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Manjunathan R, Periyaswami V, Mitra K, Rosita AS, Pandya M, Selvaraj J, Ravi L, Devarajan N, Doble M. Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein. BMC Bioinformatics 2022; 23:180. [PMID: 35578172 PMCID: PMC9108711 DOI: 10.1186/s12859-022-04724-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMPRSS2 as a therapeutic target for the inhibition of SARS-Cov-2 infection is highly promising. Hence, in the present study, we docked the binding efficacy of ten naturally available phyto compounds with known anti-viral potential with TMPRSS2. The aim is to identify the best phyto compound with a high functional affinity towards the active site of the TMPRSS2 with the aid of two different docking software. Molecular Dynamic Simulations were performed to analyse the conformational space of the binding pocket of the target protein with selected molecules. RESULTS Docking analysis using PyRx version 0.8 along with AutoDockVina reveals that among the screened phyto compounds, Genistein shows the maximum binding affinity towards the hydrophobic substrate-binding site of TMPRSS2 with three hydrogen bonds interaction ( - 7.5 kcal/mol). On the other hand, molecular docking analysis using Schrodinger identified Quercetin as the most potent phyto compound with a maximum binding affinity towards the hydrophilic catalytic site of TMPRSS2 ( - 7.847 kcal/mol) with three hydrogen bonds interaction. The molecular dynamics simulation reveals that the Quercetin-TMPRSS complex is stable until 50 ns and forms stable interaction with the protein ( - 22.37 kcal/mol of MM-PBSA binding free energy). Genistein creates a weak interaction with the loop residues and hence has an unstable binding and exits from the binding pocket. CONCLUSION The compounds, Quercetin and Genistein, can inhibit the TMPRSS2 guided priming of the spike protein. The compounds could reduce the interaction of the host cell with the type I transmembrane glycoprotein to prevent the entry of the virus. The critical finding is that compared to Genistein, Quercetin exhibits higher binding affinity with the catalytic unit of TMPRSS2 and forms a stable complex with the target. Thus, enhancing our innate immunity by consuming foods rich in Quercetin and Genistein or developing a novel drug in the combination of Quercetin and Genistein could be the brilliant choices to prevent SARS-Cov-2 infection when we consider the present chaos associated with vaccines and anti-viral medicines.
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Affiliation(s)
- Reji Manjunathan
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, Taramani Campus, University of Madras, Chennai, Tamil Nadu, India. .,Multi-Disciplinary Research Unit, Chengalpattu Government Medical College and Hospital, Chengalpattu, Tamil Nadu, 603001, India.
| | - Vijayalakshmi Periyaswami
- Department of Biotechnology and Bioinformatics, Holy Cross College, Bharathidasan University, Trichy, Tamil Nadu, India
| | - Kartik Mitra
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Arokiaraj Sherlin Rosita
- Department of Bioinformatics, Bishop Heber College (Autonomous, Bharathidasan University), Tiruchirapalli, Tamil Nadu, India
| | - Medha Pandya
- KPES Science College, Maharaja KrishnakumarSinhiji Bhavnagar University, Gujarat, India
| | - Jayaraman Selvaraj
- Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Lokesh Ravi
- Department of Botany, St. Josephs College, Bangalore, Karnataka, India
| | - Nalini Devarajan
- Central Research Laboratory, Meenakshi Ammal Dental College, Maduravoyal, Chennai, Tamil Nadu, India.
| | - Mukesh Doble
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India. .,Department of Cariology, Saveetha Dental College and Hospital, Chennai, Tamil Nadu, 600077, India.
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