Tetrazolato Ligandı ve Pt(II) Kompleksinin DNA Etkileşiminin Moleküler Doking Yöntemi ile Belirlenmesi

Fatma Okuş; Deniz Yüzbaşıoğlu; Gonca Çakmak; Nurşen Sarı; Fatma Ünal

doi:10.18016/ksutarimdoga.vi.1322613

TR EN

Tetrazolato Ligandı ve Pt(II) Kompleksinin DNA Etkileşiminin Moleküler Doking Yöntemi ile Belirlenmesi

Öz

Dünyada en çok ölüme neden olan hastalıklar arasında ikinci sırada yer alan kanserin tedavisinde platin(II) temelli ilaçlar önemli yer tutmaktadır. Yüksek etkinlik nedeniyle sıklıkla tercih edilen bu ilaçların kullanımını, yan etkileri ve direnç gelişimi gibi olumsuzluklar kısıtlamaktadır. Pt(II) iyonunu içeren moleküllerin DNA ile etkileştiği bilindiğinden, bu iyonu DNA’ya taşıyacak düşük toksisiteli bir ligandın geliştirilmesi önem kazanmıştır. Düşük toksisiteli olmaları nedeniyle ilaç çalışmalarında kullanımları desteklenen tetrazol halkası ve Schiff bazı grubu içeren ligant (tetrazolato) ve onun Pt(II) kompleksi sunulan çalışmaya konu olmuştur. Bu çalışmada tetrazolato ligandı ve onun kompleksinin farklı baz dizilimlerine sahip DNA yapıları ile etkileşimi, hem tek başına ligandın esnek olduğu “doking” ve hem de ligant-DNA yapılarının aynı anda esnek olduğu “esnek doking” yöntemleri kullanılarak araştırılması amaçlanmıştır. Bulgular, hem ligandın hem de onun Pt(II) kompleksinin tüm DNA yapılarına yüksek afinitesi olduğunu göstermektedir. Doking çalışmasındaki etkileşimler, en düşük: -5.225 kcal mol-1, en yüksek: -8.186 kcal mol-1 ve esnek doking çalışması için ise en düşük: -5.941 kcal mol-1, en yüksek: -7.967 kcal mol-1 olarak belirlenmiştir.

Anahtar Kelimeler

Determination of DNA Interaction of Tetrazolato Ligand and Pt(II) Complex by Molecular Docking

Abstract

Platinum(II) based drugs are essential in treating cancer, the second leading cause of death worldwide. These drugs, which are frequently used due to their high efficacy, are limited due to their side effects and resistance development. Since the interaction of Pt(II) with DNA is known, developing a low-toxicity ligand to carry it to DNA has gained importance. The Ligand (Tetrazolato) containing a tetrazole ring and Schiff base structures and its Pt(II) complex that are supported for use in drug development research due to their low toxicity is the main subject of this work. It is aimed at investigating the interaction of both this ligand and its Pt(II) complex with DNA structures having different base sequences by both "docking methods," in which only the ligand is flexible, and "flexible docking methods," in which the ligand and DNA structures are flexible at the same time. The data revealed that the ligand and the Pt(II) complex presented high affinity for all DNA structures. Determined interactions in docking studies ranged from the lowest: -5.225 kcal mol-1 to highest: -8.186 kcal mol-1 for the docking study, and the lowest: -5.941 kcal mol-1 to highest: -7.967 kcal mol-1 for the flexible docking study.

Keywords

Thanks

Gazi Üniversitesi’ne Schrödinger programına erişim imkânı sunduğu için teşekkür ederiz. Yükseköğretim Kurulu’na “Moleküler Farmakoloji ve İlaç Araştırmaları” öncelikli alanı kapsamında Fatma OKUŞ’a 100/2000 YÖK Doktora Bursu desteği için teşekkür ederiz.

