143
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Structural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators

, , &
Pages 12401-12410 | Received 12 Oct 2022, Accepted 03 Jan 2023, Published online: 08 Feb 2023

References

  • Anthony, C. S., Masuyer, G., Sturrock, E. D., & Acharya, K. R. (2012). structure based drug design of Angiotensin-I converting enzyme inhibitors. Current Medicinal Chemistry, 19(6), 845–855. https://doi.org/10.2174/092986712799034950
  • Bledsoe, R. K., Montana, V. G., Stanley, T. B., Delves, C. J., Apolito, C. J., McKee, D. D., Consler, T. G., Parks, D. J., Stewart, E. L., Willson, T. M., Lambert, M. H., Moore, J. T., Pearce, K. H., & Xu, H. E. (2002). Crystal structure of the glucocorticoid receptor ligand binding domain reveals a novel mode of receptor dimerization and coactivator recognition. Cell, 110(1), 93–105.
  • Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossváry, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17.
  • Cook, H., Ezzati, M., Segars, J. H., & McCarthy, K. (2010). The impact of uterine leiomyomas on reproductive outcomes. Minerva Ginecologica, 62(3), 225–236.
  • Cui, W., Aouidate, A., Wang, S., Yu, Q., Li, Y., & Yuan, S. (2020). Discovering anti-cancer drugs via computational methods. Frontiers in Pharmacology, 11, 733. https://doi.org/10.3389/fphar.2020.00733
  • Epik, Schrödinger, LLC. (2021). Protein Preparation Wizard. Epik, Schrödinger, LLC.
  • Fields, K. R., & Neinstein, L. S. (1996). Uterine myomas in adolescents: Case reports and a review of the literature. Journal of Pediatric and Adolescent Gynecology, 9(4), 195–198. https://doi.org/10.1016/S1083-3188(96)70030-X
  • Ishikawa, H., Ishi, K., Serna, V. A., Kakazu, R., Bulun, S. E., & Kurita, T. (2010). Progesterone is essential for maintenance and growth of uterine leiomyoma. Endocrinology, 151(6), 2433–2442. https://doi.org/10.1210/en.2009-1225
  • Islam, M., Afrin, S., Jones, S., & Segars, J. (2020). Selective progesterone receptor modulators—Mechanisms and therapeutic utility. Endocrine Reviews, 41(5), 1-52. https://doi.org/10.1210/endrev/bnaa012
  • Kallander, L. S., Washburn, D. G., Hoang, T. H., Frazee, J. S., Stoy, P., Johnson, L., Lu, Q., Hammond, M., Barton, L. S., Patterson, J. R., Azzarano, L. M., Nagilla, R., Madauss, K. P., Williams, S. P., Stewart, E. L., Duraiswami, C., Grygielko, E. T., Xu, X., Laping, N. J., Bray, J. D., & Thompson, S. K. (2010). Improving the developability profile of pyrrolidine progesterone receptor partial agonists. Bioorganic & Medicinal Chemistry Letters, 20(1), 371–374. https://doi.org/10.1016/j.bmcl.2009.10.092
  • Kayikci, M., Venkatakrishnan, A. J., Scott-Brown, J., Ravarani, C. N. J., Flock, T., & Babu, M. M. (2018). Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. Nature Structural & Molecular Biology, 25(2), 185–194. https://doi.org/10.1038/s41594-017-0019-z
  • Khan, J. A., Tikad, A., Fay, M., Hamze, A., Fagart, J., Chabbert-Buffet, N., Meduri, G., Amazit, L., Brion, J.-D., Alami, M., Lombès, M., Loosfelt, H., & Rafestin-Oblin, M.-E. (2013). A new strategy for selective targeting of progesterone receptor with passive antagonists. Molecular Endocrinology, 27(6), 909–924. https://doi.org/10.1210/me.2012-1328
  • Lu, P., Bevan, D. R., Leber, A., Hontecillas, R., Tubau-Juni, N., & Bassaganya-Riera, J. (2018a). Computer-aided drug discovery. Accelerated Path to Cures (pp. 7–24). Springer.
  • Lusher, S. J., Raaijmakers, H. C. A., Vu-Pham, D., Dechering, K., Lam, T. W., Brown, A. R., Hamilton, N. M., Nimz, O., Bosch, R., McGuire, R., Oubrie, A., & de Vlieg, J. (2011). Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators. The Journal of Biological Chemistry, 286(40), 35079–35086. https://doi.org/10.1074/jbc.M111.273029
  • Madauss, K. P., Grygielko, E. T., Deng, S.-J., Sulpizio, A. C., Stanley, T. B., Wu, C., Short, S. A., Thompson, S. K., Stewart, E. L., Laping, N. J., Williams, S. P., & Bray, J. D. (2007). A structural and in vitro characterization of asoprisnil: A selective progesterone receptor modulator. Molecular Endocrinology (Baltimore, Md.), 21(5), 1066–1081. https://doi.org/10.1210/me.2006-0524
  • McLachlan, A. D. (1982). Rapid comparision of protein structures. Acta Crystallographica Section A, 38(6), 871–873. https://doi.org/10.1107/S0567739482001806
