Determination of the N Protein of Nipah Virus and Its Ligands as a Potential New Anti-Nipah Viral Drug

Abstract

The purpose of this research was to produce potential inhibitors of Nipah virus by first determining the full-length 3D structure of the N-protein of the virus. Methods for Molecular Modelling using the Nipah virus sequence from UniProt KB was used since its entire structure is not yet available in the Protein Data Bank (PDB). Templates with high levels of sequence similarity and coverage were found with the use of BLAST. The whole sequence of the Nipah virus N- protein was entered into the i-TASSER system, and after ab-initio modeling was used to combine loops with functional domains, five models were projected. These models were validated with the help of Ramachandran's evaluation. Using UCSF-Chimera, we severed the connections between the loops and the functional domains of the i-TASSER model. The in-house designed tool was used to assemble these loops and pieces. After the Swiss PDB viewer had minimized the binding energies, the CASTp server figured out where the ligands would go. Once binding pockets were identified, the e-LEA3D server assisted with the development of ligand molecule designs. With the goal of creating medications that effectively suppress the spread of Nipah virus in the future, the pharmacokinetic features of each of these ligands were analyzed in further depth on the Mobyle@RPBS online site.