Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives

Güzel, Yahya; TÜRKMENOĞLU, BURÇİN

doi:10.32571/ijct.797275

Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives

Burçin TÜRKMENOĞLU, (Erzincan Binali Yıldırım Üniversitesi, Eczacılık Fakültesi, Farmasötik Temel Bilimler Anabilim Dalı, Erzincan, Türkiye)

Yahya GÜZEL (Erciyes Üniversitesi, Fen Fakültesi, Kimya Bölümü, Kayseri, Türkiye)

International Journal of Chemistry and Technology (IJCT)

4 3

Yıl: 2021 Cilt: 5 Sayı: 1 Sayfa Aralığı: 11 - 25 Metin Dili: İngilizce DOI: 10.32571/ijct.797275 İndeks Tarihi: 29-07-2022

Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives

Öz:

For the 2-hydroxydiarylamide derivative series that inhibitsserine proteases by mediating various events related to the basicprocesses of tumor invasion and metastasis in cancer, thepharmacophore (Pha) responsible for the activity was estimatedby the Molecular Conformer Electron Topological (MCET)method. The atoms in the common core structure of themolecules and template are aligned so that the remainingoriented atoms superimposition with the maximum number.Pha; in the 4D-QSAR analysis, it is selected and used torepresent the molecule that can interact best by the receptoramong all conformers. The model proposed in the training setwas verified in the external test set and the electronicidentifying values of the Pha atoms in both sets wereconsidered. With Leave One Out-Cross Validation (LOO-CV)the model proposed according to 33 molecules in the trainingset (q2 = 0.998) was validated by using 8 molecules (r2 = 0.993)in the external test set. As a result of the MCET method, theproposed pharmacophore structure was confirmed usingmolecular docking

Anahtar Kelime: Molecular docking Klopman index 2-hydroxydiarylamide derivatives MCET 4D-QSAR

2-hidroksidiarilamid türevleri için 4DQSAR'da MCET yöntemi kullanılarak belirlenen farmakoforun moleküler docking ile doğrulanması

Öz:

Pb (Kanserde tümör istilası ve metastazının temel süreçleri ile ilgili çeşitli olaylara aracılık ederek serin proteazları inhibe eden 2-hidroksidiarilamid türevi serisi için, aktiviteden sorumlu farmakofor (Pha), Moleküler Konformer Elektron Topolojik (MCET) yöntemi ile tahmin edilmiştir. Moleküllerin ve şablonun ortak çekirdek yapısındaki atomlar ile diğer yönlendirilmiş atomlar maksimum sayı olacak şekilde üst üste hizalanır. 4D-QSAR analizinde, Pha grubu tüm konformerler arasında reseptör tarafından en iyi etkileşime girebilen molekülü temsil etmek için seçilir ve kullanılır. Eğitim setinde önerilen model harici test setinde doğrulanmış ve her iki setteki Pha atomlarının elektronik tanımlayıcı değerleri dikkate alınmıştır. Bir veri dışarıda bırakılarak çapraz doğrulama (LOO-CV) ile eğitim setindeki 33 moleküle göre önerilen model (q2 = 0.998) harici test setinde 8 molekül (r2 = 0.993) kullanılarak doğrulanmıştır. MCET yönteminin bir sonucu olarak, önerilen farmakofor yapısı moleküler docking kullanılarak doğrulanmıştır.

Anahtar Kelime:

