Structural and vibrational investigations and molecular docking studies of a vinca alkoloid, vinorelbine

References

• Altinoz, M. A., Ozpinar, A., Alturfan, E. E., & Elmaci, I. (2018). Vinorelbine’s anti-tumor actions may depend on the mitotic apoptosis, autophagy and inflammation: Hypotheses with implications for chemo-immunotherapy of advanced cancers and pediatric gliomas. Journal of Chemotherapy (Florence, Italy), 30(4), 203–212.
   PubMed Web of Science ®Google Scholar
• Aronson, J. K. (Ed.). (2015). Meyler’s side effects of drugs: The international encyclopedia of adverse drug reactions and interactions. Elsevier.
   Google Scholar
• Becke, A. (1993). Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics, 98(7), 5648–5652. https://doi.org/10.1063/1.464913
   Web of Science ®Google Scholar
• Beulz-Riche, D., Grudé, P., Puozzo, C., Sautel, F., Filaquier, C., Riché, C., & Ratanasavanh, D. (2005). Characterization of human cytochrome P450 isoenzymes involved in the metabolism of vinorelbine. Fundamental and Clinical Pharmacology, 19(5), 545–553. https://doi.org/10.1111/j.1472-8206.2005.00367.x
   PubMed Web of Science ®Google Scholar
• Boichuk, S., Galembikova, A., Syuzov, K., Dunaev, P., Bikinieva, P., Aukhadieva, A., Zykova, S., Igidov, N., Gankova, K., Novikova, M., & Kopnin, P. (2021). The design, synthesis, and biological activities of pyrrole-based carboxamides: The novel tubulin ınhibitors targeting the colchicine-binding site. Molecules, 26(19), 5780. https://doi.org/10.3390/molecules26195780
   PubMed Web of Science ®Google Scholar
• Borba, A., Gómez-Zavaglia, A., & Fausto, R. (2009). Molecular structure, infrared spectra, and photochemistry of isoniazid under cryogenic conditions. The Journal of Physical Chemistry. A, 113(32), 9220–9230.
   PubMed Web of Science ®Google Scholar
• Borkakoti, N., & Palmer, R. A. (1978). The structure of the bisbenzylisoquinoline alkaloid methylwarifteine. Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, 34(2), 490–495. https://doi.org/10.1107/S0567740878003404
   Google Scholar
• Bueno, O., Gallego, J. E., Martins, S., Prota, A. E., Gago, F., Gómez-SanJuan, A., Camarasa, M.-J., Barasoain, I., Steinmetz, M. O., Díaz, J. F., Pérez-Pérez, M.-J., Liekens, S., & Priego, E.-M. (2018). High-afnity ligands of the colchicine domain in tubulin based on a structure-guided design. Scientific Reports, 8(1), 4242. https://doi.org/10.1038/s41598-018-22382-x
   PubMedGoogle Scholar
• Campos, J. A., Casado, J., & Rios, M. A. (1980). The geometry of the phenyl ring in substituted benzene molecules. A molecular orbital approach. Journal of the American Chemical Society, 102(5), 1501–1504. https://doi.org/10.1021/ja00525a005
   Web of Science ®Google Scholar
• Celik, S., Ozel, A. E., & Akyuz, S. (2016). Comparative study of antitumor active cyclo (Gly-Leu) dipeptide: A computational and molecular modeling study. Vibrational Spectroscopy, 83, 57–69. https://doi.org/10.1016/j.vibspec.2016.01.007
   Web of Science ®Google Scholar
• Celik, S., Akyuz, S., & Ozel, A. E. (2022a). Molecular modeling, DFT quantum chemical analysis, and molecular docking on edotecarin, an indolocarbazole anticancer agent. Molecular Crystals and Liquid Crystals, 1–23. https://doi.org/10.1080/15421406.2022.2084240
   Web of Science ®Google Scholar
• Celik, S., Vagifli, F., Akyuz, S., Ozkok, F., E. Ozel, A., Dosler, S., & Onul, N. (2022). Synthesis, vibrational spectroscopic investigation, molecular docking, antibacterial and antimicrobial studies of a new anthraquinone derivative compound. Spectroscopy Letters, 55(4), 259–277. https://doi.org/10.1080/00387010.2022.2056615
