Structural Flexibility in HCV NS5B Polymerase and Molecular Modelling of Anti-HCV Drugs

Abstract

Background: NS5B polymerase remains an important anti-hepatitis C virus (HCV) drug target. It has been well reported that ligand binding induces large conformational changes in the receptor. Several computational models describing polymerase dynamics have been reported. Various conformational forms have been determined by crystallography and NMR experiments and they suggest the binding of HCV inhibitors in allosteric sites might affect polymerase flexibility. Objective: In most of the cases of structure-based drug design (SBDD), only static structures have been given consideration and most molecular modeling studies have recognized the importance of flexibility. The standard virtual docking methods using rigid receptor may give misleading results as in reality many proteins undergo side-chain and/or backbone movements. The importance of HCV NS5B polymerase receptor flexibility in altering the binding site to complement the shape and binding mode of the ligand i.e. induced fit docking need to be considered. Method: The various methodologies were adopted for molecular modeling based on induced-fit docking at the well-defined inhibitor binding sites i.e. "palm" and "thumb" domain. Some of the well reported NNIs and NIs are VX-222, ANA598/Setrobuvir, CS01, aureusidin, N,N-disubstituted phenylalanine, benzothiadiazine, 6-aminoquinoline derivatives, etc. Results: These assumptions have lead to application of quantum mechanics and induced-fit docking for the development of various HCV NS5B polymerase inhibitors. This enzyme has proved to be challenging and therefore potential ligands with structural diversity have been modified to enhance selectivity and affinity. The flexible nature of HCV polymerase, reveals details about substrate-inhibitor interaction to its active site within the membrane. Conclusion: It will help to develop allosteric inhibitors into efficient drugs by understanding their indirect mode of action and complex structure-activity/kinetic relationship.

Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor

“…Benzimidazole derivatives (substituted benzo[ d ]imidazol-1-yl)methyl)benzimidamides) were considered as potential analogues for AICAR due to similarities in chemical structure (Figure 1), and could be evaluated for their antimalarial propensity. Benzimidazole derivatives have been widely used in recent years due to their wide range of pharmacological activities including antimalarial, 8 antileishmanial, 9 analgesics, 10 anticancer, 11 antitumour, 12 antimicrobial, 13 anti-inflammatory, 14 antihepatitis C virus, 15 antihelmintic, 16 antibacterial 17 and antitrypanosomal 18 activities. Although several benzimidazole derivatives have been synthesised and developed into commercially available drugs, little is known about the design of the template as an inhibitor against P falciparum ADSL ( Pf ADSL).…”