A detailed theoretical exploration on the THR-β binding affinities and antioxidant activity of some halogenated bisphenols

References

• Becke, A. D. (1992). Density‐functional thermochemistry. I. The effect of the exchange‐only gradient correction. Journal of Chemical Physics, 96, 2155.
   Web of Science ®Google Scholar
• Ahmad, S., Arshad, M. A., Ijaz, S., Khurshid, U., Rashid, F., & Azam, R. (2014). Review on methods used to determine antioxidant activity. International Journal of Multidisciplinary Research & Development, 1, 35.
   Google Scholar
• Akbaba, Y., Balaydın, H. T., Menzek, A., Göksu, S., Şahin, E., & Ekinci, D. (2013). Synthesis and biological evaluation of novel bromophenol derivatives as carbonic anhydrase inhibitors. Archiv der Pharmazie, 346(6), 447–454. https://doi.org/10.1002/ardp.201300054
   PubMed Web of Science ®Google Scholar
• Akinori, I., Sawatsubashi, S., & Yamauchi, K. (2003). Endocrine disrupting chemicals: Interference of thyroid hormone binding to transthyretins and to thyroid hormone receptors. Molecular and Cellular Endocrinology, 199, 105.
   PubMed Web of Science ®Google Scholar
• Balaydın, H. T., Gülçin, İ., Menzek, A., Göksu, S., & Şahin, E. (2010). Synthesis and antioxidant properties of diphenylmethane derivative bromophenols including a natural product. Journal of Enzyme Inhibition and Medicinal Chemistry, 25(5), 685–695. https://doi.org/10.3109/14756360903514164
   PubMed Web of Science ®Google Scholar
• Balaydın, H. T., Soyut, H., Ekinci, D., Göksu, S., Beydemir, S., Menzek, A., & Sahin, E. (2012). Synthesis and carbonic anhydrase inhibitory properties of novel bromophenols including natural products. Journal of Enzyme Inhibition and Medicinal Chemistry, 27(1), 43–50. https://doi.org/10.3109/14756366.2011.574131
   PubMed Web of Science ®Google Scholar
• Behazin, R., & Ebrahimi, A. (2018). The physicochemical properties and tyrosinase inhibitory activity of ectoine and its analogues: A theoretical study. Computational and Theoretical Chemistry, 1130, 6–14. https://doi.org/10.1016/j.comptc.2018.03.003
   Web of Science ®Google Scholar
• Bleicher, L., Aparicio, R., Nunes, F. M., Martinez, L., Gomes Dias, S. M., Figueira, A. C. M., Santos, M. A. M., Venturelli, W. H., da Silva, R., Donate, P. M., Neves, F. A., Simeoni, L. A., Baxter, J. D., Webb, P., Skaf, M. S., & Polikarpov, I. (2008). Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms. BMC Structural Biology, 8, 8. https://doi.org/10.1186/1472-6807-8-8
   PubMed Web of Science ®Google Scholar
• Buch, I., Giorgino, T., & De Fabritiis, G. (2011). Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America, 108(25), 10184–10189. https://doi.org/10.1073/pnas.1103547108
   PubMed Web of Science ®Google Scholar
• Case, D. A., Berryman, J. T., Betz, R. M., Cerutti, D. S., Cheatham, T. E., Darden, I. I. I. T. A., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T. S., LeGrand, S., Li, P., Luchko, T.,… Kollman, P. A. (2015). Amber Tools 14. University of California, San Francisco.
   Google Scholar
• Chung, L. W., Sameera, W. M. C., Ramozzi, R., Page, A. J., Hatanaka, M., Petrova, G. P., Harris, T. V., Li, X., Ke, Z., Liu, F., Li, H.-B., Ding, L., & Morokuma, K. (2015). The ONIOM method and its applications. Chemical Reviews, 115(12), 5678–5796. https://doi.org/10.1021/cr5004419
   PubMed Web of Science ®Google Scholar
• Duan, X. J., Li, X. M., & Wang, B. G. (2007). Highly brominated mono- and bis-phenols from the marine red alga Symphyocladia latiuscula with radical-scavenging activity. Journal of Natural Products, 70(7), 1210–1213. https://doi.org/10.1021/np070061b
   PubMed Web of Science ®Google Scholar
• Erin, M. K., Carbonnel, L. D., Stapleton, H. M., & Ferguson, P. L. (2018). The affinity of brominated phenolic compounds for human and zebrafish thyroid receptor β: Influence of chemical structure. Toxicological Sciences, 163, 226.