References

KAYNAKLAR Ahmad, S. (2010). Platinum–DNA interactions and subsequent cellular processes controlling sensitivity to anticancer platinum complexes. Chemistry&Biodiversity, 7(3), 543-566.
Alotaibi, S. H., & Momen, A. A. (2019). Anticancer drugs’ deoxyribonucleic acid (DNA) interactions. In Biophysical Chemistry-Advance Applications. IntechOpen.
Amjad, M. T., Chidharla, A., & Kasi, A. (2022). Cancer Chemotherapy. In StatPearls. StatPearls Publishing. Arif, R., Nayab, P. S., Abid, M., & Yadava, U. (2019). Investigation of DNA binding and molecular docking propensity of phthalimide derivatives: in vitro antibacterial and antioxidant assay. Journal of Analytical Science and Technology, 10(1), 1-9.
Ashraf, T., Ali, B., Qayyum, H., Haroone, M. S., & Shabbir, G. (2023). Pharmacological aspects of schiff base metal complexes: A critical review. Inorganic Chemistry Communications, 110449.
Berdigaliyev, N., & Aljofan, M. (2020). An overview of drug discovery and development. Future Medicinal Chemistry, 12(10), 939-947.
Boulechfar, C., Ferkous, H., Delimi, A., Djedouani, A., Kahlouche, A., Boublia, A., Darwish, A. S., Lemaoui, T., Verma, R., & Benguerba, Y. (2023). Schiff bases and their metal complexes: A review on the history, synthesis, and applications. Inorganic Chemistry Communications, 110451.
Çakmak Pehlivanlı, A., & Çakmak, G. (2022). Genotoksik etkiyi belirlemeye yönelik in silico yaklaşımlar. In F. Ünal & D. Yüzbaşıoğlu (Eds.), Genetik Toksikoloji (475-494). Nobel Akademik Yayıncılık.
Çetintaş, V. B., & Eroğlu, Z. (2013). Cisplatin direncinde etkili moleküler mekanizmalar. SDÜ Tıp Fakültesi Dergisi, 20(2), 72-79.

