Pharmacological manipulation of transcription factor protein-protein interactions: opportunities and obstacles

Frank Fontaine1, Jeroen Overman1, Mathias François1
1Division of Genomics of Development and Diseases, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, QLD 4072, Australia

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Rowinsky, 1997, Paclitaxel pharmacology and other tumor types, Semin Oncol, 24, S19-1-S-2

Galsky, 2010, Cabazitaxel, Nat Rev Drug Discov, 9, 677, 10.1038/nrd3254

Hopkins, 2002, The druggable genome, Nat Rev Drug Discov, 1, 727, 10.1038/nrd892

Kaczor, 2013, Modeling complexes of transmembrane proteins: systematic analysis of protein-protein docking tools, Mol Inform, 32, 717, 10.1002/minf.201200150

Hutchins, 2010, Systematic analysis of human protein complexes identifies chromosome segregation proteins, Science, 328, 593, 10.1126/science.1181348

Gavin, 2002, Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 141, 10.1038/415141a

Berg, 2003, Modulation of protein-protein interactions with small organic molecules, Angew Chem, 42, 2462, 10.1002/anie.200200558

Koehler, 2010, A complex task? Direct modulation of transcription factors with small molecules, Curr Opin Chem Biol, 14, 331, 10.1016/j.cbpa.2010.03.022

Mayr, 2001, Transcriptional regulation by the phosphorylation-dependent factor CREB, Nat Rev Mol Cell Biol, 2, 599, 10.1038/35085068

Coleman, 2005, Investigation of the binding determinants of phosphopeptides targeted to the SRC homology 2 domain of the signal transducer and activator of transcription 3. Development of a high-affinity peptide inhibitor, J Med Chem, 48, 6661, 10.1021/jm050513m

Arnold, 2007, Inhibitors of the interaction of a thyroid hormone receptor and coactivators: preliminary structure — activity relationships, J Med Chem, 50, 5269, 10.1021/jm070556y

Caboni, 2013, Beyond the ligand-binding pocket: targeting alternate sites in nuclear receptors, Med Res Rev, 33, 1081, 10.1002/med.21275

Vaquerizas, 2009, A census of human transcription factors: function, expression and evolution, Nat Rev Genet, 10, 252, 10.1038/nrg2538

Lee, 2000, Transcription of eukaryotic protein-coding genes, Annu Rev Genet, 34, 77, 10.1146/annurev.genet.34.1.77

Chapman, 2007, Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7, Science, 318, 1780, 10.1126/science.1145977

Arndt, 2006, Small molecule modulators of transcription, Angew Chem, 45, 4552, 10.1002/anie.200600285

Berg, 2008, Inhibition of transcription factors with small organic molecules, Curr Opin Chem Biol, 12, 464, 10.1016/j.cbpa.2008.07.023

Collingwood, 1999, Nuclear receptors: coactivators, corepressors and chromatin remodeling in the control of transcription, J Mol Endocrinol, 23, 255, 10.1677/jme.0.0230255

Endler, 2014, Coactivator recruitment of AhR/ARNT1, Int J Mol Sci, 15, 11100, 10.3390/ijms150611100

Kornberg, 2007, The molecular basis of eukaryotic transcription, Proc Natl Acad Sci, 104, 12955, 10.1073/pnas.0704138104

Zaret, 2011, Pioneer transcription factors: establishing competence for gene expression, Genes Dev, 25, 2227, 10.1101/gad.176826.111

Bianchi, 2005, HMG proteins: dynamic players in gene regulation and differentiation, Curr Opin Genet Dev, 15, 496, 10.1016/j.gde.2005.08.007

Štros, 2007, The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins, Cell Mol Life Sci, 64, 2590, 10.1007/s00018-007-7162-3

Ding, 2013, Proteome-wide profiling of activated transcription factors with a concatenated tandem array of transcription factor response elements, Proc Natl Acad Sci U S A, 110, 6771, 10.1073/pnas.1217657110

Chen, 2014, Single-molecule dynamics of enhanceosome assembly in embryonic stem cells, Cell, 156, 1274, 10.1016/j.cell.2014.01.062

Sherwood, 2014, Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape, Nat Biotechnol, 32, 171, 10.1038/nbt.2798

Rieck, 2014, PIQ-ing into chromatin architecture, Nat Biotech, 32, 138, 10.1038/nbt.2824

Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024

Perissi, 2005, Controlling nuclear receptors: the circular logic of cofactor cycles, Nat Rev Mol Cell Biol, 6, 542, 10.1038/nrm1680

Hurtado, 2011, FOXA1 is a key determinant of estrogen receptor function and endocrine response, Nat Genet, 43, 27, 10.1038/ng.730