   Web of Science ®Google Scholar
• Celik, S., Yilmaz, G., Ozel, A. E., & Akyuz, S. (2022). Structural and spectral analysis of anticancer active cyclo (Ala–His) dipeptide. Journal of Biomolecular Structure & Dynamics, 40(2), 660–672. https://doi.org/10.1080/07391102.2020.1817150
   PubMed Web of Science ®Google Scholar
• Celik, S., Akyuz, S., & Ozel, A. E. (2022b). Vibrational spectroscopic characterization and structural investigations of Cepharanthine, a natural alkaloid. Journal of Molecular Structure, 1258, 132693. https://doi.org/10.1016/j.molstruc.2022.132693
   Web of Science ®Google Scholar
• 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. https://doi.org/10.1016/j.molstruc.2021.130288
   Web of Science ®Google Scholar
• Celik, S., Akyuz, S., & Ozel, A. E. (2017). Vibrational spectroscopic and structural investigations of bioactive molecule Glycyl-Tyrosine (Gly-Tyr). Vibrational Spectroscopy, 92, 287–297. https://doi.org/10.1016/j.vibspec.2017.08.007
   Web of Science ®Google Scholar
• Celik, S., Albayrak, A. T., Akyuz, S., E., & Ozel, A. (2019). Molecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB). Journal of Biomolecular Structure & Dynamics, 37(10), 2515–2526.
   PubMed Web of Science ®Google Scholar
• Ceylan, Ü., Durgun, M., Türkmen, H., Yalçın, Ş. P., Kilic, A., & Özdemir, N. (2015). Theoretical and experimental investigation of 4-[(2-hydroxy-3-methylbenzylidene) amino] benzenesulfonamide: Structural and spectroscopic properties, NBO, NLO and NPA analysis. Journal of Molecular Structure, 1089, 222–232. https://doi.org/10.1016/j.molstruc.2015.02.042
   Web of Science ®Google Scholar
• Chengyong, W., Jinghong, X., Yanyan, W., Qing-Jie, X., Lingling, M., Yuyan, L., Hai, C., Qian, L., Quan, Z., Bo, S., & Yuxi, W. (2021). The high‐resolution X‐ray structure of vinca‐domain inhibitors of microtubules provides a rational approach for drug design. FEBS Letters, 595(2), 195–205. https://doi.org/10.1002/1873-3468.14003
   PubMed Web of Science ®Google Scholar
• Chi, S., Xie, W., Zhang, J., & Xu, S. (2015). Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin. Journal of Biomolecular Structure & Dynamics, 33(10), 2234–2254., &, ()., (), -. https://doi.org/10.1080/07391102.2014.999256
   PubMed Web of Science ®Google Scholar
• Cox, E. G., Cruickshank, D. W. J., & Smith, J. A. S. (1958). The crystal structure of benzene at -3 °C. Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences, 247(1248), 1–21.
   Google Scholar
• Debernardis, A., Alfonsi, G., Santacroce, L., Bottalico, L., Sabatini, R., Flace, P., Vermesan, D., Auteri, P., & Cagiano, R. (2009). Antiviral properties of antineoplastic drugs. From Herpes simplex-1 disappearance to a wide antiviral action: A serendipity case report. Acta Bio-Medica: Atenei Parmensis, 80(3), 265–267.
   PubMedGoogle Scholar
• Dege, N., Gökce, H., Doğan, O. E., Alpaslan, G., Ağar, T., Muthu, S., & Sert, Y. (2022). Quantum computational, spectroscopic investigations on N-(2-((2-chloro-4, 5-dicyanophenyl) amino) ethyl)-4-methylbenzenesulfonamide by DFT/TD-DFT with different solvents, molecular docking and drug-likeness researches. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 638, 128311. https://doi.org/10.1016/j.colsurfa.2022.128311
   Web of Science ®Google Scholar
• Devi, T., & R., Gayathri, S. (2010). FTIR and FT-Raman spectral analysis of paclitaxel drugs. International Journal of Pharmaceutical Sciences Review and Research, 2(2), 106–110.
