Research Article
BibTex RIS Cite
Year 2021, Volume: 8 Issue: 3, 933 - 940, 31.08.2021
https://doi.org/10.18596/jotcsa.923455

Abstract

References

  • 1. WHO. Coronavirus disease (COVID-19) pandemic [Internet]. World Health Organization; 2021 [cited 2021 Aug 5]. <URL>
  • 2. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. N Engl J Med. 2021 May 20;384(20):1885–98.
  • 3. Durdagi̇ S. Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target. Turkish Journal of Biology. 2020 Jun 21;44(SI-1):185–91.
  • 4. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul 16;583(7816):459–68.
  • 5. Idris MO, Yekeen AA, Alakanse OS, Durojaye OA. Computer-aided screening for potential TMPRSS2 inhibitors: a combination of pharmacophore modeling, molecular docking and molecular dynamics simulation approaches. Journal of Biomolecular Structure and Dynamics. 2020 Jul 16;1–19.
  • 6. Choudhary S, Malik YS, Tomar S. Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in silico Structure-Based Virtual Screening Approach. Front Immunol. 2020 Jul 10;11:1664.
  • 7. Baby K, Maity S, Mehta CH, Suresh A, Nayak UY, Nayak Y. Targeting SARS-CoV-2 Main Protease: A Computational Drug Repurposing Study. Archives of Medical Research. 2021 Jan;52(1):38–47.
  • 8. Lin S, Chen H, Ye F, Chen Z, Yang F, Zheng Y, et al. Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design. Sig Transduct Target Ther. 2020 Dec;5(1):131.
  • 9. Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, et al. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophysical Journal. 2021 Jul;120(14):2880–9.
  • 10. El Khatabi̇ K, Aanouz İ, El-Merni̇Ssi̇ R, Khaldan A, Ajana MA, Bouachrine M, et al. Designing of Novel Potential Inhibitors of a-amylase by 3D-QSAR Modeling and Molecular Docking Studies. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 May 10;469–78.
  • 11. Sulaiman M, Hassan Y, Taski̇N Tok T, Noundou XS. SYNTHESIS, ANTIBACTERIAL ACTIVITY AND DOCKING STUDIES OF BENZYL ALCOHOL DERIVATIVES. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 May 11;481–8.
  • 12. Kiliç Kurt Z. Synthesis of Novel Oxadiazole Derivatives, Molecular Properties Prediction and Molecular Docking Studies. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 Oct 30;7(3):753–74.
  • 13. Tazikeh-Lemeski E, Moradi S, Raoufi R, Shahlaei M, Janlou MAM, Zolghadri S. Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. Journal of Biomolecular Structure and Dynamics. 2021 Sep 2;39(13):4633–46.
  • 14. Jiang Y, Liu L, Manning M, Bonahoom M, Lotvola A, Yang Z-Q. Repurposing Therapeutics to Identify Novel Inhibitors Targeting 2’-O-Ribose Methyltransferase Nsp16 of SARS-CoV-2 [Internet]. 2020 May [cited 2021 Aug 8]. Note: This content is a preprint and has not been peer-reviewed.
  • 15. Vijayan V, Pant P, Vikram N, Kaur P, Singh TP, Sharma S, et al. Identification of promising drug candidates against NSP16 of SARS-CoV-2 through computational drug repurposing study. Journal of Biomolecular Structure and Dynamics. 2020 Aug 3;1–15. 16. Olsson M, Søndergard C, Rostkowski M, Jensen J. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions. J Chem Theo Comput. 2011;(2):525–37.
  • 17. Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values. J Chem Theory Comput. 2011 Jul 12;7(7):2284–95.
  • 18. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009 Dec;30(16):2785–91.
  • 19. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2009;455-61.
  • 20. Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Research. 2018 Jan 4;46(D1):D1074–82.
  • 21. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011 Dec;3(1):33.
  • 22. Maestro. Schrödinger Release 2016-4 [Internet]. Schrödinger, LLC; 2016 [cited 2021 Aug 5].
  • 23. RECOVERY Collaborative Group, Horby P, Lim WS, Emberson JR, Mafham M, Bell JL, et al. Dexamethasone in Hospitalized Patients with Covid-19. N Engl J Med. 2021 Feb 25;384(8):693–704.
  • 24. Khalili H, Nourian A, Ahmadinejad Z, Emadi Kouchak H, Jafari S, Dehghan Manshadi SA, et al. Efficacy and safety of sofosbuvir/ ledipasvir in treatment of patients with COVID-19; A randomized clinical trial. Acta Biomed. 2020 Nov 10;91(4):e2020102.
  • 25. Fürstenau M, Langerbeins P, De Silva N, Fink AM, Robrecht S, von Tresckow J, et al. COVID-19 among fit patients with CLL treated with venetoclax-based combinations. Leukemia. 2020 Aug;34(8):2225–9.
  • 26. Pollard BS, BLANCOl JC, Pollard JR. Classical Drug Digitoxin Inhibits Influenza Cytokine Storm, With Implications for Covid-19 Therapy. In Vivo. 2020;34(6):3723–30.
  • 27. Lo HS, Hui KPY, Lai H-M, He X, Khan KS, Kaur S, et al. Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir. ACS Cent Sci. 2021 May 26;7(5):792–802.

