Publications | Structural Genomics Consortium

Epigenetic targets and drug discovery Part 2: Histone demethylation and DNA methylation.

Liu K, Liu Y, Lau JL, Min J

Pharmacol. Ther.. doi: 10.1016/j.pharmthera.2015.04.001

Publication date: April 6, 2015

PMID: 25857453

Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design.

Mohanty S, Kennedy EJ, Herberg FW, Hui R, Taylor SS, Langsley G, Kannan N

Biochim. Biophys. Acta. doi: 10.1016/j.bbapap.2015.03.012

Publication date: April 3, 2015

PMID: 25847873

LLY-507, a Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2.

Nguyen H, Allali-Hassani A, Antonysamy S, Chang S, Chen LH, Curtis C, Emtage S, Fan L, Gheyi T, Li F, Liu S, Martin JR, Mendel D, Olsen JB, Pelletier L, Shatseva T, Wu S, Zhang FF, Arrowsmith CH, Brown PJ, Campbell RM, Garcia BA, Barsyte-Lovejoy D, Mader M, Vedadi M

J. Biol. Chem.. doi: 10.1074/jbc.M114.626861

Publication date: March 30, 2015

PMID: 25825497

Selective inhibitors of Cyclin-G associated kinase (GAK) as anti-HCV agents.

Kovackova S, Chang L, Bekerman E, Neveu G, Barouch-Bentov R, Chaikuad A, Heroven C, Sala M, De Jonghe SC, Knapp S, Einav S, Herdewijn P

J. Med. Chem.. doi: 10.1021/jm501759m

Publication date: March 30, 2015

PMID: 25822739

Discovery and characterization of GSK2801, a selective chemical probe for the bromodomains BAZ2A and BAZ2B.

Chen P, Chaikuad A, Bamborough P, Bantscheff M, Bountra C, Chung CW, Fedorov O, Grandi P, Jung D, Lesniak R, Lindon M, Müller S, Philpott M, Prinjha RK, Rogers CM, Selenski C, Tallant C, Werner T, Willson TM, Knapp S, Drewry DH

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b00209

Publication date: March 23, 2015

PMID: 25799074

Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures.

Pike AC, Gomathinayagam S, Swuec P, Berti M, Zhang Y, Schnecke C, Marino F, von Delft F, Renault L, Costa A, Gileadi O, Vindigni A

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1417594112

Publication date: March 23, 2015

PMID: 25831490

K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.

Dong YY, Pike AC, Mackenzie A, McClenaghan C, Aryal P, Dong L, Quigley A, Grieben M, Goubin S, Mukhopadhyay S, Ruda GF, Clausen MV, Cao L, Brennan PE, Burgess-Brown NA, Sansom MS, Tucker SJ, Carpenter EP

Science. 347(6227):1256-1259. doi: 10.1126/science.1261512

Publication date: March 13, 2015

PMID: 25766236

10-Iodo-11H-indolo[3,2-c]quinoline-6-carboxylic Acids Are Selective Inhibitors of DYRK1A.

Falke H, Chaikuad A, Becker A, Loaëc N, Lozach O, Abu Jhaisha S, Becker W, Jones PG, Preu L, Baumann K, Knapp S, Meijer L, Kunick C

J. Med. Chem.. doi: 10.1021/jm501994d

Publication date: March 2, 2015

PMID: 25730262

A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3).

Kaniskan HÜ, Szewczyk MM, Yu Z, Eram MS, Yang X, Schmidt K, Luo X, Dai M, He F, Zang I, Lin Y, Kennedy S, Li F, Dobrovetsky E, Dong A, Smil D, Min SJ, Landon M, Lin-Jones J, Huang XP, Roth BL, Schapira M, Atadja P, Barsyte-Lovejoy D, Arrowsmith CH, Brown PJ, Zhao K, Jin J, Vedadi M

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201412154

Publication date: February 27, 2015

PMID: 25728001

Ankyrin Repeats of ANKRA2 Recognize a PxLPxL Motif on the 3M Syndrome Protein CCDC8.

