Non-nucleoside NS5B Polymerase Inhibitor Research Articles

Anti-hepatitis-C virus activity and QSAR study of certain thiazolidinone and thiazolotriazine derivatives as potential NS5B polymerase inhibitors

The present study reports on evaluation of anti-HCV activity and QSAR of certain arylidenethiazolidinone derivatives as potential inhibitors of HCV-NS5B polymerase. The pursued compounds involving, 5-aryliden-3-arylacetamidothiazolidin-2,4-diones 4–6(a–f), 5-arylidine-2-(N-arylacetamido)-iminothiazolidin-4-one (10) and their rigid counterparts 5-arylidinethiazolotriazines 13–15(a–f), were synthesized and their structures confirmed by spectral and elemental analyses. The results of NS5B polymerase inhibition assay revealed compound 4e, as the most active inhibitor (IC50 = 0.035 μM), which is four folds greater than that of the reference agent, VCH-759, (IC50 = 0.14 μM). Meanwhile, compounds 4b, 4c, 5a, and 5c, and 13b, 14e and 15c displayed equipotency to 2 folds higher activity than VCH-759 (IC50 values: 0.085, 0.14, 0.14, 0.10, 0.12, 0.09 and 0.07 μM, respectively). Assessment of the anti-HCV activity (GT1a) using human hepatoma cell line (Huh-7.5) illustrates superior activity of 4e (EC50 = 3.80 μM) relative to VCH-759 (EC50 = 5.29 μM). Cytotoxicity evaluation on, Transformed normal cell lines (Human Liver Epithelial-2, THLE-2 and Proximal Tubular Epithelial, RPTEC/TERT1), demonstrate enhanced safety profile of 4e (CC50 = 102.77, 161.37 μM, respectively) compared to VCH-759 (CC50 = 61.83, 81.28 μM, respectively). Molecular docking of the synthesized derivatives to NS5B polymerase allosteric site (PDB: 2HWH) showed similar binding modes to that of the co-crystallized ligand. Moreover, QSAR models were established for the studied thiazolidinones and thiazolotriazines to investigate the molecular characteristics contributing to the observed NS5B polymerase inhibition activity. The obtained results inspire further investigations of thiazolidinones and thiazolotriazine aiming at affording more potent, safe and orally active non-nucleoside NS5B polymerase inhibitors as anti-HCV drug candidates.

Synthesis and Biological Characterization of Aryl Uracil Inhibitors of Hepatitis C Virus NS5B Polymerase: Discovery of ABT-072, a trans-Stilbene Analog with Good Oral Bioavailability.

ABT-072 is a non-nucleoside HCV NS5B polymerase inhibitor that was discovered as part of a program to identify new direct-acting antivirals (DAAs) for the treatment of HCV infection. This compound was identified during a medicinal chemistry effort to improve on an original lead, inhibitor 1, which we described in a previous publication. Replacement of the amide linkage in 1 with a trans-olefin resulted in improved compound permeability and solubility and provided much better pharmacokinetic properties in preclinical species. Replacement of the dihydrouracil in 1 with an N-linked uracil provided better potency in the genotype 1 replicon assay. Results from phase 1 clinical studies supported once-daily oral dosing with ABT-072 in HCV infected patients. A phase 2 clinical study that combined ABT-072 with the HCV protease inhibitor ABT-450 provided a sustained virologic response at 24 weeks after dosing (SVR24) in 10 of 11 patients who received treatment.

