Re-emergence of an orphan therapeutic target for the treatment of resistant prostate cancer – a thorough conformational and binding analysis for ROR-γ protein

References

• Ahmad, E. , Rabbani, G. , Zaidi, N. , Khan, M. A. , Qadeer, A. , Ishtikhar, M. , Singh, S. , & Khan, R. H. (2013). Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. Journal of Biomolecular Structure and Dynamics , 31 , 630–648.
   PubMed Web of Science ®Google Scholar
• Amadei, A. , Linssen, A. B. M. , & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Structure, Function and Genetics , 17 , 412–425. doi:10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Aranda, A. , & Pascual, A. (2001). Nuclear hormone receptors and gene expression. Physiological Reviews , 81 , 1269–1304. 0031-9333/01.
   PubMed Web of Science ®Google Scholar
• Benson, N. C. , & Daggett, V. (2008). Dynameomics: Large-scale assessment of native protein flexibility. Protein Science : A Publication of the Protein Society , 17 , 2038–2050. doi:10.1110/ps.037473.108
   PubMed Web of Science ®Google Scholar
• Carugo, O. (2001). A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science , 10 , 1470–1473. doi:10.1110/ps.690101.of
   Google Scholar
• Chen, D. , Oezguen, N. , Urvil, P. , Ferguson, C. , Dann, S. M. , & Savidge, T. C. (2016a). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances , 2 , e1501240–e1501240. doi:10.1126/sciadv.1501240
   PubMed Web of Science ®Google Scholar
• Chen, D. , Oezguen, N. , Urvil, P. , Ferguson, C. , Dann, S. M. , & Savidge, T. C. (2016b). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances , 2 , e1501240. doi:10.1126/sciadv.1501240
   PubMed Web of Science ®Google Scholar
• Cocco, S. , Monasson, R. , & Weigt, M. (2013). From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction. PLoS Computational Biology , 9 , e1003176. doi:10.1371/journal.pcbi.1003176
   PubMed Web of Science ®Google Scholar
• David, C. C., & C and Jacobs D. J. (2014). Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins. Molecular Biology , 1084 , 193–226. doi:10.1007/978-1-62703-658-0_11
   Google Scholar
• Desdouits, N. , Nilges, M. , & Blondel, A. (2015). Principal component analysis reveals correlation of cavities evolution and functional motions in proteins. Journal of Molecular Graphics and Modelling, 55 , 13–24. doi:10.1016/j.jmgm.2014.10.011
   PubMed Web of Science ®Google Scholar
• Feixas, F. , Lindert, S. , Sinko, W. , & McCammon, J. A. (2014). Exploring the Role of Receptor Flexibility in Structure-Based Drug Discovery. Journal of Biophysics Chemistry , 186 , 31–45. doi:10.1016/j.bpc.2013.10.007
   PubMed Web of Science ®Google Scholar
• Finnerty, J. (2011). Molecular dynamics meets the physical world: Thermostats and barostats. www.grs-sim.de/cms/upload/Carloni/Tutorials/FMCP/Thermostats_and_Barostats.pdf
   Google Scholar
• Fitzpatrick, J. M. , Bellmunt, J. , Fizazi, K. , Heidenreich, A. , Sternberg, C. N. , Tombal, B. , & Alcaraz, A. (2014). Optimal management of metastatic castration-resistant prostate cancer: Highlights from a European expert consensus panel. European Journal of Cancer , 50 , 1617–1627. doi:10.1016/j.ejca.2014.03.010
   PubMed Web of Science ®Google Scholar
• Fujita-sato, S. , Ito, S. , Isobe, T. , Ohyama, T. , Wakabayashi, K. , Morishita, K. , … Isono, F. (2011). Structural basis of digoxin that antagonizes roRγT receptor activity and suppresses Th17 cell differentiation and interleukin (IL) -17 production. The Journal of Biological Chemistry, 286 , 31409–31417. doi:10.1074/jbc.M111.254003
   PubMed Web of Science ®Google Scholar
• Galindo-Murillo, R. , Robertson, J. C. , Zgarbová, M. , Šponer, J. , Otyepka, M. , Jurečka, P. , & Cheatham III, T. E. (2016). Assessing the current state of amber force field modifications for DNA. Journal of Chemical Theory and Computation, 12 , 4114–4127. doi:10.1021/acs.jctc.6b00186
   PubMed Web of Science ®Google Scholar
• Genheden, S. , & Ryde, Ulf (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery , 10 , 449–461. doi:10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Goetz, A. W. , Williamson, M. J. , Xu, D. , Poole, D. , Grand, S. L. , & Walker, R. C. (2012). Routine microsecond molecular dynamics simulations with amber – Part I: Generalized born. Journal of Chemical Theory and Computation , 8 , 1542–1555.10.1021/ct200909j
