Druggability of cavity pockets within SARS-CoV-2 spike glycoprotein and pharmacophore-based drug discovery.

Future Virology
Alireza MohebbiZahra Najafimemar

Abstract

Aim: Virus spike glycoprotein of SARS-CoV-2 is a good target for drug discovery. Objective: To examine the potential for druggability of spike protein for pharmacophore-based drug discovery and to investigate the binding affinity of natural products with SARS-CoV-2 spike protein. Methods: Druggable cavities were searched though CavityPlus. A pharmacophore was built and used for hit identification. Autodock Vina was used to evaluate the hits' affinities. 10 chemical derivatives were also made from the chemical backbone to optimize the lead compound. Results: 10 druggable cavities were found within the glycoprotein spike. Only one cavity with the highest score at the binding site was selected for pharmacophore extraction. Hit identification resulted in the identification of 410 hits. Discussion: This study provides a druggable region within viral glycoprotein and a candidate compound to block viral entry.

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Software Mentioned

CavityPlus
ChemT
ADV
SwissADME
MGLTools
ZINCPharmer
CavPharmer
PaDEL
OpenBabel
Autodock Vina

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