and control groups. Targeted metabolomics revealed that plasma concentrations of LysoPC(18:0/0:0) and SM(d18:1/16:1(9Z)) were significantly higher in the lifestyle intervention group compared with the control (16.72 ± 4.75 vs. 1.34 ± 0.40 and 2.60 ± 1.24 vs. 0.40 ± 0.08, P < 0.0001). A 1 μg/mL increase in LysoPC (18:0/0:0) and SM(d18:1/16:1(9Z)) was significantly associated with decreased risk of T2D (odds ratios were 0.82 (95% CI 0.75–0.90) and 0.17 (95% CI 0.07–0.39)) in all participants after adjusting for clinical confounders. In this cross-sectional study, the plasma LysoPC(18:0/0:0) and SM(d18:1/16:1(9Z)) differ between IGT people assigned to intervention and control groups 14 years after the 6-year intervention trial, suggesting they may have been related to the long-term legacy effects of these interventions.
Menaquinone-7 alleviates mitochondrial dysfunction and senescence in senile osteoporosis by targeting the PINK1-mediated mitophagy via PXR/ERK/CREB signaling pathway
Yu Xu, Wencan Zhang, Wenpeng Xu, Shangzhi Li, Dingxin Zhang, Xiangyu Lin, Jincheng Liu, Qingyang Fu, Peijie H, Haipeng Si
, Available online  , doi: 10.1016/j.jpha.2025.101432
Abstract:
Current therapeutic strategies for senile osteoporosis inadequately address its low-turnover pathology driven by mitochondrial dysfunction and cellular senescence. This study identifies menaquinone-7 (MK-7), a vitamin K2 isoform, as a novel therapeutic agent targeting mitochondrial homeostasis in senile osteoporosis. Through RNA sequencing analysis and intramedullary adeno-associated virus (AAV)-based gene manipulation in aged mice, cellular communication network factor 2 (Ccn2) was identified as a critical mediator of MK-7’s bone-protective effects. Biochemical and proteomic assays revealed that MK-7 binds to the nuclear receptor pregnane X receptor (PXR), activating the extracellular signal-regulated kinases 1/2 (ERK1/2)/cyclic AMP-responsive element-binding protein (CREB) signaling cascade to upregulate Ccn2 in senescent bone marrow mesenchymal stem cells (BMSCs). This pathway enhanced PTEN-induced kinase 1 (PINK1)/Parkin-mediated mitophagy, reducing mitochondrial DNA damage, reactive oxygen species (mtROS), and senescence-associated secretory phenotype (SASP), while restoring metabolic function. MK-7 redirected BMSC differentiation from adipogenic to osteogenic lineages, effectively mitigating age-related bone loss in vivo. Mechanistically, MK-7 stabilized PXR via direct interaction at the F285 residue, as confirmed by drug affinity responsive target stability (DARTS), cellular thermal shift assay (CETSA), and molecular docking. PXR activation further promoted ERK1/2/CREB-dependent Ccn2 expression, which orchestrated mitochondrial quality control and cellular energy metabolism. Our findings establish MK-7 as a dual-function agent that concurrently alleviates senescence and metabolic imbalance in bone tissue, offering a safe and targeted strategy for senile osteoporosis. This study provides critical insights into the pharmacological modulation of mitochondrial pathways and highlights MK-7’s translational potential in geriatric bone health.
Angelicin: A promising tricyclic aromatic agent for ulcerative colitis through cysteine-mediated proliferation of intestinal epithelial cells
Haifan LIU, Dunfang WANG, Lin ZHU, Tao LI, Bin LIU, Jingwei SUN, Xingbo ZUO, Siyuan CHEN, Jianyao LIU, Junying XIAN, Xue FENG, Caijuan ZHANG, Weipeng YANG
, Available online  , doi: 10.1016/j.jpha.2025.101435
Abstract:
Angelicin (Ang), a natural tricyclic aromatic compound and quality marker derived from Fructus Psoraleae, exhibits significant anti-inflammatory efficacy. Fructus Psoraleae has long been utilized clinically for treating ulcerative colitis (UC). However, the specific role of Ang in UC remains poorly characterized. The present study aimed to elucidate the anti-UC effects of Ang and its underlying mechanisms. The anti-UC activity of Ang was evaluated using two UC models induced by dextran sulfate sodium (DSS) and 2,4,6-trinitrobenzenesulfonic acid (TNBS). Results demonstrated that Ang markedly inhibited the progression of UC. Microbial profiling indicated that the Ang-treated microbiome, particularly Lactobacillus murinus, provided protective effects against UC. Mechanistically, Ang facilitated proliferation of normal colonic epithelial cells, thus enhancing the intestinal mucosal barrier (IMB). Cysteine (Cys) played a crucial intermediary role by promoting glutathione (GSH) synthesis, maintaining redox homeostasis, and consequently facilitating cell proliferation. Additionally, increased Cys levels supported ribosomal biogenesis, enhancing protein translation and further stimulating cell proliferation. G-rich RNA sequence-binding factor 1 (GRSF1) was identified as a direct molecular target of Ang during ribosomal biogenesis. These findings indicated that Ang is a promising agent for promoting Cys-mediated cell proliferation, highlighting its role in maintaining redox homeostasis and protein translation. This study provides evidence supporting the future development of Ang as a therapeutic candidate for UC.
Distinct types of regulated cell death in atherosclerosis
Danyi Cao, Han Han, Deyong Yue, Guojun Shi, Yun Chen, Jiahai Shi, Guoliang Meng
, Available online  , doi: 10.1016/j.jpha.2025.101431
Abstract:
Atherosclerosis is a chronic inflammatory disorder with high morbidity and mortality, leading to serious complications like myocardial infarction and strokes. Key cell types involved in atherosclerotic lesions include vascular endothelial cells (VEC), vascular smooth muscle cells (VSMC) and macrophages. Types of regulated cell death (RCD) are significant in the development and progression of atherosclerosis, including apoptosis, autophagy, necroptosis, efferocytosis, ferroptosis, pyroptosis, parthanatos, cuproptosis, lysosome-dependent cell death, NETotic cell death, paraptosis, alkaliptosis, oxeiptosis, entotic cell death and PANoptosis. The regulatory mechanisms and the crosstalk between different types of cells during atherosclerosis are complex, and the exact molecular basis remains obscure. Currently, numerous drugs and compounds have been found to attenuate atherosclerosis by targeting RCD. The review aims to provide an overview of RCD types related to VEC, VSMC, and macrophages in atherosclerosis, providing a reliable theoretical basis of the cellular mechanisms and exploring potential therapeutic strategies.
Small molecules targeting regulated cell death for chronic kidney disease therapy
Wen-Kai Yu, Qing-Ru Zhu, Li Zhou, Xin-Lei Shen, Tian-Yang Cheng, Yi-Ni Bao, Gang Cao
, Available online  , doi: 10.1016/j.jpha.2025.101427
Abstract:

Chronic kidney disease (CKD) is a significant contributor to the global morbidity of non-communicable diseases and is predicted to become the fifth leading cause of death worldwide. However, effective treatments that directly target the underlying causes of CKD remain limited due to its complicated pathogenesis. Recent research has increasingly focused on elucidating the molecular mechanisms and identifying new therapeutic targets of CKD. In recent years, regulated cell death (RCD) has been highlighted as a central mechanism in the development and progression of CKD, suggesting that targeting specific RCD signaling pathways may offer effective strategies for CKD. Emerging research reveals that small molecules can effectively target different types of RCD in the context of CKD, including apoptosis, autophagy-dependent cell death, pyroptosis, ferroptosis and necroptosis. In this review, we summarize current understanding of the mechanism of RCD in CKD. Importantly, we emphasize the regulatory mechanism of small molecules on disturbed RCD to alleviate CKD. Taken together, this review enhances the comprehension of small molecules as modulators of RCD against CKD, which will provide new insights and potential avenues for CKD therapy.

Crebanine protects against ovariectomy-induced bone loss by targeting Sirt1 to interfere with NF-κB acetylation and ROS activity
Haojie Zhang, Xuan Zhao, Zheng Wang, Jiansen Miao, Xinli Hu, Peng Cui, Chen Jin, Xibin Zhao, Haibo Liang, Hantao Ye, Yining Xu, Xiaolong Chen, Wei Wang, Shibao Lu
, Available online  , doi: 10.1016/j.jpha.2025.101426
Abstract:
Osteoporosis, the most prevalent skeletal disorder, is primarily driven by aberrantly increased osteoclast formation and/or activity. Targeting hyperactive osteoclasts remains the cornerstone of current therapeutic strategies. Crebanine (Cre), a natural isoquinoline-derived alkaloid with diverse pharmacological activities, has not yet been explored for osteoporosis treatment. This study aimed to evaluate the therapeutic potential of Cre against ovariectomy (OVX)-induced osteoporosis and elucidate its underlying mechanisms. Cre dose-dependently inhibited in vitro osteoclast differentiation, actin ring formation, and bone resorption by downregulating nuclear factor of activated T cells 1 (NFATc1) and key osteoclast-related genes. Simultaneously, Cre enhanced osteoblast differentiation and mineralization, upregulated osteoblast marker genes, and restored hydrogen peroxide-impaired alkaline phosphatase (ALP) activity impaired by hydrogen peroxide, indicating dual regulation of bone remodeling. Mechanistically, Cre activated sirtuin 1 (Sirt1), promoting p65 deacetylation, inactivated IκB kinase (IKK), and stabilized IκBα, thus inhibiting nuclear factor-kappaB (NF-κB) signaling. Additionally, Cre reduced reactive oxygen species (ROS) by upregulating antioxidant enzymes (heme oxygenase-1 (HO-1), catalase) and suppressing nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOX1/4). Furthermore, Cre specifically bound to the predicted site of receptor activator of NF-κB (RANK), blocking RANK ligand (RANKL)-RANK interaction and disrupting downstream protein kinase B (Akt) and mitogen-activated protein kinase (MAPK) signaling pathways. In the OVX mouse model, Cre significantly attenuated bone loss and osteoclastogenesis. Crucially, Cre showed no toxicity in liver or kidney function tests. Collectively, these findings demonstrate that Cre exerts dual therapeutic effects, inhibiting osteoclastogenesis via Sirt1-mediated NF-κB/ROS suppression and promoting osteoblast activity, providing a promising therapeutic strategy for osteoporosis.
Real-Time Visualization of Drug-Target Interactions in Native Subcellular Microenvironments for Lysosome-targeted Drug Discovery
Ran Wang, Yatong Yuan, Huarong Shao, Yuehao Sun, Changcheng Lai, Mengrui Zhang, Wenjing Song, Tao Zhang, Fengfeng Zhuang, Qixin Chen, Peixue Ling, Xintian Shao
, Available online  , doi: 10.1016/j.jpha.2025.101428
Abstract:
Conventional ex vivo drug screening platforms struggle to recapitulate native subcellular microenvironments, leading to high off-target rates and compromised discovery of bioactive compounds. To address this, we developed subcellular target- tracking fluorescent-visualization-based interaction screening (SubTrack-FVIS), a platform combining super-resolution imaging with target-specific fluorescent tagging. SubTrack-FVIS first maps nanoscale spatial distributions of drug targets within living cells, then screens compound libraries to identify molecules specifically binding to target-enriched domains, and finally quantifies drug-target interactions through super- resolution imaging tracking. Compared to traditional toolbox, SubTrack-FVIS reduces off-target effects by evaluating compound binding within native subcellular architectures. When applied to the lysosomal vacuolar H+-ATPases (V-ATPase) subunit, ATP6V1A, a validated anti-cancer target, this approach identified for lysosomal alkalization fluorescent drug (LAFD) as a potent inhibitor. Super-resolution imaging revealed LAFD's dynamic binding to ATP6V1A clusters, enabling real-time visualization of V-ATPase inhibition and subsequent lysosomal destabilization. Crucially, SubTrack-FVIS uncovered LAFD's unique mechanism of blocking autophagosome-lysosome fusion, resolving autophagic flux obstruction at sub-100 nm resolution. This platform establishes a visualization framework for discovering drugs within physiological subcellular contexts while simultaneously decoding their mechanistic impacts, offering application potential for target-centric drug development.