   PubMed Web of Science ®Google Scholar
• Grant, B. J. , Rodrigues, A. P. C. , ElSawy, K. M. , Andrew McCammon, J. , & Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics , 22 , 2695–2696. doi:10.1093/bioinformatics/btl461
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D. , Curtis, D. E. , Lonie, D. C. , Vandermeerschd, T. , Zurek, E. , & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics , 4 , 1–17. doi:10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Harvey, M. J. , & De Fabritiis, G. (2009). An implementation of the smooth particle mesh Ewald method on GPU hardware. Journal of Chemical Theory and Computation , 5 , 2371–2377. doi:10.1021/ct900275y
   PubMed Web of Science ®Google Scholar
• Hu, Y. , Gupta-Ostermann, D. , & Bajorath, J. (2014). Exploring compound promiscuity patterns and multi-target activity spaces. Computational and Structural Biotechnology Journal , 9 , 1–11. doi:10.5936/csbj.201401003
   Google Scholar
• Ivanov, I. I. , Mckenzie, B. S. , Zhou, L. , Tadokoro, C. E. , Lepelley, A. , Lafaille, J. J. , … Littman, D. R. (2006). The orphan nuclear receptor ROR G T directs the differentiation program of proinflammatory IL-17 + T helper cells. Cell , 126 , 1121–1133. doi:10.1016/j.cell.2006.07.035
   PubMed Web of Science ®Google Scholar
• Jin, L. , Martynowski, D. , Zheng, S. , Wada, T. , Xie, W. , & Li, Y. (2015). Structural basis for hydroxycholesterols as natural. Molecular Endocrinology , 24 , 923–929. doi:10.1210/me.2009-0507
   Web of Science ®Google Scholar
• Johnson, A. , Johnson, T. , & Khan, A. (2012). Thermostats in molecular dynamics simulations an interest in thermostats. University of Massachusetts, Amherst, December 6th, 2012. 1–29.
   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. The Journal of Chemical Physics , 79 , 926–935. doi:10.1063/1.445869
   Web of Science ®Google Scholar
• Klepeis, J. L. , Lindorff-Larsen, K. , Dror, R. O. , & Shaw, D. E. (2009). Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology , 19 , 120–127. doi:10.1016/j.sbi.2009.03.004
   PubMed Web of Science ®Google Scholar
• Kumalo, H. M., & Soliman, M. E. (2016). Per-residue energy footprints-based pharmacophore modeling as an enhanced in silico approach in drug discovery: A case study on the identification of novel β-secretase1 (BACE1) inhibitors as anti-alzheimer agents. Cellular and Molecular Bioengineering , 9 , 175–189. doi:10.1007/s12195-015-0421-8
   Web of Science ®Google Scholar
• Kurylowicz, M. , Yu, C. H. , & Pomès, R. (2010). Systematic study of anharmonic features in a principal component analysis of gramicidin A. Biophysical Journal , 98 , 386–395. doi:10.1016/j.bpj.2009.10.034
   PubMed Web of Science ®Google Scholar
• Lagunin, A. , Stepanchikova, A. , Filimonov, D. , & Poroikov, V. (2000). PASS: Prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16 , 747–748. doi:10.1093/bioinformatics/16.8.747
   PubMed Web of Science ®Google Scholar
• Lallous, N. , Dalal, K. , Cherkasov, A. , & Rennie, P. S. (2013). Targeting alternative sites on the androgen receptor to treat castration-resistant prostate cancer. International Journal of Molecular Sciences , 14 , 12496–12519. doi:10.3390/ijms140612496
   PubMed 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 , 1950–1958. doi:10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Loeffler, H. H. , & Winn, M. D. (2013). Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain. Proteins: Structure, Function and Bioinformatics, 81 , 1931–1943. doi:10.1002/prot.24339
   Google Scholar
• Luckheeram, R. V. , Zhou, R. , Verma, A. D. , & Xia, B. (2012). Review article CD4 + T cells: Differentiation and functions, Clinical and Developmental Immunology , 2012 , 925135. doi:10.1155/2012/925135
   PubMedGoogle Scholar
• Maisuradze, G. G. , Liwo, A. , & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology , 385 , 312–329. doi:10.1016/j.jmb.2008.10.018.Principal
   PubMed Web of Science ®Google Scholar
• Molecular Biology of Cell , (n.d).
