Identification of NS2 determinants stimulating intrinsic HCV NS2 protease activity

Abstract

Hepatitis C Virus NS2-NS3 cleavage is mediated by NS2 autoprotease (NS2pro) and this cleavage is important for genome replication and virus assembly. Efficient NS2-NS3 cleavage relies on the stimulation of an intrinsic NS2pro activity by the NS3 protease domain. NS2pro activation depends on conserved hydrophobic NS3 surface residues and yet unknown NS2-NS3 surface interactions. Guided by an in silico NS2-NS3 precursor model, we experimentally identified two NS2 surface residues, F103 and L144, that are important for NS2pro activation by NS3. When analyzed in the absence of NS3, a combination of defined amino acid exchanges, namely F103A and L144I, acts together to increase intrinsic NS2pro activity. This effect is conserved between different HCV genotypes. For mutation L144I its stimulatory effect on NS2pro could be also demonstrated for two other mammalian hepaciviruses, highlighting the functional significance of this finding. We hypothesize that the two exchanges stimulating the intrinsic NS2pro activity mimic structural changes occurring during NS3-mediated NS2pro activation. Introducing these activating NS2pro mutations into a NS2-NS5B replicon reduced NS2-NS3 cleavage and RNA replication, indicating their interference with NS2-NS3 surface interactions pivotal for NS2pro activation by NS3. Data from chimeric hepaciviral NS2-NS3 precursor constructs, suggest that NS2 F103 is involved in the reception or transfer of the NS3 stimulus by NS3 P115. Accordingly, fine-tuned NS2-NS3 surface interactions are a salient feature of HCV NS2-NS3 cleavage. Together, these novel insights provide an exciting basis to dissect molecular mechanisms of NS2pro activation by NS3.

Potyviral Helper-Component Protease: Multifaced Functions and Interactions with Host Proteins

“…Similar autoinhibitory structures were also predicted for the hepatitis C virus (HCV) NS2 protease, but this protease is catalytically active as a dimer with two composite active sites, i.e., the catalytic His 143 and Glu 163 residues are provided by one monomer and the third catalytic partner (Cys 184) is provided by the other monomer [71]. In addition, the HCV NS2 cysteine protease catalytic domain is regulated by the neighboring NS3 Nterminal domain [72]. Along these lines, a protein cofactor, the N-terminal region of protein P3 (in both P3 and P3N-PIPO), may also be involved in the catalytic activity of HC-Pro (Figure 4).…”

Viral proteases as therapeutic targets

“…Host proteases ensure processing of viral structural proteins on the luminal side, whereas viral proteases process the nonstructural (NS) proteins on the cytoplasmic side ( Lohmann et al, 1996 ). The viral cysteine protease NS2 autocatalytically cleaves between NS2 and NS3 ( Isken et al, 2022 ; Santolini et al, 1995 ); the viral serine protease NS3 ensures maturation of viral proteins expressed downstream of NS3, including NS5 replication complex. NS3, which harbors not only a protease but also a helicase, requires an activating cofactor, NS4A, for proteolytic activity.…”