A novel high throughput screening assay for HCV NS3 serine protease inhibitors

Hepatitis C virus (HCV) infection is a major worldwide health problem, causing chronic hepatitis, liver cirrhosis and primary liver cancer (Hepatocellular carcinoma). HCV encodes a precursor polyprotein that is enzymatically cleaved to release the individual viral proteins. The viral non-structural proteins are cleaved by the HCV NS3 serine protease. NS3 is regarded currently as a potential target for anti-viral drugs thus specific inhibitors of its enzymatic activity should be of importance. A prime requisite for detailed biochemical studies of the protease and its potential inhibitors is the availability of a rapid reliable in vitro assay of enzyme activity. A novel assay for measurement of HCV NS3 serine protease activity was developed for screening of HCV NS3 serine protease potential inhibitors. Recombinant NS3 serine protease was isolated and purified, and a fluorometric assay for NS3 proteolytic activity was developed. As an NS3 substrate we engineered a recombinant fusion protein where a green fluorescent protein is linked to a cellulose-binding domain via the NS5A/B site that is cleavable by NS3. Cleavage of this substrate by NS3 results in emission of fluorescent light that is easily detected and quantitated by fluorometry. Using our system we identified NS3 serine protease inhibitors from extracts obtained from natural Indian Siddha medicinal plants. Our unique fluorometric assay is very sensitive and has a high throughput capacity making it suitable for screening of potential NS3 serine protease inhibitors.     

HCV NS5A-B片段的表达及在酶活性研究中的应用

目的：利用原核表达载体pBVIL1，表达丙型肝炎病毒非结构蛋白（NS3）丝氨酸蛋白酶催化底物NS5A—B小分子，为进一步研究蛋白酶活性提供方法学。方法：将PCR合成的NS5A—B（2412—2427aa）基因直接插入高效原核表达载体pBVIL1，融合表达NS5A—B片段．包涵体形式的表达产物用8mol／L脲溶解后，采用离子交换和凝胶过滤两步纯化。利用SDS—PAGE、Western blot和ELISA方法，于37℃酶催化条件下，分析NS5A—B底物的降解活性。结果：（1）构建了pBVIL1／NS5A—B重组质粒，鉴定证明NS5A—B基因片段正确地插入表达载体上：融合蛋白在转化质粒的HB101菌中得到高效表达。分离纯化重组蛋白后浓度可达0．73g／L。（2）在NS3蛋白酶作用不同时间后，用SDS—PAGE和Western blot证实，底物带可被明显降解，ELISA分析也证明，NS5A—B具有酶底物活性。结论：含有酶切位点的NS5A—B融合蛋白可被NS3丝氦酸蛋白酶有效地降解，可用作为NS3蛋白酶的底物，可替代全长NS5A—B和化学合成肽用于酶活性和酶阻断剂的研究     

聚合酶链反应诱导丙型肝炎病毒(HCV)蛋白酶活性位点的突变及突变HCVNS3/4a蛋白的表达

目的 以聚合酶链反应（PCR）突变方法诱导丙型肝炎病毒（HCV）蛋白酶活性位点ser1165的突变，获得全长非结构基因3（NS3）／4a的表达与纯化。方法 分别以NS3 N端正向引物与诱变反向引物，诱变正向引物与NS4a C端反向引物获得2个PCR产物，产物纯化后在新的PCR反应体系中加入以上2个PCR产物与NS3 N端正向引物、NS4a C端反向引物。再次PCR扩增突变模板，分别与野生型模板重组入表达载体pET26-Ub，转化大肠杆菌BL21（DE3）pCG1，诱导表达后经菌体裂解、纯清化、硫酸铵沉淀、DEAE－Sepharose、NTA纯化，Western blot分析表达蛋白的特异性及PCR诱导突变使HCV蛋白酶活性位点失活的作用。结果 获得诱导突变的模板，Western blot证实该突变可完全阻断对NS3丝氨酸蛋白酶与NS3螺旋酶间的切割，部分阻断了螺旋酶与NS4a间的切割，纯化后的HCV NS3／4a蛋白在SDS－PAGE胶上显示为双带。结论 PCR突变方法简便、有效，获得丝氨酸蛋白酶失活的NS3蛋白表达，NS3蛋白与NS4a蛋白以复合物形式存在。     

