Modeling interaction between non-structural protein 2 of Chikungunya Virus and various protein factors of innate pathway

Chikungunya virus is positive-sense single-stranded RNA virus that causes an arthropod-borne chikungunya fever, myalgia and arthralgia. Chikungunya virus belongs to the Togaviridae family, and the genus is Alphavirus. Virus-host protein interaction plays a vital role in developing vaccines and antiviral drugs. We designed the current study to establish the in-silico interaction of non-structural protein 2 (nsP2) with proteins of innate immune pathway. The nsP2 sequences of various Chikungunya virus genotypes were retrieved from National Centre for Biotechnology Institute (NCBI). The homology models of proteins were generated through a protein modeling online web server. Protein-protein interaction (PPI) between nsP2 and proteins of innate immune pathway were docked using High Ambiguity-Driven Docking (HADDOCK) webserver. The interactive residues of the bimolecular complexes were analyzed with PDBsum-Generate online webserver. Our findings revealed differentially affinity of nsP2 of various chikungunya genotypes towards key proteins of cellular innate pathway. The nsP2 of Asian genotype demonstrates relatively high interaction with interferon-beta promoter stimulator 1 (IPS-1). Similarly, nsP2 of various genotypes binds with differential affinity to tumor necrosis factor receptor-associated factor 6 (TRAF6) with the highest affinity observed for the nsP2 of the West African genotype. Bimolecular complexes of nsP2 and host proteins demonstrate the interaction of various domains of nsP2 with proteins of the innate immune pathway. Thus, it is sought that the selected panel of the proteins might be helpful to treat the viral infection as a therapeutic drug target in the future.