Rational design of antiviral drug combinations based on equipotency using HCV subgenomic replicon as an in vitro model

Combination therapy of directly acting antivirals (DAA's) for the treatment of chronic HCV infections has proven to be a highly effective strategy to cure chronic infections with this virus. Here we studied, using HCV as an example, how to best design in vitro studies that explore the combined antiviral efficiency of combinations of three or more DAA's. To that end we used a HCV NS3 protease inhibitor, a NS5A targeting compound and two non-nucleoside NS5B polymerase inhibitors (each one targeting a different drug binding site). We demonstrate, employing HCV subgenomic replicon containing Huh 9–13 hepatoma cells, that quadruple therapy with these 4 different DAA's each at 1x their EC75, results in a highly efficient inhibition of viral replication. This is further reflected in the rapid clearance of the HCV replicon from the host cell. By contrast, neither equipotent combinations that consist of either molecules alone at 4x EC75 nor triple combinations at 1.33x the EC75 resulted in clearance. In contrast to the quadruple combo, drug-resistant variants emerged under mono-treatment and in most triple combo's. These data thus demonstrate that quadruple combinations at total suboptimal concentrations [i.e. concentrations at which neither mono- nor triple therapy is sufficiently potent] result rapidly in a pronounced antiviral efficacy. Altogether, this work provides an example as to how to design studies to explore the antiviral efficacy of combinations of more than two compounds.

Physiologically Based Pharmacokinetic Modeling Suggests Limited Drug-Drug Interaction Between Clopidogrel and Dasabuvir.

Dasabuvir, a nonnucleoside NS5B polymerase inhibitor, is a sensitive substrate of cytochrome P450 (CYP) 2C8 with a potential for drug–drug interaction (DDI) with clopidogrel. A physiologically based pharmacokinetic (PBPK) model was developed for dasabuvir to evaluate the DDI potential with clopidogrel, the acyl‐β‐D glucuronide metabolite of which has been reported as a strong mechanism‐based inhibitor of CYP2C8 based on an interaction with repaglinide. In addition, the PBPK model for clopidogrel and its metabolite were updated with additional in vitro data. Sensitivity analyses using these PBPK models suggested that CYP2C8 inhibition by clopidogrel acyl‐β‐D glucuronide may not be as potent as previously suggested. The dasabuvir and updated clopidogrel PBPK models predict a moderate increase of 1.5–1.9‐fold for Cmax and 1.9–2.8‐fold for AUC of dasabuvir when coadministered with clopidogrel. While the PBPK results suggest there is a potential for DDI between dasabuvir and clopidogrel, the magnitude is not expected to be clinically relevant.

SAT-230 - Phase 1 study assessing the safety, pharmacokinetics, and antiviral activity of CC-31244, a pan-genotypic, potent non-nucleoside NS5B polymerase inhibitor for the treatment of hepatitis C virus infection

SAT-230 - Phase 1 study assessing the safety, pharmacokinetics, and antiviral activity of CC-31244, a pan-genotypic, potent non-nucleoside NS5B polymerase inhibitor for the treatment of hepatitis C virus infection

Structure-based optimization and derivatization of 2-substituted quinolone-based non-nucleoside HCV NS5B inhibitors with submicromolar cellular replicon potency

HCV NS5B polymerase is an attractive and validated target for anti-HCV therapy. Starting from our previously identified 2-aryl quinolones as novel non-nucleoside NS5B polymerase inhibitors, structure-based optimization furnished 2-alkyl-N-benzyl quinolones with improved antiviral potency by employing privileged fragment hybridization strategy. The N-(4-chlorobenzyl)-2-(methoxymethyl)quinolone derivative 5f proved to be the best compound of this series, exhibiting a selective sub-micromolar antiviral effect (EC50=0.4μM, SI=10.8) in Huh7.5.1 cells carrying a HCV genotype 2a. Considering the undesirable pharmacokinetic property of the highly substituted quinolones, a novel chemotype of 1,6-naphthyridine-4,5-diones were evolved via scaffold hopping, affording brand new structure HCV inhibitors with compound 6h (EC50 (gt2a)=2.5μM, SI=7.2) as a promising hit. Molecular modeling studies suggest that both of 2-alkyl quinolones and 1,6-naphthyridine-4,5-diones function as HCV NS5B thumb pocket II inhibitors.

