Screening of potential bio-molecules from Moringa olifera against SARS-CoV-2 main protease using computational approaches

Abstract

COVID-19 caused by SARS-CoV-2 is responsible for the deaths of millions of people worldwide. It is having devastating effects on the people of all countries. In this regard, the phytochemicals of medicinal plants could be explored to prevent this disease. M. oleifera is a miracle plant with antibacterial, antiviral, and antioxidant properties because of its high content of flavonoids, glucosides and glucosinolates. Therefore, we constructed a library of 294 phytochemicals of M. oleifera and filtered it through the FAF-Drugs4. Further, molecular docking studies of filtered phytochemicals were performed with Mpro enzyme to investigate the binding interactions. Drug likeness properties, ADMET prediction were analyzed to determine the therapeutic aspect of these compounds. Based on the binding energy score of the top 4 compounds, the results indicate that Vicenin-2 has the highest binding affinity (−8.6 kcal mol⁻¹) as compared to the reference molecule (−8.4 kcal mol⁻¹). ADMET result reveals that all top four compounds have minimal toxic effects and good absorption. Further, 500 ns molecular dynamics simulation of the top four compounds showed that Kaempferol-3-O-rutinoside and Vitexin have good stability with Mpro. These two compounds were then subjected for MMPBSA (last 50 ns) calculation to analyze the protein-ligand stability and dynamic behavior. Kaempferol-3-O-rutinoside and Vitexin showed very good binding free energy i.e. −40.136 kJ mol⁻¹ and −26.784 kJ mol⁻¹, respectively. Promising outcomes from MD simulations evidence the worth of these compounds for future drug development to combat coronavirus disease.

Communicated by Ramaswamy H. Sarma

GRAPHICAL ABSTRACT

Keywords:

• COVID-19
• Mpro
• molecular docking
• phytochemicals
• M. oleifera
• MD simulation

Acknowledgements

The authors acknowledge the Department of Botany, Kumaun University, S.S.J Campus, Almora for providing basic facilities to conduct this research work. The authors also acknowledge Kumaun University, Nainital for providing high-speed internet facilities. We also extend our acknowledgment to Rashtriya Uchchattar Shiksha Abhiyan (RUSA), Ministry of Human Resource Development, Government of India to provide Computational infrastructure for the establishment of Bioinformatics Centre in Kumaun University, S.S.J Campus, Almora.

Disclosure statement

The authors declare that there is no competing interest in this work.

Funding

There was no funding source to carry out this research work.