Longitudinal clonal resistance analysis of treatment-naïve patients with chronic Hepatitis C

HepDART 2009
06-10 December 2009
Kohala Coast, Hawaii, USA Back grey_arrow_rt.gif





Longitudinal clonal resistance analysis of treatment-naïve patients with chronic Hepatitis C (CHC) genotype 1 infection treated with MK-7009, a Novel NS3/4a Protease Inhibitor, in combination with Pegylated Interferon Alfa-2a and Ribavirin for 28 day


Reported by Jules Levin
HepDart Dec 6-10 2009 Hawaii

Richard J.O. Barnard1, Adetoun Adeniji-Adele1, Amy Himmelberger1, Richard Wiedmann2, Peggy M. Hwang3, Erin Quirk2, Nicholas Kartsonis2, Andrew W. Lee2, Robert Tipping3, Michael D. Miller1, Daria Hazuda1 1Antiviral Research, 2ID/Vaccines Clinical Research, 3Biostatistics, Merck Research Laboratories, West Point, PA, USA

Copyright © 2009 Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Whitehouse Station, N.J., U.S.A. All Rights Reserved


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ABSTRACT

Background: MK-7009 is a noncovalent competitive inhibitor of HCV NS3/4A protease which significantly improved rapid viral response (RVR) rates in CHC patients when administered in combination with pegylated interferon (peg-IFN) and ribavirin (RBV) for 28 days (i.e., "triple therapy"). We now report updated efficacy and resistance studies for patients treated with continued peg-IFN/RBV for 12 weeks total.

Methods: This is a randomized, placebo-controlled, double-blind study of MK-7009 in treatment-naïve CHC patients. MK-7009 was administered for 28 days with peg-IFN/RBV in 1 of 5 regimens: placebo, 300 mg BID, 600 mg BID, 600 mg QD, or 800 mg QD; all patients subsequently continue peg-IFN/RBV for an additional 44 weeks. HCV RNA was determined by Roche Cobas Taqman PCR with a lower limit of detection (LLOD) ∼ 10 IU/mL. RVR and complete Early Viral Response (EVR) are defined as the percentage of treated patients below LLOD at 4 and 12 weeks, respectively. For resistance studies, the NS3 region of the HCV genome was amplified by RT-PCR from RNA purified from patient plasma. Both population and clonal sequencing was performed on the resultant NS3 amplicons.

Results: 94 subjects (mean age 46.1 years, 59% male, mean baseline HCV RNA 6.70 log10 IU/mL) were randomized and treated.

The proportion of subjects who achieved RVR in the MK-7009-containing arms ranged from 69% to 82%, vs. 6% of the control (p < 0.0001 for each MK-7009 dose group, per-protocol analysis).

Preliminary data for 81 patients through Week 12 indicate continued viral suppression on peg-IFN/RBV only treatment, as 77 to 89% of subjects originally treated with triple therapy achieved EVR vs. 60% of control (per-protocol analysis).

4 patients had viral breakthrough at levels sufficient to perform resistance testing by week 12. Resistant HCV variants in the NS3/4a region of the HCV genome were detected in the three viral breakthrough patients randomized to receive MK-7009 by day 42 of the study.

Three patients had viruses that exhibited the R155K variant by week 12 of the study. The virus from one of these patients also exhibited low levels of the D168V variant. One patient exhibited a mixture of D168V/A/T by day 42 of the study. Clonal and population sequencing analysis was performed at multiple time points through week 12 from these patients where samples were available.

Conclusions: In this first study of MK-7009 in combination with peg-IFN/RBV, MK-7009 is a well-tolerated and potent inhibitor of HCV. This interim analysis indicates high rates of viral suppression to undetectable levels through 12 weeks in subjects treated with MK-7009 in combination with standard therapy for the initial 28 days. The results support further development of MK-7009 for HCV treatment. Resistance variants identified in this study were at positions 155 and 168 of the NS3/4a region.

Methods

Viral Resistance
Resistance sequencing was performed only for patients who met virological failure in Protocol 007, defined as:

· If the patient did not achieve at least 2 log10 decline in HCV viral RNA by week 4.

· If the patient has evidence of breakthrough viremia as defined by >1-log10 increase from nadir RNA (from two consecutive HCV RNA measurements)

· Plasma viral RNA of >100IU/ml in two consecutive visits after becoming undetectable

Due to the sensitivity of resistance assays, resistance analysis was performed on patient samples with HCV viral loads of >1000 IU/ml. Resistance analysis was performed at baseline, week 12 and intermediate time points based on sample availability.

Clonal Sequencing: DNA Amplicons obtained at baseline and the indicated time points were purified and cloned into a bacterial plasmid. ∼40 independent clones from each time point were sequenced


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Figure 2. MK-7009 Protocol 007 Study Design. Patients were randomized into several MK-7009 with doses groups. Patients were dosed with MK-7009 or placebo and pegylated interferon 2α (Peg-IFN) and ribavirin (RBV) for 28 days. Patients were then continued on Peg-IFN and RBV for an additional 44 weeks. Primary hypothesis: RVR rates for at least 1 MK-7009-treated group superior to placebo.

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Figure 5. Patient 1 (Genotype 1B). MK-7009 dose; 300mg b.i.d. Clonal resistance analysis (pie charts) was performed at the indicated time points. The red line denotes the limit of detection for the resistance sequencing assay

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Figure 6. Patient 2 (Genotype 1A). MK-7009 dose; 300mg b.i.d. Clonal resistance analysis (pie charts) was performed at the indicated time points. The red line denotes the limit of detection for the resistance sequencing assay. *D168V was also observed at in 1/4 amplicons by population sequencing at day 28. Clonal sequencing utilizes a different amplicon. As D168V was not amplified in the clonal analysis at day 28 (near the limit of detection of the assay), it is likely that D168V exists at very low levels at this time point.

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Figure 7. Patient 3 (Genotype 1A). MK-7009 dose; 600mg q.d. Clonal resistance analysis (pie charts) was performed at the indicated time points. The red line denotes the limit of detection for the resistance sequencing assay.

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Figure 8. Patient 4 (Genotype 1A). MK-7009 dose; 800mg b.i.d. Clonal resistance analysis (pie charts) was performed at the indicated time points. The red line denotes the limit of detection for the resistance sequencing assay.