A comprehensive review on herbal approaches for treatment of urinary tract infections: Scope and challenges
Md Saddam, Sujeet K. Mishra, Neelam Singh, Shyam Baboo Prasad, Smriti Tandon, Hemant Rawat, Ganesh Dane, Vijay Kumar, Ajay Kumar Meena, Ravindra Singh, Arjun Singh, Ch V. Narasimhaji, Narayanam Srikanth, Rabinarayan Acharya
, Available online  , doi: 10.1016/j.jpha.2025.101414
Abstract:
Urinary tract infections (UTIs) have become a major health concern globally, necessitating effective treatments for mitigating discomfort and avert complications. The uropathogens commonly associated with UTIs in humans such as Bacillus species, Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Escherichia coli (E. coli) are progressively developing resistance to current treatments and medications. The ancient wisdom of Ayurvedic medicines and its holistic approach can contribute to UTI treatment due to its lower toxicity, effectiveness against pathogens, and cost efficiency making it a viable option to complement or replace conventional treatments. This review delineates the key probable interactions between the bioactive components of antibacterial herbal drugs and UTI pathogens. Herbal drugs are rich in antioxidants such as flavonoids and polyphenols which can effectively neutralize free radicals and inhibit the formation of bacterial biofilms. These actions help alleviate oxidative stress and contribute to their anti-inflammatory effects. Certain specific herbs traditionally identified for their anti-inflammatory and antibacterial activity have been evaluated for their efficacy towards treatment of UTIs. Finally, the review addresses the challenges associated with herbal treatments of UTIs including issues related to standardization, dosage, and potential interactions with conventional medications that need to be overcome for broader acceptance and application.
Antibody screening for tumor and immune hotspot targets: the frontier of new methods and technologies
Yaping Zhou, Yitan Zou, Shaodong Lv, Dan Tan, Guangyao Li, Wenyan Fu, Changhai Lei, Mingdong Lu, Shi Hu
, Available online  , doi: 10.1016/j.jpha.2025.101417
Abstract:
Advancements in tumor immunotherapy highlight the significant potential of antibody drugs, a key category of biological agents, for treating cancer and autoimmune diseases. This paper begins by defining and classifying key targets in tumor immunity, as well as discussing their structural and functional characteristics. Subsequently, it elaborates on innovative technologies for antibody drug screening, which, when integrated with contemporary molecular biology, biotechnology, and computational biology, have substantially enhanced the efficiency and accuracy of target identification and antibody drug screening processes. Despite the promising prospects of tumor immunotherapy, certain limitations persist in its practical implementation. In conclusion, this paper offers a comprehensive examination of the cutting-edge developments in tumor immunotherapy, focusing on the aspects of tumor immunotherapy itself, critical targets for immunotherapy, and novel technologies and methodologies for antibody screening. This analysis is crucial for advancing the field of tumor immunotherapy and for enhancing both therapeutic efficacy and safety. Furthermore, research and development of antibody drugs in other domains, such as autoimmune and inflammatory diseases, can benefit from it.
Beyond conventional therapies: Gut microbiota modulation and macromolecular drugs in the battle against cardiometabolic diseases
Jingyue Wang, Jing Qu, Mengliang Ye, Ru Feng, Xiang Hui, Xinyu Yang, Jingyu Jin, Qian Tong, Xianfeng Zhang, Yan Wang
, Available online  , doi: 10.1016/j.jpha.2025.101416
Abstract:
Cardiometabolic diseases (CMDs) represent an ongoing major global health challenge, driven by complex interactions among genetic, environmental, and microbiome-related factors. While small-molecule drugs and lifestyle interventions can provide partial clinical benefits, they are possible to be constrained by the limited druggability of key target proteins, the potential for off-target effects, and difficulties in maintaining long-term adherence. In recent years, gut microbiota modulation and macromolecular drugs have emerged as promising therapeutic strategies. Gut microbiota modulation (e.g., probiotics, synbiotics, or natural products) exerts systemic metabolic and immune effects, supporting a therapeutic approach targeting multiple diseases. Meanwhile, macromolecular drugs (e.g., peptides, antibodies, and small nucleic acids) offer precise, pathway-targeted interventions. Despite advancements, limitations remain in addressing ethical considerations in microbiota modulation and optimizing targeted delivery systems, all of which may hinder clinical translation. Here, we provide a comprehensive overview of therapeutic approaches for CMDs, with a focus on obesity, type 2 diabetes mellitus (T2DM), and atherosclerosis (AS). The review is structured around three key aspects: 1) conventional therapies, including small-molecule drugs and lifestyle interventions; 2) emerging therapies, encompassing gut microbiota modulation, macromolecular drugs and their interactions; and 3) challenges and opportunities for comorbidity management, microbiota ethics and artificial intelligence (AI)-driven therapeutic optimization. We hope this review enhances the understanding of small-molecule drugs, lifestyles interventions, gut microbiota modulation and macromolecular drugs in the management of CMDs, thereby fostering medical innovation and contributing to the development of system-based comprehensive therapeutic paradigms.
Targeted nano-drug delivery systems for tumor immunotherapy
Shan Lian, Wenyong Yang, Yan Zeng, Ranran Tang, Kui Wang
, Available online  , doi: 10.1016/j.jpha.2025.101408
Abstract:
While being a safe and effective precision therapy strategy, tumor immunotherapy still fails in many patients due to immunosuppressive microenvironment. Emerging evidence has indicated that the targeted nano-drug delivery systems can accurately deliver therapeutic agents to potentiate the efficacy of immunotherapy. This review will outline recent advances in applying targeted nano-drug delivery systems in immunotherapy, with an emphasis on their crucial roles in regulating innate immunity response, adaptive immunity response, and immunogenic cell death. We will also discuss the current challenges and future opportunities for the clinical translation of targeted nano-drug delivery systems for tumor immunotherapy.
Rational design of a novel specific fluorescent substrate for monitoring hUGT1A4 activity and its application in identification of selective inhibitors
Ning Mao, Shi-Qing Li, Xiang-Lu Zhou, Cong Hu, Wen-Chao Wu, Hua Wei, Li-Wei Zou, Ling Yang
, Available online  , doi: 10.1016/j.jpha.2025.101415
Abstract:
Uridine diphosphate (UDP)-glucuronosyltransferases (UGTs) are a family of enzymes with highly similar amino acid sequences, making it challenging to distinguish between their roles. Developing selective probes and inhibitors is essential for understanding the unique functions of each isoform. In this study, we synthesized four novel naphthalimide-based fluorescent probes bearing nitrogen-containing substituents at the 4-position and identified N-(n-butyl)-4-(4-methylpiperazin-1-yl)-1,8-naphthalimide (BAD3) as a highly selective and sensitive substrate for UDP glucuronosyltransferase 1A4 (UGT1A4). Using BAD3, we established an inhibitor screening platform and identified ursolic acid (T7) as a promising lead compound from a natural product library. Structure-activity relationship (SAR) studies revealed that esterification at the 3-hydroxyl group significantly enhanced inhibitory activity, yielding two potent inhibitors, T25 and T26, while modifications at the 28-carboxyl group reduced activity. Further characterization confirmed T25 (inhibition constant (Ki) = 0.64 μM) and T26 (Ki = 0.61 μM) as selective and competitive UGT1A4 inhibitors. Molecular docking revealed that the 28-carboxyl group plays a crucial role by forming a salt bridge with Arg258 in the UGT1A4 active site. In vivo studies demonstrated that T25 significantly altered the pharmacokinetic profile of BAD3, confirming its inhibitory effect on UGT1A4 in animals. Together, BAD3 and the selective inhibitors T25/T26 serve as valuable molecular tools for studying the physiological and pharmacological roles of UGT1A4.
Unlocking Wnt’s Weak Spot: Glycosylated Nanoalbumins to Reignite Immune Responses in MSS-CRC
Xin Wei, Mingzhu Zuo, Qiongwen Liang, Shiwei Zhang, Jingmei Wang, Zhanfeng Li, Wenguang Yang, Fang Ma, Wangxiao He, Tianya Liu
, Available online  , doi: 10.1016/j.jpha.2025.101412
Abstract:
Microsatellite-stable colorectal cancer (MSS-CRC) is characterized by poor immune infiltration and immune evasion, leading to rapid tumor progression and limited efficacy of current immunotherapies. The bioinformatics analysis revealed that the hyperactivation of the Wnt/β-catenin signaling pathway in MSS-CRC is instrumental in mediating immune suppression. Although inhibiting this pathway presents a therapeutic opportunity, no Wnt inhibitors have been clinically approved due to Wnt's essential role in maintaining tissue homeostasis, with inhibition in normal cells causing significant toxicity. To address it, we discovered that Wnt activation in colorectal cancer cells enhances macropinocytosis, particularly favoring the uptake of glycosylated proteins to meet increased nutrient demands. Building on this insight, we developed a glycosylated human serum albumin (GHSA) co-assembled with carnosic acid (CA), termed glycosylated human serum albumin-carnosic acid (GHSACA), which is selectively internalized by Wnt-activated colorectal cancer cells. This approach not only reduces off-target toxicity but also effectively inhibits the Wnt pathway, resulting in notable tumor inhibition and immune reactivation in murine models, while maintaining a favorable safety profile. This strategy offers a promising therapeutic solution by combining selective Wnt inhibition with enhanced immune activation in MSS-CRC, and highlights the potential of leveraging disease-specific cellular uptake mechanisms for designing nanomedicines, advancing the development of precision-targeted cancer therapies.
Gliquidone alleviates DSS-induced ulcerative colitis in rats by targeting carnitine palmitoyltransferase 1A
Tian Tang, Ying Zhang, Xinrui Xing, Ruiqi Sun, Zhe Yu, Yuan Tian, Zunjian Zhang, Pei Zhang, Fengguo Xu
, Available online  , doi: 10.1016/j.jpha.2025.101409
Abstract:
Ulcerative colitis (UC) is an idiopathic, chronic inflammatory disorder with an increasing incidence worldwide. Due to the complex and unclear therapeutic targets, unmet UC therapeutic drugs still exist. Recently, acylcarnitine metabolism disorder has been linked to intestinal inflammation, but its role in UC remains elusive. According to our preliminary non-targeted metabolomics data, acylcarnitines (ACs) was screened as the disturbed metabolites in the different intestinal inflammation-related diseases. Here we quantified 26 ACs within liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the dextran sulfate sodium (DSS)-induced UC rat model, and found that long-chain acylcarnitines (LCACs) were increased to varying degrees. As the key metabolites of fatty acid β-oxidation (FAO), the upstream metabolites long-chain fatty acids (LCFAs) and the related metabolic enzymes were further characterized, the results showed that the rate-limiting enzyme carnitine palmitoyltransferase 1A (CPT1A)-mediated LCFAs-LCACs metabolic axis was activated sharply. Next in vitro experiments exhibited that CPT1A was significantly upregulated in both inflammatory macrophages and colonic epithelial cells, and inhibition or knockdown of CPT1A could reduce the inflammation level remarkably. Thus, we screened the pharmacologic inhibitors of CPT1A from FDA approved drugs, within molecular docking, Western blot and cell membrane chromatography (CMC) technology, gliquidone was found to inhibit CPT1A in a dose-dependent manner and exert anti-inflammatory effects in vitro. Animal experiments also showed that gliquidone alleviated DSS-induced UC significantly. In summary, our study presents that within metabolomics analysis, inhibiting CPT1A is focused to be a potential therapeutic strategy against UC, and gliquidone represents an alternative treatment.
