In silico study of androgen receptor N-terminal domain and exploration of its modulators

References

• Aguilar-Pineda, J. A., Albaghdadi, M., Jiang, W., Vera-Lopez, K. J., Nieto-Montesinos, R., Alvarez, K. L. F., Davila Del-Carpio, G., Gómez, B., Lindsay, M. E., Malhotra, R., & Lino Cardenas, C. L. (2021). Structural and functional analysis of female sex hormones against SARS-CoV-2 cell entry. International Journal of Molecular Sciences, 22(21), 11508. https://doi.org/10.3390/ijms222111508
   PubMed Web of Science ®Google Scholar
• Andersen, R. J., Mawji, N. R., Wang, J., Wang, G., Haile, S., Myung, J.-K., Watt, K., Tam, T., Yang, Y. C., Bañuelos, C. A., Williams, D. E., McEwan, I. J., Wang, Y., & Sadar, M. D. (2010). Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell, 17(6), 535–546. https://doi.org/10.1016/j.ccr.2010.04.027
   PubMed Web of Science ®Google Scholar
• Berendsen, H., Postma, J. P. M., van Gunsteren, W., DiNola, A. D., & Haak, J. R. (1984). Molecular-dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Buchanan, G., Yang, M., Harris, J. M., Nahm, H. S., Han, G., Moore, N., Bentel, J. M., Matusik, R. J., Horsfall, D. J., Marshall, V. R., Greenberg, N. M., & Tilley, W. D. (2001). Mutations at the boundary of the hinge and ligand binding domain of the androgen receptor confer increased transactivation function. Molecular Endocrinology (Baltimore, Md.), 15(1), 46–56. https://doi.org/10.1210/mend.15.1.0581
   PubMedGoogle Scholar
• Callewaert, L., Van Tilborgh, N., & Claessens, F. (2006). Interplay between two hormone-independent activation domains in the androgen receptor. Cancer Research, 66(1), 543–553. https://doi.org/10.1158/0008-5472.Can-05-2389
   PubMed Web of Science ®Google Scholar
• Chen, F., Liu, J., Huang, M., Hu, M., Su, Y., & Zhang, X. K. (2014). Identification of a New RXRα antagonist targeting the coregulator-binding site. ACS Medicinal Chemistry Letters, 5(7), 736–741. https://doi.org/10.1021/ml5000405
   PubMed Web of Science ®Google Scholar
• Chen, L., Wang, Z.-G., Aleshin, A. E., Chen, F., Chen, J., Jiang, F., Alitongbieke, G., Zeng, Z., Ma, Y., Huang, M., Zhou, H., Cadwell, G., Zheng, J.-F., Huang, P.-Q., Liddington, R. C., Zhang, X-K., & Su, Y. (2014). Sulindac-derived RXRα modulators inhibit cancer cell growth by binding to a novel site. Chemistry & Biology, 21(5), 596–607. https://doi.org/10.1016/j.chembiol.2014.02.017
   PubMedGoogle Scholar
• De Mol, E., Fenwick, R. B., Phang, C. T. W., Buzón, V., Szulc, E., de la Fuente, A., Escobedo, A., García, J., Bertoncini, C. W., Estébanez-Perpiñá, E., McEwan, I. J., Riera, A., & Salvatella, X. (2016). EPI-001, a compound active against castration-resistant prostate cancer, targets transactivation unit 5 of the androgen receptor. ACS Chemical Biology, 11(9), 2499–2505. https://doi.org/10.1021/acschembio.6b00182
   PubMed Web of Science ®Google Scholar
• Dehm, S. M., Regan, K. M., Schmidt, L. J., & Tindall, D. J. (2007). Selective role of an NH2-terminal WxxLF motif for aberrant androgen receptor activation in androgen depletion independent prostate cancer cells. Cancer Research, 67(20), 10067–10077. https://doi.org/10.1158/0008-5472.Can-07-1267
   PubMed Web of Science ®Google Scholar
• Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., & Zhang, J. Z. H. (2019). Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Frontiers in Chemistry, 7, 540. https://doi.org/10.3389/fchem.2019.00540
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H., & Pedersen, L. (1995). A smooth particle mesh ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Estébanez-Perpiñá, E., Arnold, L. A., Nguyen, P., Rodrigues, E. D., Mar, E., Bateman, R., Pallai, P., Shokat, K. M., Baxter, J. D., Guy, R. K., Webb, P., & Fletterick, R. J. (2007). A surface on the androgen receptor that allosterically regulates coactivator binding. Proceedings of the National Academy of Sciences of the United States of America, 104(41), 16074–16079. https://doi.org/10.1073/pnas.0708036104
   PubMed Web of Science ®Google Scholar
• Gallastegui, N., Mackinnon, J. A., Fletterick, R. J., & Estébanez-Perpiñá, E. (2015). Advances in our structural understanding of orphan nuclear receptors. Trends in Biochemical Sciences, 40(1), 25–35. https://doi.org/10.1016/j.tibs.2014.11.002
   PubMed Web of Science ®Google Scholar
• Hazarika, Z., & Jha, A. (2020). A comparative evaluation of docking programs using influenza endonuclease as target protein. 2020 International conference on computational performance evaluation (ComPE), Shillong, India, 2020, pp. 321-326. https://doi.org/10.1109/ComPE49325.2020.9200180
   Google Scholar