Logical design of anti-prion agents using NAGARA

To accelerate the logical drug design procedure, we created the program “NAGARA,” a plugin for PyMOL, and applied it to the discovery of small compounds called medical chaperones (MCs) that stabilize the cellular form of a prion protein (PrPC). In NAGARA, we constructed a single platform to unify the docking simulation (DS), free energy calculation by molecular dynamics (MD) simulation, and interfragment interaction energy (IFIE) calculation by quantum chemistry (QC) calculation. NAGARA also enables large-scale parallel computing via a convenient graphical user interface. Here, we demonstrated its performance and its broad applicability from drug discovery to lead optimization with full compatibility with various experimental methods including Western blotting (WB) analysis, surface plasmon resonance (SPR), and nuclear magnetic resonance (NMR) measurements. Combining DS and WB, we discovered anti-prion activities for two compounds and tegobuvir (TGV), a non-nucleoside non-structural protein NS5B polymerase inhibitor showing activity against hepatitis C virus genotype 1. Binding profiles predicted by MD and QC are consistent with those obtained by SPR and NMR. Free energy analyses showed that these compounds stabilize the PrPC conformation by decreasing the conformational fluctuation of the PrPC. Because TGV has been already approved as a medicine, its extension to prion diseases is straightforward. Finally, we evaluated the affinities of the fragmented regions of TGV using QC and found a clue for its further optimization. By repeating WB, MD, and QC recursively, we were able to obtain the optimum lead structure.

QSAR and Molecular Docking Directed Synthesis and Preliminary Evaluation of Novel Non-Nucleoside HCV NS5B Polymerase Inhibitors

In HCV genome, the NS5B RNA-dependent RNA polymerase (RdRp) plays central role in the replication. It is the most preferred target for design and screening of small molecule HCV inhibitors. From in house compound library screening using NS5B polymerase enzymatic assay, we identified some benzimidazole derivatives. The activities were predicted using the QSAR generated models. Along with QSAR predictions, molecular docking studies help to study binding of these series of compounds at allosteric pocket (AP-1). Keywords: Benzimidazole derivatives, anti-HCV agents, NS5B polymerase inhibitors, molecular docking.

Daclatasvir-containing all-oral regimens for the treatment of hepatitis C virus infection.

The treatment of chronic hepatitis C is revolutionizing rapidly. The aim of this study is to review the efficacy and safety of daclatasvir (DCV)-containing all-oral regimens in clinical studies for chronic hepatitis C treatment. Using PubMed and search terms of 'DCV,' 'hepatitis C virus (HCV) treatment,' and 'HCV NS5A inhibitors,' literature on the clinical development of DCV, as well as abstracts presented at the April 2015 annual meeting of the European Association for the Study of the Liver (EASL) and November 2014 annual meeting of the American Association for the Study of Liver Diseases were reviewed. The final search was undertaken on 14 July 2015. With its potent antiviral activity to all HCV genotypes (GT) demonstrated in preclinical, phases 1-3 studies, DCV has been acting as a very competent team player in clinical trials of all-oral regimens. It is generally safe and well tolerated with a low genetic barrier to resistance and low potential for drug-drug interaction. Administered with a non-structural protein 3 (NS3) protease inhibitor (asunaprevir, ASV) with or without a non-nucleoside NS5B polymerase inhibitor (beclabuvir, BCV), or a nucleotide NS5B polymerase inhibitor (sofosbuvir, SOF), DCV is able to achieve greater than a 90-% HCV eradication rate in both treatment-naïve and treatment-experienced patients with GT 1. A triple combination regimen with DCV/ASV/BCV results in 100% sustained virologic response (SVR) rates in HCV GT 4 treatment-naïve subjects. DCV/SOF combination also had demonstrated up to 90-% SVR rates in GT 3-infected non-cirrhotic patients. The efficacy and safety of DCV-containing all-oral regimens highlight a new era of interferon-free therapy for chronic hepatitis C.

