Beyond the catalytic site: Structural characterization of MERS-CoV nsp5 and its druggable binding pockets

Coronaviruses, including SARS-CoV (2003), MERS-CoV (2012), and SARS-CoV-2 (2019), have caused major global outbreaks, highlighting the importance of structural studies of conserved viral proteins for antiviral drug discovery. Therefore, the structural characterization of coronavirus proteins is essential for understanding their function and supporting the development of new therapeutic strategies. In present work, a structural analysis of the MERS-CoV nsp5 protein was done in detail. Specifically, here for the first time all the MERS-CoV nsp5 unique sequences were selected, then used in homology modeling and molecular dynamics methods to identify all possible binding pockets that could potentially be exploited in further drug discovery projects. Despite high overall sequence similarity, significant differences in conformational dynamics were observed, indicating that minor sequence variations can induce local structural rearrangements. This flexibility, particularly in loop regions, contributes to the formation and modulation of binding pockets. In total, seven regions with ligand-binding potential were identified. Most of the identified sites, except for the canonical catalytic site, represent previously uncharacterized binding regions distributed across the protein. Among these, pocket 3 remained highly stable throughout simulations, while pockets 4 and 5 exhibited potential cryptic behavior, showing moderate expansion into surrounding protein regions under dynamic simulation. Suggesting their binding potential to bind small ligands upon conformational rearrangement. These findings provide a comprehensive structural framework for MERS-CoV nsp5 and highlight several promising binding sites for future structure-based antiviral drug design.