   Google Scholar
• Doğan, H., Bahar, M. R., Çalışkan, E., Tekin, S., Uslu, H., Akman, F., Koran, K., Sandal, S., & Görgülü, A. O. (2022). Synthesis and spectroscopic characterizations of hexakis [(1-(4′-oxyphenyl)-3-(substituted-phenyl) prop-2-en-1-one)] cyclotriphosphazenes: Their in vitro cytotoxic activity, theoretical analysis and molecular docking studies. Journal of Biomolecular Structure and Dynamics, 40(7), 3258–3272. https://doi.org/10.1080/07391102.2020.1846621
   PubMed Web of Science ®Google Scholar
• Durgun, M., Yalçın, Ş. P., Türkmen, H., Akkurt, M., & Eroğlu, E. (2016). Structural study of 4-(2-morpholinoethanoylamino)-benzenesulfonamide by X-ray diffraction technique and DFT calculations. Bulgarian Chemical Communications, 48(1), 5–12.
   Google Scholar
• Eğlence-Bakır, S., Celik, S., Şahin, M., Ozel, A. E., Akyuz, S., & Ülküseven, B. (2021). Synthesis, molecular modelling, FT-IR, Raman and NMR characterization, molecular docking and ADMET study of new nickel (II) complex with an N4-tetradentate thiosemicarbazone. Journal of Biomolecular Structure & Dynamics, 39(12), 4212–4224.
   PubMed Web of Science ®Google Scholar
• El-Naggar, A. M., Eissa, I. H., Belal, A., & El-Sayed, A. A. (2020). Design, eco-friendly synthesis, molecular modeling and anticancer evaluation of thiazol-5 (4 H)-ones as potential tubulin polymerization inhibitors targeting the colchicine binding site. RSC Advances, 10(5), 2791–2811. https://doi.org/10.1039/c9ra10094f
   PubMed Web of Science ®Google Scholar
• Ekroos, M., & Sjögren, T. (2006). Structural basis for ligand promiscuity in cytochrome P450 3A4. Proceedings of the National Academy of Sciences, 103(37), 13682–13687. https://doi.org/10.1073/pnas.0603236103
   PubMed Web of Science ®Google Scholar
• Fishelovitch, D., Hazan, C., Shaik, S., Wolfson, H. J., & Nussinov, R. (2007). Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4. Journal of the American Chemical Society, 129(6), 1602–1611.
   PubMed Web of Science ®Google Scholar
• Flores-Holguín, N., Frau, J., & Glossman-Mitnik, D. (2019). Conceptual DFT as a chemoinformatics tool for the study of the Taltobulin anticancer peptide. BMC Research Notes, 12(1), 1–4. https://doi.org/10.1186/s13104-019-4478-7
   PubMedGoogle Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., Nakatsuji, H., Li, X., Caricato, M., Marenich, A. V., Bloino, J., Janesko, B. G., Gomperts, R., Mennucci, B., Hratchian, H. P., Ortiz, J. V., … Fox, D. J. (2016). Gaussian 16, Revision C.01. Gaussian, Inc.
   Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gregory, R. K., & Smith, I. E. (2000). Vinorelbine–A clinical review. British Journal of Cancer, 82(12), 1907–1913.
   PubMed Web of Science ®Google Scholar
• Gunasekaran, S., Seshadri, S., & Muthu, S. (2006). Vibrational spectra and normal coordinate analysis of flucytosine. Indian Journal of Pure & Applied Physics, 44, 581–586.
   Web of Science ®Google Scholar
• Hajduchova, Z., Pach, L., & Lokaj, J. (2018). Adsorption of dodecylbenzenesulfonic acid on the alumina particles in the preparation of alumina foam. Ceramics–Silikáty, 62(2), 138–145.