Nie J, Xu C, Jin J, Aka JA, Tempel W, Nguyen V, You L, Weist R, Min J, Pawson T, Yang XJ

Structure. doi: 10.1016/j.str.2015.02.001

Publication date: February 26, 2015

PMID: 25752541

Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B.

Drouin L, McGrath S, Vidler LR, Chaikuad A, Monteiro O, Tallant C, Philpott M, Rogers C, Fedorov O, Liu M, Akhtar W, Hayes A, Raynaud F, Müller S, Knapp S, Hoelder S

J. Med. Chem.. doi: 10.1021/jm501963e

Publication date: February 26, 2015

PMID: 25719566

Building a roadmap for developing combination therapies for Alzheimer's disease.

Perry D, Sperling R, Katz R, Berry D, Dilts D, Hanna D, Salloway S, Trojanowski JQ, Bountra C, Krams M, Luthman J, Potkin S, Gribkoff V, Temple R, Wang Y, Carrillo MC, Stephenson D, Snyder H, Liu E, Ware T, McKew J, Fields FO, Bain LJ, Bens C

Expert Rev Neurother. 15(3):327-33. doi: 10.1586/14737175.2015.996551

Publication date: February 25, 2015

PMID: 25708309

The 9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain.

Picaud S, Strocchia M, Terracciano S, Lauro G, Méndez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P

J. Med. Chem.. doi: 10.1021/jm501893k

Publication date: February 22, 2015

PMID: 25703523

Preclinical target validation using patient-derived cells.

Edwards AM, Arrowsmith CH, Bountra C, Bunnage ME, Feldmann M, Knight JC, Patel DD, Prinos P, Taylor MD, Sundström M, Barker P, Barsyte D, Bengtson MH, Bell C, Bowness P, Boycott KM, Buser-Doepner C, Carpenter CL, Carr AJ, Clark K, Das AM, Dhanak D, Dirks P, Ellis J, Fantin VR, Flores C, Fon EA, Frail DE, Gileadi O, O'Hagan RC, Howe T, Isaac JT, Jabado N, Jakobsson PJ, Klareskog L, Knapp S, Lee WH, Lima-Fernandes E, Lundberg IE, Marshall J, Massirer KB, MacKenzie AE, Maruyama T, Mueller-Fahrnow A, Muthuswamy S, Nanchahal J, O'Brien C, Oppermann U, Ostermann N, Petrecca K, Pollock BG, Poupon V, Prinjha RK, Rosenberg SH, Rouleau G, Skingle M, Slutsky AS, Smith GA, Verhelle D, Widmer H, Young LT

Nat Rev Drug Discov. 14(3):149-50. doi: 10.1038/nrd4565

Publication date: February 20, 2015

PMID: 25722227

Structural Insights into the Auto-regulation and Cooperativity of the Human Transcription Factor Ets-2.

Newman JA, Cooper CD, Aitkenhead H, Gileadi O

J. Biol. Chem.. doi: 10.1074/jbc.M114.619270

Publication date: February 10, 2015

PMID: 25670864

Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library.

Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201410736

Publication date: February 3, 2015

PMID: 25650139

Human prostaglandin reductase 1 (PGR1): Substrate specificity, inhibitor analysis and site-directed mutagenesis.

Mesa J, Alsina C, Oppermann U, Parés X, Farrés J, Porté S

Chem. Biol. Interact.. doi: 10.1016/j.cbi.2015.01.021

Publication date: January 22, 2015

PMID: 25619643

Clinical Utility Gene Card for: Fibrodysplasia ossificans progressiva.

Bravenboer N, Micha D, Triffit JT, Bullock AN, Ravazollo R, Bocciardi R, di Rocco M, Netelenbos JC, Ten Dijke P, Sánchez-Duffhues G, Kaplan FS, Shore EM, Pignolo RJ, Seemann P, Ventura F, Beaujat G, Eekhoff EM, Pals G

Eur. J. Hum. Genet.. doi: 10.1038/ejhg.2014.274

Publication date: January 21, 2015

PMID: 25604857

Bisubstrate Inhibitor Approach for Targeting Mitotic Kinase Haspin.

