Ligand pathways in estrogen-related receptors

References

• Abad, M. C., Askari, H., O'Neill, J., Klinger, A. L., Milligan, C., Lewandowski, F., Springer, B., Spurlino, J., & Rentzeperis, D. (2008). Structural determination of estrogen-related receptor gamma in the presence of phenol derivative compounds. The Journal of Steroid Biochemistry and Molecular Biology, 108(1–2), 44–54. https://doi.org/10.1016/j.jsbmb.2007.06.006
   PubMed Web of Science ®Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662
   PubMed Web of Science ®Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Gallo Cassarino, T., Bertoni, M., Bordoli, L., Schwede, T., Cassarino, T. G., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252. https://doi.org/10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Bortolato, A., Deflorian, F., Weiss, D. R., & Mason, J. S. (2015). Decoding the role of water dynamics in ligand-protein unbinding: CRF1R as a test case. Journal of Chemical Information and Modeling, 55(9), 1857–1866. https://doi.org/10.1021/acs.jcim.5b00440
   PubMed Web of Science ®Google Scholar
• Bowers, K., Chow, E., Xu, H., Dror, R., Eastwood, M., Gregersen, B., Klepeis, J., Kolossvary, I., Moraes, M., Sacerdoti, F., Salmon, J., Shan, Y., & Shaw, D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. In SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing.
   Google Scholar
• Bussi, G., Laio, A., & Tiwary, P. (2018). Metadynamics: A unified framework for accelerating rare events and sampling thermodynamics and kinetics. In W. Andreoni & S. Yip (Eds.), Handbook of materials modeling: Methods: theory and modeling (pp. 1–31). Springer International Publishing.
   Google Scholar
• Capelli, A. M., Bruno, A., Entrena Guadix, A., & Costantino, G. (2013). Unbinding pathways from the glucocorticoid receptor shed light on the reduced sensitivity of glucocorticoid ligands to a naturally occurring, clinically relevant mutant receptor. Journal of Medicinal Chemistry, 56(17), 7003–7014. https://doi.org/10.1021/jm400802b
   PubMed Web of Science ®Google Scholar
• Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., & Damborsky, J. (2012). CAVER 3.0: A tool for the analysis of transport pathways in dynamic protein structures. PLoS Computational Biology, 8(10), e1002708–30. https://doi.org/10.1371/journal.pcbi.1002708
   PubMed Web of Science ®Google Scholar
• Cresci, S., Huss, J. M., Beitelshees, A. L., Jones, P. G., Minton, M. R., Dorn, G. W., Kelly, D. P., Spertus, J. A., & McLeod, H. L. (2010). A pparα promoter variant impairs ERR-dependent transactivation and decreases mortality after acute coronary ischemia in patients with diabetes. PLoS One, 5(9), e12584. https://doi.org/10.1371/journal.pone.0012584
   PubMed Web of Science ®Google Scholar
• Divekar, S. D., Tiek, D. M., Fernandez, A., & Riggins, R. B. (2016). Estrogen-related receptor β (ERRβ) – renaissance receptor or receptor renaissance? Nuclear Receptor Signaling, 14(1), nrs.14002. https://doi.org/10.1621/nrs.14002
   Google Scholar
• Fischer, A., Frehner, G., Lill, M. A., & Smieško, M. (2021). Conformational changes of thyroid receptors in response to antagonists. Journal of Chemical Information and Modeling, 61(2), 1010–1019. https://doi.org/10.1021/acs.jcim.0c01403
   PubMed Web of Science ®Google Scholar
• Fischer, A., & Smieško, M. (2019). Ligand pathways in nuclear receptors. Journal of Chemical Information and Modeling, 59(7), 3100–3109. https://doi.org/10.1021/acs.jcim.9b00360
   PubMed Web of Science ®Google Scholar
• Fischer, A., & Smieško, M. (2019). Spontaneous ligand access events to membrane-bound cytochrome P450 2D6 sampled at atomic resolution. Scientific Reports, 9(1), 16411. https://doi.org/10.1038/s41598-019-52681-w
   PubMedGoogle Scholar
• Gallet, M., & Vanacker, J. M. (2010). ERR receptors as potential targets in osteoporosis. Trends in Endocrinology and Metabolism: TEM, 21(10), 637–641. https://doi.org/10.1016/j.tem.2010.06.008
   PubMed Web of Science ®Google Scholar
• Gora, A., Brezovsky, J., & Damborsky, J. (2013). Gates of enzymes. Chemical Reviews, 113(8), 5871–5923. https://doi.org/10.1021/cr300384w