   Web of Science ®Google Scholar
• Hansch, C., Sammes, P. G., & Taylor, J. B. (1990). Comprehensive medicinal chemistry: The rational design, mechanistic study & therapeutic applications of chemical compounds (Vol. 5). Pergamon Press.
   Google Scholar
• Istvan, K. (2002). Simirra, A program for simulation of IR and Raman Spectra. Chemical Research Center. (It was obtained from Dr. Gabor Keresztury in Chemical Research Center in Budapest).
   Google Scholar
• Jiao, A., Tian, S., & Lin, H. (2022). Analysis of outburst coal structure characteristics in Sanjia coal mine based on FTIR and XRD. Energies, 15(6), 1956. https://doi.org/10.3390/en15061956
   Web of Science ®Google Scholar
• Jurcik, A., Bednar, D., Byska, J., Marques, S. M., Furmanova, K., Daniel, L., Kokkonen, P., Brezovsky, J., Strnad, O., Stourac, J., Pavelka, A., Manak, M., Damborsky, J., & Kozlikova, B. (2018). CAVER Analyst 2.0: Analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. Bioinformatics (Oxford, England), 34(20), 3586–3588. https://doi.org/10.1093/bioinformatics/bty386
   PubMed Web of Science ®Google Scholar
• Kaneda, T., & Tanaka, J. (1976). The crystal structure of the ıntermolecular complex between 9-ethyladenine and ındole. Bulletin of the Chemical Society of Japan, 49(7), 1799–1804. https://doi.org/10.1246/bcsj.49.1799
   Web of Science ®Google Scholar
• Kaya Kınaytürk, N., Kalaycı, T., & Tunalı, B. (2021). Experimental and computational investigations on the molecular structure, vibrational spectra, electronic properties, and molecular electrostatic potential analysis of phenylenediamine isomers. Spectroscopy Letters, 54(9), 693–706. https://doi.org/10.1080/00387010.2021.1991381
   Web of Science ®Google Scholar
• Klots, T. D., & Collier, W. B. (1995). Heteroatom derivatives of indene Part 3. Vibrational spectra of benzoxazole, benzofuran, and indole. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 51(8), 1291–1316. https://doi.org/10.1016/0584-8539(94)00220-7
   Web of Science ®Google Scholar
• Kutlu, E., Emen, F. M., Kismali, G., Kınaytürk, N. K., Kılıç, D., Karacolak, A. I., & Demirdogen, R. E. (2021). Pyridine derivative platinum complexes: Synthesis, molecular structure, DFT and initial anticancer activity studies. Journal of Molecular Structure, 1234, 130191. https://doi.org/10.1016/j.molstruc.2021.130191
   Web of Science ®Google Scholar
• Laurent, G. J., & Shapiro, S. D. (Eds.). (2006). Encyclopedia of respiratory medicine (1st ed.). Academic Press.
   Google Scholar
• Liao, S. Y., Chen, J. C., Mo, G. Q., Zhang, C., & Zheng, K. C. (2015). A computational study of binding between 3-(4-fluorophenyl)-N-((4-fluorophenyl) sulphonyl) acrylamide and tubulin. Molecular Simulation, 41(4), 356–364. https://doi.org/10.1080/08927022.2014.894242
   Web of Science ®Google Scholar
• Lokwani, D. K., Sarkate, A. P., Karnik, K. S., Nikalje, A. P. G., & Seijas, J. A. (2020). Structure-based site of metabolism (SOM) prediction of ligand for CYP3A4 enzyme: Comparison of Glide XP and Induced Fit Docking (IFD). Molecules, 25(7), 1622. https://doi.org/10.3390/molecules25071622
   PubMed Web of Science ®Google Scholar
• Mannu, J., Jenardhanan, P., & Mathur, P. P. (2011). A computational study of CYP3A4 mediated drug interaction profiles for anti-HIV drugs. Journal of Molecular Modeling, 17(8), 1847–1854. https://doi.org/10.1007/s00894-010-0890-6
   PubMed Web of Science ®Google Scholar
• Marechal, J.-D., Yu, J., Brown, S., Kapelioukh, I., Rankin, E. M., Wolf, C. R., Roberts, G. C. K., Paine, M. J. I., & Sutcliffe, M. J. (2006). In silico and in vitro screening for inhibition of cytochrome P450 CYP3A4 by comedications commonly used by patients with cancer. Drug Metabolism and Disposition: The Biological Fate of Chemicals, 34(4), 534–538.
