Inhibitors of hepatitis C virus NS3·4A protease. Effect of P4 capping groups on inhibitory potency and pharmacokinetics

Perni, Robert B.; Chandorkar, Gurudatt; Cottrell, Kevin M.; Gates, Cynthia A.; Lin, Chao; Lin, Kai; Luong, Yu-Ping; Maxwell, John P.; Murcko, Mark A.; Pitlik, J.; Rao, Govinda; Schairer, Wayne C.; Drie, John Van; Wei, Yang

doi:10.1016/j.bmcl.2007.03.090

Cited by 19 publications

(21 citation statements)

References 19 publications

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“…Flexible ligands are also prominent in current drugs. Examples include peptido-mimetic compounds, such as Telaprevir, a current Phase III clinical candidate for HCV protease (Perni et al 2007), as well as HIV-1 protease inhibitors (King et al 2004). These ligands retain a number of rotatable bonds, whose torsion angle mobility allows for conformational readjustments upon protein binding.…”

Section: Introductionmentioning

confidence: 99%

Mapping the dynamics of ligand reorganization via 13CH3 and 13CH2 relaxation dispersion at natural abundance

2009

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Flexible ligands pose challenges to standard structure-activity studies since they frequently reorganize their conformations upon protein binding and catalysis. Here, we demonstrate the utility of side chain 13 C relaxation dispersion measurements to identify and quantify the conformational dynamics that drive this reorganization. The dispersion measurements probe methylene 13 CH 2 and methyl 13 CH 3 groups; the latter are highly prevalent side chain moieties in known drugs. Combining these side chain studies with existing backbone dispersion studies enables a comprehensive investigation of µs-ms conformational dynamics related to binding and catalysis. We perform these measurements at natural 13 C abundance, in congruence with common pharmaceutical research settings. We illustrate these methods through a study of the interaction of a phosphopeptide ligand with the peptidyl-prolyl isomerase, Pin1. The results illuminate the side-chain moieties that undergo conformational readjustments upon complex formation. In particular, we find evidence that multiple exchange processes influence the side chain dispersion profiles. Collectively, our studies illustrate how side-chain relaxation dispersion can shed light on ligand conformational transitions required for activity, and thereby suggest strategies for its optimization.

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Section: Introductionmentioning

confidence: 99%

Mapping the dynamics of ligand reorganization via 13CH3 and 13CH2 relaxation dispersion at natural abundance

2009

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“…Since no similar co-crystallized structure is publically available for telaprevir, we used PDB structure 2P59 in which the protease is co-crystallized with a telaprevir-like ligand (TLL) that has two small differences from telaprevir 22 . Its P 2 group and the P 4 capping group are slightly modified, with the P 4 providing a pyrrole NH for H-bond interactions with the protease (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease

et al. 2012

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Background & Aims It is a challenge to develop direct-acting antiviral agents (DAAs) that target the NS3/4A protease of hepatitis C virus (HCV) because resistant variants develop. Ketoamide compounds, designed to mimic the natural protease substrate, have been developed as inhibitors. However, clinical trials have revealed rapid selection of resistant mutants, most of which are considered to be pre-existing variants. Methods We identified residues near the ketoamide-binding site in X-ray structures of the genotype 1a protease, co-crystallized with boceprevir or a telaprevir-like ligand, and then identified variants at these positions in 219 genotype 1 sequences from a public database. We used side-chain modeling to assess the potential effects of these variants on the interaction between ketoamide and the protease, and compared these results with the phenotypic effects on ketoamide resistance, RNA replication capacity, and infectious virus yields in a cell culture model of infection. Results Thirteen natural binding-site variants with potential for ketoamide resistance were identified at 10 residues in the protease, near the ketoamide binding site. Rotamer analysis of amino acid side-chain conformations indicated that 2 variants (R155K and D168G) could affect binding of telaprevir more than boceprevir. Measurements of antiviral susceptibility in cell culture studies were consistent with this observation. Four variants (Q41H, I132V, R155K, and D168G) caused low-to-moderate levels of ketoamide resistance; 3 of these were highly fit (Q41H, I132V, and R155K). Conclusions Using a comprehensive sequence and structure-based analysis, we showed how natural variation in the HCV protease NS3/4A sequences might affect susceptibility to first-generation DAAs. These findings increase our understanding of the molecular basis of ketoamide resistance among naturally existing viral variants.

