The family Togaviridae includes several genera of infectious Alphaviruses that are pathogenic to humans. Apart from the well-known Chikungunya virus, other notable viruses among Alphaviruses are Eastern, Western, and Venezuelan equine encephalitis viruses (EEEV, WEEV, and VEEV, respectively). These encephalitis-causing viruses affect both equids and humans, leading to recurring outbreaks in the Americas all around the 20th century. VEEV infections affect the central nervous system, especially in children, and can even result in death. Combining with this, the history of VEEV using as a biological weapon causes the virus to get listed as a bioterrorism agent according to the Centers for Disease Control (CDC) and National Institute for Allergy and Infectious Diseases (NIAID).
The Alphaviruses contain a positive sense, single-stranded genomic RNA that has two ORFs. Those are responsible for the production of three structural (nucleocapsid C and envelope proteins E1 and E2) and four non-structural proteins (nsP1-4) individually. The nsP2 is the largest that contains a C-terminal protein that has protease and methyltransferase-like (MTL) domains and an N-terminal RNA helicase with nucleotide triphosphatase activity. The RNA helicase enzyme plays a crucial role in RNA metabolism by unwinding or rearranging RNA or ribonucleoprotein complexes in various processes like transcription, translation, splicing, etc. On the other hand, the nsP4 exhibits an RNA-dependent RNA polymerase activity. Both of these nsP2 and nsP4 are essential and are parts of the viral replicase complex.
Despite the significance of VEEV on human health, no FDA-approved drug or vaccine is available right now. Besides the structures of VEEV's nsP2 helicase (nsP2h) and nsP4 are not solved yet. For these reasons, we attempt to resolve the structures of the VEEV nsP2h and nsP4 by computational approaches. The elucidation of the structures would help to understand pathogenic mechanisms as well as to discover drugs against the virus.