Open-label phase 2 study of faldaprevir, deleobuvir and ribavirin in Japanese treatment-naive patients with chronic hepatitis C virus genotype 1 infection.

The safety and efficacy of the NS3/4A protease inhibitor faldaprevir in combination with the non-nucleoside NS5B polymerase inhibitor deleobuvir and ribavirin in Japanese treatment-naive patients with chronic genotype 1 hepatitis C virus (HCV) infection was evaluated. In this multicenter, open-label phase 2 study, patients were assigned to 8 weeks of treatment with 80 mg (group 1) or 120 mg (group 2) faldaprevir once daily (q.d.) in combination with deleobuvir 600 mg twice daily and weight-based ribavirin. This was followed by a 24-week treatment with faldaprevir 120 mg q.d. in combination with peginterferon-α-2a and ribavirin. The primary objective was safety; virological response at weeks 4 and 8 was a secondary endpoint. Twelve and 13 patients were treated in group 1 and 2, respectively; all were infected with HCV genotype 1b. All patients experienced a drug-related adverse event (AE). The frequency of individual events was generally numerically greater in group 2 than 1. The most common AEs were nausea (66.7%, group 1; 76.9%, group 2) and vomiting (33.3%, group 1; 61.5%, group 2). Virological response at weeks 4 and 8 was achieved by 11 (91.7%) patients in group 1; in group 2, 12 (92.3%) patients achieved virological response at week 4 and all at week 8. All patients who achieved the week 8 endpoint achieved sustained virological response at week 12. Faldaprevir 80 or 120 mg q.d. in combination with deleobuvir and ribavirin was tolerable and had similar efficacy in Japanese patients with HCV genotype 1 infection. ClinicalTrials.gov: NCT01528735.

Sofosbuvir and ribavirin use in wait-listed patients with hepatitis C should be selective.

Sofosbuvir and ribavirin use in wait-listed patients with hepatitis C should be selective.

Importance of very early HCV RNA kinetics for prediction of treatment outcome of highly effective all oral direct acting antiviral combination therapy

Interferon-free combination therapies lead to rapid suppression of HCV RNA early during treatment. The potential to predict virologic response and failure as well as to guide treatment duration with measurement of HCV RNA very early during treatment by highly sensitive assays is not well known.In 11 IL28B CC (rs12979860) patients infected with HCV genotype 1, who received DAA combination therapy with the NS3 protease inhibitor ABT-450/r together with the non-nucleoside NS5B polymerase inhibitor ABT-072 and ribavirin for 12 weeks, HCV RNA was assessed frequently by the RealTime HCV (ART) and the High-Pure-System/Cobas TaqMan (HPS) assays during and after treatment.Overall, at 33 of 131 time points during treatment residual HCV RNA was detectable by ART but undetectable by HPS while the converse was observed in only two samples. Of the two patients who experienced virologic relapse, one patient had residual viremia at week 6 of treatment by ART only while the other patient never had undetectable HCV RNA by the ART assay. However, residual viremia was also observed by ART as late as therapy weeks 9, 10 and 12 in patients with subsequent sustained virologic response. In patients with sustained response no viremia was observed at multiple time points during post-treatment follow up by either assay.The higher sensitivity of the ART in comparison to the HPS assay may be associated with more frequent detection of residual viremia during highly effective, interferon-free combination therapies. However, the significance of this finding in predicting virologic failure appears to be limited.

