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Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach

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Abstract

The hepatitis C virus (HCV), of the family flaviviridae, is one of the major causes of chronic liver diseases. Until the year 2012, HCV infections were treated using PEG-interferon and ribavirin combinations, which have a low cure rate and severe side effects. Currently, many direct-acting antivirals (DAAs) are available, e.g. protease inhibitors, NS5A and polymerase inhibitors. These drugs have proven to be efficient in interferon-free treatment combinations and capable of enhancing the cure rate to above 90 %. Unlike PEG-interferon and ribavirin combinations, DAAs select for resistance in HCV. The R155K mutation in the HCV was found to resist all the currently available protease inhibitors. Here, we studied biophysical parameters like pocket (cavity) geometries and stabilizing residues of HCV 1a NS3/4A protease in wild type and mutants. We also studied HCV 1a NS3/4A protease’s catalytic residues: their accessibility, energy, flexibility and binding to Phase II oral protease inhibitor vedroprevir (GS-9451), and compared these parameters between wild type and mutant(s). All these studies were performed using various bioinformatics tools (e.g. Swiss-PdbViewer and Schrödinger’s Maestro) and web servers (e.g. DoGSiteScorer, SRide, ASA-View, WHAT IF, elNémo, CABS-flex, PatchDock and PLIP). From our study, we found that introduction of R155K, A156T or D168A mutation to wild-type NS3/4A protease increases the pocket’s volume, surface (in the R155K mutant, surface decreases), lipo surface and depth and decreases the number of stabilizing residues. Additionally, differences in catalytic residues’ solvent accessibility, energy, root-mean-square deviation (RMSD) and flexibility between wild type and mutants might explain changes in the protease activity and the resistance to protease inhibitors.

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Abbreviations

HCV:

Hepatitis C virus

PDB:

Protein Data Bank

NS3:

Non-structural protein 3

NS4A:

Non-structural protein 4A

DAA:

Direct-acting antivirals

RMSD:

Root-mean-square deviation

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Acknowledgments

N.P. would like to thank EDP Department of Sakthi Sugars Ltd., Sakthi Nagar, India, for providing the computing facility for this study. N.P. would also like to thank Dr. Rituraj Purohit (CSIR-IHBT, India) for his kind help and for his critical suggestions about the manuscript. The authors would like to thank Sarah Lam for her grammatical assistance.

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Authors and Affiliations

  1. Synthetic Biology Group, Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 267 (BioQuant), 69120, Heidelberg, Germany

    Navaneethan Palanisamy

  2. The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany

    Navaneethan Palanisamy

  3. Section of Clinical Virology, Department of Medical Sciences, Uppsala University, 751 85, Uppsala, Sweden

    Navaneethan Palanisamy & Johan Lennerstrand

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  1. Navaneethan Palanisamy
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Correspondence to Navaneethan Palanisamy.

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Palanisamy, N., Lennerstrand, J. Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach. Interdiscip Sci Comput Life Sci 10, 143–156 (2018). https://doi.org/10.1007/s12539-016-0177-4

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