Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease

Abstract

The recent pandemic of severe acute respiratory syndrome–coronavirus2 (SARS-CoV-2) infection (COVID-19) has put the world on serious alert. The main protease of SARS-CoV-2 (SARS-CoV-2-M^Pro) cleaves the long polyprotein chains to release functional proteins required for replication of the virus and thus is a potential drug target to design new chemical entities in order to inhibit the viral replication in human cells. The current study employs state of art computational methods to design novel molecules by linking molecular fragments which specifically bind to different constituent sub-pockets of the SARS-CoV-2-M^Pro binding site. A huge library of 191678 fragments was screened against the binding cavity of SARS-CoV-2-M^Pro and high affinity fragments binding to adjacent sub-pockets were tailored to generate new molecules. These newly formed molecules were further subjected to molecular docking, ADMET filters and MM-GBSA binding energy calculations to select 17 best molecules (named as MP-In1 to MP-In17), which showed comparable binding affinities and interactions with the key binding site residues as the reference ligand. The complexes of these 17 molecules and the reference molecule with SARS-CoV-2-M^Pro, were subjected to molecular dynamics simulations, which assessed the stabilities of their binding with SARS-CoV-2-M^Pro. Fifteen molecules were found to form stable complexes with SARS-CoV-2-M^Pro. These novel chemical entities designed specifically according to the pharmacophoric requirements of SARS-CoV-2-M^Pro binding pockets showed good synthetic feasibility and returned no exact match when searched against chemical databases. Considering their interactions, binding efficiencies and novel chemotypes, they can be further evaluated as potential starting points for SARS-CoV-2 drug discovery.

Graphical Abstract

Communicated by Ramaswamy H. Sarma

Keywords:

• Covid-19
• main protease
• fragment-based drug discovery
• docking
• molecular dynamics

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

CC thanks Department of Science and Technology for financial assistance in the form of DST-INSPIRE Faculty award, Dr. Anuradha Chakravarti, Head, Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh for providing required infrastructure and fruitful discussions and Schrodinger for providing short term licences for some of the modules.