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ORIGINAL ARTICLE
Year : 2021  |  Volume : 12  |  Issue : 2  |  Page : 120-126

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


1 Department of Clinical Pharmacy, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
2 Department of Pharmacognosy and Phytochemistry, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia
3 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Airlangga University, Surabaya, Indonesia

Correspondence Address:
Prof. Junaidi Khotib
Nanizar Zaman Joenoes Building, Mulyorejo, Surabaya City 60115, East Java
Indonesia
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/japtr.JAPTR_88_21

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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 3CLpro inhibitors. Justicidin D had binding affinities of −8.7, −8.1, and −7.6 kcal mol−1 on RdRp, 3CLpro, 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 3CLpro and spike, respectively. Secondary metabolites of compounds from several plants were identified as potential agents for SARS-CoV-2 therapy.


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