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“…The NS4A polypeptide acts as a cofactor of NS3 serine protease for efficient polyprotein processing (30). The HCV NS3-NS4A complex is a heterodimeric serine protease that has been considered a prime target for developing direct-acting antivirals (31,32), such as novel protease inhibitors of noncovalent macrocyclic simeprevir/TMC435 (33,34), covalent linear boceprevir (BOC) (35)(36)(37), and telaprevir analog (TVR) (38,39). From an immunologic point of view, the HCV NS2 to -4A proteins are major antigens in HCV vaccines, a few of which are currently in clinical trials for induction of a protective T-cell response against HCV infection (40)(41)(42).…”

Section: Discussionmentioning

confidence: 99%

“…Marmosets infected with GBV-B developed typical viral hepatitis similar to hu- HCV NS2 to -4A/GBV-B chimera P 0 , intrahepatically M5-P 0 HCV NS2 to -4A chimeric RNA 18 M14-P 0 HCV NS2 to -4A chimeric RNA 17 P 1 , intravenously M8-P 1 Serum from M5-P 0 at wk 1 12 M22-P 1 Serum from M23-P 0 at wk 13, 23 5 M25-P 1 Serum from M23-P 0 at wk 34,38,39,43,50; rechallenged with P 1 serum from M24-P 1 at wk 5,19,20,26 34 ϩ 57 FK506-treated P 0 or P 1 infection M23-P 0 -FK506 RNA 54 M24-P 1 -FK506…”

mentioning

confidence: 99%

Infection of Common Marmosets with GB Virus B Chimeric Virus Encoding the Major Nonstructural Proteins NS2 to NS4A of Hepatitis C Virus

Zhu

Liu

et al. 2016

J Virol

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A lack of immunocompetent-small-primate models has been an obstacle for developing hepatitis C virus (HCV) vaccines and affordable antiviral drugs. In this study, HCV/GB virus B (GBV-B) chimeric virus carrying the major nonstructural proteins NS2 to NS4A (HCV NS2 to -4A chimera) was produced and used to infect common marmosets, since HCV NS2 to NS4A proteins are critical proteases and major antigens. Seven marmosets were inoculated intrahepatically with HCV NS2 to -4A chimera RNA for primary infection or intravenously injected with chimera-containing serum for passage infection. Three animals used as controls were injected with phosphate-buffered saline (PBS) or GBV-B, respectively. Six of seven HCV NS2 to -4A chimera-infected marmosets exhibited consistent viremia and one showed transient viremia during the course of follow-up detection. All six infected animals with persistent circulating viremia presented characteristics typical of viral hepatitis, including viral RNA and proteins in hepatocytes and histopathological changes in liver tissue. Viremia was consistently detected for 5 to 54 weeks of follow-up. FK506 immunosuppression facilitated the establishment of persistent chimera infection in marmosets. An animal with chimera infection spontaneously cleared the virus in blood 7 weeks following the first inoculation, but viral-RNA persistence, low-level viral protein, and mild necroinflammation remained in liver tissue. The specific antibody and T-cell response to HCV NS3 in this viremia-resolved marmoset was boosted by rechallenging, but no viremia was detected during 57 weeks of follow-up. The chimera-infected marmosets described can be used as a suitable small-primate animal model for studying novel antiviral drugs and T-cell-based vaccines against HCV infection. H epatitis C virus (HCV) infection is a global health threat thatcauses chronic hepatitis and is associated with 78% of primary hepatocellular carcinoma (1). Currently, limitations of small-primate models hamper the development of HCV vaccines and affordable antiviral drugs. Chimpanzees have been used as a uniquely reliable animal for HCV infection in past decades (2), significantly contributing to defining the infection natural history, pathogenesis, immune response, and rechallenge of HCV (3-6). However, the utility of chimpanzees has been more and more restricted by ethical concerns, and though rare, the use of this primate model in medical studies is extremely costly (2). The nonprimate animal models simulating HCV infection might potentially be mimicked with rodent hepacivirus (RHV)-infected rats (7,8), canine hepacivirus (CHV)-infected dogs (9), and equine hepacivirus (EHCV) (nonprimate hepacivirus [NPHV])-infected horses (10). HCV infection in immunocompetent mice was reported in genetically humanized mouse CD81 and occludin (OCLN) (11,12). However, the differences in infection courses and immune responses fundamentally separate these mice from HCV-infected patients.Common marmosets (Callithrix jacchus), one of the New World small ...

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Inhibitors of hepatitis C virus NS3·4A protease. Effect of P4 capping groups on inhibitory potency and pharmacokinetics

Cited by 19 publications

References 19 publications

Mapping the dynamics of ligand reorganization via 13CH3 and 13CH2 relaxation dispersion at natural abundance

Mapping the dynamics of ligand reorganization via 13CH3 and 13CH2 relaxation dispersion at natural abundance

Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease

Infection of Common Marmosets with GB Virus B Chimeric Virus Encoding the Major Nonstructural Proteins NS2 to NS4A of Hepatitis C Virus

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