VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH

İsmail Çelik; Meryem Erol; Ebru Uzunhisarcıklı; Ufuk İnce

doi:10.33483/jfpau.1073079

Araştırma Makalesi

ÇOKLU HESAPLAMALI YAKLAŞIMLA ÜÇ SARS-COV-2 İLAÇ HEDEFLERİ ÜZERİNDE SANAL TARAMA VE MOLEKÜLER DOKİNG ANALİZİ

Yıl 2022, Cilt: 46 Sayı: 2, 376 - 392, 29.05.2022

İsmail Çelik Meryem Erol Ebru Uzunhisarcıklı Ufuk İnce

https://doi.org/10.33483/jfpau.1073079

Cited By: 1

Öz

Amaç: SARS-CoV-2, üst solunum yolu enfeksiyonu ile karakterize pandemik bir virüstür ve hafif semptomlardan ciddi komplikasyonlara kadar gidebilmektedir. Bu durumda, ilaç yeniden kullanım ve bilgisayar destekli çalışmalar, acil çözümler bulmak için çok önemli hale geldi. Bu çalışmada, 8820 ilaç adayının SARS-CoV-2'nin yapısal olmayan üç protein yapısı DrugBank veri tabanından elde edilen ilaç adayları veya ilaç molekülleri ile olan ilaç-hedef etkileşimleri analiz edilmiştir.

Gereç ve Yöntem: DrugBank veri tabanından elde edilen 8820 ilaç molekülü veya ilaç adayının kapsamlı sanal tarama ve moleküler doking çalışmaları, SARS-CoV-2'nin RNA bağlayıcı proteini, 2'-O-metiltransferaz ve endoribonükleaz üzerinde gerçekleştirildi; ve her hedef için potansiyel ilaç adayları belirlendi. Yüksek Verimli Sanal Tarama (HTVS), Standard Precision (SP), Extra Precision (XP) ve Moleküler Mekanik Genelleştirilmiş Doğan Yüzey Alanı (MM-GBSA) ile sanal tarama çalışmaları yapılmıştır. Ayrıca SARS-CoV-2'nin klinik bulguları, bulaşması, patogenezi ve tedavisi hakkında bilgiler de verilmiştir.

Sonuç ve Tartışma: Her ilaç hedefi için potansiyel bileşik önerileri sunuldu. İlaç hedef proteinlerinin aktif bölgelerinin ligandlarla etkileşime girdiği kilit amino asitler hakkında bilgi verildi. Bu çalışmanın SARS-CoV-2 proteinleri üzerinde hedef bazlı ilaç geliştirme çalışmalarında faydalı olması beklenmektedir.