   Google Scholar
• Morris, G. M. , Goodsell, D. S. , Halliday, R. S. , Huey, R. , Hart, W. E. , Belew, R. K. , & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry , 19 , 1639–1662. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
   Web of Science ®Google Scholar
• Pacheco, A. B. , & HPC, L. S. U. (2012). Introduction to autodock and autodock tools . HPC Training Series Louisiana State University, Baton Rouge, LA .
   Google Scholar
• Pettersen, E. F. , Goddard, T. D. , Huang, C. C. , Couch, G. S. , Greenblatt, D. M. , Meng, E. C. , & Ferrin, T. E. (2004). UCSF Chimera? A visualization system for exploratory research and analysis. Journal of Computational Chemistry , 25 , 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Poroikov, V. , Filimonov, D. , Lagunin, A. , Gloriozova, T. , & Zakharov, A. (2007). PASS: Identification of probable targets and mechanisms of toxicity. SAR and QSAR in Environmental Research , 18 , 101–110. doi:10.1080/10629360601054032
   PubMed Web of Science ®Google Scholar
• Roberts, R. (2014). From bench to bedside: The realities of reducing global prostate cancer disparity in black men. Ecancermedicalscience , 8 , 458. doi:10.3332/ecancer.2014.458
   PubMedGoogle Scholar
• Ryckaert, J. P. , Ciccotti, G. , & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics , 23 , 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Seifert, E. (2014). OriginPro 9.1: Scientific data analysis and graphing software—software review. Journal of Chemical Information and Modeling , 54 , 1552–1552. doi:10.1021/ci500161d
   PubMed Web of Science ®Google Scholar
• Shi, Y. (2007). Orphan nuclear receptors in drug discovery. Drug Discovery Today , 12 , 440–445. doi:10.1016/j.drudis.2007.04.006
   PubMed Web of Science ®Google Scholar
• Sittel, F. , Abhinav, J. , & Gerhard, S. (2014). Principal component analysis of molecular dynamics: On the use of cartesian vs. internal coordinates. Journal of Chemical Physics, 141 , 014111. doi:10.1063/1.4885338
   PubMed Web of Science ®Google Scholar
• Skjærven, L. , Yao, X.-Q. , Scarabelli, G. , & Grant, B. J. (2014). Integrating protein structural dynamics and evolutionary analysis with Bio3D. BMC Bioinformatics , 15 , 399–410. doi:10.1186/s12859-014-0399-6
   PubMed Web of Science ®Google Scholar
• Steffen, C. , Thomas, K. , Huniar, U. , Hellweg, A. , Rubner, O. , & Schroer, A. (2010). TmoleX–a graphical user interface for TURBOMOLE. Journal of Computational Chemistry , 31 , 2967–2970. doi:10.1002/jcc
   PubMed Web of Science ®Google Scholar
• Wang, J. M. , 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 , 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, F. , Wei, Y. , Yonghui, S. , & Guowei, L. (2014). 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors. Journal of Biomolecular Structure & Dynamics , 1–20. doi:10.1080/07391102.2014.980321
   Web of Science ®Google Scholar
• Wang, J. , Zou, J. X. , Xue, X. , Cai, D. , Zhang, Y. , ... Duan, Z. (2016). ROR-γ drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer. Nature Medicine , 22 , 488–496. doi:10.1038/nm.4070
   PubMed Web of Science ®Google Scholar
• Wikipedia . (2013). Radius of gyration . https://en.wikipedia.org/wiki/Radius_of_gyration
   Google Scholar
• Wolf, A. , & Kirschner, K. N. (2013). Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain. Journal of Molecular Modeling , 19 , 539–549. doi:10.1007/s00894-012-1563-4
   PubMed Web of Science ®Google Scholar
• You, W. , Huang, Y. M. , Kizhake, S. , & Natarajan, A. (2016). Characterization of promiscuous binding of phosphor ligands to breast-cancer-gene 1 (BRCA1) C-terminal (BRCT): Molecular dynamics, free energy, entropy and inhibitor design. Plos Computational Biology , 1 , 1–25. doi:10.1371/journal.pcbi.1005057
   Web of Science ®Google Scholar