Structural Basis for Resistance of the Genotype 2b Hepatitis C Virus NS5B Polymerase to Site A Non-Nucleoside Inhibitors

Rydberg, Edwin H.; Cellucci, Antonella; Bartholomew, Linda; Mattu, Marco; Barbato, Gaetano; Ludmerer, Steven W.; Graham, Donald J.; Altamura, Sergio; Paonessa, Giacomo; Francesco, Raffaele De; Migliaccio, Giovanni; Carfı́, Andrea

doi:10.1016/j.jmb.2009.06.012

Cited by 18 publications

(32 citation statements)

References 44 publications

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“…It is also interesting to note that position 316 is under high selective pressure in this subtype, as shown by a high dN/dS ratio (equal to 16). The high frequency of mutations detected in our study sample is remarkable and suggests that their occurrence is sufficiently spread out, as previously reported (Horiike et al 1999, Qin et al 2001, Hamano et al 2005, Dutartre et al 2006, Lutchman et al 2007, Kuntzen et al 2008, McCown et al 2009, rydberg et al 2009). rIB selects for non-synonymous mutations, increasing sensitivity to IFN and leading to SVr status.…”

Section: Discussionsupporting

confidence: 87%

“…The region of the viral genome that codes for NS5B has been described as an important target in therapy with IFN and rBV (Kukolj et al 2005, Lu et al 2007, Lutchman et al 2007). The mechanisms that lead to viral resistance after IFN/ rBV treatment is still a matter of debate (Horiike et al 1999, Hadziyannis et al 2004, Kanda et al 2004, Hamano et al 2005, Hofmann et al 2007, Chung et al 2008, Kuntzen et al 2008, Kwong et al 2008, Nakamura et al 2008, Cannon et al 2009, Gaudieri et al 2009, rydberg et al 2009). For instance, Nelson et al (1995) showed that the mutations that occur in the HCV gene that codes for NS5B did not correlate with response to INF therapy, but Japanese studies associated IFN-rBV failure with mutations in the NS5B gene (Hamano et al 2005, Hmwe et al 2010 and Kuntzen et al (2008) showed that mutations conferred resistance to specifically targeted antiviral therapy drugs in treatmentnaïve patients infected with HCV genotype 1.…”

mentioning

confidence: 99%

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Association of hepatitis C virus NS5B variants with resistance to new antiviral drugs among untreated patients

Castilho

Martins

Horbach

et al. 2011

Mem. Inst. Oswaldo Cruz

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Section: Discussionsupporting

confidence: 87%

mentioning

confidence: 99%

Association of hepatitis C virus NS5B variants with resistance to new antiviral drugs among untreated patients

Castilho

Martins

Horbach

et al. 2011

Mem. Inst. Oswaldo Cruz

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“…}, where A and B denote minimal and maximal percent inhibition, respectively, C represents the EC 50 , D represents the hill slope, and x represents the compound concentration.…”

Section: Efficiency Of Replicon Clearance From Cultured Cells Hcv Rementioning

confidence: 99%

“…The potential cytotoxicities of these combined agents were also analyzed in parallel by alamarBlue staining. The 50% cytotoxic concentration (CC 50 ) values were calculated using the four-parameter logistic formula described above.…”

Section: Efficiency Of Replicon Clearance From Cultured Cells Hcv Rementioning

confidence: 99%

Effect on Hepatitis C Virus Replication of Combinations of Direct-Acting Antivirals, Including NS5A Inhibitor Daclatasvir