   PubMed Web of Science ®Google Scholar
• Faghih, Z., Fereidoonnezhad, M., Tabaei, S. M. H., Rezaei, Z., & Zolghadr, A. R. (2015). The binding of small carbazole derivative (P7C3) to protofibrils of the Alzheimer’s disease and β-secretase: Molecular dynamics simulation studies. Chemical Physics, 459, 31–39. https://doi.org/10.1016/j.chemphys.2015.07.026
   Web of Science ®Google Scholar
• Fei, L., Xie, Q., Li, X., Li, N., Chi, P., Chen, J., Wang, Z., & Hao, C. (2010). Hormone activity of hydroxylated polybrominated diphenyl ethers on human thyroid receptor-β: In vitro and in silico investigations. Environmental Health Perspectives, 118, 602.
   PubMed Web of Science ®Google Scholar
• Flodin, C., & Whitfield, F. B. (1999). Biosynthesis of bromophenols in marine algae. Water Science and Technology, 40(6), 53–58. https://doi.org/10.2166/wst.1999.0260
   Web of Science ®Google Scholar
• Frisch, M. J., Hratchian, H. P., Dennington, R. D., Todd, A., Keith, T. A., and Millam, J. (2009). GaussView 5. Gaussian, Inc.
   Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Cari-Cato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M. … Fox, D. J. (2009). Gaussian 09, revision A.02. 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
• Gordon, G. W. (1999). The diversity of naturally occurring organobromine compounds. Chemical Society Reviews, 28, 335.
   Web of Science ®Google Scholar
• Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M05-2X and M06-2X exchange-correlation functionals for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4(12), 1996–2000. https://doi.org/10.1021/ct800308k
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Hye, L. J., Lee, T. K., Kang, R. S., Shin, H. J., & Lee, H. S. (2007). The in vitro antioxidant activities of the bromophenols from the red alga Tichocarpus crinitus and phenolic derivatives. Journal of Korean Magnetic Resonance Society, 11, 56.
   Google Scholar
• Ishihara, A., Nishiyama, N., Sugiyama, S. I., & Yamauchi, K. (2003). The effect of endocrine disrupting chemicals on thyroid hormone binding to Japanese quail transthyretin and thyroid hormone receptor. General and Comparative Endocrinology, 134(1), 36–43. https://doi.org/10.1016/S0016-6480(03)00197-7
   PubMed Web of Science ®Google Scholar
• Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. Journal of Computational Chemistry, 23(16), 1623–1641. https://doi.org/10.1002/jcc.10128
   PubMed Web of Science ®Google Scholar
• Joharapurkar, A. A., Dhote, V. V., & Jain, M. R. (2012). Selective thyromimetics using receptor and tissue selectivity approaches: Prospects for dyslipidemia. Journal of Medicinal Chemistry, 55(12), 5649–5675. https://doi.org/10.1021/jm2004706
   PubMed Web of Science ®Google Scholar
• Johnson, B. G., Gill, P. M. W., Pople, J. A., & Fox, D. J. (1993). Computing molecular electrostatic potentials with the PRISM algorithm. Chemical Physics Letters, 206(1–4), 239–246. https://doi.org/10.1016/0009-2614(93)85547-2
   Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Ke, L., Li, X. M., Ji, N. Y., & Wang, B. G. (2008). Bromophenols from the marine red alga Polysiphonia urceolata with DPPH radical scavenging activity. Journal of Natural Products, 71, 28.
