Exploring effects of temperature on the catalytic site of non-structural protease 2 (nsP2) from Chikungunya virus by using molecular dynamics simulations and DFT calculations

Chikungunya virus (CHIKV) is an emerging arthropod-borne virus transmitted to humans by the bite of infected Aedes mosquitoes, responsible for more than 1 million illnesses worldwide. CHIKV is considered a significant health problem, mainly due to the lack of specific antiviral agents and vaccines. The nsP2 is an essential viral protease with a conserved catalytic dyad (Cys¹⁰¹³/His¹⁰⁸³) that processes the viral polyprotein. However, there is a study that suggests that Ser¹⁰¹⁷ could take a place in the catalysis, making it a non-papain-like protein. In this work, we decided to understand the effects of different temperatures (300 to 400K) on the distances between Ser-His-Cys residues. Thusly, the nucleophilic ion-pair formation was investigated by DFT calculations using B3LYP, M06, and ωB97X-D functionals. Moreover, we investigated an acylhydrazone inhibitor towards nsP2 in order to describe both non- and covalent binding modes. It was observed that the distances between the catalytic residues increased with an increase in temperature, therefore, decreasing the probability of generating an ion-pair. The lowest RMSD value was displayed for nsP2 at 325K and, then it was selected for further analyses. DFT calculations were capable of predicting Cys^-/His⁺ as the major ion-pair (at a distance of 3.48Å) with barrier values (ΔG^‡) ranging from 12.44 to 14.3 kcal/mol. Concerning the mechanism of action for the acylhydrazone inhibitor, the nucleophilic attack at the Michaels’ acceptor moiety is not plausible. So, it was verified that the nP2 inhibitor interacts by non-covalent mode.