TY - JOUR
T1 - Structure-based virtual screening of bioactive compounds from Indonesian medical plants against severe acute respiratory syndrome coronavirus-2
AU - Gani, Maria
AU - Nurhan, Ahmad
AU - Maulana, Saipul
AU - Siswodihardjo, Siswandono
AU - Shinta, Dewi
AU - Khotib, Junaidi
N1 - Publisher Copyright:
© 2021 Wolters Kluwer Medknow Publications. All rights reserved.
PY - 2021/4/1
Y1 - 2021/4/1
N2 - 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.
AB - 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.
KW - AutoDock Vina
KW - Indonesian herbal medicine
KW - coronavirus disease-2019
KW - infectious disease
KW - molecular docking
UR - http://www.scopus.com/inward/record.url?scp=85105398121&partnerID=8YFLogxK
U2 - 10.4103/japtr.JAPTR_88_21
DO - 10.4103/japtr.JAPTR_88_21
M3 - Article
AN - SCOPUS:85105398121
SN - 2231-4040
VL - 12
SP - 120
EP - 126
JO - Journal of Advanced Pharmaceutical Technology and Research
JF - Journal of Advanced Pharmaceutical Technology and Research
IS - 2
ER -