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Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması

Year 2021, Volume: 33 Issue: 4, 660 - 669, 30.12.2021
https://doi.org/10.7240/jeps.945430

Abstract

SARS-CoV-2’nin neden olduğu COVID-19 hastalığının bulaşma hızının ve ağır hastalık oluşturma potansiyelinin yüksek olması dolasıyla Dünya Sağlık Örgütü tarafından global bir pandemi olarak tanımlanmıştır. Günümüzde COVID-19 pandemisini önlemek amacıyla birçok ilaç çalışmaları yapılmakta olup ancak henüz tedavisine yönelik etkili ve güvenli bir ilaç mevcut değildir. Bu araştırmaların hızlı ve az maliyet ile klinik aşamalara geçmesi için SARS-CoV-2'in replikasyon ve transkripsiyon mekanizmasında etkili olan proteinlere karşı birçok bileşik bilgisayar destekli ilaç tasarımı yöntemleri ile taranmaktadır. Bu sayede, etkinliği deneysel çalışmalarla test edilmiş bileşiklerin SARS-CoV-2’e ait önemli yapısal proteinlerine yönelik etkinlikleri moleküler seviyede aydınlatılmaktadır. Bu çalışmada daha önce deneysel çalışmalar ile etkinliği belirlenmiş 32 adet kalkon türevli bileşiklerin moleküler kenetlenme yöntemi ile SARS-CoV-2 Main protease (Mpro) enzimine yönelik in siliko biyolojik etkinliği ve moleküler mekanizması incelenmiştir. Bu çalışma sonuçlarına göre, bileşik 5, 6, 14, 25 ve 32 hedef proteine ait referans bileşik (N3)’e göre SARS-CoV-2 Mpro'ya karşı daha iyi bağlanma afinitesi göstermişlerdir. Elde edilen bu veriler sonucunda, COVID-19 hastalığının tedavisine yönelik biyolojik etkinliği yüksek kimyasal bileşikler belirlenmiştir. Bu bilgiler, COVID-19 tedavisi için daha etkili antiviral ilaçların geliştirilmesi için yapılacak klinik çalışmalara rehberlik edecektir

References

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Year 2021, Volume: 33 Issue: 4, 660 - 669, 30.12.2021
https://doi.org/10.7240/jeps.945430