Anahtar Kelimeler

SARS-CoV-2, moleküler doking, sanal tarama, DrugBank

Kaynakça

1. Romano, M., Ruggiero, A., Squeglia, F., Maga, G..Berisio, R. (2020). A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells, 9(5), 1-22. [CrossRef]
2. Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W..Lu, R. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine. 382(8), 727-733.[CrossRef]
3. Cucinotta, D..Vanelli, M. (2020). WHO declares COVID-19 a pandemic. Acta bio-medica: Atenei Parmensis, 91(1), 157-160. [CrossRef]
4. Organization, W. H. (2020). Coronavirus disease 2019 (COVID-19): situation report, 82.
5. Nunes-Vaz, R. (2020). Visualising the doubling time of COVID-19 allows comparison of the success of containment measures. Global Biosecurity, 1(3). [CrossRef]
6. Woo, P. C., Lau, S. K., Lam, C. S., Lau, C. C., Tsang, A. K., Lau, J. H., Bai, R., Teng, J. L., Tsang, C. C..Wang, M. (2012). Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. Journal of Virology, 86(7), 3995-4008. [CrossRef]
7. Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H..Pei, Y.-Y. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265-269. [CrossRef]
8. Cheng, V. C., Lau, S. K., Woo, P. C..Yuen, K. Y. (2007). Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clinical Microbiology Reviews, 20(4), 660-694. [CrossRef]
9. Berry, M., Gamieldien, J..Fielding, B. C. (2015). Identification of new respiratory viruses in the new millennium. Viruses, 7(3), 996-1019. [CrossRef]
10. Liu, Y., Gayle, A. A., Wilder-Smith, A..Rocklöv, J. (2020). The reproductive number of COVID-19 is higher compared to SARS coronavirus. Journal of Travel Medicine, 27(2), 1-4. [CrossRef]
11. Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B..Huang, C.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270-273. [CrossRef]
12. Liu, T., Hu, J., Xiao, J., He, G., Kang, M., Rong, Z., Lin, L., Zhong, H., Huang, Q..Deng, A. (2020). Time-varying transmission dynamics of Novel Coronavirus Pneumonia in China. BioRxiv, 27(2), 1-4. [CrossRef]
13. Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W..Lu, R. (2020). China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727-733. [CrossRef]
14. Liu, Y., Yan, L.-M., Wan, L., Xiang, T.-X., Le, A., Liu, J.-M., Peiris, M., Poon, L. L..Zhang, W. (2020). Viral dynamics in mild and severe cases of COVID-19. The Lancet Infectious Diseases, 20(6), 656-657. [CrossRef]
15. Sah, R., Rodriguez-Morales, A. J., Jha, R., Chu, D. K., Gu, H., Peiris, M., Bastola, A., Lal, B. K., Ojha, H. C..Rabaan, A. A. (2020). Complete genome sequence of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Nepal. Microbiology Resource Announcements, 9(11). [CrossRef]
16. Cui, J., Li, F..Shi, Z.-L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology, 17(3), 181-192. [CrossRef]
17. Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., Meng, J., Zhu, Z., Zhang, Z..Wang, J. (2020). Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host & Microbe, 27(3), 325-328. [CrossRef]
18. Khan, S., Siddique, R., Shereen, M. A., Ali, A., Liu, J., Bai, Q., Bashir, N..Xue, M. (2020). Erratum: emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2. Journal of Clinical Microbiology, 58: 5, e00187-20. [CrossRef]
19. Shereen, M. A., Khan, S., Kazmi, A., Bashir, N..Siddique, R. (2020). COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. Journal of Advanced Research, 24, 91-98. [CrossRef]
20. Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W..Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China Life Sciences, 63(3), 457-460. [CrossRef] 21. Li, B., Si, H.-R., Zhu, Y., Yang, X.-L., Anderson, D. E., Shi, Z.-L., Wang, L.-F..Zhou, P. (2020). Discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing. Msphere, 5(1). [CrossRef]
22. Wan, Y., Shang, J., Graham, R., Baric, R. S..Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of Virology, 94(7). [CrossRef]
23. Jockusch, S., Tao, C., Li, X., Anderson, T. K., Chien, M., Kumar, S., Russo, J. J., Kirchdoerfer, R. N..Ju, J. (2020). A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19. Antiviral Research, 180, 104857. [CrossRef]
24. Mirza, M. U..Froeyen, M. (2020). Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of Pharmaceutical Analysis, 10(4), 320-328. [CrossRef]
25. Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W..Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269-271. [CrossRef]
26. Warren, T. K., Jordan, R., Lo, M. K., Ray, A. S., Mackman, R. L., Soloveva, V., Siegel, D., Perron, M., Bannister, R..Hui, H. C. (2016). Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature, 531(7594), 381-385. [CrossRef]
