Structural Dynamics of Zika Virus NS2B-NS3 Protease Binding to Dipeptide Inhibitors

The NS2B-NS3 viral protease is an attractive drug target against Zika virus (ZIKV) due to its importance in viral replication and maturation. Here we report the crystal structure of protease in complex with a dipeptide inhibitor, Acyl-KR-aldehyde (compound 1). The aldehyde moiety forms a covalent bond with the catalytic Ser135 of NS3. The Arg and Lys residues in the inhibitor occupy the S1 and S2 sites of the protease, respectively. Nuclear magnetic resonance studies demonstrate that the complex is in the closed conformation in solution. The chemical environment of residues surrounding the active site is sensitive to the bound inhibitor as demonstrated by the comparison with two other non-covalent dipeptides, Acyl-K-Agmatine (compound 2) and Acyl-KR-COOH (compound 3). Removing the aldehyde moiety in 1 converts the binding mode from a slow to a fast exchange regime. The structural dynamics information obtained in this study will guide future drug discovery against ZIKV and other flaviviruses. [Display omitted] •Structure and dynamics of Zika protease-inhibitor complexes are investigated•Dipeptide inhibitors bind to the protease active site•Aldehyde in the inhibitor forms a covalent bond with the catalytic residue S135•The closed conformation is suitable for structure-based drug design Li et al. present structural and dynamic studies on Zika protease in a complex with dipeptide inhibitors. The unlinked protease forms the closed conformation and the aldehyde group from the inhibitor forms a covalent bond with the side chain of S135. Compounds derived from protease substrate bind to the protease active site. Protease complexes form a stable complex in solution.