Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription

Altman, 2015, MYC disrupts the circadian clock and metabolism in cancer cells, Cell Metab., 22, 1009, 10.1016/j.cmet.2015.09.003

Amati, 2007, MYC degradation: deubiquitinating enzymes enter the dance, Nat. Cell Biol., 9, 729, 10.1038/ncb0707-729

Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106

Ayer, 1993, Mad: a heterodimeric partner for Max that antagonizes Myc transcriptional activity, Cell, 72, 211, 10.1016/0092-8674(93)90661-9

Benjamini, 1995, Controlling the false discovery rate - a practical and powerful approach to multiple testing, J. R. Stat. Soc. Series B Stat. Methodol., 57, 289, 10.1111/j.2517-6161.1995.tb02031.x

Billin, 1999, Mlx, a novel max-like BHLHZip protein that interacts with the max network of transcription factors, J. Biol. Chem., 274, 36344, 10.1074/jbc.274.51.36344

Blackwell, 1990, Sequence-specific DNA binding by the c-Myc protein, Science, 23, 1149, 10.1126/science.2251503

Blencowe, 2005, Development and application of diazirines in biological and synthetic macromolecular systems, Soft Matter., 1, 178, 10.1039/b501989c

Brautigam, 2011, Using Lamm-equation modeling of sedimentation velocity data to determine the kinetic and thermodynamic properties of macromolecular interactions, Methods, 54, 4, 10.1016/j.ymeth.2010.12.029

Calderon, 2012, Ligand-dependent corepressor (LCoR) recruitment by Kruppel-like factor 6 (KLF6) regulates expression of the cyclin-dependent kinase inhibitor CDKN1A gene, J. Biol. Chem., 287, 8662, 10.1074/jbc.M111.311605

Cascón, 2012, MAX and MYC: a heritable breakup, Cancer Res., 72, 3119, 10.1158/0008-5472.CAN-11-3891

Champely, 2018, pwr: basic functions for power analysis, R package version 1.2-2

Choi, 2017, Targeted disruption of Myc-Max oncoprotein complex by a small molecule, ACS Chem. Biol., 17, 2715, 10.1021/acschembio.7b00799

Clemons, 2010, Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles, Proc. Natl. Acad. Sci. U S A, 107, 18787, 10.1073/pnas.1012741107

Conacci-Sorrell, 2014, An overview of MYC and its interactome, Cold Spring Harb. Perspect. Med., 4, a014357, 10.1101/cshperspect.a014357

Cook, 1977, Detection of influential observation in linear regression, Technometrics, 19, 15

Dang, 2012, MYC on the path to cancer, Cell, 149, 22, 10.1016/j.cell.2012.03.003

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

Derr, 2016, End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data, Genome Res., 26, 1397, 10.1101/gr.207902.116

Devgan, V., Harris, A., Jiang, Q., and Pattison, S. (2012). Cignal reporter assay kit: a high-performance tool for assessing the functions of genes, biologics, and small molecule compounds. https://www.qiagen.com/fi/resources/download.aspx?id=6fc8144b-010b-43d8-9125-bf541a5d9c9c&lang=en.

DuPage, 2009, Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase, Nat. Protoc., 4, 1064, 10.1038/nprot.2009.95

Farrell, 2014, MYC degradation, Cold Spring Harb. Perspect. Med., 4, a014365, 10.1101/cshperspect.a014365

Felsenstein, 2016, Small molecule microarrays enable the identification of a selective, Quadruplex-binding inhibitor of MYC expression, ACS Chem. Biol., 11, 139, 10.1021/acschembio.5b00577

Felsher, 2010, MYC inactivation elicits oncogene addiction through both tumor cell-intrinsic and host-dependent mechanisms, Genes Cancer, 1, 597, 10.1177/1947601910377798

Felsher, 1999, Reversible tumorigenesis by MYC in hematopoietic lineages, Mol. Cell, 4, 199, 10.1016/S1097-2765(00)80367-6

Gabay, 2014, MYC activation is a hallmark of cancer initiation and maintenance, Cold Spring Harb. Perspect. Med., 4, a014241, 10.1101/cshperspect.a014241

Grzesiek, 1993, The importance of not saturating water in protein NMR. Application to sensitivity enhancement and NOE measurements, J. Am. Chem. Soc., 115, 12593, 10.1021/ja00079a052

Hart, 2014, Inhibitor of MYC identified in a Kröhnke pyridine library, Proc. Natl. Acad. Sci. U S A, 111, 12556, 10.1073/pnas.1319488111

Hong, 2014, Recent discoveries and applications involving small-molecule microarrays, Curr. Opin. Chem. Biol., 18, 21, 10.1016/j.cbpa.2013.09.020

Hopewell, 1995, The nerve growth factor-responsive PC12 cell line does not express the Myc dimerization partner Max, Mol. Cell. Biol., 15, 3470, 10.1128/MCB.15.7.3470

Jafari, 2014, The cellular thermal shift assay for evaluating drug target interactions in cells, Nat. Protoc., 9, 2100, 10.1038/nprot.2014.138

Jain, 2002, Sustained loss of a neoplastic phenotype by brief inactivation of MYC, Science, 297, 102, 10.1126/science.1071489

Jean-François, 2003, Improving the thermodynamic stability of the leucine zipper of max increases the stability of its b-HLH-LZ: E-box complex, J. Mol. Biol., 326, 1577, 10.1016/S0022-2836(03)00029-9

Jiang, 2009, Stabilizers of the Max homodimer identified in virtual ligand screening inhibit Myc function, Mol. Pharmacol., 76, 491, 10.1124/mol.109.054858