27. Sheahan, T. P., Sims, A. C., Graham, R. L., Menachery, V. D., Gralinski, L. E., Case, J. B., Leist, S. R., Pyrc, K., Feng, J. Y..Trantcheva, I. (2017). Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science Translational Medicine, 9(396), 1-20. [CrossRef]
28. Hillaker, E., Belfer, J. J., Bondici, A., Murad, H..Dumkow, L. E. (2020). Delayed initiation of remdesivir in a COVID‐19‐positive patient. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy, 40(6), 592-598. [CrossRef]
29. Gordon, C. J., Tchesnokov, E. P., Feng, J. Y., Porter, D. P..Götte, M. (2020). The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. Journal of Biological Chemistry, 295(15), 4773-4779. [CrossRef]
30. Furuta, Y., Komeno, T..Nakamura, T. (2017). Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proceedings of the Japan Academy, Series B, 93(7), 449-463. [CrossRef] 31. Hayden, F. G..Shindo, N. (2019). Influenza virus polymerase inhibitors in clinical development. Current Opinion in Infectious Diseases, 32(2), 176-186. [CrossRef]
32. Nagata, T., Lefor, A. K., Hasegawa, M..Ishii, M. (2015). Favipiravir: a new medication for the Ebola virus disease pandemic. Disaster Medicine and Public Health Preparedness, 9(1), 79-81. [CrossRef]
33. Dong, L., Hu, S..Gao, J. (2020). Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discoveries & Therapeutics, 14(1), 58-60. [CrossRef]
34. Syed, Y. Y. (2022). Molnupiravir: First Approval. Drugs, 82, 455–460. [CrossRef]
35. Singh, A.K., Singh, A., Singh, R., Misra, A. (2021). Molnupiravir in COVID-19: a systematic review of literature. Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 15(6), 102329. [CrossRef]
36. Parks, J. M..Smith, J. C. (2020). How to discover antiviral drugs quickly. New England Journal of Medicine, 382(23), 2261-2264. [CrossRef]
37. Egloff, M.-P., Ferron, F., Campanacci, V., Longhi, S., Rancurel, C., Dutartre, H., Snijder, E. J., Gorbalenya, A. E., Cambillau, C..Canard, B. (2004). The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proceedings of the National Academy of Sciences, 101(11), 3792-3796. [CrossRef]
38. Zeng, Z., Deng, F., Shi, K., Ye, G., Wang, G., Fang, L., Xiao, S., Fu, Z..Peng, G. (2018). Dimerization of coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity. Journal of Virology, 92(17), 1-15. [CrossRef]
39. Hu, T., Chen, C., Li, H., Dou, Y., Zhou, M., Lu, D., Zong, Q., Li, Y., Yang, C..Zhong, Z. (2017). Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9. Protein Science, 26(5), 1037-1048. [CrossRef]
40. DiNicolantonio, J. J..McCarty, M. (2020). Thrombotic complications of COVID-19 may reflect an upregulation of endothelial tissue factor expression that is contingent on activation of endosomal NADPH oxidase. Open Heart, 7(1), e001337. [CrossRef]
41. Grainger, R. G. (1971). Future Prospects in Diagnostic Radiology: Radiological Contrast Media: The Present and the Future. Proceedings of the Royal Society of Medicine, 64(3), 243-249. [CrossRef]
42. Von Ketteler, A., Herten, D. P..Petrich, W. (2012). Fluorescence Properties of Carba Nicotinamide Adenine Dinucleotide for Glucose Sensing. ChemPhysChem, 13(5), 1302-1306. [CrossRef]
43. Djabri, A., van’t Hoff, W., Brock, P., Wong, I. C., Guy, R. H..Delgado-Charro, M. B. (2015). Iontophoretic transdermal sampling of iohexol as a non-invasive tool to assess glomerular filtration rate. Pharmaceutical Research, 32(2), 590-603. [CrossRef]
44. Krafcikova, P., Silhan, J., Nencka, R..Boura, E. (2020). Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nature Communications, 11(1), 1-7. [CrossRef]
45. Chen, Y., Su, C., Ke, M., Jin, X., Xu, L., Zhang, Z., Wu, A., Sun, Y., Yang, Z..Tien, P. (2011). Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog, 7(10), e1002294. [CrossRef]
46. Ke, M., Chen, Y., Wu, A., Sun, Y., Su, C., Wu, H., Jin, X., Tao, J., Wang, Y..Ma, X. (2012). Short peptides derived from the interaction domain of SARS coronavirus nonstructural protein nsp10 can suppress the 2′-O-methyltransferase activity of nsp10/nsp16 complex. Virus Research, 167(2), 322-328. [CrossRef]
47. Rose, N. D..Regan, J. M. (2015). Changes in phosphorylation of adenosine phosphate and redox state of nicotinamide-adenine dinucleotide (phosphate) in Geobacter sulfurreducens in response to electron acceptor and anode potential variation. Bioelectrochemistry, 106, 213-220. [CrossRef]
48. Zhang, L., Li, L., Yan, L., Ming, Z., Jia, Z., Lou, Z..Rao, Z. (2018). Structural and biochemical characterization of endoribonuclease Nsp15 encoded by Middle East respiratory syndrome coronavirus. Journal of Virology, 92(22), 1-16. [CrossRef]
49. Deng, X., Hackbart, M., Mettelman, R. C., O’Brien, A., Mielech, A. M., Yi, G., Kao, C. C..Baker, S. C. (2017). Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages. Proceedings of the National Academy of Sciences, 114(21), E4251-E4260. [CrossRef]

VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH

Yıl 2022, Cilt: 46 Sayı: 2, 376 - 392, 29.05.2022

İsmail Çelik Meryem Erol Ebru Uzunhisarcıklı Ufuk İnce

https://doi.org/10.33483/jfpau.1073079

Cited By: 1

Öz

Objective: SARS-CoV-2 is a pandemic virus characterized by upper respiratory tract infection and can range from mild symptoms to severe complications. In this case, drug repurposing and computer-aided studies have become very important to find emergency solutions. In this study, drug-target interactions on three nonstructural protein structures of SARS-CoV-2 of 8820 drug candidates or drug molecules obtained from the DrugBank database were analyzed.

Material and Method: Comprehensive virtual screening and molecular docking studies from 8820 drug molecules or candidates obtained from the DrugBank database were performed on the RNA binding protein, 2'-O-methyltransferase, and endoribonuclease of SARS-CoV-2; and potential drug candidates were determined for each target. Virtual screening studies have been done with High-Throughput Virtual Screening (HTVS), Standard Precision (SP), Extra Precision (XP), and Molecular Mechanics Generalized Born Surface Area (MM-GBSA). Also, information about the clinical findings, transmission, pathogenesis, and treatment of SARS-CoV-2 has been given.

Result and Discussion: Drug-target interactions on three nonstructural protein structures of SARS-CoV-2 of 8820 drug candidates or drug molecules obtained from the DrugBank database were analyzed. Potential compound recommendations for each drug target were presented. Information was given about key amino acids where active sites of drug target proteins interact with ligands. This study is expected to be useful in target-based drug development studies on the proteins of SARS-CoV-2.