Lupien, 2010, Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance, Genes Dev, 24, 2219, 10.1101/gad.1944810

Hock, 2007, HMG chromosomal proteins in development and disease, Trends Cell Biol, 17, 72, 10.1016/j.tcb.2006.12.001

Saragosti, 1982, Fine structure of the regulatory region of simian virus 40 minichromosomes revealed by DNAase I digestion, J Mol Biol, 160, 133, 10.1016/0022-2836(82)90171-1

Jones, 1985, Sp1 binds to promoter sequences and activates herpes simplex virus ‘immediate-early’ gene transcription in vitro, Nature, 317, 179, 10.1038/317179a0

Venter, 2001, The sequence of the human genome, Science, 291, 1304, 10.1126/science.1058040

Gadgil, 2001, DNA affinity chromatography of transcription factors, Anal Biochem, 290, 147, 10.1006/abio.2000.4912

Consortium, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247

Schaefer, 2011, TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins, Nucleic Acids Res, 39, D106, 10.1093/nar/gkq945

Andersson, 2014, An atlas of active enhancers across human cell types and tissues, Nature, 507, 455, 10.1038/nature12787

Vaquerizas, 2012, How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome, Methods Mol Biol, 786, 3, 10.1007/978-1-61779-292-2_1

Boyadjiev, 2000, Online Mendelian Inheritance in Man (OMIM) as a knowledgebase for human developmental disorders, Clin Genet, 57, 253, 10.1034/j.1399-0004.2000.570403.x

Lopez-Bigas, 2006, Highly consistent patterns for inherited human diseases at the molecular level, Bioinformatics, 22, 269, 10.1093/bioinformatics/bti781

Darnell, 2002, Transcription factors as targets for cancer therapy, Nat Rev Cancer, 2, 740, 10.1038/nrc906

Francis, 2003, Nuclear receptors and the control of metabolism, Annu Rev Physiol, 65, 261, 10.1146/annurev.physiol.65.092101.142528

Ghaemmaghami, 2003, Global analysis of protein expression in yeast, Nature, 425, 737, 10.1038/nature02046

Liu, 2002, Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities, J Mol Biol, 323, 1, 10.1016/S0022-2836(02)00894-X

Janga, 2009, Transcriptional regulation shapes the organization of genes on bacterial chromosomes, Nucleic Acids Res, 37, 3680, 10.1093/nar/gkp231

Jarrett, 1993, Affinity chromatography with nucleic acid polymers, J Chromatogr, 618, 315, 10.1016/0378-4347(93)80040-B

Jiang, 2009, Methods for proteomic analysis of transcription factors, J Chromatogr A, 1216, 6881, 10.1016/j.chroma.2009.08.044

Barski, 2007, High-resolution profiling of histone methylations in the human genome, Cell, 129, 823, 10.1016/j.cell.2007.05.009

Kadonaga, 1991, Purification of sequence-specific binding proteins by DNA affinity chromatography, Methods Enzymol, 208, 10, 10.1016/0076-6879(91)08004-2

Stegmaier, 2004, Systematic DNA-binding domain classification of transcription factors, Genome Inform, 15, 276

Brivanlou, 2002, Signal transduction and the control of gene expression, Science, 295, 813, 10.1126/science.1066355

Jin, 2014, Targeting protein-protein interaction by small molecules, Annu Rev Pharmacol Toxicol, 54, 435, 10.1146/annurev-pharmtox-011613-140028

Overington, 2006, How many drug targets are there?, Nat Rev Drug Discov, 5, 993, 10.1038/nrd2199

Landry, 2008, Drugs and their molecular targets: an updated overview, Fundam Clin Pharmacol, 22, 1, 10.1111/j.1472-8206.2007.00548.x

Liu, 2014, Identifying druggable targets by protein microenvironments matching: application to transcription factors, CPT Pharmacometrics Syst Pharmacol, 3, e93, 10.1038/psp.2013.66

Alberghina, 2005, From isolation to integration, a systems biology approach for building the Silicon Cell, 13, 10.1007/b95175

Sperandio, 2010, Rationalizing the chemical space of protein-protein interaction inhibitors, Drug Discov Today, 15, 220, 10.1016/j.drudis.2009.11.007

Reynes, 2010, Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods, PLoS Comput Biol, 6, e1000695, 10.1371/journal.pcbi.1000695

Ng, 2012, Deciphering the Sox-Oct partner code by quantitative cooperativity measurements, Nucleic Acids Res, 40, 4933, 10.1093/nar/gks153

Dang, 2006, The c-Myc target gene network, Semin Cancer Biol, 16, 253, 10.1016/j.semcancer.2006.07.014

