Small-Molecule Intervention At The Dimerization Interface Of Survivin By Novel Rigidized Scaffolds

References

• Kelly RJ, Lopez-Chavez A, Citrin D, Janik JE, Morris JC. Impacting tumor cell-fate by targeting the inhibitor of apoptosis protein survivin. Mol Cancer. 2011;10:35. doi:10.1186/1476-4598-10-3521470426
   PubMed Web of Science ®Google Scholar
• Kawasaki H, Altieri DC, Lu CD, Toyoda M, Tenjo T, Tanigawa N. Inhibition of apoptosis by survivin predicts shorter survival rates in colorectal cancer. Cancer Res. 1998;58(22):5071–5074.9823313
   PubMed Web of Science ®Google Scholar
• Adida C, Berrebi D, Peuchmaur M, Reyes-Mugica M, Altieri DC. Anti-apoptosis gene, survivin, and prognosis of neuroblastoma. Lancet. 1998;351(9106):882–883. doi:10.1016/S0140-6736(05)70294-49525374
   PubMed Web of Science ®Google Scholar
• Monzo M, Rosell R, Felip E, et al. A novel anti-apoptosis gene: re-expression of survivin messenger RNA as a prognosis marker in non-small-cell lung cancers. J Clin Oncol. 1999;17(7):2100–2104. doi:10.1200/JCO.1999.17.7.210010561264
   PubMed Web of Science ®Google Scholar
• Tanaka K, Iwamoto S, Gon G, Nohara T, Iwamoto M, Tanigawa N. Expression of survivin and its relationship to loss of apoptosis in breast carcinomas. Clin Cancer Res. 2000;6(1):127–134.10656440
   PubMed Web of Science ®Google Scholar
• Chakravarti A, Zhai GG, Zhang M, et al. Survivin enhances radiation resistance in primary human glioblastoma cells via caspase-independent mechanisms. Oncogene. 2004;23(45):7494–7506. doi:10.1038/sj.onc.120804915326475
   PubMed Web of Science ®Google Scholar
• Liu BB, Wang WH. Survivin and pancreatic cancer. World J Clin Oncol. 2011;2(3):164–168. doi:10.5306/wjco.v2.i3.16421611091
   PubMedGoogle Scholar
• Wang Q, Greene MI. EGFR enhances Survivin expression through the phosphoinositide 3 (PI-3) kinase signaling pathway. Exp Mol Pathol. 2005;79(2):100–107. doi:10.1016/j.yexmp.2005.05.00215975575
   PubMed Web of Science ®Google Scholar
• Li F, Ambrosini G, Chu EY, et al. Control of apoptosis and mitotic spindle checkpoint by survivin. Nature. 1998;396(6711):580–584. doi:10.1038/251419859993
   PubMed Web of Science ®Google Scholar
• Muchmore SW, Chen J, Jakob C, et al. Crystal structure and mutagenic analysis of the inhibitor-of-apoptosis protein survivin. Mol Cell. 2000;6(1):173–182. doi:10.1016/S1097-2765(05)00019-510949038
   PubMed Web of Science ®Google Scholar
• Altieri DC. Survivin, versatile modulation of cell division and apoptosis in cancer. Oncogene. 2003;22(53):8581–8589. doi:10.1038/sj.onc.120711314634620
   PubMed Web of Science ®Google Scholar
• Schimmer AD. Inhibitor of apoptosis proteins: translating basic knowledge into clinical practice. Cancer Res. 2004;64(20):7183–7190. doi:10.1158/0008-5472.CAN-04-191815492230
   PubMed Web of Science ®Google Scholar
• Skoufias DA, Mollinari C, Lacroix FB, Margolis RL. Human survivin is a kinetochore-associated passenger protein. J Cell Biol. 2000;151(7):1575–1582. doi:10.1083/jcb.151.7.157511134084
   PubMed Web of Science ®Google Scholar
• Uren AG, Wong L, Pakusch M, et al. Survivin and the inner centromere protein INCENP show similar cell-cycle localization and gene knockout phenotype. Curr Biol. 2000;10(21):1319–1328. doi:10.1016/S0960-9822(00)00769-711084331
   PubMed Web of Science ®Google Scholar
• Jeyaprakash AA, Klein UR, Lindner D, Ebert J, Nigg EA, Conti E. Structure of a Survivin-Borealin-INCENP core complex reveals how chromosomal passengers travel together. Cell. 2007;131(2):271–285. doi:10.1016/j.cell.2007.07.04517956729
   PubMed Web of Science ®Google Scholar
• Chettiar SN, Cooley JV, Park IH, et al. Design, synthesis and biological studies of survivin dimerization modulators that prolong mitotic cycle. Bioorg Med Chem Lett. 2013;23(19):5429–5433. doi:10.1016/j.bmcl.2013.07.03423968825
   PubMed Web of Science ®Google Scholar
• Ainsztein AM, Kandels-Lewis SE, Mackay AM, Earnshaw WC. INCENP centromere and spindle targeting: identification of essential conserved motifs and involvement of heterochromatin protein HP1. J Cell Biol. 1998;143(7):1763–1774. doi:10.1083/jcb.143.7.17639864353
   PubMed Web of Science ®Google Scholar
