Abstract:
The aim of this study was to determine the full-length 3D structure of the Glyco (G) protein of
Nipah virus, followed by the De Novo drug design, which will generate ligands as prospective
Nipah virus inhibitor. Due to the unavailability of the complete structure of the Nipah virus in
RCSB-PDB, Homology modelling was adopted by using the sequence from Uni Prot KB. BLAST
assisted in the search of templates with the highest sequence similarity and coverage. After the
joining of loops with the functional domains through ab-initio modelling, the full sequence of the
Glyco (G) protein of Nipah virus was submitted in the i-TASSER server, which further predicted
five models. Ramachandran assessment helped in the validation of those models. From the i-
TASSER model, joining of the loops with the functional domains were cut off using UCSFChimera
software. These loops and fragments were joined with the help of a tool that is in house
developed. Once energy minimization has been carried out in the Swiss PDB viewer, CASTp
server provided the determination of ligand binding pockets. After pocket determination, e-
LEA3D server helped in the design of ligand molecules that will bind to those pockets. The
pharmacokinetic properties of each of those ligands were further assessed in the Mobyle@RPBS
web portal so that prospective Nipah virus inhibitor drugs can be developed in future.