Biggin, 2011, Animal transcription networks as highly connected, quantitative continua, Dev Cell, 21, 611, 10.1016/j.devcel.2011.09.008

Wells, 2007, Reaching for high-hanging fruit in drug discovery at protein-protein interfaces, Nature, 450, 1001, 10.1038/nature06526

Spencer, 1998, High-throughput screening of historic collections: observations on file size, biological targets, and file diversity, Biotechnol Bioeng, 61, 61, 10.1002/(SICI)1097-0290(199824)61:1<61::AID-BIT11>3.0.CO;2-C

Sierecki, 2013, A cell-free approach to accelerate the study of protein-protein interactions, Interface Focus, 3, 20130018, 10.1098/rsfs.2013.0018

Wu, 2014, RNAi therapies: drugging the undruggable, Sci Transl Med, 6, 240ps7, 10.1126/scitranslmed.3008362

Konstantinopoulos, 2011, Seeing the future of cancer-associated transcription factor drug targets, JAMA, 305, 2349, 10.1001/jama.2011.727

Mann, 2005, Transcription factor decoys: a new model for disease intervention, Ann N Y Acad Sci, 1058, 128, 10.1196/annals.1359.021

Li, 2014, Discovery of small-molecule inhibitors selectively targeting the DNA-binding domain of the human androgen receptor, J Med Chem, 57, 6458, 10.1021/jm500802j

Nagel-Wolfrum, 2004, The interaction of specific peptide aptamers with the DNA binding domain and the dimerization domain of the transcription factor Stat3 inhibits transactivation and induces apoptosis in tumor cells, Mol Cancer Res, 2, 170, 10.1158/1541-7786.170.2.3

Czarna, 2010, Robust generation of lead compounds for protein-protein interactions by computational and MCR chemistry: p53/Hdm2 antagonists, Angew Chem, 49, 5352, 10.1002/anie.201001343

Vogler, 2009, Bcl-2 inhibitors: small molecules with a big impact on cancer therapy, Cell Death Differ, 16, 360, 10.1038/cdd.2008.137

Bernal, 2010, A stapled p53 helix overcomes HDMX-mediated suppression of p53, Cancer Cell, 18, 411, 10.1016/j.ccr.2010.10.024

Siddiquee, 2007, An oxazole-based small-molecule Stat3 inhibitor modulates Stat3 stability and processing and induces antitumor cell effects, ACS Chem Biol, 2, 787, 10.1021/cb7001973

Turkson, 2001, Phosphotyrosyl peptides block Stat3-mediated DNA binding activity, gene regulation, and cell transformation, J Biol Chem, 276, 45443, 10.1074/jbc.M107527200

Moreira, 2007, Hot spots–a review of the protein-protein interface determinant amino-acid residues, Proteins, 68, 803, 10.1002/prot.21396

DeLano, 2000, Convergent solutions to binding at a protein-protein interface, Science, 287, 1279, 10.1126/science.287.5456.1279

Rogne, 2013, Cell signalling analyses in the functional genomics era, N Biotechnol, 30, 333, 10.1016/j.nbt.2013.01.003

Rich, 2012, A short history of the first-generation kinase inhibitors, 1085

Cusanovich, 2014, The functional consequences of variation in transcription factor binding, PLoS Genet, 10, e1004226, 10.1371/journal.pgen.1004226

Fedorov, 2006, Off-target effects by siRNA can induce toxic phenotype, RNA, 12, 1188, 10.1261/rna.28106

Dasari, 2014, Cisplatin in cancer therapy: molecular mechanisms of action, Eur J Pharmacol, 10.1016/j.ejphar.2014.07.025

Hurst, 1996, Transcription factors as drug targets in cancer, Eur J Cancer, 32A, 1857, 10.1016/0959-8049(96)00214-6

Redmond, 2009, Defining and targeting transcription factors in cancer, Genome Biol, 10, 311, 10.1186/gb-2009-10-7-311

Filippakopoulos, 2010, Selective inhibition of BET bromodomains, Nature, 468, 1067, 10.1038/nature09504

Vassilev, 2004, In vivo activation of the p53 pathway by small-molecule antagonists of MDM2, Science, 303, 844, 10.1126/science.1092472

Miyoshi, 2011, Stat3 as a therapeutic target for the treatment of psoriasis: a clinical feasibility study with STA-21, a Stat3 inhibitor, J Invest Dermatol, 131, 108, 10.1038/jid.2010.255

Kung, 2004, Small molecule blockade of transcriptional coactivation of the hypoxia-inducible factor pathway, Cancer Cell, 6, 33, 10.1016/j.ccr.2004.06.009

