1,4-Bis(2-Kloro-4-Nitrofenil)Piperazin Molekülünün Yapısının Aydınlatılması ve DNA ile Moleküler Kenetlenme Analizi

Öz

Piperazin türevi moleküller önemli antikanser aktivitelere sahiptir. Bu çalışmada 1,4-Bis(2-kloro-4-nitrofenil)piperazinin (C16H14Cl2N4O4) yapısını aydınlatmak için Spartan06 programı kullanılarak konformasyon analizi yapılmıştır. Konformasyon analizi sonucunda belirlenen konformasyonlar arasından en düşük enerjiye sahip moleküler yapı belirlenmiştir. DNA antikanser moleküller için önemli bir hedeftir. Bu nedenle 1,4-Bis(2-kloro-4-nitrofenil)piperazinin DNA (PDB ID: 1BNA) ile etkileşimi kenetlenme simülasyonları ile incelenmiştir. Molekülün elde edilen en düşük enerjili konformeri, hedef DNA ile kenetlenme simülasyonları için ligandın başlangıç geometrisi olarak alınmıştır. Sonuç olarak, DNA ile molekülün bağlanma afinitesi ve bağlanma modu değerlendirilmiştir. 1,4-Bis(2-kloro-4-nitrofenil)piperazin, DNA ile iki farklı bölgede -7.5 ve -7.4 kcal/mol bağlanma afinitelerine sahiptir. Moleküler kenetlenme çalışmalarına göre 1,4-Bis(2-kloro-4-nitrofenil)piperazinin güçlü anti-tümör etkilere sahip olduğu tahmin edilmektedir.

Anahtar Kelimeler

• Piperazin
• Antikanser
• DNA
• Konformasyon Analizi
• Moleküler Kenetlenme

Clarification Of The Structure Of 1,4-Bis(2-Chloro-4-Nitrophenyl)Piperazine Molecule And Its Molecular Docking Analysis With DNA

Abstract

Piperazine-derived molecules have important anticancer activities. In this study, conformational analysis was performed using the Spartan06 program to elucidate the structure of 1,4-Bis(2-chloro-4-nitrophenyl)piperazine (C16H14Cl2N4O4). Among the conformations determined as a result of the conformation analysis, the molecular structure with the lowest energy was determined. DNA is an important target for anticancer molecules. For this reason, the interaction of 1,4-Bis(2-chloro-4-nitrophenyl)piperazine with DNA (PDB ID: 1BNA) was investigated through docking simulations. The obtained lowest energy conformer of the title molecule was taken as the starting geometry of the ligand for docking simulations with target DNA. As a result, the binding affinity and the binding mode of the title molecule with DNA were evaluated. 1,4-Bis(2-chloro-4-nitrophenyl)piperazine has -7.5 and -7.4 kcal/mol binding affinities to DNA, in two different sites. Depending on the molecular docking studies, the 1,4-Bis(2-chloro-4-nitrophenyl)piperazine was predicted to possess strong anti-tumor effects.

Keywords

• Piperazine
• Anticancer
• DNA
• Molecular Docking
• Conformational analysis

References

1. Potten, C. S., Owen, G., & Booth, D. (2002). Intestinal stem cells protect their genome by selective segregation of template DNA strands. Journal of cell science, 115(11), 2381-2388.
2. Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a cancer journal for clinicians, 71(3), 209-249.
3. El-Deeb, I. M., & Lee, S. H. (2010). Design and synthesis of new potent anticancer pyrazoles with high FLT3 kinase inhibitory selectivity. Bioorganic & medicinal chemistry, 18(11), 3961-3973.
4. Vardanyan, R., & Hruby, V. (2016). Synthesis of best-seller drugs. Academic press.
5. Kaushik, N. K., Kaushik, N., Attri, P., Kumar, N., Kim, C. H., Verma, A. K., & Choi, E. H. (2013). Biomedical importance of indoles. Molecules, 18(6), 6620-6662.
6. Yarim, M., Koksal, M., Durmaz, I., & Atalay, R. (2012). Cancer cell cytotoxicities of 1-(4-substitutedbenzoyl)-4-(4-chlorobenzhydryl) piperazine derivatives. International journal of molecular sciences, 13(7), 8071-8085.
7. Çalışkan, B., Yılmaz, A., Evren, İ., Menevşe, S., Uludag, O., & Banoglu, E. (2013). Synthesis and evaluation of analgesic, anti-inflammatory, and anticancer activities of new pyrazole-3 (5)-carboxylic acid derivatives. Medicinal Chemistry Research, 22(2), 782-793.
8. Xia, Y., Dong, Z. W., Zhao, B. X., Ge, X., Meng, N., Shin, D. S., & Miao, J. Y. (2007). Synthesis and structure–activity relationships of novel 1-arylmethyl-3-aryl-1H-pyrazole-5-carbohydrazide derivatives as potential agents against A549 lung cancer cells. Bioorganic & medicinal chemistry, 15(22), 6893-6899.