   PubMed Web of Science ®Google Scholar
• Maren, T. H. (1976). Relations between structure and biological activity of sulfonamides. Annual Review of Pharmacology and Toxicology, 16(1), 309–327. https://doi.org/10.1146/annurev.pa.16.040176.001521
   PubMedGoogle Scholar
• Mariappan, G., & Sundaraganesan, N. (2015). Structural and vibrational spectroscopic analysis of anticancer drug mitotane using density functional theory. Materials Today: Proceedings, 2(3), 965–968.
   Google Scholar
• McQueen, C. (2010). Comprehensive toxicology(2nd Ed.). Elsevier.
   Google Scholar
• Mıhçıokur, Ö., & Özpozan, T. (2017). Molecular structure, vibrational spectroscopic analysis (IR & Raman), HOMO-LUMO and NBO analysis of anti-cancer drug sunitinib using DFT method. Journal of Molecular Structure, 1149, 27–41. https://doi.org/10.1016/j.molstruc.2017.07.064
   Web of Science ®Google Scholar
• Muthu, S., Maheswari, J. U., & Sundius, T. (2013). Molecular structural, non-linear optical, second order perturbation and Fukui studies of Indole-3-Aldehyde using density functional calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 106, 299–309. https://doi.org/10.1016/j.saa.2012.12.080
   PubMed Web of Science ®Google Scholar
• Ngan, V. K., Bellman, K., Panda, D., Hill, B. T., Jordan, M. A., & Wilson, L. (2000). Novel actions of the antitumor drugs vinflunine and vinorelbine on microtubules. Cancer Research, 60(18), 5045–5051.
   PubMed Web of Science ®Google Scholar
• O'boyle, N. M., Tenderholt, A. L., & Langner, K. M. (2008). Cclib: A library for package‐independent computational chemistry algorithms. Journal of Computational Chemistry, 29(5), 839–845.
   PubMed Web of Science ®Google Scholar
• Pangajavalli, S., Ranjithkumar, R., Sridhar, B., & Ramaswamy, S. (2017). Hirshfeld and vibrational analysis of 5-Benzyl-7a-Hydroxy-1-Methyl-2,3,5,6,7,7a-Hexahydro-1h-3a, 7-Methanoindeno [2,1-d]Pyrrolo[3,2-c]Azepine-12,13(4h)-Dione. Mechanics, Materials Science & Engineering Journal, Magnolithe, 12, 1–9.
   Google Scholar
• Pearson, R. G. (1973). Hard and soft acids and bases (Vol. 2). Van Nostrand Reinhold.
   Google Scholar
• Politzer, P., & Murray, J. S. (2002). The fundamental nature and role of the electrostatic potential in atoms and molecules. Theoretical Chemistry Accounts, 108(3), 134–142. https://doi.org/10.1007/s00214-002-0363-9
   Web of Science ®Google Scholar
• Prota, A. E., Danel, F., Bachmann, F., Bargsten, K., Buey, R. M., Pohlmann, J., Reinelt, S., Lane, H., & Steinmetz, M. O. (2014). The novel microtubule-destabilizing drug BAL27862 binds to the colchicine site of tubulin with distinct effects on microtubule organization. Journal of Molecular Biology, 426(8), 1848–1860. https://doi.org/10.1016/j.jmb.2014.02.005
   PubMed Web of Science ®Google Scholar
• Pulay, P., Fogarasi, G., Pongor, G., Boggs, J. E., & Vargha, A. (1983). Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene. Journal of the American Chemical Society, 105(24), 7037–7047. https://doi.org/10.1021/ja00362a005
   Web of Science ®Google Scholar
• Ravelli, R. B., Gigant, B., Curmi, P. A., Jourdain, I., Lachkar, S., Sobel, A., & Knossow, M. (2004). Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature, 428(6979), 198–202. https://doi.org/10.1038/nature02393
   PubMed Web of Science ®Google Scholar
• Roeges, N. P., & Baas, J. M. A. (1994). A guide to the complete interpretation of infrared spectra of organic structures (pp. 1–340). Wiley.