Characterization of NS3 protease from an Egyptian HCV genotype 4a isolate

The role of the NS3 protease in HCV replication was demonstrated by the ability of a protease inhibitor cocktail (10 μg/ml) to abolish the induced cytopathic effect in RAW macrophages upon infection with Egyptian sera. The HCV protease gene was amplified from Egyptian sera by nested PCR and cloned downstream of the CMV promotor in a mammalian expression plasmid, which was then used to transform bacteria. Colonies carrying the gene in the correct orientation were subjected to large-scale plasmid purification followed by sequencing. Phylogenetic comparison of the sequence obtained with published sequences from different genotypes confirmed that our sequence belongs to genotype 4a. Of the other genotypes, the most closely related ones were from genotype 1. Multiple alignments of protease peptides showed that the catalytic triads and binding residues for substrate, Zn2+ and the NS4 cofactor are conserved among different isolates, including ours, and confirmed the closer homology between NS3 of genotypes 4 and 1. The HCV-protease-encoding construct was successfully transcribed in both mammalian cells and mice. Mouse antibodies produced against the protease-encoding-construct detected the 18-kDa enzyme in lysates of cells transfected with the construct by Western blotting, and in the media of infected cells by ELISA.     

Comparison of three quantitative HCV RNA assays in samples from HCV genotype 1- or 4-infected patients treated with the NS3/4A protease inhibitor simeprevir

BackgroundMonitoring HCV RNA levels during treatment is an important tool for managing protease-inhibitor-based regimens, and different assays used in clinical practice can impact treatment decisions.ObjectivesThe concordance of three HCV RNA assays was determined, and their impact on treatment decisions assessed using samples from HCV genotype (GT) 1- and GT4-infected patients treated with the NS3/4A inhibitor simeprevir in combination with pegylated interferon-α/ribavirin.Study designPlasma samples collected during the simeprevir Phase III studies QUEST-1 and QUEST-2 (GT1), and RESTORE (GT4) were analyzed with the Roche High-Pure-System COBAS^® TaqMan^® HCV v2.0 (HPS), the Roche AmpliPrep COBAS^® TaqMan^® HCV v2.0 (CAP), and the Abbott RealTime HCV (ART) assay.ResultsIn GT1, of the 440 samples, 81% were undetectable (rapid virological response; RVR) by HPS at Week 4, 76% by CAP and 44% by ART. In GT4 (103 samples), RVR rates were 67% by HPS and 24% by ART. HCV RNA <25 IU/mL at Week 4 was observed for 95–96% and 92% GT1 samples and 86% and 74% GT4 samples by HPS/CAP and ART, respectively. At Week 12, assay concordance for undetectability was high in GT1 and GT4, (95–98% and 93%, respectively).ConclusionsWhile different HCV RNA assays can lead to substantially different RVR rates, a good concordance was observed with a cut-off of 25 IU/mL. Sustained virologic response rates among GT1 patients achieving RVR or <25 IU/mL at Week 4 were high and similar between assays used. At later time points, when viremia is low, assay concordance was high.     

