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In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2.
J Biomol Struct Dyn. 2020 Aug 24 [Online ahead of print]JB

Abstract

Coronavirus Disease (COVID-19) is recently declared pandemic (WHO) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The virus was named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), (Coronavirus Disease 2019). Currently, there is no specific drug for the therapy of COVID-19. So, there is a need to develop or find out the new drug from the existing to cure the COVID-19. Identification of a potent inhibitor of Methyltransferase, Endoribonuclease, Phosphatase and Main Protease enzymes of SARS CoV-2 by coumarin derivatives using insilico approach. The in silico studies were performed on maestro 12.0 software (Schrodinger LLC 2019, USA). Two thousand seven hundred fifty-five biologically active coumarin derivative was docked with above receptor proteins of SARS CoV-2. The molecular dynamic simulation of the top one ligand of respected proteins was performed. Top five ligands of each protein were taken for study. Coumarin derivatives actively interact with taken receptors and showed good docking results for Methyltransferase, Endoribonuclease, Phosphatase and Main Protease and top five compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol, respectively. The docked compounds were showed RMSD and binding stability of simulated ligands are show the potency of ligands against the SARS CoV-2. Our study provides information on drugs that may be a potent inhibitor of COVID-19 infection. Drug repurposing of the available drugs would be great help in the treatment of COVID-19 infection. The combination therapy of the finding may improve inhibitory activity. Communicated by Ramaswamy H. Sarma Highlights Coronavirus Disease (COVID-19) is recently declared pandemic (WHO) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In silico virtual screening, docking, ADME, MM-GBSA and MD simulation analysis of coumarin derivatives against Methyltransferase (MTase), Endoribonuclease(endoU), ADP ribose Phosphatase and Main Protease enzyme of SARS CoV-2. All the analysis was performed on Maestro 12.0 Schrodinger software against respective receptors. Top five compounds of coumarin derivatives s docked at the active site of Methyltransferase (MTase), Endoribonuclease(endoU), ADP ribose Phosphatase and protease and top five compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol, respectively, of SARS CoV-2. These compounds were used to analysis of binding free energy by using the Prime MM-GBSA module. All the compounds showed drug-likeness properties. MD simulation of Proteins and ligands showed binding stability and good RMSD, radius of gyration of protein, coulomb-SR and LJ-SR energy.

Authors+Show Affiliations

Chemistry Laboratory, Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Devghat, Jhalwa, Prayagraj, UP, India.Chemistry Laboratory, Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Devghat, Jhalwa, Prayagraj, UP, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32835632

Citation

Maurya, Akhilesh Kumar, and Nidhi Mishra. "In Silico Validation of Coumarin Derivatives as Potential Inhibitors Against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2." Journal of Biomolecular Structure & Dynamics, 2020, pp. 1-16.
Maurya AK, Mishra N. In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2. J Biomol Struct Dyn. 2020.
Maurya, A. K., & Mishra, N. (2020). In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2. Journal of Biomolecular Structure & Dynamics, 1-16. https://doi.org/10.1080/07391102.2020.1808075
Maurya AK, Mishra N. In Silico Validation of Coumarin Derivatives as Potential Inhibitors Against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2. J Biomol Struct Dyn. 2020 Aug 24;1-16. PubMed PMID: 32835632.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2. AU - Maurya,Akhilesh Kumar, AU - Mishra,Nidhi, Y1 - 2020/08/24/ PY - 2020/8/25/entrez PY - 2020/8/25/pubmed PY - 2020/8/25/medline KW - ADME/T KW - MD simulation KW - SARS CoV-2 KW - binding free energy KW - docking KW - inhibitor SP - 1 EP - 16 JF - Journal of biomolecular structure & dynamics JO - J. Biomol. Struct. Dyn. N2 - Coronavirus Disease (COVID-19) is recently declared pandemic (WHO) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The virus was named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), (Coronavirus Disease 2019). Currently, there is no specific drug for the therapy of COVID-19. So, there is a need to develop or find out the new drug from the existing to cure the COVID-19. Identification of a potent inhibitor of Methyltransferase, Endoribonuclease, Phosphatase and Main Protease enzymes of SARS CoV-2 by coumarin derivatives using insilico approach. The in silico studies were performed on maestro 12.0 software (Schrodinger LLC 2019, USA). Two thousand seven hundred fifty-five biologically active coumarin derivative was docked with above receptor proteins of SARS CoV-2. The molecular dynamic simulation of the top one ligand of respected proteins was performed. Top five ligands of each protein were taken for study. Coumarin derivatives actively interact with taken receptors and showed good docking results for Methyltransferase, Endoribonuclease, Phosphatase and Main Protease and top five compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol, respectively. The docked compounds were showed RMSD and binding stability of simulated ligands are show the potency of ligands against the SARS CoV-2. Our study provides information on drugs that may be a potent inhibitor of COVID-19 infection. Drug repurposing of the available drugs would be great help in the treatment of COVID-19 infection. The combination therapy of the finding may improve inhibitory activity. Communicated by Ramaswamy H. Sarma Highlights Coronavirus Disease (COVID-19) is recently declared pandemic (WHO) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In silico virtual screening, docking, ADME, MM-GBSA and MD simulation analysis of coumarin derivatives against Methyltransferase (MTase), Endoribonuclease(endoU), ADP ribose Phosphatase and Main Protease enzyme of SARS CoV-2. All the analysis was performed on Maestro 12.0 Schrodinger software against respective receptors. Top five compounds of coumarin derivatives s docked at the active site of Methyltransferase (MTase), Endoribonuclease(endoU), ADP ribose Phosphatase and protease and top five compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol, respectively, of SARS CoV-2. These compounds were used to analysis of binding free energy by using the Prime MM-GBSA module. All the compounds showed drug-likeness properties. MD simulation of Proteins and ligands showed binding stability and good RMSD, radius of gyration of protein, coulomb-SR and LJ-SR energy. SN - 1538-0254 UR - https://www.unboundmedicine.com/medline/citation/32835632/In_silico_validation_of_coumarin_derivatives_as_potential_inhibitors_against_Main_Protease_NSP10/NSP16_Methyltransferase_Phosphatase_and_Endoribonuclease_of_SARS_CoV_2_ L2 - http://www.tandfonline.com/doi/full/10.1080/07391102.2020.1808075 DB - PRIME DP - Unbound Medicine ER -
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