Drug Repurposing Against SARS-CoV-2: Targeting NSP16-NSP10 Interaction

Year 2021, Volume: 8 Issue: 3, 933 - 940, 31.08.2021
https://doi.org/10.18596/jotcsa.923455

Abstract

Drug repurposing studies played an important role for fighting with the Covid-19 pandemic. Discovering a new drug molecule for a disease takes a very long time. However, repurposing a drug molecule developed for another disease can accelerate to find new treatments for a disease. Thus, several drug repurposing studies were carried out targeting important proteins for SARS-CoV-2. In this work, Nsp16-Nsp10 interaction was targeted since this interaction is needed for SARS-CoV-2 to evade the human immune system. Therefore, docking calculations of approved 2126 drug molecules obtained from Drugbank database were performed using AutoDock VINA program. From these docking calculations, drugs Ledipasvir Elbasvir, Venetoclax, Digitoxin, Irinotecan, Dexamethasone, Acetyldigitoxin, Dactinomycin, Lumacaftor and Simeprevir have the highest docking scores. Important interactions for these drug molecules were presented.

References

  • 1. WHO. Coronavirus disease (COVID-19) pandemic [Internet]. World Health Organization; 2021 [cited 2021 Aug 5]. <URL>
  • 2. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. N Engl J Med. 2021 May 20;384(20):1885–98.
  • 3. Durdagi̇ S. Virtual drug repurposing study against SARS-CoV-2 TMPRSS2 target. Turkish Journal of Biology. 2020 Jun 21;44(SI-1):185–91.
  • 4. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul 16;583(7816):459–68.
  • 5. Idris MO, Yekeen AA, Alakanse OS, Durojaye OA. Computer-aided screening for potential TMPRSS2 inhibitors: a combination of pharmacophore modeling, molecular docking and molecular dynamics simulation approaches. Journal of Biomolecular Structure and Dynamics. 2020 Jul 16;1–19.
  • 6. Choudhary S, Malik YS, Tomar S. Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in silico Structure-Based Virtual Screening Approach. Front Immunol. 2020 Jul 10;11:1664.
  • 7. Baby K, Maity S, Mehta CH, Suresh A, Nayak UY, Nayak Y. Targeting SARS-CoV-2 Main Protease: A Computational Drug Repurposing Study. Archives of Medical Research. 2021 Jan;52(1):38–47.
  • 8. Lin S, Chen H, Ye F, Chen Z, Yang F, Zheng Y, et al. Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design. Sig Transduct Target Ther. 2020 Dec;5(1):131.
  • 9. Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, et al. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophysical Journal. 2021 Jul;120(14):2880–9.
  • 10. El Khatabi̇ K, Aanouz İ, El-Merni̇Ssi̇ R, Khaldan A, Ajana MA, Bouachrine M, et al. Designing of Novel Potential Inhibitors of a-amylase by 3D-QSAR Modeling and Molecular Docking Studies. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 May 10;469–78.
  • 11. Sulaiman M, Hassan Y, Taski̇N Tok T, Noundou XS. SYNTHESIS, ANTIBACTERIAL ACTIVITY AND DOCKING STUDIES OF BENZYL ALCOHOL DERIVATIVES. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 May 11;481–8.
