Reaction mechanisms of substrate and inhibitor with ns2b/ns3 serine protease of zika virus by mm and qm/mm simulations

Abstract

Zika virus (ZIKV) infection has become a public health concern worldwide. The recent epidemiological data have revealed a possible association of ZIKV infection with neurological manifestations in both newborn children and adults. Currently, there is no anti-ZIKV drug or vaccine available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is NS2B/NS3 serine protease that plays a crucial role to cleave the peptide bond during the viral replication process. Initially, the ZIKV NS2B/NS3 serine protease in complex with four peptide substrates were studied to investigate the binding recognition and protein-substrate interactions using conventional molecular dynamics (MD) simulations. The results indicate that the P1 and P2 positions of the substrate play a major role in binding with the enzyme, while the P3 and P4 positions show a less contribution in binding interaction. Afterwards, the cleavage reaction mechanism for the ZIKV protease with its peptide substrate (TGKRS) was studied by hybrid quantum mechanics/molecular mechanics (QM/MM) approach. QM/MM (PM6/ff14SB) free-energy simulations indicate that proton transfer from S135 to H51 and nucleophilic attack on the substrate by S135 are concerted. Importantly, higher-level QM/MM calculations also support a concerted reaction mechanism for this particular reaction. In addition, QM/MM calculations were performed to determine the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that the transfer of proton from the catalytic S135 to H51 take places in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease resembles the tetrahedral intermediate for substrate hydrolysis. Therefore, the computational approaches presented here are helpful for further designing of potent NS2B/NS3 inhibitors.