Computational study on anti-inflammatory and anti-hypertensive drug molecules interaction with base pairs

Yıl 2020, Cilt: 1 Sayı: 2, 34 - 38, 30.12.2020

Işılay Öztürk Armağan Kınal Toomas Tamm

Öz

Non-steroidal anti-inflammatory drugs (NSAIDs) and anti-hypertensive drugs have been in use for a long time for the treatment of inflammation, pain, hypertension. Besides these functions, they also show different types of other activities. Many of them exhibit critical side effects in different types of cancer such as colon, lung and breast cancer. In the present study, we computationally investigated the interactions of some nonsteroidal anti-inflammatory and anti-hypertensive drugs (acebutolol, naproxen, diflunisal, bisoprolol) with nucleobases (A, C, G, T) by employing several DFT functionals namely B3LYP, B3LYP-D2 and ωB97X-D. The main purpose of this study is was to determine the strengths of drug-DNA-base interactions that can provide insights about the side effects of the drugs. The calculations were produced the following results. Acebutolol has the highest interaction between adenine in single base-drug complexes. However, acebutolol has the strongest interaction between the guanine-cytosine base pair. The ωB97X-D method, which accounts for dispersion interaction properly, gives better results than the B3LYP and B3LYP-D2 methods.

Anahtar Kelimeler

NSAIDs, beta blockers, nucleobase, nucleobase pairs, binding energies, DFT methods

Destekleyen Kurum

this paper were performed at High Performance and Grid Computing Center (TRUBA resources)

Teşekkür

The authors thank the all calculations reported in this paper were performed at High Performance and Grid Computing Center (TRUBA resources). I.Ö. wishes to thank Armağan Kınal and Toomas Tamm.

