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In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease

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Veröffentlicht/Copyright: 1. Januar 2024
Zeitschrift für Naturforschung C
Aus der Zeitschrift Zeitschrift für Naturforschung C Band 79 Heft 1-2

Abstract

Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO–LUMO and absorption spectrum analysis have been used to evaluate the boceprevir’s toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein’s residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.

Keywords: COVID-19; 2019-nCoV MPRO; boceprevir; molecular docking; MD simulation
Corresponding author: Dipendra Sharma, Department of Physics, DDU Gorakhpur University, Gorakhpur-273009, India, E-mail:

Acknowledgements

Authors are grateful to Prof. S. N. Tiwari, Department of Physics, D.D.U. Gorakhpur University, Gorakhpur, for his insightful comments and helpful discussion. D. Sharma expresses gratitude to UGC, New Delhi, India for financial support in the form of the Start-Up Project [F.30-505/2020(BSR)].

  1. Research ethics: No human or animal participation in this work.

  2. Author contributions: G.T. performed the DFT and molecular docking calculation, helped in formal analysis, wrote the first draft of the manuscript; M.S.C. developed the idea, formal analysis, and performed the MD simulation; D.S. developed the idea, formal analysis, wrote the first draft of the manuscript, carefully examined the results, discussion and final proof of the text. The final version of the manuscript was reviewed, assembled and approved by all of the authors.

  3. Competing interests: All authors declared that there is no conflict of interest.

  4. Research funding: No funding was received for this research.

  5. Data availability: Data will be available/provided on a reasonable request.

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Received: 2023-09-03
Accepted: 2023-12-11
Published Online: 2024-01-01
Published in Print: 2024-01-29

© 2023 Walter de Gruyter GmbH, Berlin/Boston

Artikel in diesem Heft

  1. Frontmatter
  2. Research Articles
  3. In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease
  4. Analysis of the SARS-CoV-2 nsp12 P323L/A529V mutations: coeffect in the transiently peaking lineage C.36.3 on protein structure and response to treatment in Egyptian records
  5. In vitro antimicrobial and antioxidant activities, essential oil composition, and in silico molecular modeling analysis of secondary metabolites from roots of Verbascum sinaiticum
  6. Synthesis and antitumor activity of model cyclopentene-[g]annelated isoindigos
https://doi.org/10.1515/znc-2023-0117
Schlagwörter für diesen Artikel
COVID-19; 2019-nCoV MPRO; boceprevir; molecular docking; MD simulation

Artikel in diesem Heft

  1. Frontmatter
  2. Research Articles
  3. In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease
  4. Analysis of the SARS-CoV-2 nsp12 P323L/A529V mutations: coeffect in the transiently peaking lineage C.36.3 on protein structure and response to treatment in Egyptian records
  5. In vitro antimicrobial and antioxidant activities, essential oil composition, and in silico molecular modeling analysis of secondary metabolites from roots of Verbascum sinaiticum
  6. Synthesis and antitumor activity of model cyclopentene-[g]annelated isoindigos
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