Kay, 1992, Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity, J. Am. Chem. Soc., 114, 10663, 10.1021/ja00052a088

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

Kress, 2015, MYC: connecting selective transcriptional control to global RNA production, Nat. Rev. Cancer, 15, 593, 10.1038/nrc3984

Laherty, 1997, Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression, Cell, 89, 349, 10.1016/S0092-8674(00)80215-9

Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25

Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352

Liberzon, 2015, The Molecular Signatures Database (MSigDB) hallmark gene set collection, Cell Syst., 1, 417, 10.1016/j.cels.2015.12.004

Lin, 2012, Transcriptional amplification in tumor cells with elevated c-Myc, Cell, 151, 56, 10.1016/j.cell.2012.08.026

Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method, Methods, 25, 402, 10.1006/meth.2001.1262

Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8

Lu, 2010, Epithelial cell adhesion molecule regulation is associated with the maintenance of the undifferentiated phenotype of human embryonic stem cells, J. Biol. Chem., 285, 8719, 10.1074/jbc.M109.077081

Mackinnon, 2009, Target identification by diazirine photo-cross-linking and click chemistry, Curr. Protoc. Chem. Biol., 1, 55, 10.1002/9780470559277.ch090167

McKeown, 2014, Therapeutic strategies to inhibit MYC, Cold Spring Harb. Perspect. Med., 4, 10.1101/cshperspect.a014266

Mitchell, 2006, A structurally diverse library of polycyclic lactams resulting from systematic placement of proximal functional groups, Angew. Chem. Int. Ed., 45, 1722, 10.1002/anie.200503341

Molina, 2013, Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay, Science, 341, 84, 10.1126/science.1233606

Nair, 2003, X-ray structures of Myc-Max and Mad-Max recognizing DNA, Cell, 112, 193, 10.1016/S0092-8674(02)01284-9

Pajic, 2000, Cell cycle activation by c-myc in a Burkitt lymphoma model cell line, Int. J. Cancer, 87, 787, 10.1002/1097-0215(20000915)87:6<787::AID-IJC4>3.0.CO;2-6

Palmer, 1991, Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy, J. Magn. Reson., 93, 151

Pop, 2014, A small molecule that binds and inhibits the ETV1 transcription factor oncoprotein, Mol. Cancer Ther., 13, 1492, 10.1158/1535-7163.MCT-13-0689

Riss, 2013

Sauve, 2004, The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors, J. Mol. Biol., 342, 813, 10.1016/j.jmb.2004.07.058

Schleucher, 1994, A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed field gradients, J. Biomol. NMR, 4, 301, 10.1007/BF00175254

Schneider, 2012, NIH image to imageJ: 25 years of image analysis, Nat. Methods, 9, 671, 10.1038/nmeth.2089

Schuhmacher, 1999, Control of cell growth by c-Myc in the absence of cell division, Curr. Biol., 9, 1255, 10.1016/S0960-9822(99)80507-7

Shachaf, 2004, MYC inactivation uncovers pluripotent differentiation and tumour dormancy in hepatocellular cancer, Nature, 431, 1112, 10.1038/nature03043

Smith, 2015, Photoaffinity labeling in target- and binding-site identification, Future Med. Chem., 7, 159, 10.4155/fmc.14.152

Soodgupta, 2015, Small molecule MYC inhibitor conjugated to integrin-targeted nanoparticles extends survival in a mouse model of disseminated multiple myeloma, Mol. Cancer Ther., 14, 1286, 10.1158/1535-7163.MCT-14-0774-T

Soucek, 2002, Omomyc, a potential Myc dominant negative, enhances Myc-induced apoptosis, Cancer Res., 62, 3507

Soucek, 2008, Modelling Myc inhibition as a cancer therapy, Nature, 455, 679, 10.1038/nature07260

Soumillon, 2014, Characterization of directed differentiation by high-throughput single-cell RNA-Seq, bioRxiv

Speers, 2009, Activity-based protein profiling (ABPP) and click chemistry (CC)-ABPP by MudPIT mass spectrometry, Curr. Protoc. Chem. Biol., 1, 29, 10.1002/9780470559277.ch090138

Stanton, 2009, A small molecule that binds Hedgehog and blocks its signaling in human cells, Nat. Chem. Biol., 5, 154, 10.1038/nchembio.142

Stellas, 2014, Therapeutic effects of an anti-Myc drug on mouse pancreatic cancer, J. Natl. Cancer Inst., 106, 10.1093/jnci/dju320

Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Nat. Acad. Sci. U S A, 102, 15545, 10.1073/pnas.0506580102

Tsubuki, 1996, Differential inhibition of calpain and proteasome activities by peptidyl aldehydes of Di-leucine and Tri-leucine, J. Biochem., 119, 572, 10.1093/oxfordjournals.jbchem.a021280

Vegas, 2008, Small-molecule microarrays as tools in ligand discovery, Chem. Soc. Rev., 37, 1385, 10.1039/b703568n

Wang, 2015, Direct inhibition of c-Myc-Max heterodimers by celastrol and celastrol-inspired triterpenoids, Oncotarget, 6, 32380, 10.18632/oncotarget.6116

Yin, 2003, Low molecular weight inhibitors of Myc-Max interaction and function, Oncogene, 22, 6151, 10.1038/sj.onc.1206641

Zeller, 2003, An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets, Genome Biol., 4, R69, 10.1186/gb-2003-4-10-r69

Zhang, 2008, Model-based analysis of ChIP-seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137