Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease

Abstract

To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP2 protein of Venezuelan equine encephalitis virus (VEEV). The protein modeled was optimized using molecular dynamics simulation; the junction peptides of a nonstructural protein complex were then docked in order to investigate the possible protein-protein interactions between nsP2 and the proteins cleaved by nsP2. The modeling studies conducted shed light on the binding modes, and the critical interactions with the peptides provide insight into the chemical features needed to inhibit the CHIK virus infection. Energy-optimized pharmacophore mapping was performed using the junction peptides. Based on the results, we propose the pharmacophore features that must be present in an inhibitor of nsP2 protease. The resulting pharmacophore model contained an aromatic ring, a hydrophobic and three hydrogen-bond donor sites. Using these pharmacophore features, we screened a large public library of compounds (Asinex, Maybridge, TOSLab, Binding Database) to find a potential ligand that could inhibit the nsP2 protein. The compounds that yielded a fitness score of more than 1.0 were further subjected to Glide HTVS and Glide XP. Here, we report the best four compounds based on their docking scores; these compounds have IDs of 27943, 21362, ASN 01107557 and ASN 01541696. We propose that these compounds could bind to the active site of nsP2 protease and inhibit this enzyme. Furthermore, the backbone structural scaffolds of these four lead compounds could serve as building blocks when designing drug-like molecules for the treatment of Chikungunya viral fever.

Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches

“…For instance, Bassetto et al reported that Cys1013 and His1083 (the numbering is according to the CHIKV nsP2 sequence) in the homology model of the nsP2 protease were the catalytic residues compared to Cys477 and His546 in the VEEV nsP2 protease through a sequence alignment between the CHIKV nsP2 protease and the VEEV nsP2 protease. In contrast, similarly based the sequence alignment, Singh et al predicted that the active site residues interacting with the peptide substrate include Lys1045, Gly1176, His1222 and Lys1239 without explicitly identifying the catalytic residues [19]. In this work, structural alignment of the nsP2 proteases from three alphaviruses, CHIKV (PDB id: 3TRK), Venezuelan equine encephalitis virus (VEEV, PDB id:…”

“…The compounds from library NCI Diversity Set II were docked to the entire protein (the nsP2 protease) with a grid box placed at either the centre at the binding site 1 (VST1) or at the centre of the protein (VST2). The binding site 1 (Pocket 1), including the key residues for interactions (Lys1045, Gly1176, His1222 and Lys1239), was taken from the published data by Singh et al [19]. The binding modes of the compounds were ranked by their predicted binding affinities.…”

“…The envelope glycoproteins are involved with viral entry while the non-structural proteins are essential components and play a crucial role in viral replication and transcription [10,16]. Therefore, they are considered as potential targets which several studies utilized to identify potential inhibitors against CHIKV [10,[17][18][19][20][21][22].…”

“…Several studies have constructed homology models [19,24,25] of the nsP2 protease based on the counterparts of the Venezuelan equine encephalitis virus (VEEV) to assist in drug design for CHIKV, before a crystal structure of the nsP2 protease became available in late 2011. With the homology models, inhibitors of the nsP2 enzyme have been screened, allowing further compound designs based on pharmacophore models of the inhibitors [19,24,25]. The active site was predicted in the major surface groove of the C-terminaldomain region, and likely binds to the substrate polyprotein sequences in the cleavage process [10].…”

“…The key residues responsible for interactions between the nsP2 protease and ligands were established and pharmacophore features of inhibitors were suggested [19]. The structure-activity relationships of hit compounds were evaluated with predictions of CHIKV replication inhibition at low µM concentrations [25].…”