In the current study, the interaction of SARS-CoV-2 protein (A and B chains of nsp13) with different recently synthesized phenolic compounds (Sreenivasulu et al., Synthetic Communications, 2020, 112–122) has been studied. The interactions have been investigated by using molecular docking, quantum chemical and molecular dynamics simulations methods. The molecular structures of all the ligands are studied quantum chemically in terms of their optimized structures, 3-D orbital distributions, global chemical descriptors, molecular electrostatic potential plots and HOMO-LUMO orbital energies. All the ligands show reasonably good binding affinities with nsp-13 protein. The ligand L2 shows to have better binding affinities to Chain A and Chain B of nsp13 protein, which are −6.7 and −6.4 kcal/mol. The study of intermolecular interactions indicates that L2 shows different hydrophobic and hydrogen bond interactions with both chains. Furthermore, molecular dynamic simulations of the nsp13-L2 complex are obtained over a time scale of 60 ns, which indicates its stability and flexibility behavior as assessed in terms of its RMSD and RMSF graphs. The ADMET analysis also shows no violation of Lipinski rule (RO5) by studied phenolic compounds. We believe that the current findings will be further confirmed by in vitro and in vivo studies of these recent phenolic compounds for their potential as inhibitors for SARS-Co-V-2 virus.
|Original language||English (US)|
|Journal||Bioorganic and Medicinal Chemistry Letters|
|State||Published - May 8 2021|
Bibliographical noteKAUST Repository Item: Exported on 2022-06-15
Acknowledgements: The author from the University of Bisha extends their appreciation to the Deanship of Scientific Research at the University of Bisha Saudi Arabia for funding this work through COVID-19 Initiative Project under Grant Number (UB - COVID - 32 - 1441). The authors from King Khalid University of Saudi Arabia extend their appreciations to the Deanship of Scientific Research at King Khalid University for funding the work through Project (RGP.1/168/42). For computer time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.
ASJC Scopus subject areas
- Organic Chemistry
- Drug Discovery
- Pharmaceutical Science
- Molecular Medicine
- Molecular Biology
- Clinical Biochemistry