9. Xia, Y., Fan, C. D., Zhao, B. X., Zhao, J., Shin, D. S., & Miao, J. Y. (2008). Synthesis and structure–activity relationships of novel 1-arylmethyl-3-aryl-1H-pyrazole-5-carbohydrazide hydrazone derivatives as potential agents against A549 lung cancer cells. European journal of medicinal chemistry, 43(11), 2347-2353.
10. Pirol, Ş. C. (2013). Diarilpirazol Türevi Bileşiklerin Sentezi Ve Antikanser Etkilerinin Araştırılması Üzerinde Çalışmalar. Gazi Üniversitesi (Doktora Tezi), 1-114.
11. Li, X., Lu, X., Xing, M., Yang, X. H., Zhao, T. T., Gong, H. B., & Zhu, H. L. (2012). Synthesis, biological evaluation, and molecular docking studies of N, 1, 3-triphenyl-1H-pyrazole-4-carboxamide derivatives as anticancer agents. Bioorganic & medicinal chemistry letters, 22(11), 3589-3593.
12. Lee, Y. B., Gong, Y. D., Kim, D. J., Ahn, C. H., Kong, J. Y., & Kang, N. S. (2012). Synthesis, anticancer activity and pharmacokinetic analysis of 1-[(substituted 2-alkoxyquinoxalin-3-yl) aminocarbonyl]-4-(hetero) arylpiperazine derivatives. Bioorganic & medicinal chemistry, 20(3), 1303-1309.
13. Nassar, E., Abdel-Aziz, H. A., Ibrahim, H. S., & Mansour, A. M. (2011). Synthesis of diarylpyrazoles containing a phenylsulphone or carbonitrile moiety and their chalcones as possible anti-inflammatory agents. Scientia pharmaceutica, 79(3), 507-524.
14. Dekhane, D. V., Pawar, S. S., Gupta, S., Shingare, M. S., Patil, C. R., & Thore, S. N. (2011). Synthesis and anti-inflammatory activity of some new 4, 5-dihydro-1, 5-diaryl-1H-pyrazole-3-substituted-heteroazole derivatives. Bioorganic & medicinal chemistry letters, 21(21), 6527-6532.
15. Weier, R. M., Crich, J. Z., Xu, X. D., & Collins, P. W. (2003). U.S. Patent No. 6,509,361. Washington, DC: U.S. Patent and Trademark Office.
16. Bandgar, B. P., Totre, J. V., Gawande, S. S., Khobragade, C. N., Warangkar, S. C., & Kadam, P. D. (2010). Synthesis of novel 3, 5-diaryl pyrazole derivatives using combinatorial chemistry as inhibitors of tyrosinase as well as potent anticancer, anti-inflammatory agents. Bioorganic & medicinal chemistry, 18(16), 6149-6155.
17. Kuo, M. R., Morbidoni, H. R., Alland, D., Sneddon, S. F., Gourlie, B. B., Staveski, M. M., ... & Fidock, D. A. (2003). Targeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data. Journal of Biological Chemistry, 278(23), 20851-20859.
18. Kumar, S., Kumar, G., Kapoor, M., Surolia, A., & Surolia, N. (2006). Synthesis and evaluation of substituted pyrazoles: Potential antimalarials targeting the enoyl‐ACP reductase of plasmodium falciparum. Synthetic communications, 36(2), 215-226.
19. Godjayev, N. M., Akyüz, S., & Akverdieva, G. (1997). A molecular mechanics conformational study of peptide T. Journal of molecular structure, 403(1-2), 95-110.
20. Gilad, Y., & Senderowitz, H. (2014). Docking studies on DNA intercalators. Journal of chemical information and modeling, 54(1), 96-107.
21. Aminzadeh, M., Saeidifar, M., & Mansouri-Torshizi, H. (2020). Synthesis, characterization, DNA binding, cytotoxicity, and molecular docking approaches of Pd (II) complex with N, O-donor ligands as a novel potent anticancer agent. Journal of Molecular Structure, 1215, 128212.
22. Shao, Y., Molnar, L. F., Jung, Y., Kussmann, J., Ochsenfeld, C., Brown, S. T., ... & DiStasio Jr, R. A. (2006). Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics,8(27), 3172-3191.
23. Devar, M.J.S., Zoebisch, E.G., Healy, E.F., Stewart, J.J.P. (1985). AM1: A new General purposequantum mechanical molecular model. J. Am. Chem. Soc. 107, 3902-3909.
24. Trott, O., Olson, A.J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455-461.
25. Walayat, K., MOHSIN, N. U. A., Aslam, S., & Ahmad, M. (2019). An insight into the therapeutic potential of piperazine-based anticancer agents. Turkish Journal of Chemistry, 43(1), 1-23.
26. Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Sciences, 78(4), 2179-2183.
27. Celik, S., Ozkok, F., Ozel, A. E., Müge Sahin, Y., Akyuz, S., Sigirci, B. D., ... & Karaoz, E. (2020). Synthesis, FT-IR and NMR characterization, antimicrobial activity, cytotoxicity and DNA docking analysis of a new anthraquinone derivate compound. Journal of Biomolecular Structure and Dynamics, 38(3), 756-770.
28. Celik, S., E. Ozel, A., Durak, V., & Akyuz, S. (2020). Vibrational spectroscopic characterization, quantum chemical and molecular docking studies of Valyl-Methionine dipeptide. Spectroscopy Letters, 53(9), 648-663.
29. Gasymov, O. K., Celik, S., Agaeva, G., Akyuz, S., Kecel-Gunduz, S., Qocayev, N. M., ... & Aliyev, J. A. (2021). Evaluation of anti-cancer and anti-covid-19 properties of cationic pentapeptide Glu-Gln-Arg-Pro-Arg, from rice bran protein and its d-isomer analogs through molecular docking simulations. Journal of Molecular Graphics and Modelling, 108, 107999.
30. Celik, S., Ozkok, F., Ozel, A. E., Cakir, E., & Akyuz, S. (2021). Synthesis, FT-IR and NMR Characterization, Antibacterial and Antioxidant Activities, and DNA Docking Analysis of a New Vanillin-Derived imine Compound. Journal of Molecular Structure, 1236, 130288.