Molecular docking and ADMET based study to identify potential phytochemical inhibitors for papain-like protease of SARS-CoV-2

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen for the novel COVID-19 disease. SARS-CoV-2 papain-like protease (PLpro) is responsible for viral replication and host innate immunity suppression. Thus, this study aimed to explore potential phytochemical inhibitors against this dual therapeutic target using virtual screening methods. Thirty-one phytochemicals with reported anti-SARS-CoV-1 PLpro activity were used to construct the phytochemical library along with two positive controls. Molecular docking using AutoDock 4.2 was employed to calculate binding affinity and inhibition constant of each compound within the S3/S4 binding pocket of SARS-CoV-2 PLpro. Based on the docking results, twelve compounds were subjected to non-covalent interaction analysis utilizing the Discovery Studio Visualizer software. Further, their physicochemical, pharmacokinetics and toxicity descriptors were evaluated using molinspiration and pkCSM web servers, respectively. Hirsutenone from Alnus japonica and broussoflavan A from Broussonetia papyrifera, displayed the strongest binding affinity (-8.23 kcal/mol and -8.13 kcal/mol), lowest inhibition constant (920.39 nM and 1.1 μM) and highest ligand efficiency (0.34 and 0.26) among all phytochemicals towards the binding pocket of SARS-CoV-2 PLpro, demonstrating superiority to PLpro inhibitors, 3k and GRL0617 which were used as positive controls. Additionally, hirsutenone, broussoflavan A and broussochalcone A (from Broussonetia papyrifera) possessed favorable physicochemical properties for oral drug development, satisfying Lipinski’s and Veber’s rules. Furthermore, in silico pharmacokinetics and toxicity predictions revealed that the three aforementioned phytochemicals are water soluble, non-mutagenic, non-hepatotoxic and biologically safe. Hence these lead compounds might be exploited to accelerate the drug discovery process against the ongoing COVID-19 infection.