An Interferon-free Antiviral Regimen for HCV after Liver Transplantation

BackgroundHepatitis C virus (HCV) infection is the leading indication for liver transplantation worldwide, and interferon-containing regimens are associated with low response rates owing to treatment-limiting toxic effects in immunosuppressed liver-transplant recipients. We evaluated the interferon-free regimen of the NS5A inhibitor ombitasvir coformulated with the ritonavir-boosted protease inhibitor ABT-450 (ABT-450/r), the nonnucleoside NS5B polymerase inhibitor dasabuvir, and ribavirin in liver-transplant recipients with recurrent HCV genotype 1 infection.MethodsWe enrolled 34 liver-transplant recipients with no fibrosis or mild fibrosis, who received ombitasvir–ABT-450/r (at a once-daily dose of 25 mg of ombitasvir, 150 mg of ABT-450, and 100 mg of ritonavir), dasabuvir (250 mg twice daily), and ribavirin for 24 weeks. Selection of the initial ribavirin dose and subsequent dose modifications for anemia were at the investigator's discretion. The primary efficacy end point was a sustained virologic response 12 weeks after the end of treatment.ResultsOf the 34 study participants, 33 had a sustained virologic response at post-treatment weeks 12 and 24, for a rate of 97% (95% confidence interval, 85 to 100). The most common adverse events were fatigue, headache, and cough. Five patients (15%) required erythropoietin; no patient required blood transfusion. One patient discontinued the study drugs owing to adverse events after week 18 but had a sustained virologic response. Blood levels of calcineurin inhibitors were monitored, and dosages were modified to maintain therapeutic levels; no episode of graft rejection was observed during the study.ConclusionsTreatment with the multitargeted regimen of ombitasvir–ABT-450/r and dasabuvir with ribavirin was associated with a low rate of serious adverse events and a high rate of sustained virologic response among liver-transplant recipients with recurrent HCV genotype 1 infection, a historically difficult-to-treat population. (Funded by AbbVie; CORAL-I ClinicalTrials.gov number, NCT01782495.)

GI disorders: Key research at Digestive Disease Week

Digestive Disease Week (DDW) 2014, held May 3–6 in Chicago, focused on new developments in gastroenterology, liver disease, endoscopy, and gastrointestinal surgery. The annual meeting—cosponsored by the American Association for the Study of Liver Diseases (AASLD), American Gastroenterological Association (AGA), American Society for Gastrointestinal Endoscopy (ASGE), and Society for Surgery of the Alimentary Tract (SSAT)—is the largest meeting in the world for gastroenterology professionals. Following are a few key research studies presented during the meeting with a pharmacotherapy focus. Chronic hepatitis C Direct-acting antiviral agents (DAA) for hepatitis C that are associated with cure rates greater than 90% and minimal adverse effects received a signifi cant amount of attention throughout the week. With the FDA approval of simeprevir (Olysio—Janssen Therapeutics) and sofosbuvir (Sovaldi—Gilead Sciences) in late 2013 and additional oral DAA therapies anticipated for approval in 2014, research suggests that nearly all people with chronic hepatitis C can soon be treated successfully. AbbVie 3D. SAPPHIRE II (A Study to Evaluate Chronic Hepatitis C Infection in Treatment Experienced Adults) evaluated AbbVie’s interferon-free triple oral antiviral regimen “3D” containing the hepatitis C virus (HCV) protease inhibitor ABT-450, the NS5A inhibitor ombitasvir, and the nonnucleoside NS5B polymerase inhibitor dasabuvir. The twice-daily 3D combination plus ribavirin for 12 weeks in patients who did not respond to previous therapies

In vitro efficacy of approved and experimental antivirals against novel genotype 3 hepatitis C virus subgenomic replicons

