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

revised on 26.04.2020, 08:56 and posted on 27.04.2020, 12:46 by Chinmayee Choudhury

The recent pandemic of novel corona virus (nCoV) infections (COVID19) has put the world on serious alert. The main protease of nCov (nCov-MP) 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 nCov-MP binding site. A huge library of 191678 fragments was screened against the binding cavity of nCov-MP 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 property filters and MM-GBSA binding free 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 nCov-MP, were subjected to molecular dynamics simulations, which assessed the stabilities of their binding with nCov-MP. Fifteen molecules were found to form stable complexes with nCov-MP. These novel chemical entities designed specifically according to the pharmacophoric requirements of nCov-MP 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 nCov drug discovery.


DST-INSPIRE faculty grant, Department of Science and Technology, India


Email Address of Submitting Author


Post Graduate Institute of Medical Education and Research, Chandigarh



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest declared.

Version Notes

The second version includes analysis of MD simulation on all 17 complexes and also 6LU7.pdb as the reference system. similarities of the molecules with existing ChEMBL and Zinc databases are included.