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Journal of Enzyme Inhibition and Medicinal Chemistry Volume 37, 2022 - Issue 1
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Research Papers

Multi-stage structure-based virtual screening approach towards identification of potential SARS-CoV-2 NSP13 helicase inhibitors 

Mahmoud A. El Hassaba Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Salman International University (KSIU), Ras Sudr, EgyptView further author information
,
Wagdy M. Eldehnab Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, EgyptCorrespondence[email protected]
View further author information
,
Sara T. Al-Rashoodc Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaView further author information
,
Amal Alharbic Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaView further author information
,
Razan O. Eskandranic Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaView further author information
,
Hamad M. Alkahtanic Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaView further author information
,
Eslam B. Elkaeedd Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi ArabiaView further author information
&
Sahar M. Abou-Serie Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Cairo University, Cairo, EgyptView further author information
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Pages 563-572 | Received 06 Nov 2021, Accepted 20 Dec 2021, Published online: 10 Jan 2022

References

  • Wang C, Wang Z, Wang G, et al. COVID-19 in early 2021: current status and looking forward. Sig Transduct Target Ther 2021;6:114.
  • Beigel JH, Tomashek KM, Dodd LE, et al. Remdesivir for the treatment of Covid-19 — final report. New Eng J Med 2020;383:1813–26.
  • Young B, Tan TT, Leo YS. The place for remdesivir in COVID-19 treatment. Lancet Infect Dis 2021;21: 20–1.
  • Ohl ME, Miller DR, Lund BC, et al. Association of remdesivir treatment with survival and length of hospital stay among US veterans hospitalized with COVID-19. JAMA Network Open 2021;4:e2114741.
  • Zhou Y-W, Xie Y, Tang L-S, et al. Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies. Sig Transduct Target Ther 2021;6:317.
  • Chen J, Malone B, Llewellyn E, et al. Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex. Cell 2020;182:1560–73.
  • Tanner JA, Watt RM, Chai Y-B, et al. The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5' to 3' viral helicases. J Biol Chem 2003;278:39578–82.
  • Ivanov KA, Thiel V, Dobbe JC, et al. Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J Virol 2004;78:5619–32.
  • Newman JA, Douangamath A, Yadzani S, et al. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun 2021;12:4848.
  • Case DA, Cheatham TE, Darden T, et al. The amber biomolecular simulation programs. J Comput Chem 2005;26:1668–88.
  • Eberhardt J, Santos-Martins D, Tillack AF, et al. AutoDock Vina 1.2.0: new docking methods, expanded force field, and python bindings. J Chem Info Model 2021;61:3891–8.
  • Abraham MJ, Murtola T, Schulz R, et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015;1–2:19–25.
  • Schüttelkopf AW, van Aalten DMF. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004;60:1355–63.
  • Hassab MAE, Fares M, Amin MKA-H, et al. Toward the identification of potential α-ketoamide covalent inhibitors for SARS-CoV-2 main protease: fragment-based drug design and MM-PBSA calculations. Processes 2021;9:1004.
  • El Hassab MA, Shoun AA, Al-Rashood ST, et al. Identification of a new potential SARS-COV-2 RNA-dependent RNA polymerase inhibitor via combining fragment-based drug design, docking, molecular dynamics, and MM-PBSA calculations. Front Chem 2020;8:915.
  • El Hassab MA, Ibrahim TM, Al-Rashood ST, et al. In silico identification of novel SARS-COV-2 2'-O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches. J Enzyme Inhib Med Chem 2021;36:727–36.
  • El Hassab MA, Ibrahim TM, Shoun AA, et al. In silico identification of potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations. RSC Adv 2021;11:16026–33.
  • Berendsen HJC, Postma JPM, Van Gunsteren WF, et al. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684–90.
  • Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 1981;52:7182–90.
  • Kumari R, Kumar R, Lynn A. g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Info Model 2014;54:1951–62.
  • Brewerton SC. The use of protein-ligand interaction fingerprints in docking. Curr Op Drug Disc Dev 2008;11:356–64.
  • Deng Z, Chuaqui C, Singh J. Structural Interaction Fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 2004;47:337–44.
  • El-Hasab MA, El-Bastawissy EE, El-Moselhy TF. Identification of potential inhibitors for HCV NS3 genotype 4a by combining protein-ligand interaction fingerprint, 3D pharmacophore, docking, and dynamic simulation. J Biomol Struct Dyn 2018;36:1713–27.
  • El-Hassab MA, El-Bastawissy EE, El-Moselhy TF. Identification of potential inhibitors for HCV NS5b of genotype 4a by combining dynamic simulation, protein-ligand interaction fingerprint, 3D pharmacophore, docking and 3D QSAR. J Biomol Struct Dyn 2020;38:4521–35.
  • Irwin JJ, Shoichet BK. ZINC-a free database of commercially available compounds for virtual screening. J Chem Info Model 2005;45:177–82.
  • Pinzi L, Rastelli G. Molecular docking: shifting paradigms in drug discovery. Int J Mol Sci 2019;20:4331.
  • Liu X, Shi D, Zhou S, et al. Molecular dynamics simulations and novel drug discovery. Exp Op Drug Disc 2018;13:23–37.

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