Infection with genotype 3 hepatitis C virus (HCV) is common throughout the world, however no direct-acting antiviral (DAA) has been approved to treat this genotype. We therefore attempted to develop novel genotype 3 replicons to facilitate the discovery and development of new HCV therapies. A novel Huh-7-derived cell line 1C but not Lunet cells enabled the selection of a few stable colonies of a genotype 3a subgenomic replicon (strain S52). Genotypic analysis revealed a mutation of P89L in the viral NS3 protease domain, which was confirmed to enhance genotype 3a RNA replication and enable the establishment of highly replicating luciferase-encoding replicons. Secondary adaptive mutations that further enhanced RNA replication were identified in the viral NS3 and NS4A proteins. In addition, cell lines that were cured of genotype 3a replicons demonstrated higher permissiveness specifically to genotype 3a HCV replication. These novel replicons and cell lines were then used to study the activity of approved and experimental HCV inhibitors. NS3 protease and non-nucleoside NS5B polymerase inhibitors often demonstrated substantially less antiviral activity against genotype 3a compared to genotype 1b. In contrast, nucleoside analog NS5B inhibitors and host-targeting HCV inhibitors showed comparable antiviral activity between genotypes 3a and 1b. Overall, the establishment of this novel genotype 3a replicon system, in conjunction with those derived from other genotypes, will aid the development of treatment regimens for all genotypes of HCV.

A phase 2a trial of 12-week interferon-free therapy with two direct-acting antivirals (ABT-450/r, ABT-072) and ribavirin in IL28B C/C patients with chronic hepatitis C genotype 1

ABT-450 (combined with low-dose ritonavir, ABT-450/r) is a potent HCV NS3 protease inhibitor, and ABT-072 is a non-nucleoside NS5B polymerase inhibitor. The goal of this study was to evaluate the safety, tolerability, and efficacy of the peginterferon-free combination of ABT-450/r and ABT-072 with ribavirin in treatment-naïve patients with IL28B CC genotype, infected with HCV genotype 1. This was a phase 2a, multicenter, open-label, single-arm study in 11 treatment-naïve, non-cirrhotic HCV GT1-infected patients with IL28B rs12979860 genotype CC. Patients received ABT-450/r 150/100 mg once daily and ABT-072 400 mg once daily with weight-based ribavirin 1000-1200 mg/day dosed twice daily for 12 weeks. Eight (73%) patients were male, 9 (82%) were Caucasian (including 3 who self-identified as Hispanic); mean baseline HCV RNA was 6.9 log₁₀ IU/ml (range 6.5-7.3 log₁₀ IU/ml). All 11 patients completed 12 weeks of treatment and maintained HCV RNA <25 IU/ml from weeks 4 through 12 of treatment. Ten patients (91%) achieved sustained virologic response 24 weeks post-treatment, with a second patient relapsing 36 weeks post-treatment. There were no deaths, serious or severe adverse events, or premature discontinuations. Adverse events were mostly mild and the most frequent were headache, fatigue, nausea, and dry skin. A 12-week regimen of ABT-450/r and ABT-072 with ribavirin was well tolerated with 9/11 patients achieving sustained virologic response through 36 weeks of post-treatment observation. These findings suggest that peginterferon-free regimens may have the potential to cure a high proportion of HCV genotype 1-infected patients.

Exploratory Study of Oral Combination Antiviral Therapy for Hepatitis C

BackgroundThere is a need for interferon-free treatment regimens for hepatitis C virus (HCV) infection. The goal of this study was to evaluate ABT-450, a potent HCV NS3 protease inhibitor, combined with low-dose ritonavir (ABT-450/r), in addition to ABT-333, a nonnucleoside NS5B polymerase inhibitor, and ribavirin, for the treatment of HCV infection.MethodsWe conducted a 12-week, phase 2a, open-label study involving patients who had HCV genotype 1 infection without cirrhosis. All patients received ABT-333 (400 mg twice daily) and ribavirin (1000 to 1200 mg per day) and one of two daily doses of ABT-450/r. Groups 1 and 2 included previously untreated patients; group 1 received 250 mg of ABT-450 and 100 mg of ritonavir, and group 2 received 150 mg and 100 mg, respectively. Group 3, which included patients who had had a null or partial response to previous therapy with peginterferon and ribavirin, received daily doses of 150 mg of ABT-450 and 100 mg of ritonavir. The primary end point was an undetectable level of HCV RNA from week 4 through week 12 (extended rapid virologic response).ResultsA total of 17 of the 19 patients in group 1 (89%) and 11 of the 14 in group 2 (79%) had an extended rapid virologic response; a sustained virologic response 12 weeks after the end of treatment was achieved in 95% and 93% of the patients, respectively. In group 3, 10 of 17 patients (59%) had an extended rapid virologic response, and 8 (47%) had a sustained virologic response 12 weeks after therapy; 6 patients had virologic breakthrough, and 3 had a relapse. Adverse events included abnormalities in liver-function tests, fatigue, nausea, headache, dizziness, insomnia, pruritus, rash, and vomiting.ConclusionsThis preliminary study suggests that 12 weeks of therapy with a combination of a protease inhibitor, a nonnucleoside polymerase inhibitor, and ribavirin may be effective for treatment of HCV genotype 1 infection. (Funded by Abbott; ClinicalTrials.gov number, NCT01306617.)