   PubMed Web of Science ®Google Scholar
• Kitamura, S., Shinohara, S., Iwase, E., Sugihara, K., Uramaru, N., Shigematsu, H., Fujimoto, N., & Ohta, S. (2008). Affinity for thyroid hormone and estrogen receptors of hydroxylated polybrominated diphenyl ethers. Journal of Health Science, 54(5), 607–614. https://doi.org/10.1248/jhs.54.607
   Google Scholar
• Kitisripanya, N., Saparpakorn, P., Wolschann, P., & Hannongbua, S. (2011). Binding of huperzine A and galanthamine to acetylcholinesterase, based on ONIOM method. Nanomedicine: Nanotechnology, Biology and Medicine, 7(1), 60–68. https://doi.org/10.1016/j.nano.2010.08.004
   PubMed Web of Science ®Google Scholar
• Kohnke, B., Kutzner, C., & Grubmüller, H. (2020). A GPU-accelerated fast multipole method for GROMACS: Performance and accuracy. Journal of Chemical Theory and Computation, 16(11), 6938–6949. https://doi.org/10.1021/acs.jctc.0c00744
   PubMed Web of Science ®Google Scholar
• Kollitz, E. M., Carbonnel, L. D., Stapleton, H. M., & Ferguson, P. L. (2018). The affinity of brominated phenolic compounds for human and zebrafish thyroid receptor β: Influence of chemical structure. Toxicological Sciences: An Official Journal of the Society of Toxicology, 163(1), 226–239. https://doi.org/10.1093/toxsci/kfy028
   PubMed Web of Science ®Google Scholar
• Kurata, K., Taniguchii, K., Takashima, K., Hayashi, I., & Suzuki, M. (1997). Feeding-deterrent bromophenols from Odonthalia corymbifera. Phytochemistry, 45(3), 485–487. https://doi.org/10.1016/S0031-9422(97)00014-9
   Web of Science ®Google Scholar
• Lee, C., Yang, W., & Parr, R. G. (1988). Density-functional exchange-energy approximation with correct asymptotic behaviour. Physical Review B, 37(2), 785–789. https://doi.org/10.1103/PhysRevB.37.785
   PubMed Web of Science ®Google Scholar
• Leonetti, C., Butt, C. M., Hoffman, K., Miranda, M. L., & Stapleton, H. M. (2016). Concentrations of polybrominated diphenyl ethers (PBDEs) and 2,4,6-tribromophenol in human placental tissues. Environment International, 88, 23–29. https://doi.org/10.1016/j.envint.2015.12.002
   PubMed Web of Science ®Google Scholar
• Leopoldini, M., Russo, N., & Toscano, M. (2011). The molecular basis of working mechanism of natural polyphenolic antioxidants. Food Chemistry, 125(2), 288–306. https://doi.org/10.1016/j.foodchem.2010.08.012
   Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Liu, M., Hansen, P. E., & Lin, X. (2011). Bromophenols in marine algae and their bioactivities. Marine Drugs, 9(7), 1273–1292. https://doi.org/10.3390/md9071273
   PubMed Web of Science ®Google Scholar
• Maestro, V. (2017). Schrödinger Release 2017-1. Schrodinger, LLC.
   Google Scholar
• Matthieu, S., Raaka, B. M., Das, S., Fan, L., Totrov, M., Zhou, Z., Wilson, S. R., Abagyan, R., & Samuels, H. H. (2003). Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proceedings of the National Academy of Sciences of the United States of America, 100, 7354.
   PubMed Web of Science ®Google Scholar
• Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Ming, L., Hansen, P. E., & Lin, X. (2011). Bromophenols in marine algae and their bioactivities. Marine Drugs, 9, 1273.