HCV NS3 N末端部分氨基酸缺失对NS3/NS3与NS3/NS4A分子间相互作用的影响

目的旨在弄清ＮＳ３参与分子间相互作用的确切区段，为研究针对ＮＳ３的抗ＨＣＶ寡肽小分子药物的设计提供依据。方法参照ＨＣＶ中国河北株序列设计ＮＳ３引物，将其Ｎ末端的前１５个和前３０个氨基酸分别缺失掉。然后用酵母双杂交系统检测ＮＳ３／ＮＳ３及ＮＳ３／ＮＳ４Ａ分子间相互作用强度在缺失前后的变化，从而判明ＮＳ３Ｎ末端氨基酸在分子间相互作用中的意义。核苷酸序列分析采用ＡｐｐｌｉｅｄＢｉｏｓｙｓｔｅｍ３７３Ａ型自动测序仪。结果ＮＳ３Ｎ末端氨基酸缺失前后，ＮＳ３／ＮＳ３分子间及ＮＳ３／ＮＳ４Ａ分子间相互作用的强度相差有显著性（Ｐ＜０．０１），但缺失１５个氨基酸和缺失３０个氨基酸对上述相互作用强度的影响差异无显著性（Ｐ＞０．０５）。结论ＮＳ３Ｎ末端的１～３０个氨基酸在ＮＳ３／ＮＳ３及ＮＳ３／ＮＳ４Ａ分子间相互作用中有一定意义，其Ｎ末端前１５个氨基酸（ＡＰＩＴＡＹＳＱＱＴＲＧＬＬＧ）对于分子间相互作用更为关键。本研究结果将为抗ＮＳ３丝氨酸蛋白酶活性的寡肽抑制物的研究打下基础，并为抗ＨＣＶ的寡肽小分子药物的设计提供依据     

NS3 serine protease of bovine viral diarrhea virus: characterization of active site residues, NS4A cofactor domain, and protease-cofactor interactions

The gene expression of bovine viral diarrhea virus (BVDV), a pestivirus, occurs via translation of a hypothetical polyprotein that is processed cotranslationally and posttranslationally by viral and cellular enzymes. A protease located in the N-terminal region of nonstructural (NS) protein NS3 catalyzes the cleavages, leading to the release of NS4A, NS4B, NS5A, and NS5B. Our study provides experimental evidence that histidine at position 1658 and aspartic acid at position 1686 constitute together with the previously identified serine at position 1752 (S1752) the catalytic triad of the pestiviral NS3 serine protease. Interestingly, a mutant protease encompassing an exchange of the active site S1752 to threonine still showed residual activity. This finding links the NS3 protease of pestiviruses to the capsid protease of Sindbis virus. Furthermore, we observed that the minimal protease domain of NS3 encompasses about 209 amino acids. The NS3 protease was found to be sensitive to N-terminal truncation because a deletion of 6 amino acids significantly reduced the cleavage efficiency at the NS4A/4B site. Larger N-terminal deletions also impaired the activity of the enzyme with respect to the other cleavage sites but to a different degree at each site. The NS3 protease of BVDV has previously been shown to depend on NS4A as cofactor. We demonstrate here that the central region of NS4A represents the cofactor domain. Furthermore, coprecipitation studies strongly suggest an interaction between NS4A and the N-terminal region of NS3. Besides the remarkable similarities observed between the pestiviral NS3 protease and the corresponding enzyme of hepatitis C virus (HCV), our results suggest a common ancestry between these enzymes and the capsid protease of Sindbis virus.     

A transient cell-based phenotype assay for hepatitis C NS3/4A protease: application to potency determinations of a novel macrocyclic inhibitor against diverse protease sequences isolated from plasma infected with HCV

The potential of hepatitis C virus (HCV) to develop antiviral resistance renders phenotypic analysis of viral relapse or breakthrough sequences essential to the clinical evaluation of HCV antivirals. This work describes a transient assay in which clinical NS3/4A sequences are co-expressed in Huh-7 cells with a reporter whose activity is an easily quantifiable measure of protease activity. The utility of the assay was demonstrated in potency evaluations of a novel protease inhibitor against panels of NS3/4A sequences spanning genotypes 1-3. The compound was potent against genotype 1a and 1b protease sequences with sub-nanomolar to low nanomolar EC(50)s, slightly diminished in potency against genotype 2b sequences, but poorly active against genotype 3a sequences. Diverse sequences of the same HCV genotype, however, varied in response to the inhibitor as much as 30-fold, with susceptibility differences not easily attributed to specific amino acid polymorphisms. The results demonstrate the versatility of a novel phenotype assay in the evaluation of a promising new class of NS3/4A inhibitor. The results highlight further the complexity in correlating susceptibility differences with specific sequence polymorphisms, and underscore the value in direct phenotyping of clinical sequences for compound sensitivity. The assay will be useful for monitoring changes in susceptibility due to emergence of resistant virus during clinical studies of protease inhibitors.     