A comprehensive review of Intelligent Question-Answering Systems in Traditional Chinese Medicine Based on LLMs
Qilan Xu, Tong Wu, Yiwen Wang, Xingyu Li, Heshui Yu, Shixin Cen, Zheng Li
, Available online  , doi: 10.1016/j.jpha.2025.101406
Abstract:
Large language models (LLMs) are advanced deep learning models with billions or even trillions of parameters, enabling powerful natural language processing and knowledge reasoning capabilities. Their applications in the medical domain have been rapidly expanding, spanning medical research, clinical diagnosis, drug development, and patient management. As a cornerstone of China's healthcare system, traditional Chinese medicine (TCM) faces significant challenges, including difficulties in knowledge extraction, and lack of standardization. The emergence of TCM-focused LLMs presents a transformative opportunity, offering a novel technological framework to process vast amounts of TCM data, uncover hidden theoretical insights, and enhance both research and clinical applications. Despite the growing interest in AI-driven medical solutions, systematic research on LLMs in the TCM domain remains limited. This article provides a comprehensive review of LLM development, detailing their underlying mechanisms, training methodologies, and key technological advancements. It further explores the unique characteristics and diverse application scenarios of existing TCM-LLMs. Additionally, this study also conducts a horizontal comparison of the differences between intelligent question-answering (QA) systems on general LLMs and QA systems on TCM-LLMs, discusses challenges and potential risks, and offers strategic recommendations for future development. By synthesizing current advancements and addressing critical gaps, this work aims to support the continued modernization and intelligent evolution of TCM, fostering its integration into contemporary healthcare systems.
Studies and Analysis of Drug-Target Interactions by Affinity Chromatography and Related Techniques: A Review
David S. Hage, Sadia Sharmeen, B.K. Sajeeb, Harshana Olupathage, Md Masudur Rahman, Isaac Kyei, Samiul Alim, Nigar Sultana Pinky
, Available online  , doi: 10.1016/j.jpha.2025.101407
Abstract:
The characterization of drug-target interactions is a key component of drug discovery, testing, and development. Affinity chromatography is one approach that can be used for this type of analysis. For instance, this may be done by using an immobilized target as a stationary phase and a drug as the applied solute. This review will discuss the various ways in which affinity chromatographic methods have been used to examine drug-target interactions, with an emphasis on high-performance methods. The general principles of this approach and factors to consider in its use for drug-target interaction analysis will first be examined. Methods based on zonal elution or frontal analysis for binding and competition studies will then be discussed. Various techniques for kinetic studies will next be considered, along with approaches that employ secondary binding agents and hybrid techniques. In each case, the general principles and theory of an approach will be given along with examples of its use in drug-target interaction studies. Advantages or limitations of each approach will be provided as well. This information should make it possible in the future to extend these techniques to other drug-target systems of interest in biomedical research and drug testing or development.
Apatinib and silver nanoparticles synergize against gastric cancer through the PI3K/Akt signaling pathway-mediated ferroptosis
Zichang Lin, Zhenghao Deng, Jiahao Liang, Binlong Chen, Yanyan Huang, Bin Liu, Yanzhong Zhao
, Available online  , doi: 10.1016/j.jpha.2025.101400
Abstract:
Ferroptosis, a regulated form of cell death characterized by lipid peroxidation (LPO), has emerged as a promising target in cancer therapy. In this study, we detected elevated levels of glutathione (GSH) peroxidase 4 (GPX4) and solute carrier family 7 member 11 (SLC7A11) in human gastric adenocarcinoma tissues, indicating a suppression of ferroptosis in gastric cancer (GC). Apatinib (Apa), a vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitor, was found to induce ferroptosis through the classical SLC7A11/GSH/GPX4 pathway. However, long-term administration of high-dose Apa is associated with adverse side effects and the risk of drug resistance. To address these limitations, we developed a novel drug delivery system using hyaluronic acid (HA)-modified poly (lactic-co-glycolic acid) (PLGA) nanoparticles for targeted co-delivery of Apa and chitosan-coated silver nanoparticles (Chi-Ag). Our results demonstrated that the combination of Apa and Chi-Ag exerted a synergistic cytotoxic effect against GC cells. This co-delivery system evidently increased oxidative stress at the tumor site and effectively promoted ferroptosis via modulation of the phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway. In summary, we present a targeted nanoplatform that enhances the antitumor efficacy of Apa at lower dosages by leveraging ferroptosis induction. This strategy holds promise for improving the clinical outcomes in patients with GC.
Innovative perspective on the geographical origin and quality of Peucedanum praeruptorum Dunn through the integration of inorganic and organic substance profiles
Yaolei Li, Hao Wu, Jing Fan, Jinjian Huang, Hongyu Jin, Feng Wei
, Available online  , doi: 10.1016/j.jpha.2025.101405
Abstract:
The clinical efficacy of traditional Chinese medicines (TCMs) is closely linked to their genuine quality. Identifying the geographical origin and genuine characteristics of medicinal materials is pivotal for enhancing quality control and efficacy. Qianhu (Peucedanum praeruptorum Dunn), a commonly used TCM, still lacks a clear understanding of the specific connection between its quality and geographical origin. To bridge this gap, we innovatively propose a new recognition model that integrates inorganic and organic substances, using Qianhu as the model TCM. By incorporating the concepts of metallomics and metabolomics, we merge elemental fingerprint profiles with chemical component contour maps to pinpoint its geographical origin. The research findings suggested that, compared to chemometrics, machine learning with data oversampling could precisely identify Qianhu from areas like Anhui, Zhejiang, Guizhou, and Chongqing of China, especially distinguishing genuine ones. Upon this groundwork, we further introduced an innovative ensemble model that deeply integrated the optimal models for elements and chemical components, thereby substantially enhancing classification accuracy. Additionally, through variable importance analysis, we provided professional and in-depth interpretations for the elements and chemical components within the model. In summary, this study, for the first time, revealed the scientific basis of Qianhu's producing area and genuine quality through machine learning, integrating inorganic and organic factors. It provides a solid foundation for scientific and reasonable quality control and clinical application of TCMs.
Dual regulation of antiviral IFN response by Scutellariae Radix: Therapeutic implications for influenza
Li Li, Manjing Jiang, Hong Wei, Linpan Liang, Yunlong Song, Dongni Xia, Qiang Luo, Huimin Huang, Xu Li, Haisheng Yang, Lijun Ning, Ying Wu
, Available online  , doi: 10.1016/j.jpha.2025.101399
Abstract:
Scutellariae Radix (SR) is widely used in Chinese medicine for influenza treatment; however, the mechanisms underlying its effect remain unknown. Here, we report, for the first time, that the therapeutic effects of SR on influenza involve regulation of antiviral interferons (IFNs), type I and type III IFNs (IFN-Is and IFN-IIIs, respectively), particularly through the modulation of IFN-I production and its downstream effects in a cell type-specific manner. SR treatment resulted in symptomatic improvement in A/Puerto Rico/8/34 (H1N1) virus (PR8)-infected mice. It exhibited direct antiviral activity in the early stages of virus infection in PR8/A/WSN/33 (H1N1) (WSN)-infected Madin-Darby canine kidney (MDCK) cells. Next, we investigated the effects of SR on the upstream antiviral IFN pathways and downstream effects in human lung adenocarcinoma (A549) cells, human monocytic leukemia (THP-1) cells, and neutrophils (Neu). SR exhibited dual regulatory roles, enhancing the production and activity of antiviral IFNs via the nuclear factor-kappaB (NF-κB)/IFN regulatory factor 3 (IRF3) and Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathways. It also reduced IFN-I-induced neutrophil inflammation by inhibiting reactive oxygen species and neutrophil extracellular trap production, and alleviated inflammation in A549 and THP-1 cells via NF-κB/cfos or mitogen-activated protein kinase (MAPK)/c-Jun signaling. Subsequently, the importance of IFN-I/IFN-III was verified using IFN alpha and beta receptor 1 (Ifnar1)-/- and IFN lambda receptor 1(Ifnlr1)-/- mice. The absence of IFNAR or IFNLR significantly diminished the therapeutic effect of SR against influenza, highlighting its dependence on the IFN-I/IFN-III systems. Finally, a delayed drug administration experiment in PR8-infected mice revealed that the therapeutic effect of SR heavily relies on early induction of IFN. Overall, our findings offer valuable insights for the clinical utilization of SR, as well as for further exploration of antiviral treatments.
Establishment of an at-line nanofractionation-based screening platform for rapid identification of influenza PAN/PAN I38T inhibitors from Artemisiae Argyi
Yuexiang CHANG, Hao TIAN, Jia-Huan QU, Jiaming YUAN, Rongkai GU, TingTing ZHANG, Jincai WANG, Zhengjin JIANG
, Available online  , doi: 10.1016/j.jpha.2025.101402
Abstract:
The N-terminal domain of influenza viral polymerase (PAN), a highly conserved region with critical catalytic function related to viral RNA replication and transcription, is considered as a very promising anti-influenza drug target. There is an urgent need for highly efficient and rapid screening methods to identify potential PAN inhibitors (PANIs) from complex matrices. In this work, a novel high-throughput screening (HTS) platform was established by coupling high performance liquid chromatography and high-resolution mass spectrometry (HPLC-HRMS) with a fluorescence resonance energy transfer (FRET)-based endonuclease activity assay through an at-line nanofractionation system (ANF). The proposed screening platform could rapidly identify potential PANIs from plant extracts with good sensitivity (baloxavir at the half maximal inhibitory concentration (IC50) could be detected) and reliability (Z’ factor of 0.77). This platform was then successfully applied to the screening of potential inhibitors against PAN/PAN I38T from an aqueous extract of Artemisiae Argyi and 17 potential PANIs were identified. Among them, three compounds (cynarine, isochlorogenic acid B and isochlorogenic acid C) showed comparable inhibitory activity against PAN and even better activity against PAN I38T compared to baloxavir. This study not only established a novel high-throughput ANF-based PANIs screening platform, but also proved the feasibility to discover PANIs from complex TCMs, which has a great potential in future anti-influenza drug discovery.
MST4 as a Key Driver of Osteoclast Activation in Osteoporosis
Bin Zhang, Jiangjiang Zhang, Xuqiang Liu, Qiang Xu
, Available online  , doi: 10.1016/j.jpha.2025.101401
Abstract:
Osteoporosis, characterized by excessive bone resorption driven by heightened osteoclast activity, remains a major health concern with molecular mechanisms that are not fully understood. This study explores the role of mammalian Sterile 20-like kinase 4 (MST4), a member of the Sterile 20 (Ste20) kinase family, in osteoclast differentiation and function. Analysis of blood samples from osteoporosis patients revealed a significant increase in MST4 expression compared to healthy controls, with a negative correlation to bone mineral density (BMD). In vitro experiments using stem cell-derived osteoclast models showed that MST4 knockdown reduced osteoclast differentiation and bone resorption activity, whereas MST4 overexpression enhanced these processes. In vivo studies with ovariectomized (OVX) mouse models further corroborated these findings. Mechanistically, MST4 was found to promote tumor necrosis factor receptor-associated factor 6 (TRAF6) autoubiquitination through phosphorylation, a critical event for osteoclast activation. Collectively, these results identify MST4 as a key regulator of osteoclast-mediated bone resorption in osteoporosis, suggesting that targeting the MST4–TRAF6 signaling axis may offer a novel therapeutic strategy to prevent bone loss.