   PubMed Web of Science ®Google Scholar
• Mondal, S., & Mugesh, G. (2017). Novel thyroid hormone analogues, enzyme inhibitors and mimetics, and their action. Molecular and Cellular Endocrinology, 458, 91–104. https://doi.org/10.1016/j.mce.2017.04.006
   PubMed Web of Science ®Google Scholar
• Nascimento, A. S., Dias, S. M. G., Nunes, F. M., Aparício, R., Ambrosio, A. L. B., Bleicher, L., Figueira, A. C. M., Santos, M. A. M., Neto, M. D. O., Fischer, H., Togashi, M., Craievich, A. F., Garratt, R. C., Baxter, J. D., Webb, P., & Polikarpov, I. (2006). Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function. Journal of Molecular Biology, 360(3), 586–598. https://doi.org/10.1016/j.jmb.2006.05.008
   PubMed Web of Science ®Google Scholar
• Olszowy, M. (2019). What is responsible for antioxidant properties of polyphenolic compounds from plants? Plant Physiology and Biochemistry: PPB, 144, 135–143. https://doi.org/10.1016/j.plaphy.2019.09.039
   PubMed Web of Science ®Google Scholar
• Ortega-Domínguez, B., Aparicio-Trejo, O. E., García-Arroyo, F. E., León-Contreras, J. C., Tapia, E., Molina-Jijón, E., Hernández-Pando, R., Sánchez-Lozada, L. G., Barrera-Oviedo, D., & Pedraza-Chaverri, J. (2017). Curcumin prevents cisplatin-induced renal alterations in mitochondrial bioenergetics and dynamic. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 107(Pt A), 373–385. https://doi.org/10.1016/j.fct.2017.07.018
   PubMedGoogle Scholar
• Ovalle-Magallanes, B., Eugenio-Pérez, D., & Pedraza-Chaverri, J. (2017). Medicinal properties of mangosteen (Garcinia mangostana L.): A comprehensive update. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 109(Pt 1), 102–122. https://doi.org/10.1016/j.fct.2017.08.021
   PubMedGoogle Scholar
• Öztaskın, N., Taslimi, P., Maraş, A., Gülcin, İ., & Göksu, S. (2017). Novel antioxidant bromophenols with acetylcholinesterase, butyrylcholinesterase and carbonic anhydrase inhibitory actions. Bioorganic Chemistry, 74, 104–114. https://doi.org/10.1016/j.bioorg.2017.07.010
   PubMed Web of Science ®Google Scholar
• Qi, R., Walker, B., Jing, Z., Yu, M., Stancu, G., Edupuganti, R., Dalby, K. N., & Ren, P. (2019). Computational and experimental studies of inhibitor design for Aldolase A. The Journal of Physical Chemistry. B, 123(28), 6034–6041. https://doi.org/10.1021/acs.jpcb.9b04551
   PubMed Web of Science ®Google Scholar
• Ren, X. M., Guo, L. H., Gao, Y., Zhang, B. T., & Wan, B. (2013). Hydroxylated polybrominated diphenyl ethers exhibit different activities on thyroid hormone receptors depending on their degree of bromination. Toxicology and Applied Pharmacology, 268(3), 256–263. https://doi.org/10.1016/j.taap.2013.01.026
   PubMed Web of Science ®Google Scholar
• Rimarčík, J., Lukeš, V., Klein, E., & Ilčin, M. (2010). Study of the solvent effect on the enthalpies of homolytic and heterolytic N–H bond cleavage in p-phenylenediamine and tetracyano-p-phenylenediamine. Journal of Molecular Structure: Theochem, 952(1–3), 25–30. https://doi.org/10.1016/j.theochem.2010.04.002
   Web of Science ®Google Scholar
• Romero, F. A., Jones, C. T., Xu, Y., Fenaux, M., & Halcomb, R. L. (2020). The race to bash NASH: Emerging targets and drug development in a complex liver disease. Journal of Medicinal Chemistry, 63(10), 5031–5073. https://doi.org/10.1021/acs.jmedchem.9b01701
   PubMed Web of Science ®Google Scholar
• Schrödinger. (2017). Release, Schrödinger. 4: Prime. Schrödinger, LLC.
   Google Scholar
• Senthil Kumar, K., & Kumaresan, R. (2012). A DFT study on the structural, electronic properties and radical scavenging mechanisms of calycosin, glycitein, pratensein and prunetin. Computational and Theoretical Chemistry, 985, 14–22. https://doi.org/10.1016/j.comptc.2012.01.028
   Web of Science ®Google Scholar
• Shahraki, A., & Ebrahimi, A. (2019). Binding of ellagic acid and urolithin metabolites to the CK2 protein, based on the ONIOM method and molecular docking calculations. New Journal of Chemistry, 43(40), 15983–15998. https://doi.org/10.1039/C9NJ03508G
   Web of Science ®Google Scholar
• Shi, D., Li, J., Guo, S., Su, H., & Fan, X. (2009). The antitumor effect of bromophenol derivatives in vitro and Leathesia nana extract in vivo. Chinese Journal of Oceanology and Limnology, 27(2), 277–282. https://doi.org/10.1007/s00343-009-9119-x
   Web of Science ®Google Scholar
• Shigeyuki, K., Jinno, N., Suzuki, T., Sugihara, K., Ohta, S., Kuroki, H., & Fujimoto, N. (2005). Thyroid hormone-like and estrogenic activity of hydroxylated PCBs in cell culture. Toxicology, 208, 377.
