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Molecular Docking Interaction of Medicines Binding to COVID-19 Proteins

Year 2024, , 261 - 268, 04.02.2024
https://doi.org/10.18596/jotcsa.1281563

Abstract

In late 2019, in Wuhan, China, a new human coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first appeared. This virus caused the respiratory ailment known as coronavirus disease 2019 (COVID-19), which spread quickly throughout the world. Researchers from all over the world are working feverishly to comprehend SARS-CoV-2 and explore the pathophysiology of this illness to identify viable therapeutic drug candidates and treatments. This research is part of our ongoing search for an effective antiviral medication to combat this devastating illness, which necessitates work in medicinal chemistry. Every day, a sizable number of people die from the terrible disease COVID-19. This research looked at using docking theoretical calculations for dealing with the docking between medicines with proteins. Nine compounds of medicines named Aminoglutethimide, 4-aminosalicylic acid, Felbamate, Hydroflu-methiazide, Methazolamide, Modafinil, Nepafenac, Oxcarbazepine and Trichlormethiazide are used that are commonly active groups like amino group, hydroxyl, and ketone in their conformation structures. Two inhibitions of proteins in the SARS-CoV-2 virus (COVID-19) are applied (6xbg and 6xfn) for docking with nine medicines depending on the software of the Molecular operating environment package (MOE). The docking score was found to be that trichlormethiazide had a more stable value (-6.2955) and (-6.5462) with (6xbg) and (6xfn) proteins respectively.

Thanks

The Department of Chemistry, Faculty of Sciences, University of Mosul is acknowledged by the authors for its support and cooperation.

References

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  • 6. Alnoman RB, Parveen S, Hagar M, Ahmed HA, Knight JG. A new chiral boron-dipyrromethene (BODIPY)-based fluorescent probe: molecular docking, DFT, antibacterial and antioxidant approaches. J Biomol Struct Dyn [Internet]. 2020 Dec 11;38(18):5429–42. Available from: <URL>.
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  • 8. Ibrahim AA, Yahya OM, Ibrahim MA. Theoretical Prediction of Possible Drug Treatment of COVID-19 using Coumarins Containing Chloroquine Moeity. Asian J Chem [Internet]. 2020 Dec 7;32(12):3120–6. Available from: <URL>.
  • 9. Jiang F, Deng L, Zhang L, Cai Y, Cheung CW, Xia Z. Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19). J Gen Intern Med [Internet]. 2020 May 4;35(5):1545–9. Available from: <URL>.
  • 10. Zhang L, Liu Y. Potential interventions for novel coronavirus in China: A systematic review. J Med Virol [Internet]. 2020 May 3;92(5):479–90. Available from: <URL>.
  • 11. Khaerunnisa S, Kurniawan H, Awaluddin R, Suhartati S, Soetjipto S. Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study. Preprints [Internet]. 2020 Mar 13;1–14. Available from: <URL>.
  • 12. Khan SA, Zia K, Ashraf S, Uddin R, Ul-Haq Z. Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. J Biomol Struct Dyn [Internet]. 2021 May 3;39(7):2607–16. Available from: <URL>.
  • 13. Wahedi HM, Ahmad S, Abbasi SW. Stilbene-based natural compounds as promising drug candidates against COVID-19. J Biomol Struct Dyn [Internet]. 2020 May 12;39(9):3225–34. Available from: <URL>.
  • 14. Jorgensen WL. The Many Roles of Computation in Drug Discovery. Science (80- ) [Internet]. 2004 Mar 19;303(5665):1813–8. Available from: <URL>.
  • 15. Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res [Internet]. 2020 Mar 4;30(3):269–71. Available from: <URL>.
  • 16. Wang J. Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study. J Chem Inf Model [Internet]. 2020 Jun 22;60(6):3277–86. Available from: <URL>.
  • 17. Tallei TE, Tumilaar SG, Niode NJ, Fatimawali, Kepel BJ, Idroes R, et al. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Riganti C, editor. Scientifica (Cairo) [Internet]. 2020 Dec 23;2020:6307457. Available from: <URL>.
  • 18. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, et al. First Case of 2019 Novel Coronavirus in the United States. N Engl J Med [Internet]. 2020 Mar 5;382(10):929–36. Available from: <URL>.
  • 19. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell [Internet]. 2020 Apr 16;181(2):271–80. Available from: <URL>.
  • 20. Devaux CA, Rolain J-M, Colson P, Raoult D. New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19? Int J Antimicrob Agents [Internet]. 2020 May 1;55(5):105938. Available from: <URL>.
  • 21. Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, et al. In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis [Internet]. 2020 Jul 28;71(15):732–9. Available from: <URL>.
  • 22. Gong H-H, Addla D, Lv J-S, Zhou C-H. Heterocyclic Naphthalimides as New Skeleton Structure of Compounds with Increasingly Expanding Relational Medicinal Applications. Curr Top Med Chem [Internet]. 2016 Sep 26;16(28):3303–64. Available from: <URL>.
  • 23. den Boon JA, Diaz A, Ahlquist P. Cytoplasmic Viral Replication Complexes. Cell Host Microbe [Internet]. 2010 Jul 22;8(1):77–85. Available from: <URL>.
  • 24. Hackbart M, Deng X, Baker SC. Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors. Proc Natl Acad Sci [Internet]. 2020 Apr 7;117(14):8094–103. Available from: <URL>.
  • 25. Kareem AM, Al-Azzawi SN. Comparison Between Deterministic and Stochastic Model for Interaction (COVID-19) With Host Cells in Humans. Baghdad Sci J [Internet]. 2022 Oct 23;19(5):1140–7. Available from: <URL>.
  • 26. Ibrahim AA. A Theoretical Study of the Docking of Medicines with some Proteins. Baghdad Sci J [Internet]. 2023 Apr 1;20(2):483–91. Available from: <URL>.
  • 27. https://www.rcsb.org/
Year 2024, , 261 - 268, 04.02.2024
https://doi.org/10.18596/jotcsa.1281563

