The Alkaloids of Isatis indigotica as Promising Candidates against COVID-19: A Molecular Docking Simulation for Drug Development

Farnoosh Kazemi; Mahdi Mojarrab; Gholamreza Bahrami; Shahram Miraghaee; Saba Hadidi; Mohammad Bagher Maljaie

doi:10.4103/jrptps.JRPTPS_113_21

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https://doi.org/10.4103/jrptps.JRPTPS_113_21

The Alkaloids of Isatis indigotica as Promising Candidates against COVID-19: A Molecular Docking Simulation for Drug Development

Author(s):

Farnoosh Kazemi¹,

Mahdi Mojarrab²,

Gholamreza Bahrami³,

Shahram Miraghaee⁴,

Saba Hadidi^5,*,

Mohammad Bagher Maljaie^6,**

1Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran

2Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran

3Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran and Medical Biology Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran

4Medical Biology Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran

5Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran

6Kermanshah University of Medical Sciences, Kermanshah, Iran

Corresponding Authors:

Journal of Reports in Pharmaceutical Sciences:Vol. 11, issue 2; 165-81

Published online:Dec 23, 2022

Article type:Research Article

Received:Aug 11, 2021

Accepted:Feb 09, 2022

How to Cite:Farnoosh KazemiMahdi MojarrabGholamreza BahramiShahram MiraghaeeSaba HadidiMohammad Bagher Maljaieet al.The Alkaloids of Isatis indigotica as Promising Candidates against COVID-19: A Molecular Docking Simulation for Drug Development.J Rep Pharm Sci.11(2):e146235.https://doi.org/10.4103/jrptps.JRPTPS_113_21.

Abstract

Background: Due to the complexities of severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2), an effective medicinal treatment protocol for this lethal disease with a high prevalence has not been approved yet. This study aimed to explore the efficacy of the main alkaloids of Isatis indigotica, one of the richest plant sources of alkaloids against SARS-CoV-2 targets computationally.
Materials and Methods: 3D structures of the target proteins including 3CLpro; PLpro, and RdRp were downloaded from Protein Data Bank. The structures of ligands were retrieved from PubChem database or optimized by ORCA program. Ritonavir, Lopinavir, Sofosbuvir, and Remdesivir were selected as control inhibitors. Docking calculations were performed by AutoDock Vina option and top-ranked compounds were subjected to molecular dynamics simulation by Gromacs 5.1.4 simulation package.
Result: The results showed that all 15 compounds had stronger interactions with PLpro in comparison to the other enzymes. Dihydroxylisopropylidenylisatisine A binds to the active site of PLpro with highest affinity (–9.3 kcal/ mol) which is even more than the binding constants of Ritonavir and Lopinavir. Of the 15 compounds, Dihydroxylisopropylidenylisatisine A and Isatibisindosulfonic acid B had the highest tendency to bind to 3CLpro. Dihydroxylisopropylidenylisatisine A, Indirubin, Insatindibisindolamide A, Indigo, Insatindibisindolamide B, Isatibisindosulfonic acid B and Isatindosulfonic acid B had the highest RdRp binding affinity even more Remdesivir.
Conclusion: Based on the results, the highest and weakest interaction with all three enzymes was observed for Dihydroxylisopropylidenylisatisine A and Epigoitrin, respectively. Based on these findings, Dihydroxylisopropylidenylsatistine A might be potential therapeutic candidate against SARS-CoV-2.

Keywords

Alkaloids

COVID-19

isatis indigotica

molecular docking analysis

molecular dynamic simulation, protease

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Author(s):

Farnoosh Kazemi:[PubMed][Scholar]
Mahdi Mojarrab:[PubMed][Scholar]
Gholamreza Bahrami:[PubMed][Scholar]
Shahram Miraghaee:[PubMed][Scholar]
Saba Hadidi:[PubMed][Scholar]
Mohammad Bagher Maljaie:[PubMed][Scholar]