Hepatitis C Virus Nonstructural Protein 3 Protease Research Articles

Evaluating Drug Resistant Mutations to HCV NS3 Protease Inhibitors in Iranian Naïve Patients

Hepatitis C virus (HCV) is an important causative agent of acute and chronic hepatitis. The non-structural protein 3 (NS3) of HCV retains two enzymatic domains which are essential for the virus life cycle. The serine protease inhibitors have developed to improve the responses of HCV-infected patients that have an effective impact on NS3. Nonetheless, drug-resistant variants are the prominent obstruction toward therapeutic success. Sixty-eight Iranian patients infected with HCV genotypes 1a and 3a and diagnosed with chronic active hepatitis were examined. Plasma viral RNA was used to amplify and sequence the HCV NS3 gene; also, HCV viral load, molecular genotyping, and the ALT test were determined for all samples. The sequencing results were used to be analyzed by several reliable bioinformatics tools to determine the physicochemical properties, B cell epitopes, post-modification changes and secondary/tertiary structures; and evaluate the interactions with four drugs. Our results showed that 45% of patients were 1a genotype, the rest of them belonged to 3a genotype, and 70% of patients had abnormal ALT and AST levels. Several substitutions were observed in codons I52M, S102A, L132I, and S166A in 3a genotype and 40, 153 and 91 in 1a genotype. Interactions between references and sample sequences with available drugs showed that different genotypes or common mutations could not have any striking effect on the energy value of the interaction. This study displayed resistance mutations and genetic polymorphisms of NS3 region that are crucial in determining the efficiency of protease inhibitor class of drugs in Iranian HCV infected patients.

Activation of Type I and III Interferon Response by Mitochondrial and Peroxisomal MAVS and Inhibition by Hepatitis C Virus.

Sensing viruses by pattern recognition receptors (PRR) triggers the innate immune system of the host cell and activates immune signaling cascades such as the RIG-I/IRF3 pathway. Mitochondrial antiviral-signaling protein (MAVS, also known as IPS-1, Cardif, and VISA) is the crucial adaptor protein of this pathway localized on mitochondria, peroxisomes and mitochondria-associated membranes of the endoplasmic reticulum. Activation of MAVS leads to the production of type I and type III interferons (IFN) as well as IFN stimulated genes (ISGs). To refine the role of MAVS subcellular localization for the induction of type I and III IFN responses in hepatocytes and its counteraction by the hepatitis C virus (HCV), we generated various functional and genetic knock-out cell systems that were reconstituted to express mitochondrial (mito) or peroxisomal (pex) MAVS, exclusively. Upon infection with diverse RNA viruses we found that cells exclusively expressing pexMAVS mounted sustained expression of type I and III IFNs to levels comparable to cells exclusively expressing mitoMAVS. To determine whether viral counteraction of MAVS is affected by its subcellular localization we employed infection of cells with HCV, a major causative agent of chronic liver disease with a high propensity to establish persistence. This virus efficiently cleaves MAVS via a viral protease residing in its nonstructural protein 3 (NS3) and this strategy is thought to contribute to the high persistence of this virus. We found that both mito- and pexMAVS were efficiently cleaved by NS3 and this cleavage was required to suppress activation of the IFN response. Taken together, our findings indicate comparable activation of the IFN response by pex- and mitoMAVS in hepatocytes and efficient counteraction of both MAVS species by the HCV NS3 protease.

ID: 105: Activation of type I and III interferon response by mitochondrial and peroxisomal MAVS and inhibition by hepatitis C virus

Sensing viruses by pattern recognition receptors (PRR) triggers the innate immune system of the host cell and activates immune signaling cascades like the RIG-I/IRF3 pathway. Mitochondrial antiviral-signaling protein (MAVS) is the crucial adaptor protein of this pathway localized on mitochondria, peroxisomes and mitochondria associated membranes (MAMs). Activation of MAVS leads to the production of type I and type III interferon (IFN) as well as interferon stimulated genes (ISGs). To refine the role of MAVS subcellular localization for the induction of type I and III IFN responses in hepatocytes, we generated cell lines with organelle-targeted MAVS and characterized innate immune response after viral infection. We established various functional and genetic knock-out cell systems reconstituted to express exclusively mitochondrial or peroxisomal MAVS. Infection with diverse RNA viruses mounted comparable levels of type I and III IFN expression irrespective of MAVS subcellular localization. To determine whether viral counteraction of MAVS is affected in these systems we employed infection of cells with the hepatitis C virus (HCV), a major causative agent of chronic liver diseases with a high propensity to establish persistence. This virus efficiently cleaves MAVS via a viral protease residing in nonstructural protein 3 (NS3). We found that both mitochondrial and peroxisomal MAVS were efficiently cleaved by NS3 and this cleavage was required to suppress activation of the IFN response. Taken together, our findings indicate comparable activation of the IFN response by peroxisomal and mitochondrial MAVS in hepatocytes and efficient counteraction of both MAVS species by the HCV NS3 protease.

