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

Year 2021, Volume: 5 Issue: 1, 11 - 25, 30.06.2021

Burçin Türkmenoğlu Yahya Güzel

https://doi.org/10.32571/ijct.797275

Cited By: 1

Abstract

For the 2-hydroxydiarylamide derivative series that inhibits serine proteases by mediating various events related to the basic processes of tumor invasion and metastasis in cancer, the pharmacophore responsible for the activity was estimated by the Molecular Conformer Electron Topological (MCET) method. The atoms in the common core structure of the molecules and template are aligned so that the remaining oriented atoms superimposition with the maximum number. In the 4D-Quantitative Structure Activity Relationship analysis, it is selected and used to represent the molecule that can interact best by the receptor among all conformers. Despite the unknown structure of the receptor, arranging molecules on the 3D coordinate system ensures that the ligand-receptor interaction is in the same direction and in the same manner. Pha, which is a subset, was estimated by accepting / rejection step by applying Genetic Algorithm steps to the clusters formed by the atomic clusters in the 3D coordinate system. The model proposed in the training set was verified in the external test set and the electronic identifying values of the Pha atoms in both sets were considered. The model was developed by splitting the molecules into training and external test sets according to similarities of both activities and descriptors. With Leave One Out-Cross Validation the model proposed according to 33 molecules in the training set (q2 = 0.998) was validated by using 8 molecules (r2 = 0.993) in the external test set. As a result of the MCET method, the proposed pharmacophore structure was confirmed using molecular docking.

Keywords

2-hydroxydiarylamide derivatives, Molecular docking, 4D-QSAR, MCET, Klopman index

Project Number

FDK-2016-6547

References

• Referans1 World Health Organization. WHO "Cancer" February 2006 Retrieved on 2009-02-12.
• Referans2 Kang, S.; Min, H. J.; Kang, M. S.; Jung, M. G.; Kim, S. Bioorg. Med. Chem. Lett. 2013, 23, 1748-1751.
• Referans3 Min, H. J.; Lee, M. K.; Lee, J. W.; Kim, S. Biochem. Biophys. Res. Commun. 2014, 446, 1-7.
• Referans4 Hooper, J. D.; Clements, J. A.; Quigley, J. P.; Antalis, T. M. J. Biol. Chem. 2001, 276, 857-860.
• Referans5 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.
• Referans6 Szabo, R.; Wu, Q. Y.; Dickson, R. B.; Netzel-Arnett, S.; Antalis, T. M.; Bugge, T. H. Thromb. Haemost. 2003, 90, 185-193.
• Referans7 Szabo, R.; Bugge, T. H. Int. J. Biochem. Cell Biol. 2008, 40, 1297-1316.
• Referans8 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.
• Referans9 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.
• Referans10 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.
• Referans11 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.
• Referans12 Lionta, E.; Spyrou, G.; Vassilatis, D. K.; Cournia, Z. Curr. Top. Med. Chem. 2014, 14, 1923-1938.
• Referans13 Andrade, C. H.; Pasqualoto, K. F. M.; Ferreira, E. I.; Hopfinger, A. J. Molecules 2010, 15, 3281-3294.
• Referans14 Kizilcan, D. S.; Turkmenoglu, B.; Guzel, Y. Struct Chem 2020, 31, 1339–1351.
• Referans15 Alp Tokat, T., Türkmenoğlu, B., Kızılcan, D. Ş., Güzel, Y. J. Mol. Model. 2019, 25, 1-13.
• Referans16 Turkmenoglu, B.; Guzel, Y. Comput. Biol. Chem. 2018, 76, 327-337.
• Referans17 Guzel, Y.; Aslan, E.; Turkmenoglu, B.; Su, E. M. Curr. Comput-Aid. Drug. 2018, 14, 207-220.
• Referans18 Yilmaz, H.; Boz, M.; Turkmenoglu, B.; Guzel, Y. Trop. J. Pharm. Res. 2014, 13, 117-126.
• Referans19 Yilmaz, H.; Guzel, Y.; Onal, Z.; Altiparmak, G.; Kocakaya, S. O. Bull. Korean Chem. Soc. 2011, 32, 4352-4360.
• Referans20 Türkmenoğlu, B., Yılmaz, H., Su, E.M., Alp Tokat, T. Güzel, Y. Int.J. Chem. Technol. 2017, 1, 14-23.
• Referans21 Su, E. M., Turkmenoglu,B., Guzel, Y. Int. J. Innov. Stud. Sci. Eng. Technol. 2016, 02, 67-75.
• Referans22 Turkmenoglu, B.; Guzel, Y.; Su, E.M; Kizilcan, D. S. Mater. Today Commun. 2020, 25, 101583
• Referans23 Klopman, G. J. Am. Chem. Soc. 1968, 90, 223-243.
• Referans24 Salem, L. J. Am. Chem. Soc. 1968, 90, 543-552.
• Referans25 Salem, L. J. Am. Chem. Soc 1968, 90, 553-566.
• Referans26 Fujimoto, H., Fukui, K. In Chemical Reactivity and Reaction Paths, John Wiley&Sons: New York, 1974.
• Referans27 Jain, A. N. J. Comput. Aid. Mol. Des. 2007, 21, 281-306.
• Referans28 Spitzer, G. M.; Wellenzohn, B.; Laggner, C.; Langer, T.; Liedl, K. R. J. Chem. Inf. 2007, 47, 1580-1589.
• Referans29 Holt, P. A.; Chaires, J. B.; Trent, J. O. J. Chem. Inf. Model. 2008, 48, 1602-1615.