Kestav K, Lavogina D, Raidaru G, Chaikuad A, Knapp S, Uri A

Bioconjug. Chem.. doi: 10.1021/bc500464r

Publication date: January 16, 2015

PMID: 25595038

Identification of a Fragment-like Small Molecule Ligand for the Methyl-lysine Binding Protein, 53BP1.

Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV

ACS Chem. Biol.. doi: 10.1021/cb500956g

Publication date: January 15, 2015

PMID: 25590533

Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis.

Van Rechem C, Black JC, Boukhali M, Aryee MJ, Graslund S, Haas W, Benes CH, Whetstine JR

Cancer Discov. doi: 10.1158/2159-8290.CD-14-1326

Publication date: January 6, 2015

PMID: 25564516

A small molecule targeting ALK1 prevents Notch cooperativity and inhibits functional angiogenesis.

Kerr G, Sheldon H, Chaikuad A, Alfano I, von Delft F, Bullock AN, Harris AL

Angiogenesis. doi: 10.1007/s10456-014-9457-y

Publication date: January 4, 2015

PMID: 25557927

Structure-activity relationship studies of SETD8 inhibitors.

Ma A, Yu W, Xiong Y, Butler KV, Brown PJ, Jin J

Medchemcomm. 5(12):1892-1898. doi: 10.1039/C4MD00317A

Publication date: January 3, 2015

PMID: 25554733

SPOTing Acetyl-Lysine Dependent Interactions.

Picaud S, Filippakopoulos P

Microarrays (Basel). 4(3):370-88. doi: 10.3390/microarrays4030370

Publication date: January 1, 2015

PMID: 27600229

Purification and interaction analyses of two human lysosomal vitamin B12 transporters: LMBD1 and ABCD4.

Deme JC, Hancock MA, Xia X, Shintre CA, Plesa M, Kim JC, Carpenter EP, Rosenblatt DS, Coulton JW

Mol. Membr. Biol.. 31(7-8):250-61. doi: 10.3109/09687688.2014.990998

Publication date: December 24, 2014

PMID: 25535791

Recombinant renewable polyclonal antibodies.

Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury AR

MAbs. doi: 10.4161/19420862.2015.989047

Publication date: December 20, 2014

PMID: 25530082

Identification of 2,4-diamino-6,7-dimethoxyquinoline derivatives as G9a inhibitors†Electronic supplementary information (ESI) available. See DOI: 10.1039/c4md00274a.

Srimongkolpithak N, Sundriyal S, Li F, Vedadi M, Fuchter MJ

Medchemcomm. 5(12):1821-1828. doi: 10.1039/c4md00274a

Publication date: December 19, 2014

PMID: 25750706

Structural biology and chemistry of protein arginine methyltransferases.

Schapira M, Ferreira de Freitas R

Medchemcomm. 5(12):1779-1788. doi: 10.1039/c4md00269e

Publication date: December 19, 2014

PMID: 26693001

Molecular Basis of Histone Tail Recognition by Human TIP5 PHD Finger and Bromodomain of the Chromatin Remodeling Complex NoRC.

Tallant C, Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A

Structure. doi: 10.1016/j.str.2014.10.017

Publication date: December 18, 2014

PMID: 25533489

Application of in situ diffraction in high-throughput structure determination platforms.

Aller P, Sanchez-Weatherby J, Foadi J, Winter G, Lobley CM, Axford D, Ashton AW, Bellini D, Brandao-Neto J, Culurgioni S, Douangamath A, Duman R, Evans G, Fisher S, Flaig R, Hall DR, Lukacik P, Mazzorana M, McAuley KE, Mykhaylyk V, Owen RL, Paterson NG, Romano P, Sandy J, Sorensen T, von Delft F, Wagner A, Warren A, Williams M, Stuart DI, Walsh MA

Methods Mol. Biol.. 1261:233-53. doi: 10.1007/978-1-4939-2230-7_13

Publication date: December 17, 2014

PMID: 25502203

Towards a systematic analysis of human short-chain dehydrogenases/reductases (SDR): ligand identification and structure-activity relationships.