  • 12. Kiliç Kurt Z. Synthesis of Novel Oxadiazole Derivatives, Molecular Properties Prediction and Molecular Docking Studies. Journal of the Turkish Chemical Society Section A: Chemistry. 2020 Oct 30;7(3):753–74.
  • 13. Tazikeh-Lemeski E, Moradi S, Raoufi R, Shahlaei M, Janlou MAM, Zolghadri S. Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. Journal of Biomolecular Structure and Dynamics. 2021 Sep 2;39(13):4633–46.
  • 14. Jiang Y, Liu L, Manning M, Bonahoom M, Lotvola A, Yang Z-Q. Repurposing Therapeutics to Identify Novel Inhibitors Targeting 2’-O-Ribose Methyltransferase Nsp16 of SARS-CoV-2 [Internet]. 2020 May [cited 2021 Aug 8]. Note: This content is a preprint and has not been peer-reviewed.
  • 15. Vijayan V, Pant P, Vikram N, Kaur P, Singh TP, Sharma S, et al. Identification of promising drug candidates against NSP16 of SARS-CoV-2 through computational drug repurposing study. Journal of Biomolecular Structure and Dynamics. 2020 Aug 3;1–15. 16. Olsson M, Søndergard C, Rostkowski M, Jensen J. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions. J Chem Theo Comput. 2011;(2):525–37.
  • 17. Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values. J Chem Theory Comput. 2011 Jul 12;7(7):2284–95.
  • 18. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009 Dec;30(16):2785–91.
  • 19. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2009;455-61.
  • 20. Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Research. 2018 Jan 4;46(D1):D1074–82.
  • 21. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011 Dec;3(1):33.
  • 22. Maestro. Schrödinger Release 2016-4 [Internet]. Schrödinger, LLC; 2016 [cited 2021 Aug 5].
  • 23. RECOVERY Collaborative Group, Horby P, Lim WS, Emberson JR, Mafham M, Bell JL, et al. Dexamethasone in Hospitalized Patients with Covid-19. N Engl J Med. 2021 Feb 25;384(8):693–704.
  • 24. Khalili H, Nourian A, Ahmadinejad Z, Emadi Kouchak H, Jafari S, Dehghan Manshadi SA, et al. Efficacy and safety of sofosbuvir/ ledipasvir in treatment of patients with COVID-19; A randomized clinical trial. Acta Biomed. 2020 Nov 10;91(4):e2020102.
  • 25. Fürstenau M, Langerbeins P, De Silva N, Fink AM, Robrecht S, von Tresckow J, et al. COVID-19 among fit patients with CLL treated with venetoclax-based combinations. Leukemia. 2020 Aug;34(8):2225–9.
  • 26. Pollard BS, BLANCOl JC, Pollard JR. Classical Drug Digitoxin Inhibits Influenza Cytokine Storm, With Implications for Covid-19 Therapy. In Vivo. 2020;34(6):3723–30.
  • 27. Lo HS, Hui KPY, Lai H-M, He X, Khan KS, Kaur S, et al. Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir. ACS Cent Sci. 2021 May 26;7(5):792–802.
There are 26 citations in total.

Details

Primary Language English
Subjects Biochemistry and Cell Biology (Other), Chemical Engineering
Journal Section Articles
Authors

Sefer Baday 0000-0002-2913-6687

Publication Date August 31, 2021
Submission Date April 20, 2021
Acceptance Date June 21, 2021
Published in Issue Year 2021 Volume: 8 Issue: 3

Cite

Vancouver Baday S. Drug Repurposing Against SARS-CoV-2: Targeting NSP16-NSP10 Interaction. JOTCSA. 2021;8(3):933-40.