Harnessing the interactome of CHIKV in its native host environment for novel therapy targeting protein-protein interaction

"Mapping authentic virus-host interactions is a critical first step in understanding viral pathogenesis and identifying key therapeutic targets. CHIKV (CHIKV) is a re-emerging, mosquito-borne arbovirus that infects many people in Thailand and global South. Unlike other tropical viruses, CHIKV exhibits a distinct pathology, heavily targeting skeletal muscle and causing persistent muscle and joint pain. However, current studies mapping CHIKV-host protein interactions have been conducted in non-muscle cell types (e.g., kidney and liver cells) or using yeast-two-hybrid approaches, which do not capture the highly specialized cellular environment of myofibers. This gap in knowledge limits progress in CHIKV treatment. To address this, we have assembled a multidisciplinary consortium comprising clinical virologists, animal infection specialists, muscle biologists, proteomics experts, computational modelers of protein-protein interactions (PPI), and chemical synthesis specialists. In Aim 1, we will use a myotrophic adeno-associated virus (AAV) to express each of the nine CHIKV proteins, tagged with 3×HA, in intact mouse muscle. Systematic affinity purification followed by mass spectrometry will generate a comprehensive CHIKV-host PPI map. Direct interaction partners will be predicted using protein docking and AlphaFold-Multimer screening, with experimental validation. In Aim 2, we will sequence CHIKV clinical isolates archived over the past decade, correlating mutational profiles with patient severity and infectivity in mouse models. We will identify key mutations in viral genes and determine how these mutations alter PPIs. In Aim 3, we will assess the functional importance of key PPIs in viral replication and muscle pathology by manipulating host factors via AAV. Finally, Aim 4 will design and synthesize chemical and/or peptide inhibitors targeting critical PPIs and evaluate their impact on CHIKV infectivity. Together, this project will advance CHIKV research by defining interactome networks for both wild-type and mutant viral factors, while also laying the groundwork for therapeutic interventions. Our consortium is primarily based in Thailand, aiming to address the social, medical, and economic burdens associated with CHIKV infection in the region."