Structure-based virtual screening of bioactive compounds from Indonesian medical plants against severe acute respiratory syndrome coronavirus-2

Maria Gani, Ahmad Nurhan, Saipul Maulana, Siswandono Siswodihardjo, Dewi Shinta, Junaidi Khotib

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

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 (3CLpro), 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 3CLproinhibitors. Justicidin D had binding affinities of -8.7, -8.1, and -7.6 kcal mol-1on RdRp, 3CLpro, and spike, respectively. 10-methoxycamptothecin had binding affinities of -8.5 and -8.2 kcal mol-1on RdRp and spike, respectively. Inoxanthone had binding affinities of -8.3 and -8.1 kcal mol-1on RdRp and spike, respectively, while binding affinities of caribine were -9.0 and -7.5 mol-1on 3CLproand spike, respectively. Secondary metabolites of compounds from several plants were identified as potential agents for SARS-CoV-2 therapy.

Original languageEnglish
Pages (from-to)120-126
Number of pages7
JournalJournal of Advanced Pharmaceutical Technology and Research
Volume12
Issue number2
DOIs
Publication statusPublished - 1 Apr 2021

Keywords

  • AutoDock Vina
  • Indonesian herbal medicine
  • coronavirus disease-2019
  • infectious disease
  • molecular docking

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