   PubMed Web of Science ®Google Scholar
• Grebner, C., Lecina, D., Gil, V., Ulander, J., Hansson, P., Dellsen, A., Tyrchan, C., Edman, K., Hogner, A., & Guallar, V. (2017). Exploring binding mechanisms in nuclear hormone receptors by Monte Carlo and X-ray-derived motions. Biophysical Journal, 112(6), 1147–1156. https://doi.org/10.1016/j.bpj.2017.02.004
   PubMed Web of Science ®Google Scholar
• Horard, B., & Vanacker, J. M. (2003). Estrogen receptor-related receptors: Orphan receptors desperately seeking a ligand. Journal of Molecular Endocrinology, 31(3), 349–357. https://doi.org/10.1677/jme.0.0310349
   PubMed Web of Science ®Google Scholar
• Huss, J. M., Garbacz, W. G., & Xie, W. (2015). Constitutive activities of estrogen-related receptors: Transcriptional regulation of metabolism by the ERR pathways in health and disease. Biochimica et Biophysica Acta, 1852(9), 1912–1927. https://doi.org/10.1016/j.bbadis.2015.06.016
   PubMed Web of Science ®Google Scholar
• Kingsley, L. J., & Lill, M. A. (2014). Including ligand-induced protein flexibility into protein tunnel prediction. Journal of Computational Chemistry, 35(24), 1748–1756. https://doi.org/10.1002/jcc.23680
   PubMed Web of Science ®Google Scholar
• Koes, D. R., Baumgartner, M. P., & Camacho, C. J. (2013). Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. Journal of Chemical Information and Modeling, 53(8), 1893–1904. https://doi.org/10.1021/ci300604z
   PubMed Web of Science ®Google Scholar
• Li, D., Cai, Y., Teng, D., Li, W., Tang, Y., & Liu, G. (2019). Computational insights into the interaction mechanisms of estrogen-related receptor alpha with endogenous ligand cholesterol. Chemical Biology & Drug Design, 94(1), 1316–1329. https://doi.org/10.1111/cbdd.13506
   PubMed Web of Science ®Google Scholar
• Li, D., Cai, Y., Teng, D., Wu, Z., Li, W., Tang, Y., & Liu, G. (2020). Insights into the interaction mechanisms of estrogen-related receptor alpha (ERRα) with ligands via molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 38(13), 3867–3878. https://doi.org/10.1080/07391102.2019.1666034
   PubMed Web of Science ®Google Scholar
• Limongelli, V., Bonomi, M., & Parrinello, M. (2013). Funnel metadynamics as accurate binding free-energy method. Proceedings of the National Academy of Sciences of the United States of America, 110(16), 6358–6363. https://doi.org/10.1073/pnas.1303186110
   PubMed Web of Science ®Google Scholar
• Li, F., Sun, X., Cai, Y., Fan, D., Li, W., Tang, Y., & Liu, G. (2016). Computational investigation of the interaction mechanism between the estrogen related receptor α and its agonists. RSC Advances, 6(96), 94119–94127. https://doi.org/10.1039/C6RA19536A
   Web of Science ®Google Scholar
• Lynch, C., Zhao, J., Sakamuru, S., Zhang, L., Huang, R., Witt, K., Merrick, B., Teng, C., & Xia, M. (2019). Identification of compounds that inhibit estrogen-related receptor alpha signaling using high-throughput screening assays. Molecules, 24(5), 841. https://doi.org/10.3390/molecules24050841
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Paloncýova, M., Navrátilova, V., Berka, K., Laio, A., & Otyepka, M. (2016). Role of enzyme flexibility in ligand access and egress to active site: Bias-exchange metadynamics study of 1,3,7-trimethyluric acid in cytochrome P450 3A4. Journal of Chemical Theory and Computation, 12(4), 2101–2109. https://doi.org/10.1021/acs.jctc.6b00075
   PubMed Web of Science ®Google Scholar
• Pawlak, M., Lefebvre, P., & Staels, B. (2012). General molecular biology and architecture of nuclear receptors. Current Topics in Medicinal Chemistry, 12(6), 486–504. https://doi.org/10.2174/156802612799436641
   PubMed Web of Science ®Google Scholar
• Saito, K., & Cui, H. (2018). Emerging roles of estrogen-related receptors in the brain: Potential interactions with estrogen signaling. International Journal of Molecular Sciences, 19(4), 1091. https://doi.org/10.3390/ijms19041091
   PubMed Web of Science ®Google Scholar
• Schrodinger, L. C. C. (2019). Maestro Small-Molecular Drug Discovery Suite 2019–4.