Chaudhary, N. K., Guragain, B., Chaudhary, S. K., & Mishra, P. (2021). Schiff base metal complex as a potential therapeutic drug in medical science: A critical review. Bibechana, 18(1), 214-230.
Ciğerci, İ. H., Liman, R., İstifli, E. S., Akyıl, D., Özkara, A., Bonciu, E., & Colă, F. (2023). Cyto-genotoxic and behavioral effects of flubendiamide in Allium cepa root cells, Drosophila melanogaster and molecular docking studies. International Journal of Molecular Sciences, 24(2), 1565.
Cohen, S. M., & Lippard, S. J. (2001). Cisplatin: From DNA damage to cancer chemotherapy. In Progress in Nucleic Acid Research and Molecular Biology, 67, 93-130.
Dasari, S., & Tchounwou, P. B. (2014). Cisplatin in cancer therapy: Molecular mechanisms of action. European Journal of Pharmacology, 740, 364-378.
Deng, J., Yu, P., Zhang, Z., Zhang, J., Zhewen, S., Cai, M., Yuan, H., Liang, H., & Yang, F. (2019). Novel Pt (ii) complexes with modified aroyl-hydrazone Schiff-base ligands: synthesis, cytotoxicity and action mechanism. Metallomics, 11(11), 1847-1863.
Di Pasqua, A. J., Goodisman, J., & Dabrowiak, J. C. (2012). Understanding how the platinum anticancer drug carboplatin works: From the bottle to the cell. Inorganica Chimica Acta, 389, 29-35.
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.
Du, L., Geng, C., Zeng, Q., Huang, T., Tang, J., Chu, Y., & Zhao, K. (2023). Dockey: a modern integrated tool for large-scale molecular docking and virtual screening. Briefings in Bioinformatics, 24(2), bbad047.
Ebosie, N. P., Ogwuegbu, M. O. C., Onyedika, G. O., & Onwumere, F. C. (2021). Biological and analytical applications of Schiff base metal complexes derived from salicylidene-4-aminoantipyrine and its derivatives: a review. Journal of the Iranian Chemical Society, 1-31.
Fan, J. Y., Fu, A. L., & Zhang, L. (2019). Progress in molecular docking. Quantitative Biology, 7(2), 83-89. Faraj, E. M., & Jumaa, F. H. (2022). Preparation, diagnostics and biological evaluation of new Schiff base and tetrazole derivatives. Materials Today: Proceedings, 49, 3549-3557.
Feng, Y., Yan, Y., He, J., Tao, H., Wu, Q., & Huang, S.-Y. (2022). Docking and scoring for nucleic acid–ligand interactions: Principles and current status. Drug Discovery Today, 27(3), 838-847.
Frey, P. A. (2004). Low Barrier Hydrogen Bonds. In W. J. Lennarz & M. D. Lane (Eds.), Encyclopedia of Biological Chemistry (594-598). Elsevier.
Ghosh, S. (2019). Cisplatin: The first metal based anticancer drug. Bioorganic Chemistry, 88, Article 102925.
Hah, S. S., Stivers, K. M., de Vere White, R. W., & Henderson, P. T. (2006). Kinetics of carboplatin− DNA binding in genomic DNA and bladder cancer cells as determined by accelerator mass spectrometry. Chemical Research in Toxicology, 19(5), 622-626.
Husunet, M. T., Mısırlı, R. Ç., Istıflı, E. S., & Ila, H. B. (2022). Investigation of the genotoxic effects of patent blue V (E131) in human peripheral lymphocytes and in silico molecular docking. Drug and Chemical Toxicology, 45(4), 1780-1786.
Ince Yardimci, A., Istifli, E. S., Acikbas, Y., Liman, R., Yagmurcukardes, N., Yilmaz, S., & Ciğerci, İ. H. (2022). Synthesis and characterization of single‐walled carbon nanotube: Cyto‐genotoxicity in Allium cepa root tips and molecular docking studies. Microscopy Research and Technique, 85(9), 3193-3206.
Ji, S., Shao, H., Han, Q., Seiler, C. L., & Tretyakova, N. Y. (2017). Reversible DNA–Protein Cross‐Linking at Epigenetic DNA Marks. Angewandte Chemie International Edition, 56(45), 14130-14134.
Jireš, J., Gibala, P., Kalášek, S., Douša, M., & Doubský, J. (2021). The determination of two analogues of 4-(azidomethyl)-1, 1'-biphenyl as potential genotoxic impurities in the active pharmaceutical ingredient of several sartans containing a tetrazole group. Journal of Pharmaceutical and Biomedical Analysis, 205, 114300.
Johnson, T. O., Akinsanmi, A. O., Ejembi, S. A., Adeyemi, O. E., Oche, J.-R., Johnson, G. I., & Adegboyega, A. E. (2023). Modern drug discovery for inflammatory bowel disease: The role of computational methods. World Journal of Gastroenterology, 29(2), 310.
