Molecular docking based comparative study of antiviral compounds on SARS-CoV-2 spike protein

Abstract

The urgent need for effective therapeutic interventions against SARS-CoV-2 has prompted extensive exploration of potential drug candidates. Among the viral proteins, the spike (S) protein presents an attractive target due to its critical role in viral entry and infection. In this study, we employed molecular docking techniques to investigate the binding affinities and interaction profiles of a panel of active compounds against the SARS-CoV-2 spike protein. Utilising computational simulations, we assessed the binding properties of these compounds within the receptor-binding domain (RBD) and other key regions of the spike protein. Our comparative analysis elucidates the differential binding patterns and identifies promising lead compounds with high binding affinity and favourable interaction profiles. Furthermore, we discuss the implications of these findings for the development of potential therapeutics targeting the SARS-CoV-2 spike protein. Using molecular docking and the Lipinski five rule, this study illustrates possible compounds with strong binding affinities, their molecular interactions, for both naturally occurring and man-made drugs. Computational approach is applied, and it is concluded that, drugs like Withanolide, Dihydroergocristine, Fenebrutinib, and Ergotamine shows binding energies between −8.3 and −9.1 kcal/mol, and are possible candidate for anti covid drug.

Graphical Abstract

Keywords:

• SARS-CoV-2
• covid-19
• spike protein
• molecular docking
• natural medicine

Ethical approval

This study does not involve any study with human or animal subjects.

Disclosure statement

The authors declare no conflicts of interest.

Additional information

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.