Classification models of HCV NS3 protease inhibitors based on support vector machine (SVM).

Inhibition of the hepatitis C virus (HCV) non-structural protein 3 (NS3) serine protease by molecule inhibitors is an attractive strategy for the treatment of hepatitis C. We built four classification models based on a dataset of 413 HCV NS3 protease inhibitors using support vector machine method. The best performing model obtains the best prediction performance for the test set with prediction accuracy, sensitivity (SE), specificity (SP) and Matthews correlation coefficient (MCC) of 90.76%, 92.21%, 88.10% and 0.799, respectively. The number of rotatable bonds (NRotBond), charge and electronegativity related properties were found to be correlated with the bioactivity of the inhibitors. The ECFP_4 analyses of structural features were performed and it was found that the cyclopropyl with acylsulfonamide group was the unique substructure in the active inhibitors. The method with dataset split by Kohonen's self-organizing map and descriptors selected by SVMAttributeEval presented in this study can be employed in virtual screening for discovering novel inhibitors of HCV NS3 protease.

Molecular Docking Investigation of the Binding Interactions of Macrocyclic Inhibitors with HCV NS3 Protease and its Mutants (R155K, D168A and A156V)

Hepatitis C Virus (HCV) non-structural protein 3 (NS3) protease drug resistance poses serious challenges on the design of an effective treatment. Substrate Envelope Hypothesis, "the substrates of HCV NS3/4A protease have a consensus volume inside the active site called substrate envelope" is used to design potent and specific drugs to overcome this problem. Using molecular docking, we studied the binding interaction of the different inhibitors and protein and evaluated the effect of three different mutations (R155K, D168A and A156V) on the binding of inhibitors. P2-P4 macrocycles of 5A/5B and modified 5A/5B hexapeptide sequences have the best scores against the wild-type protein -204.506 and -206.823kcal/mole, respectively. Also, charged P2-P4 macrocycles of 3/4A and 4A/4B hexapeptide sequences have low scores with the wild-type protein -200.467 and -203.186kcal/mole, respectively. R155K mutation greatly affects the conformation of the compounds inside the active site. It inverts its orientations, and this is because the large and free side chain of K155 which restricts the conformation of the large P2-P4 macrocycle. The conformation of charged P2-P4 macrocycle of 3/4A hexapeptide sequence in wild-type, A156V and D168A proteins is nearly equal; while that of charged P2-P4 macrocycle of 4A/4B hexapeptide sequence is different. Nevertheless, these compounds have a slight increase of Van der Waals volume compared to that of substrates, they are potent against mutations and have good scores. Therefore, the suggested drugs can be used as an effective treatment solving HCV NS3/4A protease drug resistance problem.

HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor

Viruses sometimes mimic host proteins and hijack the host cell machinery. Hepatitis C virus (HCV) causes liver fibrosis, a process largely mediated by the overexpression of transforming growth factor (TGF)-β and collagen, although the precise underlying mechanism is unknown. Here, we report that HCV non-structural protein 3 (NS3) protease affects the antigenicity and bioactivity of TGF-β2 in (CAGA)9-Luc CCL64 cells and in human hepatic cell lines via binding to TGF-β type I receptor (TβRI). Tumor necrosis factor (TNF)-α facilitates this mechanism by increasing the colocalization of TβRI with NS3 protease on the surface of HCV-infected cells. An anti-NS3 antibody against computationally predicted binding sites for TβRI blocked the TGF-β mimetic activities of NS3 in vitro and attenuated liver fibrosis in HCV-infected chimeric mice. These data suggest that HCV NS3 protease mimics TGF-β2 and functions, at least in part, via directly binding to and activating TβRI, thereby enhancing liver fibrosis.

