Nonstructural Proteins of Alphavirus-Potential Targets for Drug Development

Abstract

Alphaviruses are enveloped, positive single-stranded RNA viruses, typically transmitted by arthropods. They often cause arthralgia or encephalitic diseases in infected humans and there is currently no targeted antiviral treatment available. The re-emergence of alphaviruses in Asia, Europe, and the Americas over the last decade, including chikungunya and o'nyong'nyong viruses, have intensified the search for selective inhibitors. In this review, we highlight key molecular determinants within the alphavirus replication complex that have been identified as viral targets, focusing on their structure and functionality in viral dissemination. We also summarize recent structural data of these viral targets and discuss how these could serve as templates to facilitate structure-based drug design and development of small molecule inhibitors.

Keywords: alphavirus replication; nonstructural protein; protease inhibitors.

Figure 1

(A) Schematic representation of the alphavirus genome showing the RNA sequence open reading frames (ORFs). The (*) indicates the position of opal termination codon; (B) schematic representation of non-structural polyprotein (nsP2) processing by nsP2 protease. Early processing of P1234 produces P123 and nsP4 which associate to form the early replication complex (RC), which performs negative-sense RNA synthesis. P123 is further processed to produce the individual nsPs, which associate to form mature RC that regulates positive-sense RNA synthesis and transcription of subgenomic 26S RNA.

Figure 2

(A) Illustration of superposed structures of papain and chikungunya virus (CHIKV) nsP2 proteases (Protein Data Bank (PDB) 9PAD and 3TRK respectively). The structure of papain protease is presented as a solid, blue ribbon. The structure of CHIKV nsP2 protease is presented as solid, green ribbon. The domain common for both proteases is highlighted in dark colors and is enlarged subsequently to show the conserved catalytic dyad; (B) alignment of nsP2 cleavage sites. The nomenclature of Berger and Schechter is used to identify residues on the amino (P1, P2, etc.) or carboxy (P1′, P2′, etc.) termini of the scissile bond. The arrow indicates the location of the cleavage site. Cleavage sites between the non-structural proteins contain a common motif, AG(A/C)↓(G/Y/A) [55]. Abbreviations: Chikungunya virus (CHIKV), o’nyong’nyong virus (ONNV), semliki forest virus (SFV), ross river virus (RRV), sindbis virus (SINV) and Venezuelan equine encephalitis virus (VEEV).