  • Melis, G., Neri, M., Piras, B., Paoletti, A., Ajossa, S., Pilloni, M., Marotto, M., Corda, V., Saba, A., Giancane, E., & Mais, V. (2018). Vilaprisan for treating uterine fibroids. Expert Opinion on Investigational Drugs, 27(5), 497–505. https://doi.org/10.1080/13543784.2018.1471134
  • Moravek, M., & Bulun, S. (2015). Endocrinology of uterine fibroids. Current Opinion in Obstetrics & Gynecology, 27(4), 276–283. https://doi.org/10.1097/GCO.0000000000000185
  • Moroni, R., Ferriani, R., Candido-dos-Reis, F., Brito, L., & Vieira, C. (2014). Pharmacological treatment of uterine fibroids. Annals of Medical and Health Sciences Research, 4(9), 185. https://doi.org/10.4103/2141-9248.141955
  • Murji, A., Whitaker, L., Chow, T., & Sobel, M. (2017). Selective progesterone receptor modulators (SPRMs) for uterine fibroids. Cochrane Database of Systematic Reviews, 2017(4), 1-81. https://doi.org/10.1002/14651858.CD010770.pub2
  • Pavone, D., Clemenza, S., Sorbi, F., Fambrini, M., & Petraglia, F. (2018). Epidemiology and risk factors of uterine fibroids. Best Practice & Research. Clinical Obstetrics & Gynaecology, 46, 3–11. https://doi.org/10.1016/j.bpobgyn.2017.09.004
  • Petit-Topin, I., Fay, M., Resche-Rigon, M., Ulmann, A., Gainer, E., Rafestin-Oblin, M.-E., & Fagart, J. (2014). Molecular determinants of the recognition of ulipristal acetate by oxo-steroid receptors. The Journal of Steroid Biochemistry and Molecular Biology, 144, 427–435. https://doi.org/10.1016/j.jsbmb.2014.08.008
  • Prada-Gracia, D., Huerta-Yepez, S., & Moreno-Vargas, L. M. (2016). Application of computational methods for anticancer drug discovery, design, and optimization. Boletin Medico Del Hospital Infantil de Mexico, 73(6), 411–423. https://doi.org/10.1016/j.bmhimx.2016.10.006
  • Raaijmakers, H. C. A., Versteegh, J. E., & Uitdehaag, J. C. M. (2009). The X-ray structure of RU486 bound to the progesterone receptor in a destabilized agonistic conformation. The Journal of Biological Chemistry, 284(29), 19572–19579. https://doi.org/10.1074/jbc.M109.007872
  • Rabe, T., Saenger, N., Ebert, A., Roemer, T., Tinneberg, H., De Wilde, R., & Wallwiener, M. (2018). Selective progesterone receptor modulators for the medical treatment of uterine fibroids with a focus on ulipristal acetate. Biomed Research International, 2018, 1–12.
  • Sastry, G. M., 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
  • Schrödinger, L., & DeLano, W. (2020). The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
  • Schrödinger, LLC. (2021a). LigPrep. Schrödinger, LLC.
  • Schrödinger, LLC. (2021b). Glide. Schrödinger, LLC.
  • Schrödinger, LLC. (2021c). Prime. Schrödinger, LLC.
  • Stewart, E. A. (2001). Uterine fibroids. Lancet (London, England), 357(9252), 293–29 8. https://doi.org/10.1016/S0140-6736(00)03622-9
  • Sumathi, K., Ananthalakshmi, P., Roshan, M. N., & Sekar, K. (2006). 3dSS: 3D structural superposition. Nucleic Acids Research, 34(Web Server issue), W128–W132. https://doi.org/10.1093/nar/gkl036
  • Taylor, D., & Leppert, P. (2012). Treatment for uterine fibroids: Searching for effective drug therapies. Drug Discovery Today: Therapeutic Strategies, 9(1), 41–49.
  • Thompson, S. K., Washburn, D. G., Frazee, J. S., Madauss, K. P., Hoang, T. H., Lapinski, L., Grygielko, E. T., Glace, L. E., Trizna, W., Williams, S. P., Duraiswami, C., Bray, J. D., & Laping, N. J. (2009). Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists. Bioorganic & Medicinal Chemistry Letters, 19(16), 4777–4780. https://doi.org/10.1016/j.bmcl.2009.06.055
  • Yoshida, S., Ohara, N., Xu, Q., Chen, W., Wang, J., Nakabayashi, K., Sasaki, H., Morikawa, A., & Maruo, T. (2010). Cell-type specific actions of progesterone receptor modulators in the regulation of uterine leiomyoma growth. Seminars in Reproductive Medicine, 28(3), 260–273.
  • Zheng, L., Xia, K., & Mu, Y. (2019). Ligand binding induces agonistic-like conformational adaptations in helix 12 of progesterone receptor ligand binding domain. Frontiers in Chemistry, 7, 315. https://doi.org/10.3389/fchem.2019.00315
  • Zhou, Y., Zhang, Y. T., Lian, X. C., Li, F. C., Wang, C. X., Zhu, F., Qiu, Y. Q., & Chen, Y. Z. (2022). Therapeutic target database update 2022: Facilitating drug discovery with enriched comparative data of targeted agents. Nucleic Acids Research, 50(D1), D1398–D1407. https://doi.org/10.1093/nar/gkab953

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.