A wide range of NS3/4A protease catalytic efficiencies in HCV-infected individuals

The hepatitis C virus (HCV) NS3/4A protease acts as an antagonist of virus-induced interferon (IFN) regulatory factor (IRF)-3 activation and IFN-beta expression. The NS3/4A protease performs this function by cleaving Cardif and TRIF proteins to block retinoic-acid-inducible gen I (RIG-I) and toll-like receptor (TLR)-3 signaling, respectively. NS3/4A protease inhibition can prevent Cardif and/or TRIF inactivation during HCV infection, thereby maintaining the innate immune response. Thus, differences in NS3/4A protease catalytic efficiency could be related to viral pathogenicity. In this study, we analyzed the catalytic efficiency of the most abundant NS3/4A protease isolated from each of 12 individuals infected with HCV genotypes 1b, 1a, 3a, 4a or 4d. A diversity of NS3/4A protease catalytic efficiencies (up to a six-fold difference) was found in the analyzed samples. The genotype 1b NS3/4A proteases displayed the highest catalytic efficiencies. However, within this genotype up to three-fold differences were observed. Cross-genotypic interactions between the NS3 protease domain and the NS4A cofactor peptide were also investigated. Overall, catalytic efficiencies of NS3 proteases cross-interacting with NS4A cofactors from heterologous genotypes were as efficient as the homologous NS3/4A interactions. Of the 28 heterologous interactions tested, only 6 resulted in deleterious or nonfunctional enzymes. Nonfunctional interactions were not genotype-specific, suggesting that enhancement of NS3 catalytic efficiency by the NS4A cofactor depends on a few specific amino acid residues. Characterization of the proteolytic activities of individual NS3/4A proteases should provide clues for understanding HCV-host interactions, as well as assisting in the development of new classes of NS3/4A protease inhibitors.     

The acidic sequence of the NS4A cofactor regulates ATP hydrolysis by the HCV NS3 helicase

In flaviviruses and hepatitis C virus (HCV), the NS3 gene encodes the N-terminal protease (NS3pro) and the C-terminal helicase (NS3hel). In HCV, the downstream NS4A is required for the NS3pro activity and exhibits a conserved EFDEMEE motif. To identify the role of this motif, we compared the ATPase and helicase activities of NS3 alone with those of the NS3-NS4A constructs. Our results suggest that the EFDEMEE motif is essential for regulating the ATPase activity of NS3hel. It is likely that this motif interferes with the ATP-binding site of NS3hel. It is becoming clear that NS4A functions as a cofactor of both proteinase and helicase in HCV.     

HCV非结构蛋白3真核表达载体pcDNA3.1(-)/NS3的构建

目的：构建HCV NS3基因真核表达载体，为进一步研究和解析HCV NS3基因诱发不死化人肝细胞癌化的机制准备了条件。方法：将含HCV全长基因的pBRTM/HCV1-3011质粒转化感受态菌JM109并扩增；提取pBRTM/HCV1-3011质粒；从pBRTM/HCV1-3011质粒中PCR扩增出HCV NS3片段；并将其插入到克隆载体pMD18-T中，再与表达载体pcDNA3.1(-)重组，以得到重组的真核表达载体pcDNA3.1(-)/NS3；最后限制性酶切鉴定HCV NS3表达载体。结果：从pBRTM/HCV1-3011质粒中扩增出的HCV NS3片段大小正确，经测序证明其碱基序列为编码目的基因的正确序列；凝胶电泳结果证明已将此片段克隆到pcDNA3.1/NS3内。结论：成功地构建了HCV NS3基因的真核表达载体pcDNA3.1(-)/NS3。     

Extent of HCV NS3 protease variability and resistance-associated mutations assessed by next generation sequencing in HCV monoinfected and HIV/HCV coinfected patients