967 PRECLINICAL CHARACTERIZATION OF SCH 900518, A NOVEL MECHANISM-BASED INHIBITOR OF HCV NS3 PROTEASE

Small molecule hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease inhibitors have shown antiviral activity as monotherapy and in combination with pegylated interferon-alfa and ribavirin in clinical trials; however, clinical efficacy can be limited by inadequate drug exposure and development of viral resistance. Improvement in inhibitor potency and pharmacokinetic properties offers opportunities to overcome such limitations and to further increase SVR. Methods: Inhibition of HCV NS3 protease was measured using a single-chain NS3 (3-181)/4A protease. The antiviral effect and resistance study of protease inhibitors were evaluated using genotype 1b HCV replicon cells. Results: Combination of medicinal chemistry and structure-based design has led to the discovery of SCH 900518, a novel ketoamide protease inhibitor which forms a reversible covalent bond with the active site serine with an inhibition constant (K i *) of 7 nM. SCH 900518 showed a 10-fold improvement in replicon potency (EC 90 = 40 nM) compared to boceprevir and telaprevir. In biochemical assays, SCH 900518 was active against proteases of genotypes 1a, 1b, 2, and 3. A 2-week treatment with 5× EC 90 of the inhibitor reduced replicon RNA by 3-log. High exposures of SCH 900518 had minimal effects on a variety of human normal and tumor cell lines. Selection of replicon cells with SCH 900518 resulted in outgrowth of several major resistant mutants (T54A/S, A156S/T/V). Preclinical cross-resistance studies demonstrated that the majority of mutations against boceprevir and telaprevir showed similar fold loss of activity against all three inhibitors; however, SCH 900518 retained more activity against these mutants due to its higher intrinsic potency. Combination treatment with interferon-alfa enhanced inhibition of replicon RNA and suppressed emergence of resistant replicon colonies, supporting the use of SCH 900518/peginterferon combination therapy in the clinic. Conclusions: The preclinical characterization of SCH 900518 supports its progression toward clinical evaluation of safety, pharmacokinetic, and pharmacodynamic parameters.

Inhibition of dsRNA-induced signaling in hepatitis C virus-infected cells by NS3 protease-dependent and -independent mechanisms.

The recent establishment of a robust hepatitis C virus (HCV) cell culture system permits analysis of virus-host interactions during HCV infection. Here, we report that HCV genotype 2a (JFH-1) infection fails to induce IFN-beta or IFN-stimulated gene expression in Huh-7 cells, and that it blocks IFN-beta and IFN-stimulated gene production after transfection of synthetic dsRNA. Overexpression of individual components of the dsRNA-signaling pathway in HCV-infected and uninfected cells indicates that HCV inhibits IFN-beta promoter activity by inactivating the mitochondrial antiviral signaling protein/IFN-beta promoter stimulator 1 (MAVS/IPS-1), while leaving the IFN-induced Janus kinases-signal transducers and activators of transcription (JAK-STAT) signaling pathway intact. We also show that MAVS/IPS-1-dependent IFN-beta promoter activity in HCV-infected cells is fully restored by the nonstructural protein 3 (NS3) protease inhibitor BILN2061. In contrast, synthetic dsRNA-induced IFN-beta promoter activity is not restored by BILN2061, although it is partially restored by overexpression of RIG-I. These results support recently reported evidence that the HCV NS3 protease blunts the ability of HCV to induce IFN-beta promoter activity by proteolytically cleaving MAVS/IPS-1. The results also suggest that HCV blocks the synthetic dsRNA-induced signaling pathway at a point upstream of MAVS/IPS-1, and that it does so by an NS3-independent mechanism.

Structure-activity relationships for the selectivity of hepatitis C virus NS3 protease inhibitors.

The selectivity of hepatitis C virus (HCV) non-structural protein 3 (NS3) protease inhibitors was determined by evaluating their inhibitory effect on other serine proteases (human leukocyte elastase (HLE), porcine pancreatic elastase (PPE), bovine pancreatic chymotrypsin (BPC)) and a cysteine protease (cathepsin B). For these peptide inhibitors, the P1-side chain and the C-terminal group were the major determinants of selectivity. Inhibitors with electrophilic C-terminal residues were generally non-selective while compounds with non-electrophilic C-terminal residues were more selective. Furthermore, compounds with P1 aminobutyric acid residues were non-selective, while 1-aminocyclopropane-1-carboxylic acid (ACPC) and norvaline-based inhibitors were generally selective. The most potent and selective inhibitors of NS3 protease tested contained a non-electrophilic phenyl acyl sulfonamide C-terminal residue. HLE was most likely to be inhibited by the HCV protease inhibitors, in agreement with similar substrate specificities for these enzymes. The identified structure-activity relationships for selectivity are of significance for design of selective HCV NS3 protease inhibitors.

