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Molecular Docking Investigation of the Binding Interactions of Macrocyclic Inhibitors with HCV NS3 Protease and its Mutants (R155K, D168A and A156V)

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Abstract

Hepatitis C Virus (HCV) non-structural protein 3 (NS3) protease drug resistance poses serious challenges on the design of an effective treatment. Substrate Envelope Hypothesis, “the substrates of HCV NS3/4A protease have a consensus volume inside the active site called substrate envelope” is used to design potent and specific drugs to overcome this problem. Using molecular docking, we studied the binding interaction of the different inhibitors and protein and evaluated the effect of three different mutations (R155K, D168A and A156V) on the binding of inhibitors. P2–P4 macrocycles of 5A/5B and modified 5A/5B hexapeptide sequences have the best scores against the wild-type protein −204.506 and −206.823 kcal/mole, respectively. Also, charged P2–P4 macrocycles of 3/4A and 4A/4B hexapeptide sequences have low scores with the wild-type protein −200.467 and −203.186 kcal/mole, respectively. R155K mutation greatly affects the conformation of the compounds inside the active site. It inverts its orientations, and this is because the large and free side chain of K155 which restricts the conformation of the large P2–P4 macrocycle. The conformation of charged P2–P4 macrocycle of 3/4A hexapeptide sequence in wild-type, A156V and D168A proteins is nearly equal; while that of charged P2–P4 macrocycle of 4A/4B hexapeptide sequence is different. Nevertheless, these compounds have a slight increase of Van der Waals volume compared to that of substrates, they are potent against mutations and have good scores. Therefore, the suggested drugs can be used as an effective treatment solving HCV NS3/4A protease drug resistance problem.

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Abbreviations

HCV:

Hepatitis C Virus

NS3:

Non-structural protein 3

NS4A:

Non-structural protein 4A

FDA:

Food and drug administration

PEG IFN-α:

Pegylated interferon α

HIV-1:

Human immunodeficiency virus-1

PM3:

Parameterization model, version 3

MM3:

Molecular mechanics 3

MO-G:

Molecular orbital package

NS:

Non-structural protein

PMF:

Potential of mean force

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Authors and Affiliations

  1. Biophysics Department, Faculty of Science, University of Cairo, Giza, 11757, Egypt

    Ahmed A. Ezat, Nihal S. El-Bialy & Hamdy I. A. Mostafa

  2. Spectroscopy Department, National Research Centre, Dokki, Cairo, 12311, Egypt

    Medhat A. Ibrahim

Authors
  1. Ahmed A. Ezat
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  2. Nihal S. El-Bialy
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  3. Hamdy I. A. Mostafa
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  4. Medhat A. Ibrahim
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Correspondence to Ahmed A. Ezat.

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Ezat, A.A., El-Bialy, N.S., Mostafa, H.I.A. et al. Molecular Docking Investigation of the Binding Interactions of Macrocyclic Inhibitors with HCV NS3 Protease and its Mutants (R155K, D168A and A156V). Protein J 33, 32–47 (2014). https://doi.org/10.1007/s10930-013-9538-6

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