Structure-based virtual screening of bioactive compounds from Indonesian medical plants against severe acute respiratory syndrome coronavirus-2
Maria Apriliani Gani, Ahmad Dzulfikri Nurhan, Saipul Maulana, Siswandono Siswodihardjo, Dewi Wara Shinta, Junaidi Khotib
Abstract
ABSTRACT Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a virus that causes the infectious disease coronavirus disease-2019. Currently, there is no effective drug for the prevention and treatment of this virus. This study aimed to identify secondary metabolites that potentially inhibit the key proteins of SARS-CoV-2. This was an in silico molecular docking study of several secondary metabolites of Indonesian herbal plant compounds and other metabolites with antiviral testing history. Virtual screening using AutoDock Vina of 216 Lipinski rule-compliant plant metabolites was performed on 3C-like protease (3CL pro ), RNA-dependent RNA polymerase (RdRp), and spike glycoprotein. Ligand preparation was performed using JChem and Schrödinger's software, and virtual protein elucidation was performed using AutoDockTools version 1.5.6. Virtual screening identified several RdRp, spike, and 3CL pro inhibitors. Justicidin D had binding affinities of −8.7, −8.1, and −7.6 kcal mol −1 on RdRp, 3CL pro , and spike, respectively. 10-methoxycamptothecin had binding affinities of −8.5 and −8.2 kcal mol −1 on RdRp and spike, respectively. Inoxanthone had binding affinities of −8.3 and −8.1 kcal mol −1 on RdRp and spike, respectively, while binding affinities of caribine were −9.0 and −7.5 mol −1 on 3CL pro and spike, respectively. Secondary metabolites of compounds from several plants were identified as potential agents for SARS-CoV-2 therapy.