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

Author(s): Vaishali M. Patil*, Satya Prakash Gupta.

Journal Name: Current Chemical Biology

Volume 12 , Issue 1 , 2018

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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.

Keywords: Hepatitis C virus, HCV NS5B polymerase, molecular dynamics, structure-based drug design, flexibility docking, HCV inhibitors.

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Article Details

VOLUME: 12
ISSUE: 1
Year: 2018
Page: [65 - 87]
Pages: 23
DOI: 10.2174/2212796812666180423155559

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