HCV quasispecies variability represents the background for the selection of mutations and for the development of drug resistance. Natural aminoacid changes in NS3, associated with reduced protease inhibitor susceptibility, have been observed in treatment-naïve patients. Massively parallel sequencing has been used to analyze NS3 quasispecies in patients infected with HCV genotype 1, naive to anti-HCV treatment, with/without HIV-coinfection, to establish the genetic heterogeneity and the presence of amino acid substitutions at positions responsible for drug resistance. Genomes carrying substitutions represented either predominant or minority components of viral quasispecies, and were observed in 85.7% of patients. Multiple substitutions, frequently associated on the same haplotype, were observed in 46.4% of patients. High resistance combinations were not detected, neither on the same genome, nor in the whole quasispecies. Heterogeneity of HCV NS3 was lower in HIV-coinfected as compared to HCV-monoinfected patients, but factors underlying this difference remain to be established. Although the relevance of naturally occurring mutations with respect of resistance development and probability of success of direct acting antivirals is questioned, UDPS may be beneficial to help understanding viral dynamics, providing high resolution view of viral diversity.     

Hepatitis C virus NS3/4A protease blocks IL-28 production

Type I interferons (IFNs), including IFN-α, -β, and -ω, play a critical role in innate immune responses against viral infection. IFN-λ, including IL-29, IL-28A, and IL-28B, recently identified as a new subfamily of IFN named type III IFN, has also been demonstrated to suppress virus replication in vitro and in vivo. However, the molecular mechanisms that regulate the induction of type III IFNs during viral infection remain elusive. Here, we demonstrate that IL-28 (IFN-λ 2/3) IFN production, similar to type I IFN, represents a primary and direct host response to HCV genomic RNA transfection. IL-28 (IFN-λ2/3) induction by HCV genomic RNA was dependent upon the activation of NF-κB and IRF3. We identified a minimal IL-28 promoter region consisting of putative NF-κB and IRF3-binding sites. Furthermore, we showed that HCV infection can inhibit HCV genomic RNA-induced IL-28 expression, and that the viral NS3/4A protease activity was responsible for this inhibitory effect. Our results present important evidence for the control of type III IFN response by HCV, and shed more light on the molecular mechanisms underlying the persistence of HCV infection.     

HCV NS5A基因在hepG2细胞中的表达以及对PI3K的影响

目的：探讨HCV—NS5A对PI3K表达的影响。方法：应用PCR技术从含有HCV全长开放阅读框的质粒中获得NS5A全长基因片段，利用基因重组技术将其克隆至真核表达载体pcDNA3．0（-）中。通过酶切、PCR及测序鉴定，NS5A基因已正确插入到pcDNA3．0（-）中，再利用脂质体转染HepG2细胞。结果：经RT—PCR及Western blot检测，HCV的NS5A基因在HepG2细胞中获得表达，而且在表达重组NS5A的转染HepG2细胞中，检测到PI3K蛋白的表达。结论：NS5A可在体外激活PI3K及其信号通路。     

活体荧光成像监测HCV NS3/4A蛋白在小鼠体内的瞬时表达

目的建立HCV NS3/4A蛋白酶在小鼠体内可视化表达模型。方法利用水动力转染技术将融合基因NS3/4A-Fluc转染至小鼠肝脏,建立目的基因的瞬时表达模型,通过RT-PCR方法检测目的基因Fluc及NS3/4A的RNA表达水平,以及通过Western blot方法检测目的基因NS3/4A-Fluc的蛋白表达水平。结果建立了通过报告基因Fluc反映HCV NS3/4A蛋白酶的瞬时表达可视化小鼠模型。结论成功建立了可用于评价NS3/4A蛋白酶的可视化小鼠模型。     

Phylogenetic and structural analysis of HCV nonstructural protein 4A from Pakistani patients

Hepatitis C virus nonstructural protein, NS4A, is a small protein comprising of about 54 amino acids. Despite its small size, it plays key role in many viral and cellular functions. The most important of which is its role as the co-factor of viral serine protease and helicase (NS3). Our study examines the phylogenetic and structural analysis of this coding region after isolation from Pakistani HCV patient samples. Phylogenetic analysis of the gene revealed that Pakistani 3a HCV strains do not show significant divergence from those reported from the rest of the world. The findings of this study also depict that NS4A sequence is conserved within genotypes, whereas it shows variations among different genotypes. While predicting the tertiary structure of the protein two important mutations (H28Y & E32G) were observed when comparing the Pakistani sequences with that of a reference HCV (genotype 3a) strain NZL (D17763). These mutations were observed in the central domain of NS4A which is responsible for interaction with NS3. Taken together, these mutations within the NS4A coding region can play an important role in the binding capacity of NS4A with HCV serine protease NS3.     