   Google Scholar
• Rowland, P., Blaney, F. E., Smyth, M. G., Jones, J. J., Leydon, V. R., Oxbrow, A. K., Lewis, C. J., Tennant, M. G., Modi, S., Eggleston, D. S., Chenery, R. J., & Bridges, A. M. (2006). Crystal structure of human cytochrome P450 2D6. The Journal of Biological Chemistry, 281(11), 7614–7622.
   PubMed Web of Science ®Google Scholar
• Scozzafava, A., Carta, F., & Supuran, C. T. (2013). Secondary and tertiary sulfonamides: A patent review (2008–2012). Expert Opinion on Therapeutic Patents, 23(2), 203–213. https://doi.org/10.1517/13543776.2013.742065
   PubMed Web of Science ®Google Scholar
• Sebhaoui, J., El Bakri, Y., Lai, C. H., Karthikeyan, S., Anouar, E. H., Mague, J. T., & Essassi, E. M. (2021). Unexpected synthesis of novel 2-pyrone derivatives: crystal structures, Hirshfeld surface analysis and computational studies. Journal of Biomolecular Structure & Dynamics, 39(13), 4859–4877.
   PubMed Web of Science ®Google Scholar
• Sevrioukova, I. F., & Poulos, T. L. (2010). Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir. Proceedings of the National Academy of Sciences of the United States of America, 107(43), 18422–18427. https://doi.org/10.1073/pnas.1010693107
   PubMed Web of Science ®Google Scholar
• Sevrioukova, I. F., & Poulos, T. L. (2015). Current approaches for investigating and predicting cytochrome P450 3A4-ligand interactions. İn E. G. Hrycay & S. M. Bandiera (Eds.), Monooxygenase, peroxidase and peroxygenase properties and mechanisms of cytochrome P450, 851, 83–105. Springer.
   Google Scholar
• Shao, Y., Molnar, L. F., Jung, Y., Kussmann, J., Ochsenfeld, C., Brown, S. T., Gilbert, A. T., Slipchenko, L. V., Levchenko, S. V., O’Neill, D. P., DiStasio Jr, R. A., Lochan, R. C., Wang, T., Beran, G. J., Besley, N. A., Herbert, J. M., Yeh Lin, C., Van Voorhis, T., Hung Chien, S., … Head-Gordon, M. (2006). Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics, 8(27), 3172–3191. https://doi.org/10.1039/B517914A
   PubMed Web of Science ®Google Scholar
• Silverstein, M., Basseler, G. C., & Morill, C. (1981). Spectrometric ıdentification of organic compounds. Wiley.
   Google Scholar
• Socrates, G. (1980). Infrared characteristic group frequencies. Wiley-Interscience Publication.
   Google Scholar
• Stewart, J. J. (1989). Optimization of parameters for semiempirical methods I. Method. Journal of Computational Chemistry, 10(2), 209–220. https://doi.org/10.1002/jcc.540100208
   Web of Science ®Google Scholar
• Stewart, J. J. (1989). Optimization of parameters for semiempirical methods II. Applications. Journal of Computational Chemistry, 10(2), 221–264.