Pelosi

Voss

Liu

et al. 2012

Antimicrob Agents Chemother

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Three hepatitis C virus (HCV) inhibitors, asunaprevir (ASV; BMS-650032), daclatasvir (DCV; BMS-790052), and BMS-791325, each targeting a different nonstructural protein of the virus (NS3, NS5A, and NS5B, respectively), have independently demonstrated encouraging preclinical profiles and are currently undergoing clinical evaluation. Since drug-resistant variants have rapidly developed in response to monotherapy with almost all direct-acting antiviral agents (DAAs) for HCV, the need for combination therapies to effectively eradicate the virus from infected patients is clear. These studies demonstrated the additivesynergistic effects on replicon inhibition and clearance of combining NS3 protease or NS5B RNA polymerase inhibitors with the first-in-class, NS5A replication complex inhibitor daclatasvir (DCV) and reveal new resistance pathways for combinations of two small-molecule inhibitors that differ from those that develop during monotherapy. The results suggest that under a specific selective pressure, a balance must be reached in the fitness costs of substitutions in one target gene when substitutions are also present in another target gene. Further synergies and additional novel resistance substitutions were observed during triple-combination treatment relative to dual-drug therapy, indicating that, in combination, HCV inhibitors can exert cross-target influences on resistance development. Enhanced synergies in replicon inhibition and a reduced frequency of resistance together lend strong support to the utility of combinations of DAAs for the treatment of HCV, and the identification of altered resistance profiles during combination treatment provides useful information for monitoring resistance in the clinic. H epatitis C virus (HCV) is a positive-stranded RNA virus in theFlaviviridae family of enveloped virions which affects an estimated 170 million people worldwide and is the major cause of chronic hepatitis. Currently, approximately 50% of patients infected with genotype 1 (gt 1), the most prevalent form of the virus, fail to achieve a sustained reduction in viral load with therapy employing pegylated alpha interferon (IFN-␣) plus ribavirin (alfa/RBV) (52,54,56). A substantial fraction (20%) of chronically infected patients develop serious progressive liver disease, including cirrhosis or hepatocellular carcinoma. alfa/RBV treatment is associated with a high incidence (Ͼ30%) of adverse effects, some of which are of sufficient severity to cause patients to discontinue therapy (56). Despite the recent approval of two new direct-acting antiviral agents (DAAs), boceprevir and telaprevir, for use in combination with alfa/RBV (18, 47), their use may be limited by poor efficacy in some patient populations, inconvenient 3-times-daily dosing of the DAA, and association with side effects, including anemia, rash, and gastrointestinal effects, in addition to the well-documented spectrum of adverse effects associated with alfa/RBV. Although addition of these DAAs to the standard of care for HCV represents a significant i...

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“…In the absence of an NNI-1 ligand, helix A of the mobile ⌳1 loop occupies the known indole-binding site (10,20), as has been observed in other structures (6,26,32,47) on May 9, 2018 by guest http://jvi.asm.org/ mational preference at this position could impact inhibitor affinity; this is, however, highly speculative and requires further structural studies for clarification. Interestingly, the Ala499 variant has been suggested as a possible cause of benzimidazole resistance (42). The NNI-2 sites of the 1a and 1b complexes with compound 4 are also identical, with the exception of the side chain conformations of a couple of solvent-exposed polar side chains that do not make direct binding contacts with inhibitors at this site (4).…”

Section: Analysis Of Nni-1 -2 and -4mentioning

confidence: 99%

1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus

Nyanguile¹,

Devogelaere²,

Vijgen³

et al. 2010

J Virol

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The RNA-dependent RNA polymerase (NS5B) of hepatitis C virus (HCV) is an unusually attractive target for drug discovery since it contains five distinct drugable sites. The success of novel antiviral therapies will require nonnucleoside inhibitors to be active in at least patients infected with HCV of subtypes 1a and 1b. Therefore, the genotypic assessment of these agents against clinical isolates derived from genotype 1-infected patients is an important prerequisite for the selection of suitable candidates for clinical development. Here we report the 1a/1b subtype profiling of polymerase inhibitors that bind at each of the four known nonnucleoside binding sites. We show that inhibition of all of the clinical isolates tested is maintained, except for inhibitors that bind at the palm-1 binding site. Subtype coverage varies across chemotypes within this class of inhibitors, and inhibition of genotype 1a improves when hydrophobic contact with the polymerase is increased. We investigated if the polymorphism of the palm-1 binding site is the sole cause of the reduced susceptibility of subtype 1a to inhibition by 1,5-benzodiazepines by using reverse genetics, X-ray crystallography, and surface plasmon resonance studies. We showed Y415F to be a key determinant in conferring resistance on subtype 1a, with this effect being mediated through an inhibitor-and enzyme-bound water molecule. Binding studies revealed that the mechanism of subtype 1a resistance is faster dissociation of the inhibitor from the enzyme.

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Structural Basis for Resistance of the Genotype 2b Hepatitis C Virus NS5B Polymerase to Site A Non-Nucleoside Inhibitors

Cited by 18 publications

References 44 publications

Association of hepatitis C virus NS5B variants with resistance to new antiviral drugs among untreated patients

Association of hepatitis C virus NS5B variants with resistance to new antiviral drugs among untreated patients

Effect on Hepatitis C Virus Replication of Combinations of Direct-Acting Antivirals, Including NS5A Inhibitor Daclatasvir

1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus

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