Anahtar Kelimeler

SARS-CoV-2, molecular docking, virtual screening, DrugBank

Kaynakça

1. Romano, M., Ruggiero, A., Squeglia, F., Maga, G..Berisio, R. (2020). A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells, 9(5), 1-22. [CrossRef]
2. Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W..Lu, R. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine. 382(8), 727-733.[CrossRef]
3. Cucinotta, D..Vanelli, M. (2020). WHO declares COVID-19 a pandemic. Acta bio-medica: Atenei Parmensis, 91(1), 157-160. [CrossRef]
4. Organization, W. H. (2020). Coronavirus disease 2019 (COVID-19): situation report, 82.
5. Nunes-Vaz, R. (2020). Visualising the doubling time of COVID-19 allows comparison of the success of containment measures. Global Biosecurity, 1(3). [CrossRef]
6. Woo, P. C., Lau, S. K., Lam, C. S., Lau, C. C., Tsang, A. K., Lau, J. H., Bai, R., Teng, J. L., Tsang, C. C..Wang, M. (2012). Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. Journal of Virology, 86(7), 3995-4008. [CrossRef]
7. Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H..Pei, Y.-Y. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265-269. [CrossRef]
8. Cheng, V. C., Lau, S. K., Woo, P. C..Yuen, K. Y. (2007). Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clinical Microbiology Reviews, 20(4), 660-694. [CrossRef]
9. Berry, M., Gamieldien, J..Fielding, B. C. (2015). Identification of new respiratory viruses in the new millennium. Viruses, 7(3), 996-1019. [CrossRef]
10. Liu, Y., Gayle, A. A., Wilder-Smith, A..Rocklöv, J. (2020). The reproductive number of COVID-19 is higher compared to SARS coronavirus. Journal of Travel Medicine, 27(2), 1-4. [CrossRef]
11. Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B..Huang, C.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270-273. [CrossRef]
12. Liu, T., Hu, J., Xiao, J., He, G., Kang, M., Rong, Z., Lin, L., Zhong, H., Huang, Q..Deng, A. (2020). Time-varying transmission dynamics of Novel Coronavirus Pneumonia in China. BioRxiv, 27(2), 1-4. [CrossRef]
13. Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W..Lu, R. (2020). China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727-733. [CrossRef]
14. Liu, Y., Yan, L.-M., Wan, L., Xiang, T.-X., Le, A., Liu, J.-M., Peiris, M., Poon, L. L..Zhang, W. (2020). Viral dynamics in mild and severe cases of COVID-19. The Lancet Infectious Diseases, 20(6), 656-657. [CrossRef]
15. Sah, R., Rodriguez-Morales, A. J., Jha, R., Chu, D. K., Gu, H., Peiris, M., Bastola, A., Lal, B. K., Ojha, H. C..Rabaan, A. A. (2020). Complete genome sequence of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in Nepal. Microbiology Resource Announcements, 9(11). [CrossRef]
16. Cui, J., Li, F..Shi, Z.-L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology, 17(3), 181-192. [CrossRef]
17. Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., Meng, J., Zhu, Z., Zhang, Z..Wang, J. (2020). Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host & Microbe, 27(3), 325-328. [CrossRef]
18. Khan, S., Siddique, R., Shereen, M. A., Ali, A., Liu, J., Bai, Q., Bashir, N..Xue, M. (2020). Erratum: emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2. Journal of Clinical Microbiology, 58: 5, e00187-20. [CrossRef]
19. Shereen, M. A., Khan, S., Kazmi, A., Bashir, N..Siddique, R. (2020). COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. Journal of Advanced Research, 24, 91-98. [CrossRef]
20. Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W..Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China Life Sciences, 63(3), 457-460. [CrossRef] 21. Li, B., Si, H.-R., Zhu, Y., Yang, X.-L., Anderson, D. E., Shi, Z.-L., Wang, L.-F..Zhou, P. (2020). Discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing. Msphere, 5(1). [CrossRef]
22. Wan, Y., Shang, J., Graham, R., Baric, R. S..Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of Virology, 94(7). [CrossRef]
23. Jockusch, S., Tao, C., Li, X., Anderson, T. K., Chien, M., Kumar, S., Russo, J. J., Kirchdoerfer, R. N..Ju, J. (2020). A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19. Antiviral Research, 180, 104857. [CrossRef]
24. Mirza, M. U..Froeyen, M. (2020). Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of Pharmaceutical Analysis, 10(4), 320-328. [CrossRef]
25. Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W..Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269-271. [CrossRef]
26. Warren, T. K., Jordan, R., Lo, M. K., Ray, A. S., Mackman, R. L., Soloveva, V., Siegel, D., Perron, M., Bannister, R..Hui, H. C. (2016). Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys. Nature, 531(7594), 381-385. [CrossRef]