Inhibition of HCV NS3 protease by RNA aptamers in cells

Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in vitro. To utilize these aptamers in vivo, we constructed a G9 aptamer expression system in cultured cells, using the cytomegarovirus enhancer + chicken beta-actin globin (CAG) promoter. By conjugating the cis-acting genomic human hepatitis delta virus (HDV) ribozyme and G9-II aptamer, a chimeric HDV ribozyme-G9-II aptamer (HA) was constructed, which was used to produce stable RNA in vivo and to create tandem repeats of the functional unit. To target the transcribed RNA aptamers to the cytoplasm, the minimal mutant of constitutive transport element (CTE), derived from type D retroviruses, was conjugated at the 3' end of HA (HAC). Transcript RNAs from (HA)(n) and (HAC)(n) were processed into the G9-II aptamer unit by the cis-acting HDV ribozyme, both in vitro and in vivo. Efficient protease inhibition activity of HDV ribozyme-G9-II aptamer expression plasmid was demonstrated in HeLa cells. Protease inhibition activity level of tandem chimeric aptamers, (HA)(n) and (HAC)(n), rose with the increase of n from 1 to 4.

Construction of the dual-functional RNA ligand against HCV NS3 protease and helicase.

Non-structural protein 3 (NS3) of hepatitis C virus (HCV) contains two distinct activities, protease and helicase which are essential for the HCV replication. In the previous study, we succeeded to obtain RNA aptamers, G9-I, G9-II and G9-III specific for the NS3 protease domain (delta NS3) by in vitro selection (1). As the result of mutational analysis in G9-I, we could obtain the minimum length of RNA structure, delta NEO-III maintaining the full inhibitional activity as shown in G9-I. Furthermore, we created a bi-functional novel RNA ligand, NEO-III-14U which was constructed by connecting delta NEO-III with (U)14 at the 3' terminal. NEO-III-14U was able to inhibit the unwinding of duplex DNA catalyzed by the Full-NS3 helicase activity as well as the protease activity in vitro. Consequently, we could obtain the dual-functional RNA ligand which could inhibit both NS3 protease and helicase activities essential for the HCV proliferation.

Virus-specific cofactor requirement and chimeric hepatitis C virus/GB virus B nonstructural protein 3.

GB virus B (GBV-B) is closely related to hepatitis C virus (HCV) and causes acute hepatitis in tamarins (Saguinus species), making it an attractive surrogate virus for in vivo testing of anti-HCV inhibitors in a small monkey model. It has been reported that the nonstructural protein 3 (NS3) serine protease of GBV-B shares similar substrate specificity with its counterpart in HCV. Authentic proteolytic processing of the HCV polyprotein junctions (NS4A/4B, NS4B/5A, and NS5A/5B) can be accomplished by the GBV-B NS3 protease in an HCV NS4A cofactor-independent fashion. We further characterized the protease activity of a full-length GBV-B NS3 protein and its cofactor requirement using in vitro-translated GBV-B substrates. Cleavages at the NS4A/4B and NS5A/5B junctions were readily detectable only in the presence of a cofactor peptide derived from the central region of GBV-B NS4A. Interestingly, the GBV-B substrates could also be cleaved by the HCV NS3 protease in an HCV NS4A cofactor-dependent manner, supporting the notion that HCV and GBV-B share similar NS3 protease specificity while retaining a virus-specific cofactor requirement. This finding of a strict virus-specific cofactor requirement is consistent with the lack of sequence homology in the NS4A cofactor regions of HCV and GBV-B. The minimum cofactor region that supported GBV-B protease activity was mapped to a central region of GBV-B NS4A (between amino acids Phe22 and Val36) which overlapped with the cofactor region of HCV. Alanine substitution analysis demonstrated that two amino acids, Val27 and Trp31, were essential for the cofactor activity, a finding reminiscent of the two critical residues in the HCV NS4A cofactor, Ile25 and Ile29. A model for the GBV-B NS3 protease domain and NS4A cofactor complex revealed that GBV-B might have developed a similar structural strategy in the activation and regulation of its NS3 protease activity. Finally, a chimeric HCV/GBV-B bifunctional NS3, consisting of an N-terminal HCV protease domain and a C-terminal GBV-B RNA helicase domain, was engineered. Both enzymatic activities were retained by the chimeric protein, which could lead to the development of a chimeric GBV-B virus that depends on HCV protease function.

