In silico investigation of hepatitis c virus: a novel perspective into targeted viral inhibition of NS3 helicase, NS 3/4a protease and NS5b RNA dependent RNA polymerase.

Abstract

Hepatitis C Virus (HCV) is an escalating global healthcare and economic burden that requires extensive intervention to alleviate its control. Over the years, drug design efforts have produced many anti-HCV drugs; however, due to drug resistance brought on by numerous genetic variations of the virus and lack of specificity and stability, current drugs are rendered ineffective. The situation has been further intensified by the absence of a viable vaccine. For these reasons, continuous HCV research is imperative for the design and development of promising inhibitors that address the challenges faced by present antiviral therapies. Moreover, exposure of previously neglected viral protein targets can offer another potentially valuable therapeutic route in drug design research. Structure-based drug design approaches accentuate the development of small inhibitor molecules that interact with therapeutic targets through non-covalent interactions. The unexpected discovery of covalent inhibitors and their distinctive nature of instigating complete and irreversible inhibition of targets have shifted attention away from the use of non-covalent drugs in antiviral treatment. This has led to significant progress in understanding covalent inhibition regarding their underlying mechanism of action and in the design of novel covalent inhibitors that work against biological targets. However, due to difficulties arising in its application and resultant safety, the pharmaceutical industry were reluctant to pursue this strategy. With the use of rational drug design, a novel strategy was then proposed known as selective covalent inhibition. Due to the lack of competent protocols and information, little is known regarding selective covalent inhibition This study investigates three biological HCV targets, NS3 protease, RNA helicase and NS5B RNAdependent RNA polymerase. With constantly evolving viruses like HCV, computational methods including molecular modelling and docking, virtual screening and molecular dynamic simulations have allowed chemists to screen millions of compounds to filter out potential lead drugs. These in silico approaches have allowed Computer-Aided Drug Design as a cost-effective strategy to accelerate the process of drug discovery. The above techniques, with numerous other computational tools were employed in this study to fill the gap in HCV drug research by providing insights into the structural and dynamic changes that describe the mechanism of selective covalent inhibition and pharmacophoric features that lead to unearthing of potential small inhibitor molecules against Hepatitis C. v The first study (Chapter 4) provides a comprehensive review on HCV NS3/4A protein, current therapies and covalent inhibition as well as introduces a technical guideline that provides a systematic approach for the design and development of potent, selective HCV inhibitors. The second study (Chapter 5) provides a comprehensive understanding concerning the implications of selective covalent inhibition on the activity of HCV NS5B RNA-dependent RNA polymerase, with respect to key components required for viral replication, when bound to a target-specific small inhibitor molecule. The third study (Chapter 6) is preliminary investigation that uses Pharmacophore-based virtual screening as an efficient tool for the discovery of improved potential HCV NS3 helicase inhibitors. The pharmacophoric features were created based on the highly contributing amino acid residues that bind with highest affinity to the weak inhibitor, quercetin. These residues were identified based on free energy footprints obtained from molecular dynamic and thermodynamic calculations. Post molecular dynamic analysis and appropriate drug-likeness properties of the three top-hit compounds revealed that ZINC02495613 could be a more effective potential HCV helicase inhibitor; however, further validation steps are still required. This study offers a comprehensive in silico perspective to fill the gap in rational drug design research against HCV, thus providing an insight into the mechanism of selective covalent inhibition, uncovering a previously neglected viral target and identifying possible antiviral drugs. To this end, the work presented in this report is considered a fundamental platform to advance research toward the design and development of novel and selective anti-HCV drugs.