Volume 10 Issue 6
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Article Navigation >  Journal of Pharmaceutical Analysis  > 2020  >  10(6): 546-559
Mubarak A. Alamri, Muhammad Tahir ul Qamar, Muhammad Usman Mirza, Safar M. Alqahtani, Matheus Froeyen, Ling-Ling Chen. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches[J]. Journal of Pharmaceutical Analysis, 2020, 10(6): 546-559. doi: 10.1016/j.jpha.2020.08.012
Citation: Mubarak A. Alamri, Muhammad Tahir ul Qamar, Muhammad Usman Mirza, Safar M. Alqahtani, Matheus Froeyen, Ling-Ling Chen. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches[J]. Journal of Pharmaceutical Analysis, 2020, 10(6): 546-559. doi: 10.1016/j.jpha.2020.08.012
shu

Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches

doi: 10.1016/j.jpha.2020.08.012

  • a. Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkarj, Saudi Arabia;

  • b. College of Life Science and Technology, Guangxi University, Nanning, China;

  • c. Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium;

  • d. Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China

Funds:

This work was supported by the Starting Research Grant for High-level Talents from Guangxi University and the Postdoctoral Project from Guangxi University. Authors would like to thank Guangxi University, Prince Sattam Bin Abdulaziz University and University of Leuven for providing necessary facilities to conduct this research.

  • Received Date: Mar. 25, 2020
  • Accepted Date: Aug. 24, 2020
  • Rev Recd Date: Aug. 23, 2020
  • Available Online: Jan. 24, 2022
  • Publish Date: Dec. 10, 2020
    Abstract
  • The papain-like protease (PLpro) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro, which can be further developed as potential pan-PLpro based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PLpro were explored, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7,000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PLpro, and showed consistent interaction profile with SARS-CoV PLpro and MERS-CoV PLpro as well. Conclusively, the reported SARS-CoV-2 PLpro specific compounds could serve as seeds for developing potent pan-PLpro based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.
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