27. Sheahan, T. P., Sims, A. C., Graham, R. L., Menachery, V. D., Gralinski, L. E., Case, J. B., Leist, S. R., Pyrc, K., Feng, J. Y..Trantcheva, I. (2017). Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science Translational Medicine, 9(396), 1-20. [CrossRef]
28. Hillaker, E., Belfer, J. J., Bondici, A., Murad, H..Dumkow, L. E. (2020). Delayed initiation of remdesivir in a COVID‐19‐positive patient. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy, 40(6), 592-598. [CrossRef]
29. Gordon, C. J., Tchesnokov, E. P., Feng, J. Y., Porter, D. P..Götte, M. (2020). The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. Journal of Biological Chemistry, 295(15), 4773-4779. [CrossRef]
30. Furuta, Y., Komeno, T..Nakamura, T. (2017). Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase. Proceedings of the Japan Academy, Series B, 93(7), 449-463. [CrossRef] 31. Hayden, F. G..Shindo, N. (2019). Influenza virus polymerase inhibitors in clinical development. Current Opinion in Infectious Diseases, 32(2), 176-186. [CrossRef]
32. Nagata, T., Lefor, A. K., Hasegawa, M..Ishii, M. (2015). Favipiravir: a new medication for the Ebola virus disease pandemic. Disaster Medicine and Public Health Preparedness, 9(1), 79-81. [CrossRef]
33. Dong, L., Hu, S..Gao, J. (2020). Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discoveries & Therapeutics, 14(1), 58-60. [CrossRef]
34. Syed, Y. Y. (2022). Molnupiravir: First Approval. Drugs, 82, 455–460. [CrossRef]
35. Singh, A.K., Singh, A., Singh, R., Misra, A. (2021). Molnupiravir in COVID-19: a systematic review of literature. Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 15(6), 102329. [CrossRef]
36. Parks, J. M..Smith, J. C. (2020). How to discover antiviral drugs quickly. New England Journal of Medicine, 382(23), 2261-2264. [CrossRef]
37. Egloff, M.-P., Ferron, F., Campanacci, V., Longhi, S., Rancurel, C., Dutartre, H., Snijder, E. J., Gorbalenya, A. E., Cambillau, C..Canard, B. (2004). The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proceedings of the National Academy of Sciences, 101(11), 3792-3796. [CrossRef]
38. Zeng, Z., Deng, F., Shi, K., Ye, G., Wang, G., Fang, L., Xiao, S., Fu, Z..Peng, G. (2018). Dimerization of coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity. Journal of Virology, 92(17), 1-15. [CrossRef]
39. Hu, T., Chen, C., Li, H., Dou, Y., Zhou, M., Lu, D., Zong, Q., Li, Y., Yang, C..Zhong, Z. (2017). Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9. Protein Science, 26(5), 1037-1048. [CrossRef]
40. DiNicolantonio, J. J..McCarty, M. (2020). Thrombotic complications of COVID-19 may reflect an upregulation of endothelial tissue factor expression that is contingent on activation of endosomal NADPH oxidase. Open Heart, 7(1), e001337. [CrossRef]
41. Grainger, R. G. (1971). Future Prospects in Diagnostic Radiology: Radiological Contrast Media: The Present and the Future. Proceedings of the Royal Society of Medicine, 64(3), 243-249. [CrossRef]
42. Von Ketteler, A., Herten, D. P..Petrich, W. (2012). Fluorescence Properties of Carba Nicotinamide Adenine Dinucleotide for Glucose Sensing. ChemPhysChem, 13(5), 1302-1306. [CrossRef]
43. Djabri, A., van’t Hoff, W., Brock, P., Wong, I. C., Guy, R. H..Delgado-Charro, M. B. (2015). Iontophoretic transdermal sampling of iohexol as a non-invasive tool to assess glomerular filtration rate. Pharmaceutical Research, 32(2), 590-603. [CrossRef]
44. Krafcikova, P., Silhan, J., Nencka, R..Boura, E. (2020). Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nature Communications, 11(1), 1-7. [CrossRef]
45. Chen, Y., Su, C., Ke, M., Jin, X., Xu, L., Zhang, Z., Wu, A., Sun, Y., Yang, Z..Tien, P. (2011). Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog, 7(10), e1002294. [CrossRef]
46. Ke, M., Chen, Y., Wu, A., Sun, Y., Su, C., Wu, H., Jin, X., Tao, J., Wang, Y..Ma, X. (2012). Short peptides derived from the interaction domain of SARS coronavirus nonstructural protein nsp10 can suppress the 2′-O-methyltransferase activity of nsp10/nsp16 complex. Virus Research, 167(2), 322-328. [CrossRef]
47. Rose, N. D..Regan, J. M. (2015). Changes in phosphorylation of adenosine phosphate and redox state of nicotinamide-adenine dinucleotide (phosphate) in Geobacter sulfurreducens in response to electron acceptor and anode potential variation. Bioelectrochemistry, 106, 213-220. [CrossRef]
48. Zhang, L., Li, L., Yan, L., Ming, Z., Jia, Z., Lou, Z..Rao, Z. (2018). Structural and biochemical characterization of endoribonuclease Nsp15 encoded by Middle East respiratory syndrome coronavirus. Journal of Virology, 92(22), 1-16. [CrossRef]
49. Deng, X., Hackbart, M., Mettelman, R. C., O’Brien, A., Mielech, A. M., Yi, G., Kao, C. C..Baker, S. C. (2017). Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages. Proceedings of the National Academy of Sciences, 114(21), E4251-E4260. [CrossRef]