Cross-genotypic interaction between hepatitis C virus NS3 protease domains and NS4A cofactors

Background/Aims: Hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease requires NS4A as a cofactor. This cofactor activity has been mapped to the central region of NS4A which interacts with the N-terminus of NS3 protease. To investigate whether this interaction is conserved among different genotypes of HCV, cross-genotypic characterization were performed to delineate the importance of NS4A cofactor function in relation to the molecular evolution of HCV.Methods: Active NS3 protease domains of genotype 1–3 (representing five subtypes: 1a, 1b, 2a, 2b and 3a) were produced and purified from bacterial cells. NS4A cofactor-dependent in vitro trans cleavage assays were established using the in vitro translated recombinant protein substrates. These substrates contained the junction site of NS4A/NS4B, NS4B/NS5A or NS5A/NS5B.Results: Our data revealed that NS3 proteases crossinteracted with NS4A cofactors derived from different genotypes, although the genotype 2 cofactor was less efficient, which could be due to greater genetic variations in this region. Furthermore, the corresponding region in hepatitis G virus (HGV) NS4A was found to provide weak cofactor activity for HCV NS3 protease. Surprisingly, a synthetic substrate peptide from the NS4B/NS5A junction was also found to enhance HCV NS3 protease activity in a dose-dependent manner.Conclusion: Our study suggests that the NS4A cofactor function is well conserved among HCV. It is likely that other HCV-related viruses may have developed similar strategies to regulate their protease activity.

Nucleoside Triphosphatase and RNA Helicase Activities Associated with GB Virus B Nonstructural Protein 3

GB virus B (GBV-B) is a positive-stranded RNA virus that belongs to the Flaviviridae family. This virus is closely related to hepatitis C virus (HCV) and causes acute hepatitis in tamarins (Saguinus species). Nonstructural protein 3 (NS3) of GBV-B contains sequence motifs predictive of three enzymatic activities: serine protease, nucleoside triphosphatase (NTPase), and RNA helicase. The N-terminal serine protease has been characterized and shown to share similar substrate specificity with the HCV NS3 protease. In this report, a full-length GBV-B NS3 protein was expressed in Escherichia coli and purified to homogeneity. This recombinant protein was shown to possess polynucleotide-stimulated NTPase and double-stranded RNA (dsRNA) unwinding activities. Both activities were abolished by a single amino acid substitution, from the Lys (K) residue in the conserved walker motif A (or Ia) “AXXXXGK210S” to an Ala (A), confirming that they are intrinsic to GBV-B NS3. Kinetic parameters (Km and kcat) for hydrolysis of various NTPs or dNTPs were obtained. The dsRNA unwinding activity depends on the presence of divalent metal ions and ATP and requires an RNA duplex substrate with 3′ unpaired regions (RNAs with 5′ unpaired regions only or with blunt ends are not suitable substrates for this enzyme). This indicates that GBV-B NS3 RNA helicase unwinds dsRNA in the 3′ to 5′ direction. Direct interaction of the GBV-B NS3 protein with a single-stranded RNA was established using a gel-based RNA bandshift assay. Finally, a homology model of GBV-B NS3 RNA helicase domain based on the 3-dimensional structure of the HCV NS3 helicase that shows a great similarity in overall structure and surface charge distribution between the two proteins was proposed.

GB virus B and hepatitis C virus NS3 serine proteases share substrate specificity

GB virus B (GBV-B) is a recently discovered virus responsible for hepatitis in tamarins (Saguinus species). GBV-B belongs to the Flaviviridae family and is closely related to the human pathogen hepatitis C virus (HCV). Nonstructural protein 3 (NS3) of HCV has been shown to encompass a serine protease domain required for viral maturation. GBV-B and HCV share only about 30% of the amino acid sequence within the NS3 protease domain. The catalytic triad is conserved, and the residue Phe-154, presumed to be a crucial amino acid for determining the S1 specificity pocket of the HCV NS3 protease, is also conserved. We have expressed a synthetic gene encoding the GBV-B NS3 protease domain in Escherichia coli and have characterized the purified recombinant protein for its activity on HCV substrates. We have shown that the NS3 region of the GBV-B genome actually encodes a serine protease that, despite the low sequence homology, shares substrate specificity with the HCV NS3 protease.