Best, 2004, Identification of small-molecule antagonists that inhibit an activator: coactivator interaction, Proc Natl Acad Sci U S A, 101, 17622, 10.1073/pnas.0406374101

Tinsley, 2013, New NSAID targets and derivatives for colorectal cancer chemoprevention, Recent Results Cancer Res, 191, 105, 10.1007/978-3-642-30331-9_6

Lehmann, 1997, Peroxisome proliferator-activated receptors alpha and gamma are activated by indomethacin and other non-steroidal anti-inflammatory drugs, J Biol Chem, 272, 3406, 10.1074/jbc.272.6.3406

Yin, 1998, The anti-inflammatory agents aspirin and salicylate inhibit the activity of I(kappa)B kinase-beta, Nature, 396, 77, 10.1038/23948

Blondrath, 2014, The ppargamma cofactor RIP140 regulates BACE1 gene expression, Alzheimers Dement, 10, P326, 10.1016/j.jalz.2014.05.299

Zschiedrich, 2008, Coactivator function of RIP140 for NFkappaB/RelA-dependent cytokine gene expression, Blood, 112, 264, 10.1182/blood-2007-11-121699

Rosell, 2011, Role of nuclear receptor corepressor RIP140 in metabolic syndrome, Biochim Biophys Acta, 1812, 919, 10.1016/j.bbadis.2010.12.016

Lichty, 2005, Comparison of affinity tags for protein purification, Protein Expr Purif, 41, 98, 10.1016/j.pep.2005.01.019

Benayoun, 2009, A post-translational modification code for transcription factors: sorting through a sea of signals, Trends Cell Biol, 19, 189, 10.1016/j.tcb.2009.02.003

Nilsson, 1987, A synthetic IgG-binding domain based on staphylococcal protein A, Protein Eng, 1, 107, 10.1093/protein/1.2.107

Bedouelle, 1988, Production in Escherichia coli and one-step purification of bifunctional hybrid proteins which bind maltose. Export of the Klenow polymerase into the periplasmic space, Eur J Biochem, 171, 541, 10.1111/j.1432-1033.1988.tb13823.x

Smith, 1988, Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase, Gene, 67, 31, 10.1016/0378-1119(88)90005-4

Tessier, 1991, Enhanced secretion from insect cells of a foreign protein fused to the honeybee melittin signal peptide, Gene, 98, 177, 10.1016/0378-1119(91)90171-7

Luo, 2014, Single-step protease cleavage elution for identification of protein-protein interactions from GST pull-down and mass spectrometry, Proteomics, 14, 19, 10.1002/pmic.201300315

Macarron, 2006, Critical review of the role of HTS in drug discovery, Drug Discov Today, 11, 277, 10.1016/j.drudis.2006.02.001

Fox, 2004, High-throughput screening: searching for higher productivity, J Biomol Screen, 9, 354, 10.1177/1087057104265290

Ertl, 2008, Natural product-likeness score and its application for prioritization of compound libraries, J Chem Inf Model, 48, 68, 10.1021/ci700286x

Feher, 2003, Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry, J Chem Inf Comput Sci, 43, 218, 10.1021/ci0200467

Osada, 2009

Koes, 2012, Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists, PLoS One, 7, e32839, 10.1371/journal.pone.0032839

Pagliaro, 2004, Emerging classes of protein-protein interaction inhibitors and new tools for their development, Curr Opin Chem Biol, 8, 442, 10.1016/j.cbpa.2004.06.006

Barnard, 2008, Development and implementation of split-GFP-based bimolecular fluorescence complementation (BiFC) assays in yeast, Biochem Soc Trans, 36, 479, 10.1042/BST0360479

Kenworthy, 2001, Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy, Methods, 24, 289, 10.1006/meth.2001.1189

Gradinaru, 2010, Fluorescence anisotropy: from single molecules to live cells, Analyst, 135, 452, 10.1039/b920242k

Almholt, 2004, Changes in intracellular cAMP reported by a Redistribution assay using a cAMP-dependent protein kinase-green fluorescent protein chimera, Cell Signal, 16, 907, 10.1016/j.cellsig.2004.01.006

Almholt, 2004, Nuclear export inhibitors and kinase inhibitors identified using a MAPK-activated protein kinase 2 redistribution screen, Assay Drug Dev Technol, 2, 7, 10.1089/154065804322966270

Malki, 2010, Shuttling of SOX proteins, Int J Biochem Cell Biol, 42, 411, 10.1016/j.biocel.2009.09.020

Stumpf, 2008, Estimating the size of the human interactome, Proc Natl Acad Sci U S A, 105, 6959, 10.1073/pnas.0708078105