Computational Studies of Drugs Used in Covid-19

Abstract

In this article, the computational studies in the literature of the drugs used in the treatment of Covid-19 disease, which has affected the world, are brought together. Combination studies of Favipiravir (F), Hydroxychloroquine (H) and Oseltamivir (O) molecules for Covid-19 were examined. The combinations created are F + H, F + O, H + O and F + H + O. Between the combination of the two inhibitors, it was found that the F + H combination showed good binding affinity. Similarly, a further significant increase in F + H + O, binding affinity with the protein of interest was observed for the three combination drugs. As a result, studies have been obtained confirming the results of the molecular docking, the stronger binding affinity of the combination drug

Keywords

• Covid-19
• favipiravir
• chloroquine
• hydroxychloroquine
• oseltamivir

Covid-19’da Kullanılan İlaçların Hesapsal Çalışmaları

Abstract

Bu yazıda dünyayı etkisi altına alan Covid-19 hastalığının tedavisinde kullanılan ilaçların literatürde olan hesapsal çalışmaları bir araya getirilmiştir. Covid-19 için Favipiravir (F), Hidroksiklorokin (H) ve Oseltamivir (O) moleküllerin kombinasyon çalışmaları incelenmiştir. Oluşturulan kombinasyonlar F + H, F + O, H + O ve F + H + O şeklindedir. İki inhibitörün kombinasyonu arasında, F + H kombinasyonun iyi bağlanma afinitesi gösterdiğine ulaşılmıştır. Benzer şekilde, üç kombinasyon ilaç için F+H+O, ilgili protein ile bağlanma afinitesinde daha fazla önemli artış gözlenmiştir. Sonuç olarak, moleküler yerleştirmenin sonuçları, kombinasyon ilacının daha güçlü bağlanma afinitesini doğrulayan çalışmalar elde edilmiştir.

Keywords

• Covid-19
• favipiravir
• klorokin
• hidroksiklorokin
• osteltamivir

References

1. Baron S., Fons M., & Albrecht T. (1996). Viral Pathogenesis. Medical Microbiology, 4th edition.
2. Ben-Zvi I., Kivity S., Langevitz P., & Shoenfeld Y. (2012). Hydroxychloroquine: From Malaria to Autoimmunity. Clinical Reviews in Allergy & Immunology, 42(2), 145-153.
3. Burley S. K., Berman H. M., … & Zardecki C. (2019). RCSB Protein Data Bank: Biological Macromolecular Structures Enabling Research and Education in Fundamental Biology, Biomedicine, Biotechnology and Energy. Nucleic Acids Research, 47(D1), D464–D474.
4. Cai Q., Yang M., Li, D., Chen J., Shu D., Xia J., ... & Liu L. (2020). Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study. Engineering, 6(10), 1192-1198.
5. Cao Y. C., Deng Q. X., & Dai S. X. (2020). Remdesivir for Severe Acute Respiratory Syndrome Coronavirus 2 Causing COVID-19: An Evaluation of the Evidence. Travel Medicine And Infectious Disease, 35, 101647.
6. Chan J. F. W., Yao Y., Yeung M. L., Deng W., Bao L., Jia L., ... & Yuen K. Y. (2015). Treatment with Lopinavir/Ritonavir or Interferon-β1b Improves Outcome of MERS-CoV Infection in a Nonhuman Primate Model of Common Marmoset. The Journal of Infectious Diseases, 212(12), 1904-1913.
7. Chowdhury P., Pathak P. (2020). Neuroprotective Immunity by Essential Nutrient “Choline” for the Prevention of SARS CoV2 Infections: An In Silico Study by Molecular Dynamics Approach. Chemical Physics Letters, 761, 138057.
8. Chowdhury P. (2020a). In silico Investigation of Phytoconstituents from Indian Medicinal Herb ‘Tinospora cordifolia (giloy)’ Against SARS-CoV-2 (COVID-19) by Molecular Dynamics Approach. Journal of Biomolecular Structure and Dynamics, 1-18.