Joseph, F., Martins, E., Harriet, K., Ermias, T., & Xiang, W. (2015). Green chemistry strategies for drug discovery. In E. Peterson & J. Manley (Eds.), The business case for green chemistry in drug discovery (Vol. 46, 291-296). Royal Society of Chemistry.
Kelland, L. (2007). The resurgence of platinum-based cancer chemotherapy. Nature Reviews Cancer, 7(8), 573-584.
Kumar, J., Rai, A., & Raj, V. (2017). A comprehensive review on the pharmacological activity of schiff base containing derivatives. Organic & Medicinal Chemistry International Journal, 1(3), 88-102.
Lee, S., & Shanti, A. (2021). Effect of exogenous ph on cell growth of breast cancer cells. International Journal of Molecular Sciences, 22(18), 9910.
Leyva-Ramos, S., & Cardoso-Ortiz, J. (2021). Recent developments in the synthesis of tetrazoles and their pharmacological relevance. Current Organic Chemistry, 25(3), 388-403.
Liman, R., Kursunlu, A. N., Ozmen, M., Arslan, S., Mutlu, D., Istifli, E. S., & Acikbas, Y. (2022). Synthesis of water soluble symmetric and asymmetric pillar [5] arene derivatives: Cytotoxicity, apoptosis and molecular docking studies. Journal of Molecular Structure, 1265, 133482.
Lin, R., Zhang, J., Xu, R., Yuan, C., Guo, L., Liu, P., Fang, Y., & Cui, B. (2023). Developments in molecular docking technologies for application of polysaccharide-based materials: A review. Critical Reviews in Food Science and Nutrition, 1-13.
Martinho, N., Santos, T. C., Florindo, H. F., & Silva, L. C. (2019). Cisplatin-membrane interactions and their influence on platinum complexes activity and toxicity. Frontiers in Physiology, 9, 1898.
Morris, G. M., & Lim-Wilby, M. (2008). Molecular docking. Molecular modeling of proteins, 365-382.
Murray, D., & Mirzayans, R. (2020). Cellular responses to platinum-based anticancer drugs and UVC: Role of p53 and implications for cancer therapy. International Journal of Molecular Sciences, 21(16), 5766.
Nemati, L., Keypour, H., Shahabadi, N., Hadidi, S., & Gable, R. W. (2021). Synthesis, characterization and DNA interaction of a novel Pt (II) macroacyclic Schiff base complex containing the piperazine moiety and its cytotoxicity and molecular docking. Journal of Molecular Liquids, 337, 116292.
Ogbonna, E. N., Paul, A., Farahat, A. A., Terrell, J. R., Mineva, E., Ogbonna, V., Boykin, D. W., & Wilson, W. D. (2023). X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. ACS Bio & Med Chem Au, 3(4), 335-348.
Oun, R., Moussa, Y. E., & Wheate, N. J. (2018). The side effects of platinum-based chemotherapy drugs: a review for chemists. Dalton Transactions, 47(19), 6645-6653.
Özkan, H. (2019). N-Alkillenmiş Tetrazol Türevi Bileşiklerin Absorpsiyon, Dağılım, Metabolizma ve Atılım (ADME) Özelliklerinin Araştırılması. Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 14(2), 384-394.
Piasentin, N., Milotti, E., & Chignola, R. (2020). The control of acidity in tumor cells: a biophysical model. Scientific Reports, 10(1), 13613.
Potlitz, F., Link, A., & Schulig, L. (2023). Advances in the discovery of new chemotypes through ultra-large library docking. Expert Opinion on Drug Discovery, 18(3), 303-313.
Pradeep, S. D., Gopalakrishnan, A. K., Manoharan, D. K., Soumya, R. S., Gopalan, R. K., & Mohanan, P. V. (2023). Isatin derived novel Schiff bases: An efficient pharmacophore for versatile biological applications. Journal of Molecular Structure, 1271, 134121.
Protas, A. V., Popova, E. A., Mikolaichuk, O. V., Porozov, Y. B., Mehtiev, A. R., Ott, I., Alekseev, G. V., Kasyanenko, N. A., & Trifonov, R. E. (2018). Synthesis, DNA and BSA binding of Pd (II) and Pt (II) complexes featuring tetrazolylacetic acids and their esters. Inorganica Chimica Acta, 473, 133-144.
Raiber, E.-A., Portella, G., Martínez Cuesta, S., Hardisty, R., Murat, P., Li, Z., Iurlaro, M., Dean, W., Spindel, J., & Beraldi, D. (2018). 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells. Nature Chemistry, 10(12), 1258-1266.
Reedijk, J., & Lohman, P. (1985). Cisplatin: synthesis, antitumour activity and mechanism of action. Pharmaceutisch Weekblad, 7, 173-180.
Repasky, M. P., Shelley, M., & Friesner, R. A. (2007). Flexible ligand docking with Glide. Current Protocols in Bioinformatics, 18(1), 8.12. 11-18.12. 36.
