Natural Variation in Drug Susceptibility to HCV Polymerase Inhibitors in Treatment-naïve HCV Patient Isolates

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From Journal of Viral Hepatitis

Natural Variation in Drug Susceptibility to HCV Polymerase Inhibitors in Treatment-naïve HCV Patient Isolates

S.-C. C. Sun; A. Bae; X. Qi; J. Harris; K. A. Wong; M. D. Miller; H. Mo

Posted: 12/27/2011; J Viral Hepat. 2011;18(12):861-870. © 2011 Blackwell Publishing

Abstract and Introduction

Abstract

To assess the natural variation in drug susceptibility among treatment-naïve hepatitis C virus (HCV) patient isolates, the susceptibilities of chimeric replicons carrying the HCV NS5B polymerase from up to 51 patient isolates against a panel of diverse HCV nonnucleoside polymerase inhibitors were evaluated using a replicon-based transient replication assay. Some patient to patient variation in susceptibility to the panel of three HCV nonnucleoside polymerase inhibitors was observed. Linear regression and correlation analyses revealed no correlations among the susceptibilities to the polymerase inhibitors tested. Our results suggest that variable antiviral responses to HCV nonnucleoside polymerase inhibitors may be observed because of the natural variation in baseline susceptibility. In addition, the lack of correlation among the susceptibilities to three classes of HCV polymerase inhibitors evaluated here supports their possible combined use in a combination therapy strategy


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In this study, the sensitivity of up to 51 clinical baseline isolates from untreated HCV GT-1-infected patients to a panel of nonnucleoside HCV polymerase inhibitors was determined to investigate the effect of HCV genetic diversity on the inhibitor's antiviral potency. Some natural variation in susceptibility among these isolates was observed with all three different classes of HCV polymerase inhibitors tested (benzofuran, benzothiadiazine and thiophene carboxylic acid). The degree of the variation in EC50 was slightly different among these three drug classes of nonnucleoside HCV polymerase inhibitors. The EC50 values in the 95th percentile were 4.5-, 6.0- and 7.5-fold higher than the 5th percentile EC50 values for the thiophene carboxylic acid, benzofuran and benzothiadiazine, respectively. Interestingly, no significant difference in sensitivity between GT-1a and GT-1b was observed for the tested benzofuran and thiophene carboxylic acid. In contrast, the benzothiadiazine was significantly more potent against GT-1b than GT-1a. The differential potency against GT-1a vs GT-1b for only the benzothiadiazine, and the high assay reproducibility for the reference standard suggests that the natural variation in drug susceptibility observed among baseline clinical isolates is not caused by assay variation. In addition, the results in the study are consistent with the findings of previous reports that described variable activity for HCV nonnucleoside polymerase inhibitors among clinical baseline isolates using similar phenotypic analysis assays.[38,39]

Given the observation of the natural variation in drug susceptibility to these three classes of nonnucleoside inhibitors, it is possible that this natural variation may cause variable antiviral response among different patients. For example, one dose may be optimal for patients containing more sensitive variants, but this same dose may be suboptimal for patients who have less susceptible variants. Indeed, variable response to some of the HCV nonnucleoside polymerase inhibitors among different patients has been observed in clinical studies, especially in lower-dose groups. Furthermore, consistent with the in vitro findings of less potent activity against GT-1a than GT-1b for the benzothiadiazines in this study, the response in HCV GT-1a-infected patients was poorer than the GT-1b-infected patients during monotherapy with ABT-333 and ANA-598 (both benzothiadiazines).[9,10] In addition to the susceptibility of baseline isolates, the pharmacokinetics of the drug also influences response. The natural variation in drug susceptibility coupled with pharmacokinetic information could be used to predict the response to drug treatment and provide guidance on the drug concentration needed for achieving a maximal response. If sufficiently high levels of drug exposure relative to the cluster of EC50 values is achieved, the natural variation in drug susceptibility would be of less concern. Finally, the natural variation in baseline susceptibility could provide a threshold for defining abnormal reductions in drug susceptibility and serve as an indicator for an increased probability of drug resistance.

Sequence analysis of NS5B revealed C316N and S556G double mutants in 2 of the 14 GT-1b isolates. Phenotypic analysis of the one isolate with sufficient replication capacity to test drug susceptibility had the highest EC50 against the benzofuran. This finding is consistent with previous reports, demonstrating that C316N confers a low-level of resistance to the benzofuran.[26] However, the benzofuran susceptibility of this isolate was well within the natural variation of the GT-1a isolates and it had wild-type susceptibility to the benzothiadiazine tested in this study. Similarly, no significant change in EC50 to the benzothiadiazine was seen in the isolate containing S556S/G. Previous studies showed that both C316N and S556G were associated with reduced susceptibility to other compounds of the benzothiadiazine class.[23,24,26] The discrepancy may be due to the fact that the benzothiadiazine compound tested in this study has subtle differences in chemical structure with the benzothiadiazine compounds in previous studies resulting in a slightly different interaction with the NS5B polymerase.

In contrast to the above three GT-1b isolates, NS5B sequence analysis did not identify any of the mutations that are known to confer resistance to the tested compounds in 52 of 55 patient samples (41 GT-1a and 11 of 14 GT-1b). In addition, no clear pattern of the NS5B sequence was revealed in baseline clinical isolates with higher EC50 values (data not shown). Thus, the natural variation in drug susceptibility observed in this study may be caused by the intrinsic genetic diversity of HCV.

The mean EC50 values derived from each baseline clinical isolate against the benzofuran, benzothiadiazine and thiophene carboxylic acid were compared between drugs using the statistical regression analysis of correlation. Overall, the correlation was poor between any of the three compounds. These results suggest that the HCV variants which are less susceptible to one of these three classes of nonnucleoside polymerase inhibitors may not be less sensitive to the other two different classes of nonnucleoside polymerase inhibitors. Therefore, a combination of two or three different classes of nonnucleoside polymerase inhibitors may be advantageous for maximal antiviral response and reducing the selection of resistance. However, other aspects including synergistic/antagonistic inhibitory effects, drug–drug interactions and overlapping toxicity profiles should be taken into consideration for potential combination therapy strategies. The lack of correlation between two different classes of nonnucleotide polymerase inhibitors agrees with the fact that these three nonnucleoside inhibitors target different sites of the HCV polymerase and also exhibit different resistance profiles.

In summary, the activity of three classes of nonnucleoside polymerase inhibitors (benzofuran, benzothiadiazine and thiophene carboxylic acid) against a panel of baseline clinical isolates was evaluated using a replicon-based transient replication assay. Some variation in drug susceptibility was observed for all three classes of nonnucleoside polymerase inhibitors. However, there was no correlation between susceptibilities from one compound to another among those tested. Our findings suggest that the existing natural variation in baseline susceptibility should be taken into account for the optimal dose selection for the development of future nonnucleoside polymerase inhibitors. The lack of correlation between drug susceptibilities supports the combination of these different classes of HCV nonnucleotide polymerase inhibitors in the clinic.

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