• Lens SM, Vader G, Medema RH. The case for Survivin as mitotic regulator. Curr Opin Cell Biol. 2006;18(6):616–622. doi:10.1016/j.ceb.2006.08.01616962308
   PubMed Web of Science ®Google Scholar
• Wendt MD, Sun C, Kunzer A, et al. Discovery of a novel small molecule binding site of human survivin. Bioorg Med Chem Lett. 2007;17(11):3122–3129. doi:10.1016/j.bmcl.2007.03.04217391963
   PubMed Web of Science ®Google Scholar
• Berezov A, Cai Z, Freudenberg JA, et al. Disabling the mitotic spindle and tumor growth by targeting a cavity-induced allosteric site of survivin. Oncogene. 2012;31(15):1938–1948. doi:10.1038/onc.2011.37721892210
   PubMed Web of Science ®Google Scholar
• Park IH, Li C. Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: a survivin example. J Phys Chem B. 2010;114(15):5144–5153. doi:10.1021/jp911085d20337446
   PubMed Web of Science ®Google Scholar
• AMBER [computer program]. Version 11: University of California, San Francisco; 2010.
   Google Scholar
• Pearlman DA, Case DA, Caldwell JW, et al. 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. Comput Phys Commun. 1995;91(1–3):1–41. doi:10.1016/0010-4655(95)00041-D
   Web of Science ®Google Scholar
• Case DA, Cheatham TE, Darden T, et al. The Amber biomolecular simulation programs. J Comput Chem. 2005;26(16):1668–1688. doi:10.1002/(ISSN)1096-987X16200636
   PubMed Web of Science ®Google Scholar
• Verdecia MA, Huang H, Dutil E, Kaiser DA, Hunter T, Noel JP. Structure of the human anti-apoptotic protein survivin reveals a dimeric arrangement. Nat Struct Biol. 2000;7(7):602–608. doi:10.1038/7792910876248
   PubMedGoogle Scholar
• Sun C, Nettesheim D, Liu Z, Olejniczak ET. Solution structure of human survivin and its binding interface with Smac/Diablo. Biochemistry. 2005;44(1):11–17. doi:10.1021/bi048517115628841
   PubMed Web of Science ®Google Scholar
• Pang YP, Xu K, Yazal JE, Prendergas FG. Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach. Protein Sci. 2000;9(10):1857–1865.11106157
   PubMed Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174. doi:10.1002/(ISSN)1096-987X15116359
   PubMed Web of Science ®Google Scholar
• Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 2006;25(2):247–260. doi:10.1016/j.jmgm.2005.12.00516458552
   PubMed Web of Science ®Google Scholar
• Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006;65(3):712–725. doi:10.1002/prot.v65:316981200
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79(2):926–935. doi:10.1063/1.445869
   Web of Science ®Google Scholar
• Wu XW, Brooks BR. Self-guided Langevin dynamics simulation method. Chem Phys Lett. 2003;381(3–4):512–518. doi:10.1016/j.cplett.2003.10.013
   Web of Science ®Google Scholar
• Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23(3):327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald - an N.Log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98(12):10089–10092. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Shao JY, Tanner SW, Thompson N, Cheatham TE. Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J Chem Theory Comput. 2007;3(6):2312–2334. doi:10.1021/ct700119m26636222
   PubMed Web of Science ®Google Scholar
• Shao J. Amber archive. Available from: http://archiveambermdorg/200808/0008html.
   Google Scholar
• Boeckler FM, Joerger AC, Jaggi G, Rutherford TJ, Veprintsev DB, Fersht AR. Targeted rescue of a destabilized mutant of p53 by an in silico screened drug. Proc Natl Acad Sci U S A. 2008;105(30):10360–10365. doi:10.1073/pnas.080532610518650397
   PubMed Web of Science ®Google Scholar
• Jez JM, Ferrer JL, Bowman ME, Dixon RA, Noel JP. Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase. Biochemistry. 2000;39(5):890–902. doi:10.1021/bi991489f10653632
   PubMed Web of Science ®Google Scholar
• Molecular Operating Environment (MOE) [computer program]. Version 2012: chemical Computing Group Inc.. 1010 Sherbooke St. West, Montreal, QC, Canada.
   Google Scholar
• Bauer MR, Ibrahim TM, Vogel SM, Boeckler FM. Evaluation and optimization of virtual screening workflows with DEKOIS 2.0–a public library of challenging docking benchmark sets. J Chem Inf Model. 2013;53(6):1447–1462. doi:10.1021/ci400115b23705874
   PubMed Web of Science ®Google Scholar
• Ligprep [computer program]. Version 2.4: schrödinger, LLC. New York, NY; 2010.