Kaynakça

• Abbas, H. (2017). First-principles study of interaction of serine with nucleobases of DNA and RNA, 105–111. https://doi.org/10.1007/s10867-016-9436-1
• Abdolahi, N., Aghaei, M., Soltani, A., Azmoodeh, Z., Balakheyli, H., & Heidari, F. (2018). Adsorption of Celecoxib on B 12 N 12 fullerene: Spectroscopic and DFT/TD-DFT study. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 204, 348–353. https://doi.org/10.1016/j.saa.2018.06.077
• Armakovic, S., Armakovic, S. J., Šetrajcic, J. P., & Šetrajcic, I. J. (2012). Active components of frequently used β-blockers from the aspect of computational study. Journal of Molecular Modeling, 18(9), 4491–4501. https://doi.org/10.1007/s00894-012-1457-5
• Aubrey-Medendorp, C., Swadley, M. J., & Li, T. (2008). The polymorphism of indomethacin: An analysis by density functional theory calculations. Pharmaceutical Research, 25(4), 953–959. https://doi.org/10.1007/s11095-007-9346-9
• Azizi, H., & Zoha, T. (2018). An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis : conformers , binding energies , and charge transfer. Applied Biological Chemistry, 61(2), 209–226. https://doi.org/10.1007/s13765-018-0348-6
• Badawi, H. M., & Förner, W. (2014). Analysis of the molecular structure and vibrational spectra of the indole based analgesic drug indomethacin. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 123, 447–454. https://doi.org/10.1016/j.saa.2013.12.044
• Brouwers, L., Iskar, M., Zeller, G., Noort, V. Van, & Bork, P. (2011). Network Neighbors of Drug Targets Contribute to Drug Side-Effect Similarity, 6(7). https://doi.org/10.1371/journal.pone.0022187
• Brown, B. M. (1994). P22 Arc : Energetics and Cooperativity of DNA Binding. Caflisch, A. (2009). Quantum Mechanical Methods for Drug Design, (November). https://doi.org/10.2174/156802610790232242
• Carvalho, M. A., Arruda, E. G. R., Profirio, D. M., Gomes, A. F., Gozzo, F. C., Formiga, A. L. B., & Corbi, P. P. (2015). Chemical and spectroscopic characterizations, ESI-QTOF mass spectrometric measurements and DFT studies of new complexes of palladium(II) with tryptamine and mefenamic acid. Journal of Molecular Structure, 1100, 6–13. https://doi.org/10.1016/j.molstruc.2015.07.020
• Chinnasamy, K., Saravanan, M., & Poomani, K. (2020). Evaluation of binding and antagonism / downregulation of brilanestrant molecule in estrogen receptor- α via quantum mechanics / molecular mechanics , molecular dynamics and binding free energy calculations. Journal of Biomolecular Structure and Dynamics, 38(1), 219–235. https://doi.org/10.1080/07391102.2019.1574605
• Editor, G., Hobza, P., Cozzi, F., Annunziata, R., Benaglia, M., Kim, K., … Hobza, P. (2008). acid bases. https://doi.org/10.1039/b805489b Emamian, S. (2015). Understanding the molecular mechanism and regioselectivity in the synthesis of celecoxib via a domino reaction: A DFT study. Journal of Molecular Graphics and Modelling, 60, 155–161. https://doi.org/10.1016/j.jmgm.2015.05.006
• Farca, A., Iacoviə, C., Vineler, E., Chi, V., Stiufiuc, R., & Lucaciu, C. M. (2016). The Influence of Molecular Structure Modifications on Vibrational Properties of Some Beta Blockers: A Combined Raman and DFT Study. Journal of Spectroscopy, 2016. https://doi.org/10.1155/2016/3137140
• Ghosh, D., Kosenkov, D., Vanovschi, V., Williams, C. F., Herbert, J. M., Gordon, M. S., … Krylov, A. I. (2010). Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method : Theory and Application to Nucleobase Oligomers, 12739–12754. Huq, F. (2008). Molecular modelling analysis of the metabolism of oseltamivir. Asian Journal of Chemistry, 20(4), 3121–3126. https://doi.org/10.3923/ajb.2008.109.117
• Iacovit, C., Vint, E., Chis, V., & Lucaciu, C. M. (2016). The Influence of Molecular Structure Modifications on Vibrational Properties of Some Beta Blockers : A Combined Raman and DFT Study, 2016.
• Karaman, R., Dajani, K., & Hallak, H. (2012). Computer-assisted design for atenolol prodrugs for the use in aqueous formulations, 1523–1540. https://doi.org/10.1007/s00894-011-1180-7
• Kell, D. B., & Oliver, S. G. (2014). How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Frontiers in Pharmacology, 5(October), 1–32. https://doi.org/10.3389/fphar.2014.00231
• King, M. D., Ouellette, W., & Korter, T. M. (2011). Noncovalent Interactions in Paired DNA Nucleobases Investigated by Terahertz Spectroscopy and Solid-State Density Functional Theory, 9467–9478. https://doi.org/10.1021/jp111878h
• Kong, H., Sun, Q., Wang, L., Tan, Q., Zhang, C., Sheng, K., & Xu, W. (2014). Atomic-scale investigation on the facilitation and inhibition of guanine tautomerization at Au(111) surface. ACS Nano, 8(2), 1804–1808. https://doi.org/10.1021/nn4061918
• Kov, A., & Rode, J. E. (2017). Benchmarking density functionals in conjunction with Grimme ’ s dispersion correction for noble gas dimers, (September 2016). https://doi.org/10.1002/qua.25358
• Lee, W., & Engels, B. (2014). The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate. https://doi.org/10.1021/bi401308j
• Lin, Y., Li, G., Mao, S., & Chai, J. (2013). Long-Range Corrected Hybrid Density Functionals with Improved Dispersion Corrections. https://doi.org/10.1021/ct300715s
• Martínez-Araya, J. I., Salgado-Morán, G., & Glossman-Mitnik, D. (2013). Computational nanochemistry report on the oxicams - Conceptual DFT indices and chemical reactivity. Journal of Physical Chemistry B, 117(21), 6339–6351. https://doi.org/10.1021/jp400241q Morgado, C., Vincent, M. A., Hillier, I. H., & Shan, X. (2007). Can the DFT-D method describe the full range of noncovalent interactions found in large biomolecules ? w, 448–451. https://doi.org/10.1039/b615263e
• Musa, K. A. K., & Eriksson, L. A. (2008). Theoretical Study of the Phototoxicity of Naproxen and the Active Form of Nabumetone, 10921–10930. Mutter, S. T., Margiotta, N., Papadia, P., & Platts, J. A. (2015). Computational evidence for structural consequences of kiteplatin damage on DNA. Journal of Biological Inorganic Chemistry, 20(1), 35–48. https://doi.org/10.1007/s00775-014-1207-5
• S, I. N. D. R. N. (2017). What are NSAIDs? Australian Rheumatology Association, (February), 2–5. Saji, R. S., Prasana, J. C., Muthu, S., George, J., Kuruvilla, T. K., & Raajaraman, B. R. (2020). Spectroscopic and quantum computational study on naproxen sodium. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 226. https://doi.org/10.1016/j.saa.2019.117614
• Sharma, R. P., Kumar, S., Venugopalan, P., Ferretti, V., Tarushi, A., Psomas, G., & Witwicki, M. (2016). RSC Advances drug mefenamic acid : a concerted study including synthesis , physicochemical characterization and. RSC Advances, 6, 88546–88558. https://doi.org/10.1039/C6RA14706B
• Shoute, L. C. T., & Loppnow, G. R. (2018). between EvaGreen dye and dsDNA †, 4772–4780. https://doi.org/10.1039/c7cp06058k
• Sigel, A., Operschall, B. P., & Sigel, H. (2014). Comparison of the p -stacking properties of purine versus pyrimidine residues . Some generalizations regarding selectivity, 691–703. https://doi.org/10.1007/s00775-013-1082-5
• Sirajuddin, M., Ali, S., & Badshah, A. (2013). Journal of Photochemistry and Photobiology B : Biology Drug – DNA interactions and their study by UV – Visible , fluorescence spectroscopies and cyclic voltametry. Journal of Photochemistry & Photobiology, B: Biology, 124, 1–19. https://doi.org/10.1016/j.jphotobiol.2013.03.013
• Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. (2014). Computational Methods in Drug Discovery, (January), 334–395. Souri, M., & Mohammadi, A. K. (2017). Investigation of solvent effect on adenine-thymine base pair interaction. Journal of Molecular Liquids, 230, 169–174. https://doi.org/10.1016/j.molliq.2017.01.021
• Wenthold, P. G., & Squires, R. R. (2005). Bond Dissociation Energies of F2 and HF2 A Gas-Phase Experimental and G2, 2002–2005. https://doi.org/10.1021/j100007a034