   PubMed Web of Science ®Google Scholar
• Shulin, Z., Bao, L., Linhananta, A., & Liu, W. (2013). Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization. Journal of Molecular Graphics and Modelling, 44, 155.
   PubMed Web of Science ®Google Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon parser interfacE. BMC Research Notes, 5, 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Stapleton, H. M., Eagle, S., Sjödin, A., & Webster, T. F. (2012). Serum PBDEs in a North Carolina toddler cohort: Associations with handwipes, house dust, and socioeconomic variables. Environmental Health Perspectives, 120(7), 1049–1054. https://doi.org/10.1289/ehp.1104802
   PubMed Web of Science ®Google Scholar
• Thangaraj, S. K., Arola, H., Tullila, A., Nevanen, T. K., Rouvinen, J., & Jänis, J. (2019). Quantitation of thyroid hormone binding to anti-thyroxine antibody fab fragment by native mass spectrometry. ACS Omega, 4(20), 18718–18724. https://doi.org/10.1021/acsomega.9b02659
   PubMed Web of Science ®Google Scholar
• Trummal, A., Lipping, L., Kaljurand, I., Koppel, I. A., & Leito, I. (2016). Acidity of strong acids in water and dimethyl sulfoxide. The Journal of Physical Chemistry. A, 120(20), 3663–3669. https://doi.org/10.1021/acs.jpca.6b02253
   PubMed Web of Science ®Google Scholar
• Vanessa, D., Grimaldi, M., Pons, J. L., Boulahtouf, A., Maire, A. L., Cavailles, V., Labesse, G., Bourguet, W., & Balaguer, P. (2012). Structural and mechanistic insights into bisphenols action provide guidelines for risk assessment and discovery of bisphenol A substitutes. Proceedings of the National Academy of Sciences of the United States of America, 109, 14930.
   PubMed Web of Science ®Google Scholar
• Vreven, T., Byun, K. S., Komáromi, I., Dapprich, S., M, J. A., Jr., Morokuma, K., & Frisch, M. J. (2006). Combining quantum mechanics methods with molecular mechanics methods in ONIOM. Journal of Chemical Theory and Computation, 2(3), 815–826. https://doi.org/10.1021/ct050289g
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, W., Okada, Y., Shi, H., Wang, Y., & Okuyama, T. (2005). Structures and aldose reductase inhibitory effects of bromophenols from the red alga Symphyocladia l atiuscula. Journal of Natural Products, 68(4), 620–622. https://doi.org/10.1021/np040199j
   PubMed Web of Science ®Google Scholar
• Wanyi, Z., Feng, X., Ban, S., Lin, W., & Li, Q. (2010). Synthesis and biological activity of halophenols as potent antioxidant and cytoprotective agents. Bioorganic and Medicinal Chemistry Letters, 20, 4132.
   PubMed Web of Science ®Google Scholar
• Wright, J. S., Johnson, E. R., & DiLabio, G. A. (2001). Predicting the activity of phenolic antioxidants: Theoretical method, analysis of substituent effects, and application to major families of antioxidants. Journal of the American Chemical Society, 123(6), 1173–1183. https://doi.org/10.1021/ja002455u
   PubMed Web of Science ®Google Scholar
• Xu, N., Fan, X., Yan, X., Li, X., Niu, R., & Tseng, C. K. (2003). Antibacterial bromophenols from the marine red alga Rhodomela confervoides. Phytochemistry, 62(8), 1221–1224. https://doi.org/10.1016/s0031-9422(03)00004-9
   PubMed Web of Science ®Google Scholar
• Xu, X., Song, F., Wang, S., Li, S., Xiao, F., Zhao, J., Yang, Y., Shang, S., Yang, L., & Shi, J. (2004). Dibenzyl bromophenols with diverse dimerization patterns from the brown alga Leathesia nana. Journal of Natural Products, 67(10), 1661–1666. https://doi.org/10.1021/np0400609
   PubMed Web of Science ®Google Scholar
• Zhong, D., Wang, H., Liu, M., Li, X., Huang, M., Zhou, H., Lin, S., Lin, Z., & Yang, B. (2015). Ganoderma lucidum polysaccharide peptide prevents renal ischemia reperfusion injury via counteracting oxidative stress. Scientific Reports, 5, 16910. https://doi.org/10.1038/srep16910
   PubMed Web of Science ®Google Scholar