Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors

• Published in: Antiviral research 2018-12, Vol.160, p.17-24
• Main Authors: Phoo, Wint Wint, Zhang, Zhenzhen, Wirawan, Melissa, Chew, Edwin Jun Chen, Chew, Alvin Bing Liang, Kouretova, Jenny, Steinmetzer, Torsten, Luo, Dahai
• Format: Article
• Language: English
• Subjects: Drug discovery; Flaviviral protease; NS3 protease; Peptide inhibitors; Protease inhibitor; X-ray crystallography; Zika virus
• ISSN: 0166-3542; 1872-9096
• DOI: 10.1016/j.antiviral.2018.10.006

Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of protease inhibitors, we report three high-resolution co-crystal structures of bZiPro with peptidomimetic inhibitors composed of a P1-P4 segment and different P1′ residues. Compounds 1 and 2 possess small P1′ groups that are split off by bZiPro, which could be detected by mass spectrometry. On the other hand, the more potent compound 3 contains a bulky P1′ benzylamide structure that is resistant to cleavage by bZiPro, demonstrating that presence of an uncleavable C-terminal cap contributes to a slightly improved inhibitory potency. The N-terminal phenylacetyl residue occupies a position above the P1 side chain and therefore stabilizes a horseshoe-like backbone conformation of the bound inhibitors. The P4 moieties show unique intra- and intermolecular interactions. Our work reports the detailed binding mode interactions of substrate-analogue inhibitors within the S4-S1′ pockets and explains the preference of bZiPro for basic P1-P3 residues. These new structures of protease-inhibitor complexes will guide the design of more effective NS2B-NS3 protease inhibitors with improved potency and bioavailability. •Crystal structures of unlinked ZIKV protease (bZiPro) with three peptide inhibitors were determined at high resolution.•The inhibitor 3 is the longest peptidic inhibitor co-crystallised with flaviviral protease.•The susceptibility of the inhibitor for cleavage between P1 and P1′ affects the inhibition efficiency of the compound.•The structural characterization of S4-S1 and -S1′ pockets reported here is useful for antivirals against ZIKV.