   Web of Science ®Google Scholar
• Stewart, J. J. (1991). Optimization of parameters for semiempirical methods. İİİ extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, İn, Sn, Sb, Te, Hg, Tl, Pb, and Bi. Journal of Computational Chemistry, 12(3), 320–341. https://doi.org/10.1002/jcc.540120306
   Web of Science ®Google Scholar
• Stewart, J. J. (2004). Optimization of parameters for semiempirical methods IV: Extension of MNDO, AM1, and PM3 to more main group elements. Journal of Molecular Modeling, 10(2), 155–164. https://doi.org/10.1007/s00894-004-0183-z
   PubMed Web of Science ®Google Scholar
• Stravodimou, A., Zaman, K., & Voutsadakis, I. A. (2014). Vinorelbine with or without trastuzumab in metastatic breast cancer: A retrospective single institution series. ISRN Oncology, 2014, 1–7. https://doi.org/10.1155/2014/289836
   Google Scholar
• Subhani, S., & Jamil, K. (2015). Molecular docking of chemotherapeutic agents to CYP3A4 in non-small cell lung cancer. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 73, 65–74. https://doi.org/10.1016/j.biopha.2015.05.018
   PubMed Web of Science ®Google Scholar
• Subramanian, N., Sundaraganesan, N., Sudha, S., Aroulmoji, V., Sockalingam, G. D., & Bergamin, M. (2011). Experimental and theoretical investigation of the molecular and electronic structure of anticancer drug camptothecin. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 78(3), 1058–1067. https://doi.org/10.1016/j.saa.2010.12.049
   PubMed Web of Science ®Google Scholar
• Sundius, T. (1990). Molvib-A flexible program for force field calculations. Journal of Molecular Structure, 218, 321–326. https://doi.org/10.1016/0022-2860(90)80287-T
   Web of Science ®Google Scholar
• Sundius, A. T. (2002). Scaling of ab initio force fields by MOLVIB. Vibrational Spectroscopy, 29(1–2), 89–95. https://doi.org/10.1016/S0924-2031(01)00189-8
   Web of Science ®Google Scholar
• Thirunavukkarasu, K., Rajkumar, P., Selvaraj, S., Suganya, R., Kesavan, M., Gunasekaran, S., & Kumaresan, S. (2018). Vibrational (FT-IR and FT-Raman), electronic (UV–Vis), NMR (1H and 13C) spectra and molecular docking analyses of anticancer molecule 4-hydroxy-3-methoxycinnamaldehyde. Journal of Molecular Structure, 1173, 307–320. https://doi.org/10.1016/j.molstruc.2018.07.003
   Web of Science ®Google Scholar
• Topletz, A. R., Dennison, J. B., Barbuch, R. J., Hadden, C. E., Hall, S. D., & Renbarger, J. L. (2013). The relative contributions of CYP3A4 and CYP3A5 to the metabolism of vinorelbine. Drug Metabolism and Disposition, 41(9), 1651–1661. https://doi.org/10.1124/dmd.113.051094
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: İmproving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461.
   PubMed Web of Science ®Google Scholar
• Waldman, S. A., & Terzic, A. (2008). Pharmacology and therapeutics: Principles to practice (1st Ed.). Elsevier.
   Google Scholar
• Wang, Z., Wang, X., Li, Y., Lei, T., Wang, E., Li, D., Kang, Y., Zhu, F., & Hou, T. (2019). farPPI: A webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB (GB) SA methods. Bioinformatics (Oxford, England), 35(10), 1777–1779. https://doi.org/10.1093/bioinformatics/bty879
   PubMed Web of Science ®Google Scholar
• Williams, P. A., Cosme, J., Vinkovic, D. M., Ward, A., Angove, H. C., Day, P. J., Vonrhein, C., Tickle, I. J., & Jhoti, H. (2004). Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science (New York, N.Y.), 305(5684), 683–686.
   PubMed Web of Science ®Google Scholar
• Yano, J. K., Wester, M. R., Schoch, G. A., Griffin, K. J., Stout, C. D., & Johnson, E. F. (2004). The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-Å resolution. The Journal of Biological Chemistry, 279(37), 38091–38094.
   PubMed Web of Science ®Google Scholar
• Zhurko, G. A. (2005). Chemcraft - Graphical program for visualization of quantum chemistry computations. https://chemcraftprog.com
   Google Scholar