   Google Scholar
• Shaw, D. E., Grossman, J. P., Bank, J. A., Batson, B., Butts, J. A., Chao, J. C., Deneroff, M. M., Dror, R. O., Even, A., Fenton, C. H., Forte, A., Gagliardo, J., Gill, G., Greskamp, B., Ho, C. R., Ierardi, D. J., Iserovich, L., Kuskin, J. S., Larson, R. H., Layman, T., Lee, L. S., Lerer, A. K., Li, C., Killebrew, D., Mackenzie, K. M., Mok, S. Y., Moraes, M. A., Mueller, R., Nociolo, L. J., Peticolas, J. L., Quan, T., Ramot, D., Salmon, J. K., Scarpazza, D. P., Ben Schafer, U., Siddique, N., Snyder, C. W., Spengler, J., Tang, P. T., Theobald, M., Toma, H., Towles, B., Vitale, B., Wang, S. C., & Young, C. (2014). Anton 2: Raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In SC'14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (pp. 41–53).
   Google Scholar
• Shen, J., Li, W., Liu, G., Tang, Y., & Jiang, H. (2009). Computational insights into the mechanism of ligand unbinding and selectivity of estrogen receptors. The Journal of Physical Chemistry. B, 113(30), 10436–10444. https://doi.org/10.1021/jp903785h
   PubMed Web of Science ®Google Scholar
• Shiau, A. K., Barstad, D., Loria, P. M., Cheng, L., Kushner, P. J., Agard, D. A., & Greene, G. L. (1998). The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell, 95(7), 927–937. https://doi.org/10.1016/S0092-8674(00)81717-1
   PubMed Web of Science ®Google Scholar
• Studer, G., Rempfer, C., Waterhouse, A. M., Gumienny, R., Haas, J., & Schwede, T. (2020). QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics (Oxford, England), 36(6), 1765–1771. https://doi.org/10.1093/bioinformatics/btz828
   PubMed Web of Science ®Google Scholar
• Suetsugi, M., Su, L., Karlsberg, K., Yuan, Y. C., & Chen, S. (2003). Flavone and isoflavone phytoestrogens are agonists of estrogen-related receptors. Molecular Cancer Research : MCR, 1(13), 981–991.
   PubMed Web of Science ®Google Scholar
• Sun, H., Li, Y., Shen, M., Li, D., Kang, Y., & Hou, T. (2017). Characterizing drug-target residence time with metadynamics: How to achieve dissociation rate efficiently without losing accuracy against time-consuming approaches. Journal of Chemical Information and Modeling, 57(8), 1895–1906. https://doi.org/10.1021/acs.jcim.7b00075
   PubMed Web of Science ®Google Scholar
• Trapl, D., & Spiwok, V. (2020). Analysis of the results of metadynamics simulations by metadynminer and metadynminer3d. arXiv preprint arXiv:2009.02241, 1–11.
   Google Scholar
• Tripathi, M., Yen, P. M., & Singh, B. K. (2020). Estrogen-related receptor alpha: An under-appreciated potential target for the treatment of metabolic diseases. International Journal of Molecular Sciences, 21(5), 1645. https://doi.org/10.3390/ijms21051645
   PubMed Web of Science ®Google Scholar
• Wei, W., Schwaid, A. G., Wang, X., Wang, X., Chen, S., Chu, Q., Saghatelian, A., & Wan, Y. (2016). Ligand activation of ERRα by cholesterol mediates statin and bisphosphonate effects. Cell Metabolism, 23(3), 479–491. https://doi.org/10.1016/j.cmet.2015.12.010
   PubMed Web of Science ®Google Scholar
• Yao, B., Zhang, S., Wei, Y., Tian, S., Lu, Z., Jin, L., He, Y., Xie, W., & Li, Y. (2020). Structural insights into the specificity of ligand binding and coactivator assembly by estrogen-related receptor β. Journal of Molecular Biology, 432(19), 5460–5472. https://doi.org/10.1016/j.jmb.2020.08.007
   PubMed Web of Science ®Google Scholar