Computational Studies of Drugs Used in Covid-19

Yıl 2021, Cilt: 8 Sayı: 1, 93 - 107, 30.06.2021

Fatma Aloğlu , Zeynep Şilan Turhan

https://doi.org/10.48138/cjo.944469

Öz

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

Anahtar Kelimeler

Covid-19, favipiravir, chloroquine, hydroxychloroquine, oseltamivir

Covid-19’da Kullanılan İlaçların Hesapsal Çalışmaları

Öz

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.

Anahtar Kelimeler

Covid-19, favipiravir, klorokin, hidroksiklorokin, osteltamivir

Kaynakça

• Baron S., Fons M., & Albrecht T. (1996). Viral Pathogenesis. Medical Microbiology, 4th edition.
• Ben-Zvi I., Kivity S., Langevitz P., & Shoenfeld Y. (2012). Hydroxychloroquine: From Malaria to Autoimmunity. Clinical Reviews in Allergy & Immunology, 42(2), 145-153.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.