[Frontiers in Bioscience 13, 3857-3868, May 1, 2008]

4-Thiazolidinones: a novel class of hepatitis C virus NS5B polymerase inhibitors

Neerja Kaushik-Basu1, Alain Bopda-Waffo1, Tanaji T. Talele2, Amartya Basu1, Ye Chen1, S. Guniz Kucukguzel3

1Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, 2Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, St. John's University, Jamaica, NY 11439, 3Marmara University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Haydarpasa, 34668 Istanbul, Turkey

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Materials and Methods
3.1. Synthesis of inhibitors
3.2. Purification of recombinant replicase proteins
3.3. RNA-dependent RNA polymerase (RdRp) assay
3.4. Cross-linking of NS5B to TP
3.5. Determination of the Ki and mode of inhibition
3.6. Molecular modeling
4. Results
4.1. Expression and purification of recombinant replicase proteins
4.2. Identification of 4-Thiazolidinones as inhibitors of HCV NS5B RdRp activity
4.3. Mechanism of inhibition
4.4. Molecular docking and analysis of the binding mode of compound 6
5. Discussion
6. Acknowledgement
7. References
1. ABSTRACT

In a quest to identify novel compounds targeting HCV viral replicase, we evaluated a new series of 4-thiazolidinone derivatives (18 compounds). Our in vitro NS5B RdRp inhibition analysis with a series of 2¢ ,4¢ -difluoro-4-hydroxybiphenyl-3-carboxylic acid (2-(5-nitro-2-furyl / substituted phenyl)-4-thiazolidinone-3-yl) amides (1-7) yielded IC50 values ranging between 45-75 microM. Of these, lead compound 6: 2¢ ,4¢ -difluoro-4-hydroxybiphenyl-3-carboxylic acid(2-(2-fluorophenyl)-4-thiazolidinone-3-yl)amide exhibited an IC50 value of 48 microM and inhibited NS5B non-competitively with respect to UTP and exhibited a mixed mode of inhibition with respect to RNA. Molecular docking of thiazolidinone derivatives within the allosteric site of NS5B yielded significant correlation between their calculated binding affinity and IC50 values. Taken together, these data suggest that the 4-thiazolidinone scaffold may be optimized for generating new analogues with improved anti-NS5B potency.