Profiling cytotoxicity of nanofractionated elapid snake venoms in human cell lines representing different tissues
Haifeng Xu, Mátyás A. Bittenbinder, Julien Slagboom, Nicholas R. Casewell, Paul Jennings, Jeroen Kool
, Available online  , doi: 10.1016/j.jpha.2025.101398
Abstract:
Elapid snakebites cause severe toxicity, predominantly neurotoxicity and general cytotoxicity. However, the specific cellular impacts of individual venom toxins remain largely underexplored. This study developed a high-throughput platform for profiling cytotoxicity from elapid venoms, focusing on nanofractionation analytics to enhance selectivity and toxin identification. Elapid Venoms were tested on four human cell lines, representing kidney (RPTEC/TERT1), liver (HepaRG), endothelial (iPSC-EC), and skin (HaCaT) tissues. Cytotoxic effects were assessed through cell coverage, viability, and metabolic assays in both crude and nanofractionated venom samples. Nanofractionation revealed selective cytotoxicity in venom components, notably phospholipases A2 (PLA2s) and three-finger toxins (3FTxs), which impaired membrane integrity and cellular metabolism. Crude B. multicinctus venom displayed specific cytotoxicity toward liver and skin cells but not kidney or endothelial cells. Cytotoxicity of nanofractionated B. multicinctus venom was lost, likely due to denaturing conditions of the reversed-phase separation. Fractionation after size exclusion chromatography (SEC) for post-column bioassaying to avoid toxin denaturation yielded bioactive fractions, with 3FTxs, PLA2s, and Kunitz-type serine protease (KUNs) likely responsible for the observed cell permeability disruption, extracellular matrix (ECM) degradation, and metabolic loss. This integrated analytical workflow, combining nanofractionation with high-throughput cytotoxicity assays and venomics, enabled rapid identification of venom components with cell type-specific toxicity. Our findings contribute to understanding elapid venom toxicity and can aid in developing targeted snakebite treatments focusing on cytotoxicity responsible for tissue-specific damage.
Development and validation of a static multiple light scattering (SMLS) method for real-time colloidal stability assessment in nanoparticle formulations
Haiyang Shen, Shiqi Huang, Renjie Li, Hongliang Wang, Yanfang Yang, Yuling Liu, Jun Ye, Xiaohai Ma
, Available online  , doi: 10.1016/j.jpha.2025.101396
Abstract:
This study presents the first development and validation of a static multiple light scattering (SMLS)-based method for real-time, non-invasive assessment of nanoparticle colloidal stability. Nanoparticles, leveraging their nanoscale advantages (e.g., targeted delivery, enhanced drug solubility, and controlled release), hold transformative potential in treating diseases. However, their clinical success hinges on colloidal stability, which dictates in vivo behavior, safety, and regulatory compliance. While dynamic light scattering (DLS) remains widely used, its inability to monitor dynamic transformations and reliance on sample dilution limit its accuracy. Here, we pioneer the application of SMLS to systematically evaluate colloidal stability across standardized particles and commercial nanoparticle formulations (liposomes, nanoparticles, micelles, and nanoemulsions). Results demonstrate that SMLS captures destabilization kinetics (aggregation, sedimentation, creaming) in real-time without dilution, even at high concentrations, while DLS fails to distinguish polydisperse systems due to time-point sampling. The Turbiscan stability index (TSI) quantifies instability mechanisms, correlating with particle size distribution broadening. This first comprehensive validation of SMLS for nanoparticles reveals its superiority in reflecting native-state behavior, exemplified by minimal or the variations in the average transmission (ΔT) or backscattering intensity (ΔBS) fluctuations and low TSI values in four commercial formulations. By addressing a critical technological gap, this study establishes SMLS as an indispensable tool for optimizing nanoparticle design, ensuring compliance with U.S. Food and Drug Administration (FDA) in-use stability guidelines, and accelerating clinical translation.
FPS_P/N: A two-dimensional mass spectrometry utilization program with precursor ion determination for accurately distinguishing anthocyanin from other flavonoids
Ya-Hui Ge, Lili Zhang, Shilin Gong, Wen Miao, Li Zhang, Weibin Bai, Jian-Lin Wu, Na Li
, Available online  , doi: 10.1016/j.jpha.2025.101385
Abstract:
Anthocyanins, a unique class of flavonoids with flavylium skeletons, are valued for antioxidant properties. However, distinguishing anthocyanins from co-existing flavonoids using conventional automated tandem mass spectrometry (MS) analysis methods remains challenging. This difficulty arises from low specificity of MS features and confusion of precursor ions, leading to substantial false confidence annotations. To address it, we have developed the strategy of positive (POS)-to-negative (NEG) primary MS (MS1) intensity ratios detecting with fast polarity switching (FPS), termed FPS-POS/NEG, to determine their specific precursor ions. Moreover, we developed an automated program leveraging FPS-POS/NEG strategy (FPS_P/N) streamlining i) screening candidate pool with molecular networking analysis from MS1 and secondary MS (MS2), ii) determining precursor ions with FPS-POS/NEG, and iii) annotation with MS2. This program enables simultaneous capture of positive and negative signals in a single run and accurate determination of precursor ions for anthocyanins (5.98 to 9.28) and other flavonoids (-2.52 to 2.08). The underlying mechanisms were elucidated by difference in protonated and deprotonated Gibbs free energy and in-source fragmentation (ISF). FPS-POS/NEG strategy was validated across a broad pH range (0.1%-2% formic acid) and demonstrated high alignment accuracy (retention time difference, 0.011 min) and consistency (relative standard deviation (RSD), 0.38%-4.62%). Using blueberry, 20 anthocyanins (nonacylated and acylated) and 14 additional flavonoids were annotated. With two-dimensional integration of positive and negative MS1 intensities with intensity ratios, FPS_P/N program provides a novel way to identify anthocyanins from other flavonoids. We anticipate this innovative method will enhance the high-throughput qualification of anthocyanins and other flavonoids in complex samples.
Promising TNF-α inhibitors: Targeting pathogenic TNF-α/TNFR signaling to restore Th17/Treg balance in rheumatoid arthritis
Jiajie Kuai, Zhuo Chen, Ju He, Fengling Wang, Wei Wei
, Available online  , doi: 10.1016/j.jpha.2025.101382
Abstract:
The pleiotropic regulatory effect of tumor necrosis factor-alpha (TNF-α), an essential cytokine involved in immune regulation, is of significant importance in the immune response. TNF-α inhibitors have been widely used in rheumatoid arthritis (RA) and other autoimmune diseases since their introduction into clinical practice. However, the tradeoff between its excellent efficacy and adverse drug reactions (ADR) remains a problem. T cells, especially the T helper cell 17 (Th17)/regulatory T (Treg) cells balance, are crucial for the treatment of autoimmune diseases including RA. This review explores the mechanisms by which TNF-α/TNF receptor (TNFR) signaling induces Th17/Treg imbalance in RA. This review synthesizes current knowledge to facilitate an improved understanding of the causes of ADR, such as infection caused by TNF-α inhibitors in clinical practice. Moreover, our findings offer a reference for exploring potential TNF-α/TNFR signaling inhibitory strategies from the perspective of regulating T cell balance.
Breaking the boundaries of affinity selection-mass spectrometry: From ligand screening to target-ligand interaction insights
Pamella Christina Ortega de Oliveira, Bruno Sérgio do Amaral, Carmen Lucia Cardoso, Quezia Bezerra Cass, Marcela Cristina De Moraes
, Available online  , doi: 10.1016/j.jpha.2025.101379
Abstract:
Affinity selection mass spectrometry (AS-MS) has emerged as a powerful label-free technique for identifying and characterizing ligand-target interactions. This review explores the diverse applications of AS-MS in drug discovery, including its role in selective screening, binding site characterization, and quantitative affinity determination. We discuss the use of AS-MS for determining equilibrium dissociation constants (KD) and competitive binding parameters (ACE50), highlighting its ability to rank ligand affinities efficiently. The review also examines AS-MS applications in fragment-based drug discovery, screening for molecular glues, and investigating interactions with membrane proteins. Moreover, we address key technical challenges, including competitive binding effects, protein stability, and ligand dissociation kinetics, along with recent advancements in automation and artificial intelligence (AI) integration. Rather than providing a comprehensive literature review, this work aims to broaden the applicability of AS-MS assays and encourage researchers to explore its use in underutilized contexts. By providing rapid and high-sensitivity affinity measurements, AS-MS continues to expand its role in drug discovery and structural biology, complementing conventional biophysical techniques.
Latest surface plasmon resonance advances for G protein-coupled receptors
Giulia De Soricellis, Enrica Calleri, Sofia Salerno, Gloria Brusotti, Sara Tengattini, Caterina Temporini, Gabriella Massolini, Francesca Rinaldi
, Available online  , doi: 10.1016/j.jpha.2025.101381
Abstract:
G protein-coupled receptors (GPCRs) are a big family of membrane proteins which represent one of the main classes of drug targets. However, their investigation presents several challenges, among which their instability outside the membrane environment. Different strategies for the drug discovery of this target are available, and surface plasmon resonance (SPR) stands out as one of the most informative and widespread binding assays, with many advantages such as real-time and label-free analyses resulting in the definition of both affinity and kinetic constants. This review covers the applications of SPR in GPCR drug discovery of the last 10 years and classifies the papers based on the immobilization strategy on the SPR sensor chip to maintain receptor stability. In particular, GPCR immobilization can occur in its native membrane by immobilizing whole cells or membrane fragments, using membrane mimetics (such as lipoparticles, lentiviral particles, liposomes, lipoproteins, nanodiscs, or planar lipid membranes) or immobilizing the isolated receptor stabilized by the use of detergents or engineering approaches. Different examples were considered and pros and cons of each strategy were presented.
Tumor-associated macrophages in hepatocellular carcinoma: Cellular plasticity and therapy resistance in crosstalk
Tianhao Zhang, Xi Zhao, Tingting Gao, Fang Ma
, Available online  , doi: 10.1016/j.jpha.2025.101384
Abstract:
Hepatocellular carcinoma (HCC) is the predominant type of liver cancer. There are different risk factors for HCC including viral infection, liver fibrosis, non-alcoholic fatty liver disease, environmental factors and genomic alterations. The tumor microenvironment (TME) has been proposed as a potent regulator of tumor malignancy comprised of normal and cancerous cells. Macrophages are among the most abundant cells in the TME, known as tumor-associated macrophages (TAMs) that can control proliferation, metastasis, immune reactions and therapy response of tumor cells. In the present review, the function of TAMs in the regulation of HCC progression was evaluated. TAMs are prognostic factors in HCC that increase in TAM infiltration into TME can cause undesirable outcome in patients. Moreover, M2 polarization of macrophages can impair function of other immune cells such as T cells and natural killer cells to mediate immune evasion. TAMs demonstrate association with other biological events including autophagy and glycolysis. There is mutual interaction between TAMs and exosomes that TAM-mediated exosome secretion regulates HCC progression, while exosomes derived from other cells can also affect TAMs. Inhibition of macrophage recruitment, their depletion and increasing M1 polarization are promising approaches in HCC therapy. The natural products and nanostructures have been also recently introduced for the regulation of macrophages in HCC therapy.