Activation of dengue protease autocleavage at the NS2B-NS3 junction by recombinant NS3 and GST-NS2B fusion proteins

Dengue virus possesses a protease complex made up of the non-structural proteins NS2B and NS3. This protease complex catalyzes autocleavage (cis) at the junction between NS2A and NS2B as well as between NS2B and NS3. It also catalyzes trans cleavage at the junctions between NS3 and NS4A as well as NS4B and NS5. The cis cleavage at the NS2B-NS3 junction has been demonstrated in Escherichia coli by linking a 40-residue hydrophilic segment of NS2B to a NS3 N-terminal protease domain carrying the NS2B-NS3 cleavage site. To explore whether the hydrophilic segment could be further shortened, residues from both N- and C-termini of the NS2B hydrophilic segment were deleted. The results indicate that the four C-terminal's consecutive Glu residues could be deleted, each one leading to a further loss of activity, whereas the N-terminal boundary needed to be absolutely preserved. To examine whether an NS2B peptide could be expressed independently and added to activate the NS3 protease domain, the hydrophilic region of NS2B was fused to the C-terminus of glutathione-S-transferase (GST). This recombinant protein was soluble in bacteria and easily purified by affinity chromatography. Without removing the GST, the fusion protein activated the NS3 protease domain allowing it to function at the adjacent NS2B-NS3 junction. Thus, the findings reported below have produced a feasible alternative for the assay of dengue viral protease and this should facilitate the development of a screening method for inhibitors of dengue protease.     

52 例病毒性肝炎患者肝组织中丙型肝炎病毒 RNA 和 HCAg-NS3 的测定

应用地高辛标记探针原位杂交法和单克隆抗ＨＣＶ－ＮＳ３－ＨＲＰ建立直接酶标免疫组化法分别测定５２例肝炎患者肝组织ＨＣＶＲＮＡ和ＨＣＡｇ－ＮＳ３。结果抗ＨＣＶ阳性组ＨＣＶＲＮＡ检出率５７．１％（１６／２８），ＨＣＡｇ－ＮＳ３检出率５３．６％（１５／２８）；抗ＨＣＶ阴性组其两项检出率均为１２．５％（３／２４）。肝组织中ＨＣＶＲＮＡ阳性物呈蓝紫色细小颗粒存在于肝细胞核或胞浆内，其在肝小叶中的分布可分为３型，即弥漫型、局灶型、散在型。肝组织中ＨＣＡｇ－ＮＳ３阳性物呈棕黄色细小颗粒分布于肝细胞核或胞浆内，以单个或数个阳性细胞散布于肝小叶中。２３例ＨＣＶＲＮＡ或／和ＨＣＡｇ－ＮＳ３阳性病例以肝炎后肝硬化（ＬＣ）病例占多数（１４／２３），其次为慢性重型肝炎（ＣＳＨ）和中度慢性肝炎（ＣＡＨ）。此两种检测方法具有较高符合率（９０．４％，４７／５２），表明病毒核酸及其表达产物均存在于肝细胞内，与ＨＣＶ感染密切相关。这为ＨＣＶ感染诊断提供了直接依据，有利于研究ＨＣＶ感染中病毒复制、慢性化进程、抗病毒治疗监测及重叠感染时病毒相互关系。     

Influence of hepatitis C virus (HCV) genotypes on HCV recombinant immunoblot assay patterns.

Ninety-six patients with chronic hepatitis C were studied. A second-generation recombinant immunoblot assay detected anti-NS4 antibodies significantly more often in patients infected by hepatitis C virus genotype 1 than in patients infected by other types. By a third-generation recombinant immunoblot assay, the prevalences of the four antibodies measured did not differ according to the hepatitis C virus genotype.