Rosenberg, B., Vancamp, L., Trosko, J. E., & Mansour, V. H. (1969). Platinum compounds: a new class of potent antitumour agents. Nature, 222(5191), 385-386.
Sakthi, M., & Ramu, A. (2017). Synthesis, structure, DNA/BSA binding and antibacterial studies of NNO tridentate Schiff base metal complexes. Journal of Molecular Structure, 1149, 727-735.
Saritha, T. J., & Metilda, P. (2021). Synthesis, Spectroscopic characterization and biological applications of some novel Schiff base transition metal (II) complexes derived from Curcumin moiety. Journal of Saudi Chemical Society, 101245.
Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in Biology and Medicine, 137, 104851.
Shekhar, S., Khan, A. M., Sharma, S., Sharma, B., & Sarkar, A. (2022). Schiff base metallodrugs in antimicrobial and anticancer chemotherapy applications: a comprehensive review. Emergent Materials, 5(2), 279-293.
Singh, H. L., Dhingra, N., & Bhanuka, S. (2023). Synthesis, spectral, antibacterial and QSAR studies of tin and silicon complexes with Schiff base of amino acids. Journal of Molecular Structure, 1287, 135670.
Sinha, S., & Vohora, D. (2018). Drug discovery and development: An overview. Pharmaceutical Medicine and Translational Clinical Research, 19-32.
Soldatović, T. V., Šmit, B., Mrkalić, E. M., Matić, S. L., Jelić, R. M., Serafinović, M. Ć., Gligorijević, N., Čavić, M., Aranđelović, S., & Grgurić-Šipka, S. (2023). Exploring heterometallic bridged Pt (II)-Zn (II) complexes as potential antitumor agents. Journal of Inorganic Biochemistry, 240, 112100.
Stanzione, F., Giangreco, I., & Cole, J. C. (2021). Use of molecular docking computational tools in drug discovery. Progress in Medicinal Chemistry, 60, 273-343.
Swietach, P., Vaughan-Jones, R. D., Harris, A. L., & Hulikova, A. (2014). The chemistry, physiology and pathology of pH in cancer. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1638), 20130099.
Tao, X., Huang, Y. K., Wang, C., Chen, F., Yang, L. L., Ling, L., Che, Z. M., & Chen, X. G. (2020). Recent developments in molecular docking technology applied in food science: a review. International Journal of Food Science and Technology, 55(1), 33-45.
Tarai, S. K., Mandal, S., Bhaduri, R., Pan, A., Biswas, P., Bhattacharjee, A., & Moi, S. C. (2023). Bioactivity, molecular docking and anticancer behavior of pyrrolidine based Pt (II) complexes: Their kinetics, DNA and BSA binding study by spectroscopic methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 287, 122059.
Tripathi, A., & Misra, K. (2017). Molecular docking: A structure-based drug designing approach. JSM Chem, 5(2), 1042-1047.
Vishwakarma, R., Gadipelly, C., & Mannepalli, L. K. (2022). Advances in Tetrazole Synthesis – An Overview. ChemistrySelect, 7(29), e202200706.
Ward, C., Meehan, J., Gray, M. E., Murray, A. F., Argyle, D. J., Kunkler, I. H., & Langdon, S. P. (2020). The impact of tumour pH on cancer progression: strategies for clinical intervention. Exploration of Targeted Anti-tumor Therapy, 1(2), 71.
Yu, Y., Xu, S., He, R., & Liang, G. (2023). Application of molecular simulation methods in food science: status and prospects. Journal of Agricultural and Food Chemistry, 71(6), 2684-2703.

Details

Primary Language

Turkish

Subjects

Animal Cell and Molecular Biology

Journal Section

Research Article

Authors

Fatma Okuş
0000-0001-7648-9584
Türkiye

Deniz Yüzbaşıoğlu ^*
0000-0003-2756-7712
Türkiye

Gonca Çakmak
0000-0002-6283-5404
Türkiye

Nurşen Sarı
0000-0002-4764-7747
Türkiye

Fatma Ünal
0000-0002-7468-6186
Türkiye

Early Pub Date

March 11, 2024

Publication Date

June 30, 2024

Submission Date

July 4, 2023

Acceptance Date

December 3, 2023

Published in Issue

Year 2024 Volume: 27 Number: 3

DOI

https://doi.org/10.18016/ksutarimdoga.vi.1322613

IZ

https://izlik.org/JA87PS48DS

Cite

RIS / Bibtex

APA

Okuş, F., Yüzbaşıoğlu, D., Çakmak, G., Sarı, N., & Ünal, F. (2024). Tetrazolato Ligandı ve Pt(II) Kompleksinin DNA Etkileşiminin Moleküler Doking Yöntemi ile Belirlenmesi. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 27(3), 528-540. https://doi.org/10.18016/ksutarimdoga.vi.1322613

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