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

1. World Health Organization. WHO "Cancer" February 2006 Retrieved on 2009-02-12
2. Kang, S.; Min, H. J.; Kang, M. S.; Jung, M. G.; Kim, S. Bioorg. Med. Chem. Lett. 2013, 23, 1748-1751.
3. Min, H. J.; Lee, M. K.; Lee, J. W.; Kim, S. Biochem. Biophys. Res. Commun. 2014, 446, 1-7.
4. Hooper, J. D.; Clements, J. A.; Quigley, J. P.; Antalis, T. M. J. Biol. Chem. 2001, 276, 857-860.
5. Netzel-Arnett, S.; Hooper, J. D.; Szabo, R.; Madison, E. L.; Quigley, J. P.; Bugge, T. H.; Antalis, A. M. Cancer Metastasis Rev. 2003, 22, 237-258.
6. Szabo, R.; Wu, Q. Y.; Dickson, R. B.; Netzel-Arnett, S.; Antalis, T. M.; Bugge, T. H. Thromb. Haemost. 2003, 90, 185-193.
7. Szabo, R.; Bugge, T. H. Int. J. Biochem. Cell Biol. 2008, 40, 1297-1316.
8. Kim, S.; Kang, H. Y.; Nam, E. H.; Choi, M. S.; Zhao, X. F.; Hong, C. S.; Lee, J. W.; Lee, J. H.; Park, Y. K. Carcinogenesis 2010, 31, 597-606.
9. Larzabal, L.; Nguewa, P. A.; Pio, R.; Blanco, D.; Sanchez, B.; Rodriguez, M. J.; Pajares, M. J.; Catena, R.; Montuenga, L. M.; Calvo, A. Br. J. Cancer. 2011, 105, 1608-1614.
10. Jung, H.; Lee, K. P.; Park, S. J.; Park, J. H.; Jang, Y. S.; Choi, S. Y.; Jung, J. G.; Jo, K.; Park, D. Y.; Yoon, J. H.; Park, J. H.; Lim, D. S.; Hong, G. R.; Choi, C.; Park, Y. K.; Lee, J. W.; Hong, H. J.; Kim, S.; Park, Y. W. Oncogene. 2008, 27, 2635-2647.
11. Ou-Yang, S. S.; Lu, J. Y.; Kong, X. Q.; Liang, Z. J.; Luo, C.; Jiang, H. L. Acta Pharmacol. Sin. 2012, 33, 1131-1140.
12. Lionta, E.; Spyrou, G.; Vassilatis, D. K.; Cournia, Z. Curr. Top. Med. Chem. 2014, 14, 1923-1938.
13. Andrade, C. H.; Pasqualoto, K. F. M.; Ferreira, E. I.; Hopfinger, A. J. Molecules 2010, 15, 3281-3294.
14. Kizilcan, D. S.; Turkmenoglu, B.; Guzel, Y. Struct Chem 2020, 31, 1339–1351
15. Alp Tokat, T., Türkmenoğlu, B., Kızılcan, D. Ş., Güzel, Y. J. Mol. Model. 2019, 25, 1-13.
16. Turkmenoglu, B.; Guzel, Y. Comput. Biol. Chem. 2018, 76, 327-337.
17. Guzel, Y.; Aslan, E.; Turkmenoglu, B.; Su, E. M. Curr. Comput-Aid. Drug. 2018, 14, 207-220.
18. Yilmaz, H.; Boz, M.; Turkmenoglu, B.; Guzel, Y. Trop. J. Pharm. Res. 2014, 13, 117-126.
19. Yilmaz, H.; Guzel, Y.; Onal, Z.; Altiparmak, G.; Kocakaya, S. O. Bull. Korean Chem. Soc. 2011, 32, 4352-4360.
20. Türkmenoğlu, B., Yılmaz, H., Su, E.M., Alp Tokat, T. Güzel, Y. Int.J. Chem. Technol. 2017, 1, 14-23.
21. Su, E. M., Turkmenoglu, B., Guzel, Y. Int. J. Innov. Stud. Sci. Eng. Technol. 2016, 02, 67-75.
22. Turkmenoglu, B.; Guzel, Y.; Su, E.M; Kizilcan, D. S. Mater. Today Commun. 2020, 25, 101583
23. Klopman, G. J. Am. Chem. Soc. 1968, 90, 223-243.
24. Salem, L. J. Am. Chem. Soc. 1968, 90, 543-552.
25. Salem, L. J. Am. Chem. Soc 1968, 90, 553-566.
26. Fujimoto, H., Fukui, K. In Chemical Reactivity and Reaction Paths, John Wiley&Sons: New York, 1974.
27. Jain, A. N. J. Comput. Aid. Mol. Des. 2007, 21, 281- 306.
28. Spitzer, G. M.; Wellenzohn, B.; Laggner, C.; Langer, T.; Liedl, K. R. J. Chem. Inf. 2007, 47, 1580-1589.
29. Holt, P. A.; Chaires, J. B.; Trent, J. O. J. Chem. Inf. Model. 2008, 48, 1602-16158. Ghorbani, M.; Seyedin, O.; Aghamohammadhassan, M. J. Environ. Manage. 2020, 254, 109814-109919.

APA	TÜRKMENOĞLU B, Güzel Y (2021). Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. , 11 - 25. 10.32571/ijct.797275
Chicago	TÜRKMENOĞLU BURÇİN,Güzel Yahya Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. (2021): 11 - 25. 10.32571/ijct.797275
MLA	TÜRKMENOĞLU BURÇİN,Güzel Yahya Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. , 2021, ss.11 - 25. 10.32571/ijct.797275
AMA	TÜRKMENOĞLU B,Güzel Y Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. . 2021; 11 - 25. 10.32571/ijct.797275
Vancouver	TÜRKMENOĞLU B,Güzel Y Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. . 2021; 11 - 25. 10.32571/ijct.797275
IEEE	TÜRKMENOĞLU B,Güzel Y "Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives." , ss.11 - 25, 2021. 10.32571/ijct.797275
ISNAD	TÜRKMENOĞLU, BURÇİN - Güzel, Yahya. "Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives". (2021), 11-25. https://doi.org/10.32571/ijct.797275

APA	TÜRKMENOĞLU B, Güzel Y (2021). Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. International Journal of Chemistry and Technology (IJCT), 5(1), 11 - 25. 10.32571/ijct.797275
Chicago	TÜRKMENOĞLU BURÇİN,Güzel Yahya Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. International Journal of Chemistry and Technology (IJCT) 5, no.1 (2021): 11 - 25. 10.32571/ijct.797275
MLA	TÜRKMENOĞLU BURÇİN,Güzel Yahya Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. International Journal of Chemistry and Technology (IJCT), vol.5, no.1, 2021, ss.11 - 25. 10.32571/ijct.797275
AMA	TÜRKMENOĞLU B,Güzel Y Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. International Journal of Chemistry and Technology (IJCT). 2021; 5(1): 11 - 25. 10.32571/ijct.797275
Vancouver	TÜRKMENOĞLU B,Güzel Y Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives. International Journal of Chemistry and Technology (IJCT). 2021; 5(1): 11 - 25. 10.32571/ijct.797275
IEEE	TÜRKMENOĞLU B,Güzel Y "Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives." International Journal of Chemistry and Technology (IJCT), 5, ss.11 - 25, 2021. 10.32571/ijct.797275
ISNAD	TÜRKMENOĞLU, BURÇİN - Güzel, Yahya. "Confirmation by molecular docking of the pharmacophore defined as 4D-QSAR using the MCET method for the 2-hydroxydiarylamide derivatives". International Journal of Chemistry and Technology (IJCT) 5/1 (2021), 11-25. https://doi.org/10.32571/ijct.797275