Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies

Mohammed Ali Dahhas; Hamad M Alkahtani; Ajamaluddin Malik; Abdulrahman A Almehizia; Ahmed H Bakheit; Siddique Akber Ansar; Abdullah S AlAbdulkarim; Lamees S Alrasheed; Mohammad A Alsenaidy

doi:10.1016/j.jsps.2022.12.007

Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies

Saudi Pharm J. 2023 Feb;31(2):228-244. doi: 10.1016/j.jsps.2022.12.007. Epub 2022 Dec 16.

Authors

Mohammed Ali Dahhas¹, Hamad M Alkahtani², Ajamaluddin Malik³, Abdulrahman A Almehizia⁴, Ahmed H Bakheit², Siddique Akber Ansar², Abdullah S AlAbdulkarim¹, Lamees S Alrasheed², Mohammad A Alsenaidy¹

Affiliations

¹ Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
² Department of Pharmaceutical Chemistry, Department Chairman, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
³ Department of Biochemistry, College of Science, King Saud University. King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia.
⁴ Department of Pharmaceutical Chemistry, P.O. Box 2457, Riyadh 11451, Saudi Arabia.

Abstract

MERS-CoV belongs to the coronavirus group. Recent years have seen a rash of coronavirus epidemics. In June 2012, MERS-CoV was discovered in the Kingdom of Saudi Arabia, with 2,591 MERSA cases confirmed by lab tests by the end of August 2022 and 894 deaths at a case-fatality ratio (CFR) of 34.5% documented worldwide. Saudi Arabia reported the majority of these cases, with 2,184 cases and 813 deaths (CFR: 37.2%), necessitating a thorough understanding of the molecular machinery of MERS-CoV. To develop antiviral medicines, illustrative investigation of the protein in coronavirus subunits are required to increase our understanding of the subject. In this study, recombinant expression and purification of MERS-CoV (PLpro), a primary goal for the development of 22 new inhibitors, were completed using a high throughput screening methodology that employed fragment-based libraries in conjunction with structure-based virtual screening. Compounds 2, 7, and 20, showed significant biological activity. Moreover, a docking analysis revealed that the three compounds had favorable binding mood and binding free energy. Molecular dynamic simulation demonstrated the stability of compound 2 (2-((Benzimidazol-2-yl) thio)-1-arylethan-1-ones) the strongest inhibitory activity against the PLpro enzyme. In addition, disubstitutions at the meta and para locations are the only substitutions that may boost the inhibitory action against PLpro. Compound 2 was chosen as a MERS-CoV PLpro inhibitor after passing absorption, distribution, metabolism, and excretion studies; however, further investigations are required.

Keywords: 3CLpro, 3-Chymotrypsin -like Protease; ADMET, Absorption, distribution, metabolism, excretion and toxicity; CFR, Case fatality rate; DTT, Dithiothreitol; Drug Design; Drug Discovery; E. coli, Escherichia coli; EDTA, Ethylenediaminetetraacetic acid; HCoV-, Human Coronavirus; HIA, Human intestinal absorption; His-tag, Histidine tag; IPTG, Isopropyl b-D-1-thiogalactopyranoside; Inhibitors; Kan, Kanamicyn; LB, Luria–Bertani; MD, Molecular dynamic; MERS-CoV PLpro Inhibitors; MOE, Molecular Operating Environment; MPLpro, MERS papain-like protease; Molecular Docking; Molecular dynamic simulation; Ni-NTA, Nickel-nitrilotri; Nonstructural proteins; PLIF, Protein- ligand interaction fingerprint; Papain-like protease; Protease; RMSD, Root Mean Square Deviation; RMSF, Root Mean Square Fluctuation; pp1a, Polyprotein 1a; pp1b, Polyprotein 1b.