• He, Y., Hwang, D. J., Ponnusamy, S., Thiyagarajan, T., Mohler, M. L., Narayanan, R., & Miller, D. D. (2021). Exploration and biological evaluation of basic heteromonocyclic propanamide derivatives as SARDs for the treatment of enzalutamide-resistant prostate cancer. Journal of Medicinal Chemistry, 64(15), 11045–11062. https://doi.org/10.1021/acs.jmedchem.1c00439
   PubMed Web of Science ®Google Scholar
• Jorgensen, W., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Kagami, L. P., das Neves, G. M., Timmers, L., Caceres, R. A., & Eifler-Lima, V. L. (2020). Geo-measures: A PyMOL plugin for protein structure ensembles analysis. Computational Biology and Chemistry, 87, 107322. https://doi.org/10.1016/j.compbiolchem.2020.107322
   PubMed Web of Science ®Google Scholar
• Le Moigne, R., Zhou, H.-J., Obst, J. K., Banuelos, C. A., Jian, K., Williams, D., Virsik, P., Andersen, R. J., Sadar, M., Perabo, F., & Chi, K. N. (2019). Lessons learned from the metastatic castration-resistant prostate cancer phase I trial of EPI-506, a first-generation androgen receptor N-terminal domain inhibitor. Journal of Clinical Oncology, 37(7_suppl), 257–257. https://doi.org/10.1200/JCO.2019.37.7_suppl.257
   PubMedGoogle Scholar
• Li, H., Ban, F., Dalal, K., Leblanc, E., Frewin, K., Ma, D., Adomat, H., Rennie, P. S., & Cherkasov, A. (2014). Discovery of small-molecule inhibitors selectively targeting the DNA-binding domain of the human androgen receptor. Journal of Medicinal Chemistry, 57(15), 6458–6467. https://doi.org/10.1021/jm500802j
   PubMed Web of Science ®Google Scholar
• Li, Y., Lambert, M. H., & Xu, H. E. (2003). Activation of nuclear receptors: A perspective from structural genomics. Structure (London, England: 1993), 11(7), 741–746. https://doi.org/10.1016/s0969-2126(03)00133-3
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Mandelkow, E. M., & Mandelkow, E. (2012). Biochemistry and cell biology of tau protein in neurofibrillary degeneration. Cold Spring Harbor Perspectives in Medicine, 2(7), a006247–a006247. https://doi.org/10.1101/cshperspect.a006247
   PubMed Web of Science ®Google Scholar
• Moigne, R. L., Banuelos, C. A., Mawji, N. R., Tam, T., Wang, J., Jian, K., Andersen, R. J., Cesano, A., Sadar, M. D., Zhou, H.-J., & Virsik, P. (2019). EPI-7386 is a novel N-terminal domain androgen receptor inhibitor for the treatment of prostate cancer. Annals of Oncology, 30(503P), v189–v190. https://doi.org/10.1093/annonc/mdz244.065
   Google Scholar
• Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1-3), 1–41. https://doi.org/10.1016/0010-4655(95)00041-D
   Web of Science ®Google Scholar
• Puhl, A. C., Milton, F. A., Cvoro, A., Sieglaff, D. H., Campos, J. C. L., Bernardes, A., Filgueira, C. S., Lindemann, J. L., Deng, T., Neves, F. A. R., Polikarpov, I., & Webb, P. (2015). Mechanisms of peroxisome proliferator activated receptor γ regulation by non-steroidal anti-inflammatory drugs. Nuclear Receptor Signaling, 13(1), e004. https://doi.org/10.1621/nrs.13004
   PubMedGoogle Scholar
• Roe, D. R., & Cheatham, T. E. 3rd. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Sadar, M. D., Williams, D. E., Mawji, N. R., Patrick, B. O., Wikanta, T., Chasanah, E., Irianto, H. E., Soest, R. V., & Andersen, R. J. (2008). Sintokamides A to E, chlorinated peptides from the sponge Dysidea sp. that inhibit transactivation of the N-terminus of the androgen receptor in prostate cancer cells. Organic Letters, 10(21), 4947–4950. https://doi.org/10.1021/ol802021w
   PubMed Web of Science ®Google Scholar
• Saha, D., Borah, N. J., & Jha, A. N. (2023). Molecular scaffold recognition of drug molecules against essential genes of Leishmania donovani using biocomputing approach. South African Journal of Botany, 162, 52–63. https://doi.org/10.1016/j.sajb.2023.08.067
   Web of Science ®Google Scholar
• Shaffer, P. L., Jivan, A., Dollins, D. E., Claessens, F., & Gewirth, D. T. (2004). Structural basis of androgen receptor binding to selective androgen response elements. Proceedings of the National Academy of Sciences of the United States of America, 101(14), 4758–4763. https://doi.org/10.1073/pnas.0401123101
   PubMed Web of Science ®Google Scholar
• Sladek, F. M. (2003). Nuclear receptors as drug targets: New developments in coregulators, orphan receptors and major therapeutic areas. Expert Opinion on Therapeutic Targets, 7(5), 679–684. https://doi.org/10.1517/14728222.7.5.679
   PubMed Web of Science ®Google Scholar
• Weatherman, R. V., Fletterick, R. J., & Scanlan, T. S. (1999). Nuclear-receptor ligands and ligand-binding domains. Annual Review of Biochemistry, 68(1), 559–581. https://doi.org/10.1146/annurev.biochem.68.1.559
   PubMedGoogle Scholar