   Google Scholar
• Maestro [computer program]. Version 9.1: schrödinger, LLC. New York, NY; 2010.
   Google Scholar
• Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997;267(3):727–748. doi:10.1006/jmbi.1996.08979126849
   PubMed Web of Science ®Google Scholar
• Jones G, Willett P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol. 1995;245(1):43–53. doi:10.1016/S0022-2836(95)80037-97823319
   PubMed Web of Science ®Google Scholar
• Jones G, Willett P, Glen RC. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comput-Aided Mol Des. 1995;9(6):532–549. doi:10.1007/BF001243248789195
   PubMed Web of Science ®Google Scholar
• Hartshorn MJ, Verdonk ML, Chessari G, et al. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem. 2007;50(4):726–741. doi:10.1021/jm061277y17300160
   PubMed Web of Science ®Google Scholar
• Berthold MR, Cebron N, Dill F, et al. KNIME: the Konstanz information miner In: Studies in Classification, Data Analysis, and Knowledge Organization (GFKL 2007). Heidelberg-Berlin: Springer-Verlag; 2007.
   Google Scholar
• Ibrahim TM, Bauer MR, Boeckler FM. Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets. J Cheminform. 2014;6(Suppl 1):p19. doi:10.1186/1758-2946-6-S1-P19
   PubMedGoogle Scholar
• Ibrahim TM, Bauer MR, Dorr A, Veyisoglu E, Boeckler FM. pROC-chemotype plots enhance the interpretability of benchmarking results in structure-based virtual screening. J Chem Inf Model. 2015;55(11):2297–2307. doi:10.1021/acs.jcim.5b0047526434782
   PubMed Web of Science ®Google Scholar
• Shiraishi M, Aramaki Y, Seto M, et al. Discovery of novel, potent, and selective small-molecule CCR5 antagonists as anti-HIV-1 agents: synthesis and biological evaluation of anilide derivatives with a quaternary ammonium moiety. J Med Chem. 2000;43(10):2049–2063. doi:10.1021/jm990626410821717
   PubMed Web of Science ®Google Scholar
• Junker A, Schepmann D, Yamaguchi J, et al. Diverse modifications of the 4-methylphenyl moiety of TAK-779 by late-stage Suzuki-Miyaura cross-coupling. Org Biomol Chem. 2014;12(1):177–186. doi:10.1039/C3OB41873A24217712
   PubMed Web of Science ®Google Scholar
• Vogel SM, Bauer MR, Boeckler FM. DEKOIS: demanding evaluation kits for objective in silico screening–a versatile tool for benchmarking docking programs and scoring functions. J Chem Inf Model. 2011;51(10):2650–2665. doi:10.1021/ci200154921774552
   PubMed Web of Science ®Google Scholar
• Boeckler FM, Bauer MR, Ibrahim TM, Vogel SM. Use of DEKOIS 2.0 to gain insights for virtual screening. J Cheminform. 2014;6(Suppl 1):O24. doi:10.1186/1758-2946-6-S1-O2424765123
   PubMedGoogle Scholar
• Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007;35(Databaseissue):D198–D201. doi:10.1093/nar/gkl99917145705
   PubMed Web of Science ®Google Scholar
• Hopkins AL, Groom CR, Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov Today. 2004;9(10):430–431. doi:10.1016/S1359-6446(04)03069-715109945
   PubMed Web of Science ®Google Scholar
• Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. J Mol Biol. 2002;322(2):339–355. doi:10.1016/S0022-2836(02)00777-512217695
   PubMed Web of Science ®Google Scholar
• Abadi AH, Ibrahim TM, Abouzid KM, et al. Design, synthesis and biological evaluation of novel pyridine derivatives as anticancer agents and phosphodiesterase 3 inhibitors. Bioorg Med Chem. 2009;17(16):5974–5982. doi:10.1016/j.bmc.2009.06.06319628397
   PubMed Web of Science ®Google Scholar
• Abadi A, Al-Deeb O, Al-Afify A, El-Kashef H. Synthesis of 4-alkyl (aryl)-6-aryl-3-cyano-2(1H)-pyridinones and their 2-imino isosteres as nonsteroidal cardiotonic agents. Farmaco. 1999;54(4):195–201. doi:10.1016/S0014-827X(99)00004-X10384712
   PubMedGoogle Scholar
• Minlon H. A simple modification of the wolff-kishner reduction. J Am Chem Soc. 1946;68(12):2487–2488. doi:10.1021/ja01216a013
   Web of Science ®Google Scholar
• Shi F, Tu S, Fang F, Li T. One-pot synthesis of 2-amino-3-cyanopyridine derivatives under microwave irradiation without solvent. ARKIVOC. 2005;i:137–142.
   Web of Science ®Google Scholar