Targeting SH3GL1 for Prognosis and Immune Response in Breast Cancer
Si Si, Hong Yu, Hao Zhang, Jianqiao Yin, Ziwei Li, Ning Wang, Xiaopeng Yu
, Available online  , doi: 10.1016/j.jpha.2025.101377
Abstract:
The cuproptosis-related gene (CRG) SH3GL1 is identified as a pivotal regulator in breast cancer (BRCA) progression and immune regulation in this study. Through gene expression profiling and meta-analysis of public datasets, SH3GL1 was found to be overexpressed in BRCA tumor tissues and correlated with poor prognosis. Single-cell RNA sequencing pinpointed SH3GL1's expression in epithelial cells and its critical interactions with immune cells, particularly T cells and monocytes. Functional experiments confirmed SH3GL1’s role in promoting immune cell migration and modulating drug sensitivity. Moreover, high SH3GL1 expression was linked to reduced immunotherapy response, as revealed by TIDE scoring, suggesting its contribution to the immune microenvironment complexity in high-risk BRCA groups. These results emphasize SH3GL1's dual role as a prognostic biomarker and a target for therapeutic intervention in BRCA, providing new insights into personalized cancer treatment approaches.
Antimicrobial sonodynamic therapy: recent advances and challenges in new therapeutic approaches to antimicrobials
Linyu Xue, Shidian Ran, Jindie Huang, Xiaorui Wei, Xingrui Yan, Tongchuan He, Hongmei Zhang, Mengqin Gu
, Available online  , doi: 10.1016/j.jpha.2025.101375
Abstract:
Pathogenic microorganisms pose significant threat to global health. In particular, conventional antibiotic treatments run the risk of exacerbating bacterial resistance. Antimicrobial sonodynamic therapy (aSDT), which combines sonosensitizers and low-intensity ultrasound (US), has opened up new avenues for the treating drug-resistant bacteria. The appeal of this therapy lies in its ability to focus US energy toward the deep-seated site of bacterial infection sites, it locally activates sonosensitizers and generates cytotoxic reactive oxygen species (ROS), which ultimately induces bacterial death. In the last decade, aSDT has been rapidly developed due to its good penetrative, biocompatibility and targeting properties. This paper highlights the recent aSDT advances in antimicrobial applications. We review aSDT mechanisms and sonosensitizers types, and propose relevant strategies to improve aSDT effects in terms of improving hypoxia and combining applications with other therapies. Furthermore, we summarize the potential obstacles and opportunities for the advancement of aSDT, and provide a deeper understanding of sonodynamic therapy (SDT) for antimicrobial applications, thereby promoting further innovation and clinical application.
Synergistic antibacterial and anti-inflammatory potentials of dual-loaded self-healing hydrogel for methicillin-resistant Staphylococcus aureus-infected wound healing
Sangyu Hu, Weigang Zhong, Yuzhu Pei, Yutong Zhou, Jianfeng Wang, Xuming Deng, Zihao Teng, Lei Xu
, Available online  , doi: 10.1016/j.jpha.2025.101376
Abstract:
The emergence of drug-resistant bacterial infection and persistent biofilm colonization pose a rigorous challenge to effective wound healing and regeneration, necessitating the innovative therapeutic strategies to combat these pressing clinical crises. Herein, nortriptyline, a novel FDA-approved tricyclic antidepressant was uncovered to effectively potentiate bactericidal activities of β-lactam antibiotics against methicillin-resistant Staphylococcus aureus (MRSA). Mechanistically, nortriptyline functions by disrupting the microbial iron homeostasis and potentiation of Fenton chemistry-mediated oxidative stress, concomitant with metabolic reprogramming via TCA cycle dysregulation and membrane destabilization. To enhance combination therapy-mediated therapeutic potential in wound management, the dual-loaded self-healing hydrogel OHA-PLL@AN was engineered to exhibit excellent biocompatibility and antibacterial potentials through molecular cross-linking of oxidized hyaluronic acid (OHA) and ε-polylysine (PPL). The therapeutic efficacy of OHA-PLL@AN was further validated in a murine model with MRSA-infected cutaneous wounds. OHA-PLL@AN therapy significantly attenuated the inflammatory response, concurrently promoting angiogenesis and accelerating the cutaneous wounds healing. Collectively, these findings underscore the dual drug-loaded self-healing hydrogel OHA-PLL@AN with anti-infection and anti-inflammatory properties as a novel therapeutic strategy for drug-resistant bacterial infected wounds therapy.
Luteolin attenuates RA-associated chronic pain by targeting the LDHA/H3K9la/NFATC2 axis to suppress Th17 cell differentiation and central infiltration
Yuepeng Jiang, Yang Zhao, Xiao Ma, Xiaoxuan Zhao, Mengjia Zheng, Junjun Wen, Cunrui Yuan, Xinyi Ding, Chengping Wen
, Available online  , doi: 10.1016/j.jpha.2025.101373
Abstract:
Chronic joint pain in rheumatoid arthritis (RA) represents a persistent therapeutic challenge, and although luteolin (LUT) exhibits established anti-inflammatory properties, its precise mechanism for alleviating RA-associated chronic pain remains undefined. Through systematic investigation in collagen-induced arthritis (CIA) mice, we demonstrated that LUT administration effectively attenuated chronic pain by modulating spinal cluster of differentiation 4 positive T (CD4+ T) cell dynamics and suppressing microglial activation. Integrated multi-omics profiling (cleavage under targets and tagmentation, RNA sequencing (RNA-seq), and metabolomics) coupled with functional validation revealed nuclear factor of activated T cells 2 (NFATC2) as the central transcriptional regulator governing T helper 17 (Th17) cell differentiation and spinal infiltration through protein kinase C epsilon (PRKCE)-signal transducer and activator of transcription 3 (STAT3) signaling transduction. Significantly, our mechanistic studies uncovered a previously unrecognized epigenetic cascade: LUT-mediated suppression of lactate dehydrogenase A (LDHA) activity disrupts glycolysis-fueled histone h3 lysine 9 lactylation (H3K9la), thereby epigenetically silencing NFATC2 transcription. Translational studies using RA patient-derived CD4+ T cells confirmed LUT's capacity to normalize pathological hyperactivity of the LDHA/H3K9la/NFATC2 axis, concomitantly regulating CD4+ T dynamics. Biophysical validation through molecular docking, surface plasmon resonance, and molecular dynamics simulations established LUT's direct binding to LDHA with high affinity. Collectively, these findings delineate a novel therapeutic paradigm wherein LUT alleviates RA-associated chronic pain by orchestrating Th17 differentiation and migratory capacity through coordinated blockade of the LDHA-H3K9la-NFATC2 signaling network, highlighting its potential as a disease-modifying agent for chronic pain management in RA.
A comprehensive narrative review of Epimedium and its bioactive compounds in respiratory diseases
Lanlan Song, Changyu Lei, Cheng Zheng, Yichen Liu, Jian Liu, Dan Yao, Xiaoying Huang
, Available online  , doi: 10.1016/j.jpha.2025.101374
Abstract:
Respiratory diseases pose a significant global health challenge due to their high morbidity and mortality rates. Traditional Chinese medicine (TCM), particularly the herb Epimedium, has demonstrated therapeutic potential in managing these diseases. This review systematically evaluates evidence from both in vitro and in vivo studies to assess the effects of Epimedium and its bioactive compounds, including Icariin (ICA), Icariside I (ICS I), Icariside II (ICS II), Icaritin (ICT), and others, on respiratory diseases. The synthesis of current literature reveals that these compounds exhibit anti-inflammatory, antioxidant, and immunomodulatory activities, as well as other effects crucial for the management of respiratory diseases. Further research is needed to fully understand and harness the therapeutic potential of Epimedium and its bioactive compounds in respiratory diseases.
Astrocytes: Unveiling their role in the molecular mechanism of natural antidepressants
Shimeng Lv, Ruirui Shang, Xia Zhong, Yitong Lu, Haonan Gao, Guangheng Zhang, Linghui Kong, Yunhao Yi, Yufei Huang, Yuexiang Ma, Jing Teng, Sheng Wei
, Available online  , doi: 10.1016/j.jpha.2025.101370
Abstract:
Depression, an emotional disorder characterized by persistent low mood and loss of pleasure, can be alleviated by mainstream clinical drugs (such as selective serotonin reuptake inhibitors). However, issues such as delayed efficacy, significant individual differences, and adverse reactions remain. Compared to traditional single-target drugs, natural products have shown unique potential in depression intervention due to their synergistic multi-component effects and multi-target, multi-pathway regulation. As the most abundant glial cells in the central nervous system, astrocytes are deeply involved in the pathology of depression and have become important targets for the antidepressant effects of natural products. Although existing studies have revealed the regulatory effects of natural products on the function of astrocytes, there is still a lack of systematic categorization and mechanism integration. This review comprehensively summarized the molecular mechanisms by which natural products regulated astrocyte function through a systematic literature review, objectively analyzes key bottlenecks in current translational research, and aims to provide a theoretical basis and technical pathway for optimizing depression treatment paradigms and promoting the clinical translation of natural product research.
Mechanisms and therapeutic potential of YTHDF readers: linking epitranscriptomics to cancer
Na Deng, Qiang Sun, Shuying Wang, Shiheng Jia, Cheng Zheng, Fanglin Wang, Shuang Ma, Heng Zhou, Weiwei Liu
, Available online  , doi: 10.1016/j.jpha.2025.101371
Abstract:
YT521-B homology domain-containing family paralogs (YTHDFs), as RNA epigenetic modification effector proteins, fully or partially participate in N6-methyladenosine (m6A), N1-methyladenosine (m1A), and 5-methylcytosine (m5C) modifications, which play critical roles in tumor biology and contribute to obtaining and maintaining cancer hallmarks relying on their characteristic protein structures. Accumulating evidence has underscored the involvement of YTHDFs in manipulating RNA stability, translation, and RNA metabolism, thereby influencing tumor initiation, progression, and anti-tumor treatment efficacy through independent RNA epigenetic modification pathways. This review aims to illustrate the essential regulatory mechanisms and pathological consequences of YTHDFs in tumorigenesis and therapeutic resistance. Additionally, we highlight the potential of targeting YTHDFs for cancer therapy, offering promising avenues for the elimination of tumor cells and the amelioration of tumor treatment efficacy.
Exploring TGFBR3 in disease pathogenesis: Mechanisms, clinical implications, and pharmacological modulation
Hui Song, Jinjiang Chou, Peng Zhao, Meijun Chen, Jue Yang, Xiaojiang Hao
, Available online  , doi: 10.1016/j.jpha.2025.101372
Abstract:
Transforming growth factor beta (TGF-β) receptor 3 (TGFBR3), or betaglycan, is a transmembrane proteoglycan that serves as a coreceptor for TGF-β ligands, modulating TGF-β signaling in a context-dependent manner. Its extracellular domain can undergo proteolytic cleavage, yielding a 120 kDa soluble isoform (sTGFBR3) that antagonizes TGF-β signaling by sequestering ligands. Through this dual role, TGFBR3 exerts profound influence over various physiological and pathological processes, including cell survival, stemness, differentiation, cancer metastasis, chemoresistance, and fibrosis, underscoring its significance as both a biomarker and therapeutic target. Despite its significance, regulatory mechanisms, particularly tissue-specific expression, cross-talk with other pathways and post-translational modifications, remain poorly defined. A current thorough review of the prognostic and therapeutic implications of TGFBR3 is still lacking. In this review, we systematically examine the structural features of TGFBR3, and their functional relevance, providing an in-depth analysis of its dysregulation and molecular roles in diseases such as cancer, nervous system disorders, cardiovascular diseases (CVDs), diabetes and infectious diseases. Current experimental approaches are critically evaluated, and gaps in existing literature are highlighted to identify priorities for future research. By synthesizing emerging insights, this review aims to inform the development of TGFBR3-targeted therapies and support the design of innovative clinical and preclinical strategies.
