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Published on: July 15, 2019
Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19)
Raghvendra Dubey1, Kushagra Dubey2
1Department of Pharmaceutical Chemistry, Matoshri Institute of Pharmacy, Yeola, Nashik, Maharashtra 423401, India.
Background:
COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many people have been contaminated by environmental contamination and transmission from one human to another until now.
Objective:
The objective of the present work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein), using molecular docking approach.
Methods:
The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations.
Result:
The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore, and H Bond score of nicotiflorin and standard inhibitor X77 were observed as -173.058, -127.302, -21.9398 and -156.913,-121.296,-5.7369, respectively.
Conclusion:
Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.
Insights
This study explored nicotiflorin, a flavonoid, as a potential inhibitor for the COVID-19 main protease (6W63). Molecular docking revealed nicotiflorin exhibits stronger binding affinity than the standard inhibitor X77, suggesting therapeutic potential.
Area of Science:
- Biochemistry
- Computational Chemistry
- Pharmacology
Background:
- The novel coronavirus (COVID-19) pandemic emerged in December 2019.
- Human-to-human transmission and environmental contamination facilitate COVID-19 spread.
- Identifying effective antiviral agents is crucial for managing the pandemic.
Purpose of the Study:
- To evaluate the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid.
- To assess nicotiflorin's interaction with the main protease (3Clpro protein, 6W63) of SARS-CoV-2.
- To utilize molecular docking to predict binding affinity and interactions.
Main Methods:
- Protein structure (6W63) obtained from the Protein Data Bank.
- Molecular docking performed using Molegro Virtual Docker (MVD) software.
- Ligand structure prepared using Chem 3D and energy minimized with MM2 force field.
Main Results:
- Nicotiflorin demonstrated a higher MolDock score (-173.058) compared to the standard inhibitor X77 (-156.913).
- Nicotiflorin exhibited superior Rerank and H Bond scores (-127.302, -21.9398) versus X77 (-121.296, -5.7369).
- Molecular docking confirmed greater binding affinity of nicotiflorin to the viral protein 6W63.
Conclusions:
- Flavonoid nicotiflorin shows promising inhibitory potential against the SARS-CoV-2 main protease (6W63).
- Nicotiflorin's affinity for viral protein 6W63 surpasses that of the standard inhibitor X77.
- Further preclinical and clinical evaluations are recommended to assess nicotiflorin's safety and efficacy for COVID-19 treatment.