Toplam 47 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	İngilizce
Konular	Eczacılık ve İlaç Bilimleri
Bölüm	Araştırma Makalesi
Yazarlar	İsmail Çelik 0000-0002-8146-1663 Meryem Erol 0000-0001-5676-098X Ebru Uzunhisarcıklı 0000-0002-7088-7490 Ufuk İnce 0000-0002-7316-4802
Yayımlanma Tarihi	29 Mayıs 2022
Gönderilme Tarihi	14 Şubat 2022
Kabul Tarihi	19 Nisan 2022
Yayımlandığı Sayı	Yıl 2022 Cilt: 46 Sayı: 2

Kaynak Göster

APA	Çelik, İ., Erol, M., Uzunhisarcıklı, E., İnce, U. (2022). VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH. Journal of Faculty of Pharmacy of Ankara University, 46(2), 376-392. https://doi.org/10.33483/jfpau.1073079
AMA	Çelik İ, Erol M, Uzunhisarcıklı E, İnce U. VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH. Ankara Ecz. Fak. Derg. Mayıs 2022;46(2):376-392. doi:10.33483/jfpau.1073079
Chicago	Çelik, İsmail, Meryem Erol, Ebru Uzunhisarcıklı, ve Ufuk İnce. “VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH”. Journal of Faculty of Pharmacy of Ankara University 46, sy. 2 (Mayıs 2022): 376-92. https://doi.org/10.33483/jfpau.1073079.
EndNote	Çelik İ, Erol M, Uzunhisarcıklı E, İnce U (01 Mayıs 2022) VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH. Journal of Faculty of Pharmacy of Ankara University 46 2 376–392.
IEEE	İ. Çelik, M. Erol, E. Uzunhisarcıklı, ve U. İnce, “VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH”, Ankara Ecz. Fak. Derg., c. 46, sy. 2, ss. 376–392, 2022, doi: 10.33483/jfpau.1073079.
ISNAD	Çelik, İsmail vd. “VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH”. Journal of Faculty of Pharmacy of Ankara University 46/2 (Mayıs 2022), 376-392. https://doi.org/10.33483/jfpau.1073079.
JAMA	Çelik İ, Erol M, Uzunhisarcıklı E, İnce U. VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH. Ankara Ecz. Fak. Derg. 2022;46:376–392.
MLA	Çelik, İsmail vd. “VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH”. Journal of Faculty of Pharmacy of Ankara University, c. 46, sy. 2, 2022, ss. 376-92, doi:10.33483/jfpau.1073079.
Vancouver	Çelik İ, Erol M, Uzunhisarcıklı E, İnce U. VIRTUAL SCREENING AND MOLECULAR DOCKING ANALYSIS ON THREE SARS-COV-2 DRUG TARGETS BY MULTIPLE COMPUTATIONAL APPROACH. Ankara Ecz. Fak. Derg. 2022;46(2):376-92.

Cited By

IN SILICO EVALUATION OF SARS-COV-2 PAPAIN-LIKE PROTEASE INHIBITORY ACTIVITY OF SOME FDA-APPROVED DRUGS

Ankara Universitesi Eczacilik Fakultesi Dergisi

https://doi.org/10.33483/jfpau.1311496

Kapak Resmi İndir

Makale Dosyaları

Tam Metin

Kapsam ve Amaç

Ankara Üniversitesi Eczacılık Fakültesi Dergisi, açık erişim, hakemli bir dergi olup Türkçe veya İngilizce olarak farmasötik bilimler alanındaki önemli gelişmeleri içeren orijinal araştırmalar, derlemeler ve kısa bildiriler için uluslararası bir yayım ortamıdır. Bilimsel toplantılarda sunulan bildiriler supleman özel sayısı olarak dergide yayımlanabilir. Ayrıca, tüm farmasötik alandaki gelecek ve önceki ulusal ve uluslararası bilimsel toplantılar ile sosyal aktiviteleri içerir.