TMC647055, a Potent Nonnucleoside Hepatitis C Virus NS5B Polymerase Inhibitor with Cross-Genotypic Coverage

Hepatitis C virus (HCV) infection is a major global health burden and is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma. There remains an unmet medical need for efficacious and safe direct antivirals with complementary modes of action for combination in treatment regimens to deliver a high cure rate with a short duration of treatment for HCV patients. Here we report the in vitro inhibitory activity, mode of action, binding kinetics, and resistance profile of TMC647055, a novel and potent nonnucleoside inhibitor of the HCV NS5B RNA-dependent RNA polymerase. In vitro combination studies with an HCV NS3/4A protease inhibitor demonstrated potent suppression of HCV RNA replication, confirming the potential for combination of these two classes in the treatment of chronic HCV infection. TMC647055 is a potent nonnucleoside NS5B polymerase inhibitor of HCV replication with a promising in vitro biochemical, kinetic, and virological profile that is currently undergoing clinical evaluation.

A novel HCV NS3 protease mutation selected by combination treatment of the protease inhibitor boceprevir and NS5B polymerase inhibitors

Boceprevir (SCH 503034) is an orally active novel inhibitor of the hepatitis C virus (HCV) NS3 protease currently in clinical development for the treatment of hepatitis C. In this in vitro study, we demonstrate that combination of boceprevir with a nucleoside analog or a non-nucleoside HCV NS5B polymerase inhibitor was superior to treatment by single agents in inhibiting viral RNA replication in replicon cells. In the presence of boceprevir (at 5×EC90), the addition of 2′-C-methyl-adenosine or an indole-N-acetamide targeting the polymerase finger-loop site (at 1×EC90) significantly reduced the emergence of resistant replicon colonies. A higher dose (5×EC90) of either of the polymerase inhibitors in combination with boceprevir suppressed replicon resistance further to below detectable levels. Sequencing analysis of replicon cells selected by the combination treatment revealed known resistance mutations to the two polymerase inhibitors but no previously reported resistance mutations to boceprevir. Interestingly, a novel mutation (M175L) in the protease domain was identified. The dually resistant replicon cells were monitored for over 30 passages and sensitivity to polymerase inhibitors was found to decrease over time in a manner that correlated with the increasing prevalence of specific resistance mutations. Importantly, these cells remained sensitive to interferon-α and different classes of polymerase inhibitors. These findings support the rationale for clinical evaluation of combination treatment of HCV protease and polymerase inhibitors.

Identification and structure-based optimization of novel dihydropyrones as potent HCV RNA polymerase inhibitors

A novel class of non-nucleoside HCV NS5B polymerase inhibitors has been identified from screening. A co-crystal structure revealed an allosteric binding site in the protein that required a unique conformational change to accommodate inhibitor binding. Herein we report the structure–activity relationships (SARs) of this novel class of dihydropyrone-containing compounds that show potent inhibitory activities against the HCV RNA polymerase in biochemical assays.