9. Chowdhury, P. (2020b). Repurposing the Combination Drug of Favipiravir, Hydroxychloroquine and Oseltamivir as a Potential Inhibitor against SARS-CoV-2: A Computational Study. ArXiv Preprint arXiv, 2012.00652.
10. Costanzo M., Giglio M. A. R. D., Roviello G. N. (2020). SARS-CoV-2: Recent Reports on Antiviral Therapies Based on Lopinavir/Ritonavir, Darunavir/Umifenovir, Hydroxychloroquine, Remdesivir, Favipiravir and other Drugs for the Treatment of the New Coronavirus. Current Medicinal Chemistry, 27, 4536-4541.
11. Deng X., John S. E. St., Osswald H. L., …& Bake S. C.(2014). Coronaviruses Resistant to a 3C-Like Protease Inhibitor are Attenuated for Replication and Pathogenesis, Revealing a Low Genetic Barrier but High Fitness Cost of Resistance. Journal of Virology, 88, 11886 –11898.
12. Doi K., Ikeda M., Hayase N., Moriya K., Morimura N. (2020). Nafamostat Mesylate Treatment in Combination with Favipiravir for Patients Critically ill with Covid-19: A Case Series. Critical Care, 24(1), 1-4.
13. Dyall J., Coleman C. M., Hart B. J., ... & Johansen L. M. (2014). Repurposing of Clinically Developed Drugs for Treatment of Middle East Respiratory Syndrome Coronavirus Infection. Antimicrobial Agents and Chemotherapy, 58(8), 4885-4893.
14. Fried M. W., Shiffman M. L., Reddy K. R., ... & Craxi A. (2002). Peginterferon Alfa-2a Plus Ribavirin for Chronic Hepatitis C Virus Infection. New England Journal of Medicine, 347(13), 975-982.
15. Furuta Y., Takahashi K., Fukuda Y., …& Shiraki K. (2002). In-Vitro and In-Vivo Activities of Anti-influenza Virus Compound T-705. Antimicrob. Agents Chemother, 46, 977–981.
16. Gupta M. K., Vemula S., Donde R., Gouda G., Behera L., Vadde R. (2020). In-silico Approaches to Detect Inhibitors of the Human Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Ion Channel. Journal of Biomolecular Structure and Dynamics, 1-11.
17. Hendaus M. A. (2020). Remdesivir in the Treatment of Coronavirus Disease 2019 (COVID-19): A Simplified Summary. Journal of Biomolecular Structure and Dynamics, 1-6.
18. Hurt A. C., Ernest J., Deng Y. M., Lannello P., Besselaar T. G., Birch C., ... & Barr I. G. (2009). Emergence and Spread of Oseltamivir-resistant A (H1N1) Influenza Viruses in Oceania, South East Asia and South Africa. Antiviral research, 83(1), 90-93.
19. Jiang F., Deng L., Zhang L., Cai Y., Cheung C. W., Xia Z. (2020). Review of the Clinical Characteristics of Coronavirus Disease 2019 (COVID-19). Journal of General Internal Medicine, 35(5), 1545–1549.
20. Kapoor G., Saigal S., Elongavan A. (2017). Action and Resistance Mechanisms of Antibiotics: A Guide for Clinicians. J Anaesthesiol Clin. Pharmacol, 33(3), 300-305.
21. Khan R. J., Jha R. K., Amera G. M.,…& Singh A. K. (2020). Targeting SARS-CoV-2; A Systematic Drug Repurposing Approach to Identify Promising Inhibitors Against 3C-like Proteinase and 2’-o-ribose methyltransferase. Journal of Biomoleular Structure and Dynamics, 1–14.
22. Muralidharan N., Sakthivel R., Velmurugan D., Gromiha M. M. (2020). Computational Studies of Drug Repurposing and Synergism of Lopinavir, Oseltamivir and Ritonavir Binding with SARS-CoV-2 Protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1-6.
23. Mayo S. L., Olafson B. D., Goddard W. A. (1990). DREIDING: A Generic Force Field For Molecular Simulations. Journal of Physical chemistry, 94(26), 8897-8909.
24. Panyod S., Ho C. T., Sheen L. Y. (2020). Dietary Therapy and Herbal Medicine for COVID-19 Prevention: A Review and Perspective. Journal of traditional and complementary medicine, 10,(4), 420–427.
25. Ter Meulen J., Van Den Brink E. N., Cox F., ... & Goudsmit J. (2006). Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants. PLoS Med, 3(7), e237.
26. Velavan T. P., Meyer C. G. (2020). The COVID‐19 Epidemic. Tropical Medicine & International Health, 25(3), 278. Woo P. C., Lau S. K., Chu C. M., Chan K. H., Tsoi H. W., Huang Y., ... & Yuen K. Y. (2005). Characterization and Complete Genome Sequence of A Novel Coronavirus, Coronavirus HKU1, from Patients with Pneumonia. Journal of Virology, 79(2), 884-895.
27. Wu F., Zhao S., Yu B., Chen Y. M., Wang W., Song Z. G., ... & Zhang Y. Z. (2020). A New Coronavirus Associated with Human Respiratory Disease in China. Nature, 579(7798), 265-269.
28. Yin W., Mao C., Luan X., Shen D. D., Shen Q., Su H., ... & Xu H. E. (2020). Structural Basis for Inhibition of the RNA-dependent RNA Polymerase from SARS-CoV-2 by Remdesivir. Science, 368(6498), 1499-1504.