Advances in aptamer technology for target-based drug discovery
Yingxian Cui, Yifan Chen, Youbo Zhang, Liqin Zhang
, Available online  , doi: 10.1016/j.jpha.2025.101369
Abstract:
Aptamer therapeutics represent a class of target-based therapies that leverage their high specificity and affinity for diverse molecular targets. As single-stranded DNA or RNA oligonucleotides, aptamers offer advantages in therapeutic applications. A critical aspect of aptamer drug development is the selection process, which has seen significant advancements through various in vitro selection methods, including Systematic Evolution of Ligands by Exponential Enrichment and its emerging variations. Recent progress has also introduced functional screening strategies that directly identify pharmacologically active aptamers, accelerating drug discovery. The applications of aptamers in disease treatment are expanding across oncology, neurodegenerative disorders, infectious diseases and other diseases. Aptamers exhibit versatile mechanisms of action, including blocking interactions, recruiting protein machinery, and inhibiting target functions. By addressing key limitations and presenting future directions, this review provides a comprehensive perspective on the recent evolving landscape of aptamer technology and its transformative potential in modern medicine.
Pharmacological mechanisms of natural products with antidepressant effects: A focus on the programmed cell death regulation
Guangheng Zhang, Shimeng Lv, Shengchuan Bao, Weijie Zhao, Yunhao Yi, Haonan Gao, Xia Zhong, Xiangyu Li, Fengzhao Liu, Yitong Lu, Siyuan Sun, Jing Teng
, Available online  , doi: 10.1016/j.jpha.2025.101356
Abstract:
Depression is a prevalent mental disorder characterized by persistent disinterest and a depressed mood, with severe cases potentially leading to suicide. In recent years, the incidence of depression has steadily increased, making it the second-largest global health burden. The pathogenesis of depression involves a series of complex pathological mechanisms, although the key underlying causes remain unclear. Programmed cell death (PCD), including apoptosis, autophagy, pyroptosis, ferroptosis, and necroptosis, involves highly organized gene expression processes that may influence the occurrence and development of depression by regulating cellular fate. Furthermore, numerous studies have shown that natural products can modulate PCDs through various signaling pathways, presenting significant potential for managing depression. Natural products offer benefits such as cost-effectiveness, fewer side effects, and other advantages, making them viable supplements or alternatives to traditional antidepressant drugs. To explore this potential, we reviewed studies demonstrating the antidepressant effects of natural products through multi-target modulation of PCDs. In addition, we discussed the toxicity and clinical applications of these natural products. This study highlights that diverse core biological pathways and targets are involved in determining the fate of depression-associated brain cells, including the PI3K/Akt signaling pathway, caspase-8, GSDMD, and others. In conclusion, the multi-target mechanisms of PCD regulation by natural products may provide a promising foundation for the future development of novel antidepressant medications.
Ferroptosis and retinal ganglion cell death in glaucoma: Mechanisms and therapeutic approaches
Minggao Qin, Xueqin He, Weiwen Qiu, Yanjing Peng, Yequan Liao, Jusen Zhao, Lianxiang Luo, Qiuli Zhang
, Available online  , doi: 10.1016/j.jpha.2025.101355
Abstract:
Glaucoma represents a predominant worldwide etiology of permanent vision impairment; it is clinically manifested through progressive neuronal atrophy in retinal ganglion cells (RGCs) and is accompanied by axonal degeneration in the optic pathway. Given the limited efficacy of conventional intraocular pressure-lowering therapies in halting RGC degeneration, the exploration of novel neuroprotective strategies has become imperative. An increasing amount of research emphasizes the pathogenic role of ferroptosis, a metal ion-associated programmed cellular demise mechanism recently implicated in neurodegenerative cascades, as a pivotal executor of RGC demise and putative central mechanism in glaucomatous pathology. This comprehensive review systematically examines the mechanistic interplay between ferroptosis and established contributors to glaucomatous optic neuropathy, including oxidative stress, mitochondrial dysfunction, glutamate excitotoxicity, and neuroinflammation. We provide evidence demonstrating that retinal ferroptosis is associated with the death of RGCs and discuss current therapeutic strategies to mitigate retinal ferroptosis, including treatments with natural products and gene therapy. Furthermore, by understanding ferroptosis, we provide insights into potential therapeutic targets and offer valuable directions for future research and clinical applications.
CRISPR screening redefines therapeutic target identification and drug discovery with precision and scalability
Yao He, Xiao Tu, Yuxin Xue, Yuxuan Chen, Bengui Ye, Xiaojie Li, Dapeng Li, Zhihui Zhong, Qixing Zhong
, Available online  , doi: 10.1016/j.jpha.2025.101357
Abstract:
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 screening technology is redefining the landscape of drug discovery and therapeutic target identification by providing a precise and scalable platform for functional genomics. The development of extensive single-guide RNA (sgRNA) libraries enables high-throughput screening (HTS) that systematically investigates gene-drug interactions across the genome. This powerful approach has found broad applications in identifying drug targets for various diseases, including cancer, infectious diseases, metabolic disorders, and neurodegenerative conditions, playing a crucial role in elucidating drug mechanisms and facilitating drug screening. Despite challenges like off-target effects, data complexity, and ethical or regulatory concerns, ongoing advancements in CRISPR technology and bioinformatics are steadily overcoming these limitations. Additionally, by integrating with organoid models, artificial intelligence (AI), and big data technologies, CRISPR screening expands the scale, intelligence, and automation of drug discovery. This integration boosts data analysis efficiency and offers robust support for uncovering new therapeutic targets and mechanisms. This review outlines the fundamental principles and applications of CRISPR screening technology, delves into specific case studies and technical challenges, and highlights its expanding role in drug discovery and target identification. It also examines the potential for clinical translation and addresses the associated ethical and regulatory considerations.
Development of a dual-chamber derivatization method for the determination of cyanide in sodium nitroprusside and its preparation via HS-GC-ECD
Jinqi Zheng, Xinyu Zhao, Caixia Li, Chenxiao Yan, Pingping Chen, Xiao Gu, Liya Hong, Su Zeng
, Available online  , doi: 10.1016/j.jpha.2025.101353
Abstract:
The acute toxicity of cyanide and its pharmaceutical residues, has fueled interest in the development of analytical methods for its determination, particularly for sodium nitroprusside (SNP), a widely used vasodilator with potential cyanide residues. In this study, a dual-chamber derivatization bottle was designed to establish an interconnected gas environment, thereby facilitating chloramine T-mediated cyanide conversion to cyanogen chloride (CNCl) without direct contact with SNP. Subsequent determination of the analytes was undertaken using a headspace gas chromatography electron capture detector (HS-GC-ECD). The challenges of analyzing cyanide and the rapid degradation of SNP were addressed simultaneously. The method was subjected to rigorous validation, encompassing specificity, linearity, limits of detection (LOD), limit of quantification (LOQ), accuracy, precision, and robustness. The validation process revealed a notable degree of linearity within the range of 0.012-1.56 μg/mL, with a LOQ of 12.0 ng/mL. The method was found to be both accurate and precise, thus satisfying the requisite criteria. This method facilitates reliable cyanide monitoring in degradation-prone pharmaceuticals.
The role of NRF2 in human cancers: Pre-clinical insights paving the way for clinical trials
Yi Pei, Jianqiao Yin, Jiamei Liu, Dongze Liu, Qianlong Wu, Xue Cai, Mingming Han, Yu Tian, Liyu Yang, Shengye Liu
, Available online  , doi: 10.1016/j.jpha.2025.101358
Abstract:
Tumorigenesis is viewed as a complex, multistep process in which genetic mutations play a crucial role. The genetic mutations cause notable changes, not only in the biological behavior of tumor cells but also in their reactions to treatment. Nuclear factor erythroid 2-related factor 2 (NRF2) is one of the most disrupted molecular pathways in human cancers, and during cancer development, the expression of this factor rises to enhance survival rates. The NRF2 seems crucial for shielding tumor cells from apoptosis and oxidative harm, while promoting pro-survival autophagy to increase the survival rate. Crucially, NRF2 plays a dual role in enhancing both the growth and metastasis of cancer cells, and the upregulation of this factor boosts the stemness and cancer-stem cell characteristics of tumor cells, while also promoting drug resistance and radioresistance. The elevation of glycolysis, activation of epithelial-mesenchymal transition (EMT), and inhibition of ferroptosis are additional features of NRF2 upregulation in human cancers. Among the different pathways that control NRF2, non-coding RNA transcripts play a significant role, and by altering NRF2 expression, they influence tumor development. The pharmacological modulation of NRF2 can occur through both direct and indirect methods; in the direct method, NRF2 is inhibited, whereas in the indirect method, the regulators and associated pathways of NRF2, like KEAP1, are influenced. The nanoparticles have been engineered to inhibit NRF2 in decreasing tumorigenesis. Consequently, the clinical application of current discoveries can enhance cancer treatment capabilities for patients in the near future
Phytomedicine-mediated time-dependent inactivation of CYP3A4 by chemical modification
Xu Mao
, Available online  , doi: 10.1016/j.jpha.2025.101352
Abstract:
Cytochromes P450 (CYP)3A4 as the richest P450 enzyme is responsible for the metabolism of about 50% drugs. However, severe drug-drug interactions (DDIs) frequently occur when CYP3A4 is strongly inhibited by xenobiotics, which is one of the major reasons for the withdrawal of already marketed drugs. Compared to reversible inhibition, time-dependent inactivation (TDI), including mechanism-based inactivation (MBI), quasi-irreversible inactivation, and affinity-labeling inactivation, results from chemical modification of the host enzyme by electrophilic inactivators or electrophilic intermediates and is more likely to result in adverse clinical consequences. Increasing phytomedicines have been identified as time-dependent inactivators of CYP3A4 with the rapid growth of global consumption of natural products. According to vast experimental and theoretical studies, functional groups with chemical reactivity existing in phytomedicines are mainly involved in TDI of CYP3A4. For better understanding of the structure-activity relationship between phytomedicine and CYP3A4, we systematically summarize chemical mechanisms of TDI, including furan, thiophene, acetylenes, and methylenedioxyphenyl (MDP)-containing phytomedicineinduced MBI, MDP, alkylamine, and hydrazine-containing phytomedicine-induced quasi-irreversible inactivation, and iminium-containing phytomedicine-induced affinity-labeling inactivation, and comprehensively classify known natural CYP3A4 time-dependent inactivators, including polyphenols, alkaloids, terpenoids, and coumarins, which will offer the guidance and evidence for rational drug combinations and avoiding TDI-based DDIs in clinics.
Recent advances in nanomaterial-based optical biosensors and their biomedical and biopharmaceutical applications
Mengjia Xu, Lutfun Nahar, Kenneth J. Ritchie, Chenxu Wang, Li Cheng, Zimiao Wu, Satyajit D. Sarker, Mingquan Guo
, Available online  , doi: 10.1016/j.jpha.2025.101349
Abstract:
Optical biosensors are gaining popularity owing to their portability, miniaturization, no requirement for additional attachments and rapid responsiveness. These features render them suitable for various applications including at-home diagnostics, pharmacology, and continuous molecular monitoring. The integration of functionalized lowdimensional nanomaterials (zero-dimensional (0D), 1D, 2D, and 3D) has redirected focus towards the design, fabrication and optimization of optical biosensors. This review summarizes the fundamental mechanisms underlying optical biosensing. The key mechanisms include localized surface plasmon resonance (LSPR), photoluminescence (PL), surface enhancement Raman scattering (SERS), nanozymebased colorimetric strategies, chemiluminescence, bioluminescence and electrochemiluminescence. The advantages of various low-dimensional nanomaterials for different types of optical biosensors are presented. This comparison emphasizes their potential superiority in targeted biosensing applications. Therefore, promoting optical biosensing techniques and recent developments in advanced biosensing strategies for biomedical research and biopharmaceutical applications is necessary to establish their future directions.