Abstract

References

  • 1. World Health Organization (WHO). Coronavirus Disease (COVID-19) Situation Reports [Internet]. 2020. Available from: <URL>.
  • 2. Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet [Internet]. 2020 Feb 15;395(10223):470–3. Available from: <URL>.
  • 3. Xu X, Chen P, Wang J, Feng J, Zhou H, Li X, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci [Internet]. 2020 Mar 21;63(3):457–60. Available from: <URL>.
  • 4. Mali SN, Pratap AP, Thorat BR. The Rise of New Coronavirus Infection-(COVID-19): A Recent Update. Eurasian J Med Oncol [Internet]. 2020;4(1):35–41. Available from: <URL>.
  • 5. Hagar M, Chaieb K, Parveen S, Ahmed HA, Alnoman RB. N-alkyl 2-pyridone versus O-alkyl 2-pyridol: Ultrasonic synthesis, DFT, docking studies and their antimicrobial evaluation. J Mol Struct [Internet]. 2020 Jan 5;1199:126926. Available from: <URL>.
  • 6. Alnoman RB, Parveen S, Hagar M, Ahmed HA, Knight JG. A new chiral boron-dipyrromethene (BODIPY)-based fluorescent probe: molecular docking, DFT, antibacterial and antioxidant approaches. J Biomol Struct Dyn [Internet]. 2020 Dec 11;38(18):5429–42. Available from: <URL>.
  • 7. Liu C, Ma Y, Zhao J, Nussinov R, Zhang Y-C, Cheng F, et al. Computational network biology: Data, models, and applications. Phys Rep [Internet]. 2020 Mar 3;846:1–66. Available from: <URL>.
  • 8. Ibrahim AA, Yahya OM, Ibrahim MA. Theoretical Prediction of Possible Drug Treatment of COVID-19 using Coumarins Containing Chloroquine Moeity. Asian J Chem [Internet]. 2020 Dec 7;32(12):3120–6. Available from: <URL>.
  • 9. Jiang F, Deng L, Zhang L, Cai Y, Cheung CW, Xia Z. Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19). J Gen Intern Med [Internet]. 2020 May 4;35(5):1545–9. Available from: <URL>.
  • 10. Zhang L, Liu Y. Potential interventions for novel coronavirus in China: A systematic review. J Med Virol [Internet]. 2020 May 3;92(5):479–90. Available from: <URL>.
  • 11. Khaerunnisa S, Kurniawan H, Awaluddin R, Suhartati S, Soetjipto S. Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study. Preprints [Internet]. 2020 Mar 13;1–14. Available from: <URL>.
  • 12. Khan SA, Zia K, Ashraf S, Uddin R, Ul-Haq Z. Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. J Biomol Struct Dyn [Internet]. 2021 May 3;39(7):2607–16. Available from: <URL>.
  • 13. Wahedi HM, Ahmad S, Abbasi SW. Stilbene-based natural compounds as promising drug candidates against COVID-19. J Biomol Struct Dyn [Internet]. 2020 May 12;39(9):3225–34. Available from: <URL>.
  • 14. Jorgensen WL. The Many Roles of Computation in Drug Discovery. Science (80- ) [Internet]. 2004 Mar 19;303(5665):1813–8. Available from: <URL>.