Abstract

References

  • [1] Grifoni, A., Weiskopf, D. . (2020). Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell, 181(7), 1489-1501.e15.
  • [2] Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565-574
  • [3] Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., Meng, J., Zhu, Z., Zhang, Z., Wang, J., Sheng, J., Quan, L., Xia, Z., Tan, W., Cheng, G., & Jiang, T. (2020). Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host & Microbe, 27(3), 325-328.
  • [4] Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of M pro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289-293
  • [5] Amin, M., & Abbas, G. (2020). Docking study of chloroquine and hydroxychloroquine interaction with RNA binding domain of nucleocapsid phospho-protein – an in silico insight into the comparative efficacy of repurposing antiviral drugs. Journal of Biomolecular Structure and Dynamics, 1-13.
  • [6] Banerjee, R., Perera, L., & Tillekeratne, L. M. V. (2021). Potential SARS-CoV-2 main protease inhibitors. Drug Discovery Today, 26(3), 804-816.
  • [7] Cui, W., Yang, K., & Yang, H. (2020). Recent Progress in the Drug Development Targeting SARS-CoV-Main Protease as Treatment for COVID-19. Frontiers in Molecular Biosciences, 7.
  • [8] Kumar, D., Kumari, K., Vishvakarma, V. K., Jayaraj, A., Kumar, D., Ramappa, V. K., Patel, R., Kumar, V., Dass, S. K., Chandra, R., & Singh, P. (2020). Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 1-15.
  • [9] Li, Z., Li, X., Huang, Y.-Y., Wu, Y., Liu, R., Zhou, L., Lin, Y., Wu, D., Zhang, L., Liu, H., Xu, X., Yu, K., Zhang, Y., Cui, J., Zhan, C.-G., Wang, X., & Luo, H.-B. (2020). Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs. Proceedings of the National Academy of Sciences, 117(44), 27381-27387.
  • [10] Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409-412.
  • [11] Elkhalifa, D., Al-Hashimi, I., Al Moustafa, A.-E., & Khalil, A. (2021). A comprehensive review on the antiviral activities of chalcones. Journal of Drug Targeting, 29(4), 403-419
  • [12] Jo, S., Kim, S., Shin, D. H., & Kim, M.-S. (2020). Inhibition of SARS-CoV 3CL protease by flavonoids. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 145-151.
  • [13] Solnier, J., & Fladerer, J.-P. (2020). Flavonoids: A complementary approach to conventional therapy of COVID-19? Phytochemistry Reviews, 1-23.
  • [14] Tatar, G., Salmanli, M., Dogru, Y., & Tuzuner, T. (2021). Evaluation of the effects of chlorhexidine and several flavonoids as antiviral purposes on SARS-CoV-2 main protease: Molecular docking, molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 1-10.
  • [15] Marquina, S., Maldonado-Santiago, M., Sánchez-Carranza, J. N., Antúnez-Mojica, M., González-Maya, L., Razo-Hernández, R. S., & Alvarez, L. (2019). Design, synthesis and QSAR study of 2′-hydroxy-4′-alkoxy chalcone derivatives that exert cytotoxic activity by the mitochondrial apoptotic pathway. Bioorganic & Medicinal Chemistry, 27(1), 43-54
  • [16] Bukhari, S. N. A., Butt, A. M., Amjad, M. W. B., Ahmad, W., Shah, V. H., & Trivedi, A. R. (2013). Synthesis and evaluation of chalcone analogues based pyrimidines as angiotensin converting enzyme inhibitors. Pakistan Journal of Biological Sciences: PJBS, 16(21), 1368-1372.
  • [17] Israf, D. A., Khaizurin, T. A., Syahida, A., Lajis, N. H., & Khozirah, S. (2007). Cardamonin inhibits COX and iNOS expression via inhibition of p65NF-kappaB nuclear translocation and Ikappa-B phosphorylation in RAW 264.7 macrophage cells. Molecular Immunology, 44(5), 673-679.
  • [18] Yamamoto, T., Yoshımura, M., Yamaguchı, F., Kouchı, T., Tsujı, R., Saıto, M., Obata, A., & Kıkuchı, M. (2004). Anti-allergic Activity of Naringenin Chalcone from a Tomato Skin Extract. Bioscience, Biotechnology, and Biochemistry, 68(8), 1706-1711.
  • [19] Aoki, N., Muko, M., Ohta, E., & Ohta, S. (2008). C-Geranylated Chalcones from the Stems of Angelica keiskei with Superoxide-Scavenging Activity. Journal of Natural Products, 71(7), 1308-1310.
  • [20] Abdullah, M. I., Mahmood, A., Madni, M., Masood, S., & Kashif, M. (2014). Synthesis, characterization, theoretical, anti-bacterial and molecular docking studies of quinoline based chalcones as a DNA gyrase inhibitor. Bioorganic Chemistry, 54, 31-37.
  • [21] Kurşun-Aktar, B. S., Oruç-Emre, E. E., Karaküçük-İyi̇doğan, A., Yağlioğlu, A. Ş., Demi̇rtaş, İ., & Teki̇n, Ş. (2017). Synthesis and structure-activity relationship study: Anticancer chalcones derived from 4′-morpholinoacetophenone. Marmara Pharmaceutical Journal, 21(4), 949-960
  • [22] Kurşun Aktar, B. S., Oruç-Emre, E. E., Demirtaş, I., Yaglioglu, A. S., Guler, C., Adem, S., & Karaküçük Iyidoğan, A. (2017). Synthesis of novel fluorinated chalcones derived from 4′-morpholinoacetophenone and their antiproliferative effects. Journal of Molecular Structure, 1149, 632-639.
  • [23] Ambinter, Search and Inquire chemicals online www.ambinter.com
  • [24] Khalil, O. M. (2011). Synthesis of some chalcones and pyrazolines carrying morpholinophenyl moiety as potential anti-inflammatory agents. Archiv Der Pharmazie, 344(4), 242-247.
  • [25] Aktar, B. S. K., Oruç-Emre, E. E., Demi̇rtaş, İ., Yağlioğlu, A. Ş., İyi̇doğan, A. K., Güler, Ç., & Adem, Ş. (2018). Synthesis and biological evaluation of novel chalcones bearing morpholine moiety as antiproliferative agents. Turkısh Journal Of Chemıstry, 42(2), 482-492.
  • [26] Marshall, G. R. (1987). Computer-Aided Drug Design. Annual Review of Pharmacology and Toxicology, 27(1), 193-213.
  • [27] Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., … Baker, N. A. (2018). Improvements to the APBS biomolecular solvation software suite. Protein Science: A Publication of the Protein Society, 27(1), 112-128
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  • [29] Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785-2791.
  • [30] Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717.
  • [31] Ullrich, S., & Nitsche, C. (2020). The SARS-CoV-2 main protease as drug target. Bioorganic & Medicinal Chemistry Letters, 30(17), 127377.
There are 31 citations in total.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Research Articles
Authors

Gizem Tatar 0000-0001-6642-6870

Bedriye Seda Kurşun Aktar 0000-0002-1492-3266

Publication Date December 30, 2021
Published in Issue Year 2021 Volume: 33 Issue: 4

Cite

APA Tatar, G., & Kurşun Aktar, B. S. (2021). Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması. International Journal of Advances in Engineering and Pure Sciences, 33(4), 660-669. https://doi.org/10.7240/jeps.945430
AMA Tatar G, Kurşun Aktar BS. Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması. JEPS. December 2021;33(4):660-669. doi:10.7240/jeps.945430
Chicago Tatar, Gizem, and Bedriye Seda Kurşun Aktar. “Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi Ile Aydınlatılması”. International Journal of Advances in Engineering and Pure Sciences 33, no. 4 (December 2021): 660-69. https://doi.org/10.7240/jeps.945430.
EndNote Tatar G, Kurşun Aktar BS (December 1, 2021) Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması. International Journal of Advances in Engineering and Pure Sciences 33 4 660–669.
IEEE G. Tatar and B. S. Kurşun Aktar, “Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması”, JEPS, vol. 33, no. 4, pp. 660–669, 2021, doi: 10.7240/jeps.945430.
ISNAD Tatar, Gizem - Kurşun Aktar, Bedriye Seda. “Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi Ile Aydınlatılması”. International Journal of Advances in Engineering and Pure Sciences 33/4 (December 2021), 660-669. https://doi.org/10.7240/jeps.945430.
JAMA Tatar G, Kurşun Aktar BS. Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması. JEPS. 2021;33:660–669.
MLA Tatar, Gizem and Bedriye Seda Kurşun Aktar. “Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi Ile Aydınlatılması”. International Journal of Advances in Engineering and Pure Sciences, vol. 33, no. 4, 2021, pp. 660-9, doi:10.7240/jeps.945430.
Vancouver Tatar G, Kurşun Aktar BS. Kalkon Türevli Bileşiklerin Covid-19 Tedavisine Yönelik SARS-CoV-2 Main Protease Enzimine Karşı Bağlanma Mekanizmasının Moleküler Kenetlenme Yöntemi ile Aydınlatılması. JEPS. 2021;33(4):660-9.