A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum.

Journal of Molecular Liquids
Sajjad AhmadMuzammil Hasan Najmi

Abstract

The nucleocapsid (N) protein of SARS-COV-2, a virus responsible for the current COVID-19 pandemic, is considered a potential candidate for the design of new drugs and vaccines. The protein is central to several critical events in virus production, with its highly druggable nature and rich antigenic determinants making it an excellent anti-viral biomolecule. Docking-based virtual screening using the Asinex anti-viral library identified binding of drug molecules at three specific positions: loop 1 region, loop 2 region and β-sheet core pockets, the loop 2 region being the most common binding and stable site for the bulk of the molecules. In parallel, the protein was characterized by vaccine design perspective and harboured three potential B cell-derived T cell epitopes: PINTNSSPD, GVPINTNSS, and DHIGTRNPA. The epitopes are highly antigenic, virulent, non-allergic, non-toxic, bind with good affinity to the highly prevalent DRB*0101 allele and show an average population coverage of 95.04%. A multi-epitope vaccine ensemble which was 83 amino acids long was created. This was highly immunogenic, robust in generating both humoral and cellular immune responses, thermally stable, and had good physicochemical properties that could be easi...Continue Reading

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Methods Mentioned

BETA
in silico methodology
X-ray

Software Mentioned

ERRAT
WaterSwap
AllerTOP
UCSF Chimera
GalaxyRefine
VMD
MMPBSA
IFNepitope
AutoDock4
3Dpro

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