A novel method for screening antihyperuricemic drugs by combining aptamer sensor array, exonuclease III-DNA walker and linear discriminant analysis
Shiquan Zheng, Jiale Ke, Hanren Chen, Huaze Shao, Fengxin Zheng, Runhui Zhang, Zean Zhao, Jianxin Pang, Lihong Liu
, Available online  , doi: 10.1016/j.jpha.2025.101345
Abstract:
The lack of a cell-based screening method limits urate-lowering drug development. A novel method combining aptamer sensor array (ASA), exonuclease III (Exo III)- powered 3D DNA walker (DW), and linear discriminant analysis (LDA) was developed for detecting uric acid (UA) in cell lysates, referred to as ASA–Exo III-DW–LDA. Three aptamers (Apts) with different affinities for UA and its structurally similar compound, xanthine (Xan), were used to design the ASA. The combination of ASA and Exo III-DW enabled the detection of UA at the picomolar level, whereas LDA was employed to differentiate UA signals from the mixed signals of UA and Xan. Significantly, Pearson correlation analysis revealed a strong correlation between our method and the 14C radioactive labeling method for urate anion exchanger 1 (URAT1) inhibitors, with r = 0.9880 for lesinurad and r = 0.9777 for benzbromarone. Using our method, kaempferol was identified as a promising hit compound for inhibiting the URAT1, because of its low half-maximal inhibitory concentration (IC50) (18.96 μM) low toxicity in mouse renal tubular epithelial cells (mTECs), and significant uratelowering effect in hyperuricemic mice at 5 mg/kg. Overall, this method is sensitive, cost-effective and safe, offering a novel strategy for routine urate-lowering drug screening in standard laboratories.
Applications of quantitative 13C NMR in pharmaceutical analysis: From small molecule drugs to biopolymers
Qi Tang, Sinan Wang, Xiongqi Zhai, Seon Beom Kim, Prabhakar Achanta, Gonzalo R. Malca-Garcia, Yuzo Nishizaki, Yi Wang, Yu Tang
, Available online  , doi: 10.1016/j.jpha.2025.101346
Abstract:
Chemical integrity is indispensable for advancing healthcare by ensuring the availability of high quality, safe, and effective pharmaceutical products. Ingredient quantification is particularly pivotal in this process. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for both qualitative and quantitative analysis for complex systems. Compared with 1D quantitative 1H NMR (1H qNMR), quantitative 13C NMR (13C qNMR) holds some unique advantages. This technique offers a broader chemical shift range and the resulting much lesser signal overlap compare to 1H NMR spectroscopy. This review summarizes relevant studies on the use of 13C qNMR as a quantification technique, along with a focus on quantitative principles, influencing factors, and technical improvements of 13C NMR. The review also highlights its applicability in quantifying diverse molecular structures in pharmaceutical analysis. In addition, potential of low-field NMR, artificial intelligence (AI)-driven method development, and hyphenation of NMR with other techniques for 13C qNMR analysis is discussed and summarized as well. As a versatile method, 13C qNMR holds great potential, and ongoing research is expected to unlock its full capabilities and expand its range of applications.
Equivariant graph neural network-based accurate and ultra-fast virtual screening of small molecules targeting miRNA-protein complex
Huabei Wang, Zhimin Zhang, Guangyang Zhang, Ming Wen, Hongmei Lu
, Available online  , doi: 10.1016/j.jpha.2025.101339
Abstract:
MicroRNAs (miRNAs) are small RNA molecules with significant therapeutic potential for treating various diseases, underscoring the need for effective methods to screen drugs targeting disease-associated miRNAs. In this study, we introduce miRPVS, a rapid virtual screening approach designed to identify small molecule drugs targeting miRNA-protein complex. miRPVS identifies binding pockets on the surface of these complexes, expanding the scope of potential small molecule targets. It employs an equivariant graph neural network model to extract 3D structure features of small molecules, enabling accurate prediction of docking scores. Using miRPVS, four complexes involved in pri-miRNA cleaving, pre-miRNA transport, and mRNA depress were identified as promising targets. For each target, hit compounds were screened from the ZINC20 database, which contains approximately 600 million druglike small molecules. MiRPVS predicted the docking score for these compounds, with Pearson correlation coefficients between predicted and experimentally docked scores comparable to those obtained through twice docking. Notably, the average deviation was only 0.67% across the four complexes. Remarkably, the entire screening process for all four complexes was completed in 14 h using just four V100 GPUs. Additionally, we integrated AlphaFold3-predicted structures into the miRPVS workflow, enabling virtual screening of small molecules against miRNA-protein complexes without experimentally determined structures. miRPVS demonstrated performance comparable to traditional docking methods while significantly reducing computational time and resource requirements. This innovative approach holds great promise for accelerating the discovery of small molecule drugs targeting miRNA-regulated pathways, addressing a critical gap in miRNA therapeutics.
Screening of tyrosine phosphatase SHP2 (PTPN11) inhibitors from natural products with therapeutic potential for receptor tyrosine kinase-driven cancer
Lingfeng Chen, Di Ke, Zheng Jiang, Ruixiang Luo, Jie Li, Lulu Zheng, Guang Liang
, Available online  , doi: 10.1016/j.jpha.2025.101335
Abstract:
Src homology 2 domain-containing phosphatase 2 (SHP2) is a pivotal regulator linking receptor tyrosine kinase (RTK) signaling. Abnormal SHP2 activity has been associated with tumorigenesis and metastasis. Although some SHP2-targeting modulators have entered clinical trials, FDA-approved SHP2 targeting drugs are still not available. Herein, we describe cooperative biochemical inhibition experiments that facilitate the identification of both catalytic and allosteric SHP2 inhibitors using an in-house natural product (NP) library. Based on this screening methodology, structurally diverse sets of NPs were characterized, among which dihydrotanshinone I (DHT) potently inhibited the wild-type SHP2 protein tyrosine phosphatase (PTP) domain and gain-of-function SHP2 variants. Trichostatin A (TSA) bound to the “tunnel” binding site, acting as an allosteric inhibitor. This study illustrates an optimized screening methodology and tactics to identify novel SHP2 modulators from NPs and provides a foundation for further NP-based drug development for the treatment of RTK-driven cancer.
Unraveling pyrrolizidine alkaloid-induced liver damage with an integrative spatial lipidomics framework
Yilin Chen, Jie Xu, Thomas Ka-Yam LAM, Yanqiao Xie, Jianing Wang, Aizhen Xiong, Zhengtao Wang, Zongwei Cai, Linnan Li, Li Yang
, Available online  , doi: 10.1016/j.jpha.2025.101340
Abstract:
Pyrrolizidine alkaloids (PAs), a class of secondary metabolites widely distributed in plants and the accidental ingestion or improper use of foods and herbs containing PAs, can lead to irreversible liver damage. Considering that the toxic mechanism of PAs is closely associated with metabolism, the hepatotoxicity was analyzed from the perspective of lipid metabolism. An integrated analytical approach was employed, combining mass spectrometry imaging (MSI) with liquid chromatography-mass spectrometry (LC-MS), to comprehensively investigate the spatial and temporal dynamics of lipid metabolites during PA exposure. The final lipidomics results combined with RNA sequencing showed that time-dependent changes in metabolite levels after the administration of PAs, involving the pathways of fatty acids, glycerophospholipids, glycerolipids and sphingolipids. Among them, phosphatidylcholines (PC), phosphatidylethanolamines (PE), phosphatidylinositols (PI) and sphingomyelins (SM) were downregulated to varying degrees within 0 to 24 h, while phosphatidylglycerol (PG), ceramides (Cer), diacylglycerols (DG) and triacylglycerols (TG) were upregulated. Notably, certain lipids exhibited distinct spatial distributions; for example, elevated levels of TG (56:13) were localized near the hepatic portal vein. Subsequently, the changes of lipid subclasses recovered within 24 to 48 h. Transcriptome RNA sequencing was used to enrich for key pathway-related differential genes Pemt, Gpat, etc. to explain the regulation of the hepatotoxic lipid pathway. The integration of MSI with LC-MS spectroscopy of endogenous metabolites provided intuitive insights into the alterations and spatial distribution of lipid metabolism in mice. Consequently, this study may enhance specific assessments and facilitate early diagnosis of acute toxicity associated with PAs.
Oblique-incidence Reflectivity Difference Technology Identifies the Antiviral Drug Ribavirin as an Inhibitor of Lung Tumor Progression by Targeting AMPK Signaling
Jiani Gao, Yiwen Zheng, Yicheng Wang, Dong Xie, Yijiu Ren
, Available online  , doi: 10.1016/j.jpha.2025.101306
Abstract:
Lung cancer takes the lead in terms of global cancer incidence and mortality rates. 5'-Adenosine monophosphate (AMP)-activated protein kinase (AMPK) serves as a universally conserved energy sensor throughout evolution checkpoint that orchestrates energy balance and metabolic homeostasis. However, AMPK activation has a complex, dual function in both the onset and advancement of lung cancer. Despite its protumorigenic effects, targeting AMPK with inhibitors to suppress cancer progression remains a critical area of research. An innovative high-content screening platform integrating small-molecule microarrays (SMMs) with oblique-incidence reflectivity difference (OI-RD) optical detection was established for AMPK inhibitor discovery. Alterations in the interfacial refractive index revealed that Ribavirin, an antiviral drug, has a high affinity for AMPK. Ribavirin binds directly to AMPK, suppressing its activation in mouse and human cells. By inhibiting AMPK phosphorylation, Ribavirin affects the downstream phosphorylation of mechanistic target of rapamycin complex 1 (mTORC1) and eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1), thereby regulating tumor cell proliferation and apoptosis. These results identify Ribavirin as a new AMPK inhibitor with potential utility in lung cancer therapy.
Perturbation response scanning of drug-target networks: Drug repurposing for multiple sclerosis
Yitan Lu, Ziyun Zhou, Qi Li, Bin Yang, Xing Xu, Yu Zhu, Mengjun Xie, Yuwan Qi, Fei Xiao, Wenying Yan, Zhongjie Liang, Qifei Cong, Guang Hu
, Available online  , doi: 10.1016/j.jpha.2025.101304
Abstract:
Combined with elastic network model, the perturbation response scanning (PRS) has emerged as a robust technique for pinpointing allosteric interactions within proteins. Here, we proposed the PRS analysis of drug-target networks (DTNs), which could provide a promising avenue in network medicine. We demonstrated the utility of the method by introducing a deep learning and network perturbation-based framework, for drug repurposing of multiple sclerosis (MS). First, the MS comorbidity network was constructed by performing a random walk with restart algorithm based on shared genes between MS and other diseases as seed nodes. Then, based on topological analysis and functional annotation, the neurotransmission module was identified as the “therapeutic module” of MS. Further, perturbation scores of drugs on the module were calculated by constructing the DTN corresponding to the module and introducing the PRS analysis, giving a list of repurposable drugs for MS. Mechanism of action analysis both at pathway and structural levels screened dihydroergocristine as a candidate drug of MS by targeting a serotonin receptor of HTR2B. Finally, we established a cuprizone-induced chronic mouse model to evaluate the alteration of HTR2B in mouse brain regions and observed that HTR2B was significantly reduced in the cuprizone-induced mouse cortex. These findings proved that the network perturbation modeling is a promising avenue for drug repurposing of MS. As a useful systematic method, our approach can also be used to discover the new molecular mechanism and provide effective candidate drugs for other complex diseases.