  • 15. Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res [Internet]. 2020 Mar 4;30(3):269–71. Available from: <URL>.
  • 16. Wang J. Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study. J Chem Inf Model [Internet]. 2020 Jun 22;60(6):3277–86. Available from: <URL>.
  • 17. Tallei TE, Tumilaar SG, Niode NJ, Fatimawali, Kepel BJ, Idroes R, et al. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. Riganti C, editor. Scientifica (Cairo) [Internet]. 2020 Dec 23;2020:6307457. Available from: <URL>.
  • 18. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, et al. First Case of 2019 Novel Coronavirus in the United States. N Engl J Med [Internet]. 2020 Mar 5;382(10):929–36. Available from: <URL>.
  • 19. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell [Internet]. 2020 Apr 16;181(2):271–80. Available from: <URL>.
  • 20. Devaux CA, Rolain J-M, Colson P, Raoult D. New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19? Int J Antimicrob Agents [Internet]. 2020 May 1;55(5):105938. Available from: <URL>.
  • 21. Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, et al. In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis [Internet]. 2020 Jul 28;71(15):732–9. Available from: <URL>.
  • 22. Gong H-H, Addla D, Lv J-S, Zhou C-H. Heterocyclic Naphthalimides as New Skeleton Structure of Compounds with Increasingly Expanding Relational Medicinal Applications. Curr Top Med Chem [Internet]. 2016 Sep 26;16(28):3303–64. Available from: <URL>.
  • 23. den Boon JA, Diaz A, Ahlquist P. Cytoplasmic Viral Replication Complexes. Cell Host Microbe [Internet]. 2010 Jul 22;8(1):77–85. Available from: <URL>.
  • 24. Hackbart M, Deng X, Baker SC. Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors. Proc Natl Acad Sci [Internet]. 2020 Apr 7;117(14):8094–103. Available from: <URL>.
  • 25. Kareem AM, Al-Azzawi SN. Comparison Between Deterministic and Stochastic Model for Interaction (COVID-19) With Host Cells in Humans. Baghdad Sci J [Internet]. 2022 Oct 23;19(5):1140–7. Available from: <URL>.
  • 26. Ibrahim AA. A Theoretical Study of the Docking of Medicines with some Proteins. Baghdad Sci J [Internet]. 2023 Apr 1;20(2):483–91. Available from: <URL>.
  • 27. https://www.rcsb.org/
There are 27 citations in total.

Details

Primary Language English
Subjects Physical Chemistry
Journal Section RESEARCH ARTICLES
Authors

Ammar Ibrahim 0000-0002-7085-4074

Entesar Sullıman This is me

Maher A Ibrahım This is me

Publication Date February 4, 2024
Submission Date April 12, 2023
Acceptance Date October 31, 2023
Published in Issue Year 2024

Cite

Vancouver Ibrahim A, Sullıman E, Ibrahım MA. Molecular Docking Interaction of Medicines Binding to COVID-19 Proteins. JOTCSA. 2024;11(1):261-8.