Comparative two-dimensional NKG2A/CD94 cell membrane chromatography for screening NK cell immune checkpoint inhibitors
Yanting Li, Yanqiu Gu, Weiyue Zhang, Tianhua Li, Chun Chen, Chengliang Wang, Yifeng Chai, Xueqin Ma, Xiaofei Chen
, Available online  , doi: 10.1016/j.jpha.2025.101259
Abstract:
The natural killer (NK) group 2 member A/C-type lectin domain family 4 member A (NKG2A/CD94) heterodimeric receptor is commonly recognized as a crucial immune checkpoint in NK cells. Currently, there is a notable lack of small-molecule inhibitors specifically targeting NKG2A that have progressed to clinical trials, and established screening methodologies for identifying such inhibitors remain limited. Cell membrane chromatography (CMC) is a biochromatographic technique that leverages the specific interactions between membrane receptors and their ligands. In this study, a comprehensive two-dimensional (2D) NKG2A/CD94 and HEK293 CMC comparative analysis system was developed to screen for selective NKG2A/CD94 ligands derived from Echinacea purpurea (L.) Moench and Alpinia katsumadai Hayata. The comprehensive 2D CMC comparative analysis system demonstrated superior selection performance, resulting in the successful screening and identification of five compounds. Of these compounds, chicoric acid and alpinetin exhibited greater binding affinity for the NKG2A/CD94 CMC column compared to the HEK293 CMC column, leading to their selection for further efficacy verification. Surface plasmon resonance (SPR) analysis revealed that chicoric acid and alpinetin exhibit binding affinities of 12.9 and 9.49 μM, to NKG2A/CD94. Molecular docking analyses and pharmacological investigations further demonstrated that both compounds could influence NK cell activation by interacting with the NKG2A/CD94. These findings suggest their potential as novel NKG2A/CD94 immune checkpoint inhibitors. Additionally, the comprehensive 2D CMC system serves as a robust and practical platform for drug discovery, and could be applied to other immune checkpoint receptor models.
Discovery of anthraquinones as potent Notum inhibitors for treating osteoporosis by integrating biochemical, phytochemical, computational, and experimental assays
Jia Guo, Yuqing Song, Mengru Sun, Jun Qian, Dihang See, Tian Tian, Yunqing Song, Wei Liu, Hongping Deng, Yao Sun, Guangbo Ge, Yongfang Zhao
, Available online  , doi: 10.1016/j.jpha.2025.101256
Abstract:
Osteoporosis, a severe systemic skeletal disorder characterized by decreased bone mineral density, leads to increased risks of bone fragility and fracture. Although some herbal medicines are clinically used for treating osteoporosis, the crucial anti-osteoporotic constituents and their mechanisms have not been well-elucidated. Notum, a negative regulator of Wnt/β-catenin signaling, has been validated as a druggable target for enhancing cortical bone thickness and alleviating osteoporosis. Herein, we showcase an efficient strategy for uncovering the key anti-Notum constituents from herbal medicines via integrating biochemical, phytochemical, computational, and cellular assays. Following screening the anti-Notum potentials of herbal medicines, Polygonum multiflorum Thunb. (PM), a commonly used anti-osteoporosis herb, showed potent and competitive inhibition against Notum. Phytochemical profiling coupling with docking-based virtual screening suggested that three anthraquinones, including rhein, emodin, and chrysophanol, showed high binding-potency towards Notum. Biochemical assays validated that three anthraquinones were strong competitive inhibitors of Notum, while rhein was the most potent one (IC50 = 9.98 nM). Cellular investigations demonstrated that rhein markedly promoted osteoblast differentiation in dexamethasone-challenged MC3T3-E1 osteoblasts, while RNA sequencing showed that rhein remarkably regulated Wnt signaling-related and osteogenic differentiation-related genes. In vivo tests showed that rhein displayed favorable safety profiles in healthy mice and this agent significantly elevated bone mineral density, augmented trabecula and cortical bone thickness in dexamethasone-induced osteoporotic mice. Collectively, this study showcases an efficient strategy for uncovering the key anti-Notum constituents from herbal medicines, while rhein was identified as a naturally occurring Notum inhibitor that shows favorable safety profiles and impressive anti-osteoporosis effects.
Uncovering the covalent inhibitors of SARS-CoV-2 Mpro in Tibetan edible herb Rhodiola crenulata and their synergistic anti-Mpro mechanism
Guang-Hao Zhu, Ya-Ni Zhang, Yuan Xiong, Xu-Dong Hou, Qing-Guang Zhang, Zhao-Qin Zhang, Xiao-Yu Zhuang, Wei-Dong Zhang, Guang-Bo Ge
, Available online  , doi: 10.1016/j.jpha.2025.101224
Abstract:
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) has been validated as a therapeutic target for antiviral drug development, given its critical role in the viral life cycle. SARS-CoV-2 Mpro contains 12 cysteine residues, which are susceptible to covalent modification by nucleophilic entities. In this study, we showcase an efficient strategy to uncover the key covalent inhibitors of SARS-CoV- 2 Mpro from herbal extracts and decipher their synergistic anti-Mpro mechanisms. Preliminary screening identified Rhodiola crenulata root (RCR), a well-known Tibetan herb, showing the most potent time-dependent inhibition against SARS-CoV-2 Mpro. By integrating fluorescence resonance energy transfer (FRET)-based biochemical assay with phytochemical and chemoproteomic profiling, we efficiently identified thirteen Mpro covalent inhibitors from the crude extract of RCR. Among these, rhodiosin and gallic acid were validated as the key anti-Mpro constituents, due to their strong anti-Mpro effects and high abundance in RCR. Remarkably, their combination exhibited a pronounced synergy in Mpro inhibition. Further intact protein mass measurements and top-down mass spectrometry (MS) analysis, complemented by biophysical methods, elucidated how these two compounds work in concert. Our findings revealed that rhodiosin functions as an allosteric inhibitor, disrupting Mpro dimerization and significantly facilitating the covalent modification of Mpro by gallic acid. Collectively, the covalent SARS-CoV-2 Mpro inhibitors are efficiently identified from a Tibetan herb, while a phytochemical combination with synergistic anti-Mpro effects and their unique allosteric-induced cooperative modification mechanism are revealed.
Targeted protein degradation: A promising approach for cancer treatment
Muhammad Zafar Irshad Khan, Adila Nazli, Iffat Naz, Dildar Khan, Ihsan-ul Haq, Jian-Zhong Chen
, Available online  , doi: 10.1016/j.jpha.2023.09.004
Abstract:
Targeted protein degradation (TPD) is a promising approach that has the ability to address disease-causing proteins. Compared to traditional inhibition, proteolysis targeting chimera (PROTAC) technology offers various benefits, including the potential to target mutant and overexpressed proteins along with characteristics to target undruggable proteomes. A significant obstacle to the ongoing effective treatment of malignancies is cancer drug resistance, which is developed frequently by mutated or overexpressed protein targets and causes current remedies to continuously lose their effectiveness. The effective use of PROTACs to degrade targets that have undergone mutations and conferred resistance to first-line cancer therapies has attracted much research attention. To find novel/effective treatments, we analyzed the advancements in PROTACs aimed at cancer resistance and targets. This review provides a description of how PROTAC-based anticancer drugs are currently being developed and how to counter resistance if developed to PROTAC technology. Moreover, modern technologies related to protein degradation, including autophagy-targeting chimeras (AUTAC), lysosome-targeting chimeras (LYTAC), antibody-based PROTAC (AbTAC), Glue-body chimeras (GlueTAC), transcription-factor-targeting chimeras (TRAFTAC), RNA-PROTAC, aptamer-PROTAC, Photo-PROTAC, folate-PROTAC, and in-cell click-formed proteolysis targeting chimeras (CLIPTACs), have been discussed along with their mechanisms of action.
Caenorhabditis elegansdeep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks
Nguyen Hoang Anh, Young Cheol Yoon, Young Jin Min, Nguyen Phuoc Long, Cheol Woon Jung, Sun Jo Kim, Suk Won Kim, Eun Goo Lee, Daijie Wang, Xiao Wang, Sung Won Kwon
, Available online  , doi: https://doi.org/10.1016/j.jpha.2022.06.006
Abstract:
Lipidomics coverage improvement is essential for functional lipid and pathway construction. powerful approach to discovering organism lipidome is to combine various data acquisitions, uch as full scan (full MS), data-dependent acquisition (DDA), and data-independent acquisition DIA). Caenorhabditis elegans(C. elegans) is a useful model for discovering toxic-induced etabolism, high-throughput drug screening, and a variety of human disease pathways. To etermine the lipidome of C. elegans and investigate lipid disruption from the molecular to the ystem biology level, we used integrative data acquisition. The methyl-tert-butyl ether method was sed to extract L4 stage C. elegans after exposure to triclosan (TCS), perfluorooctanoic acid, and nanopolystyrene (nPS). Full MS, DDA, and DIA integrations were performed to comprehensively profile the C. elegans lipidome by Q-Exactive Plus mass spectrometry. All annotated lipids were then analyzed using lipid ontology and pathway analysis. We annotated up to 940 lipids from 20 lipid classes involved in various functions and pathways. The biological investigations revealed that when C. elegans were exposed to nPS, lipid droplets were disrupted, whereas plasma membrane-functionalized lipids were likely changed in the TCS treatment group. The nPS treatment caused a significant disruption in lipid storage. Triacylglycerol, glycerophospholipid, and ether class lipids were those primarily hindered by toxicants. Finally, toxicant exposure frequently involves numerous lipid-related pathways, including the PI3K/AKT pathway. In conclusion, an integrative data acquisition strategy was used to characterize the C. elegans lipidome, providing valuable biological insights needed for hypothesis generation and validation.
article
Innovative diabetes mellitus treatment strategies: Mesenchymal stem cell-based therapy and its impact on pro- and anti-inflammatory cytokines modulation
Amin Ullah, Yutao Wu, Rajeev K. Singla, Weidong Tian, Bairong Shen
, Available online  , doi: 10.1016/j.jpha.2025.101497
Abstract:
Diabetes mellitus (DM) is a metabolic condition defined by chronic hyperglycemia with serious complications, including retinopathy, neuropathy, cardiopathy, and nephropathy. DM often accelerates inflammatory responses, which traditional treatments frequently fail to control. Chronic inflammation, with an imbalance between pro-inflammatory and anti-inflammatory cytokines, causes pancreatic β-cell failure and tissue damage. Mesenchymal stem cells (MSCs) are emerging as a promising therapy because of their capacity to control immune responses and stimulate tissue repair. Interleukin-1β (IL-1β), IL-17, IL-6, and tumor necrosis factor-α (TNF-α) have crucial roles in the diabetes-associated inflammatory environment. MSC therapies reduce levels of pro-inflammatory cytokines and increase levels of anti-inflammatory cytokines, such as IL-10, IL-4, IL-13, and transforming growth factor-β (TGF-β), reducing inflammation and promoting wound healing. Moreover, the dual functions in inflammation and tissue repair of key cytokines, including TGF-β, IL-6, IL-2, IL-33, and IL-8, provide both challenges and opportunities in MSC therapy. This review explores innovative MSC-based therapies for treating DM, focusing on their modulation of pro- and anti-inflammatory cytokines. MSCs may help reduce diabetic complications by restoring the cytokine balance, increasing insulin sensitivity, and protecting organs. However, the unique source of MSCs and the complex cytokine milieu in DM warrant additional research to improve treatment strategies and ensure long-term safety and efficacy. By highlighting the potential of MSCs to improve DM treatment and enhance patient outcomes, this review attempts to provide a thorough understanding of the molecular mechanisms by which MSCs regulate cytokine activity.