Bhatia C, Oerum S, Bray J, Kavanagh KL, Shafqat N, Yue W, Oppermann U

Chem. Biol. Interact.. doi: 10.1016/j.cbi.2014.12.013

Publication date: December 16, 2014

PMID: 25526675

Crystal Structure of Sphingosine Kinase 1 with PF-543.

Wang J, Knapp S, Pyne NJ, Pyne S, Elkins JM

ACS Med Chem Lett. 5(12):1329-33. doi: 10.1021/ml5004074

Publication date: December 11, 2014

PMID: 25516793

CSB interacts with SNM1A and promotes DNA interstrand crosslink processing.

Iyama T, Lee SY, Berquist BR, Gileadi O, Bohr VA, Seidman MM, McHugh PJ, Wilson DM

Nucleic Acids Res.. doi: 10.1093/nar/gku1279

Publication date: December 10, 2014

PMID: 25505141

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.

Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R

Nat. Genet.. doi: 10.1038/ng.3165

Publication date: December 8, 2014

PMID: 25485837

A global assessment of cancer genomic alterations in epigenetic mechanisms.

Shah MA, Denton EL, Arrowsmith CH, Lupien M, Schapira M

Epigenetics Chromatin. 7(1):29. doi: 10.1186/1756-8935-7-29

Publication date: December 4, 2014

PMID: 25484917

Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor.

England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE

Medchemcomm. 5(12):1879-1886. doi: 10.1039/C4MD00291A

Publication date: December 1, 2014

PMID: 26682034

Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures.

Chatterjee S, Zagelbaum J, Savitsky P, Sturzenegger A, Huttner D, Janscak P, Hickson ID, Gileadi O, Rothenberg E

Nat Commun. 5:5556. doi: 10.1038/ncomms6556

Publication date: November 25, 2014

PMID: 25418155

Nanog requires BRD4 to maintain murine embryonic stem cell pluripotency and is suppressed by bromodomain inhibitor JQ1 together with Lefty1.

Horne G, Stewart H, Dickson J, Knapp S, Ramsahoye B, Chevassut T

Stem Cells Dev.. doi: 10.1089/scd.2014.0302

Publication date: November 13, 2014

PMID: 25393219

Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia.

Xu B, On DM, Ma A, Parton T, Konze KD, Pattenden SG, Allison DF, Cai L, Rockowitz S, Liu S, Liu Y, Li F, Vedadi M, Frye SV, Garcia BA, Zheng D, Jin J, Wang GG

Blood. doi: 10.1182/blood-2014-06-581082

Publication date: November 13, 2014

PMID: 25395428

The Humoral Immune Response to HCV: Understanding is Key to Vaccine Development.

Cashman SB, Marsden BD, Dustin LB

Front Immunol. 5:550. doi: 10.3389/fimmu.2014.00550

Publication date: November 10, 2014

PMID: 25426115

Identification and Characterization of a Small-Molecule Inhibitor of Death-Associated Protein Kinase 1.

Wilbek TS, Skovgaard T, Sorrell FJ, Knapp S, Berthelsen J, Strømgaard K

Chembiochem. doi: 10.1002/cbic.201402512

Publication date: November 7, 2014

PMID: 25382253

Small Molecules Dorsomorphin and LDN-193189 Inhibit Myostatin/GDF8 Signaling and Promote Functional Myoblast Differentiation.

Horbelt D, Boergermann JH, Chaikuad A, Alfano I, Williams E, Lukonin I, Timmel T, Bullock AN, Knaus P

J. Biol. Chem.. doi: 10.1074/jbc.M114.604397

Publication date: November 3, 2014

PMID: 25368322

Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation.

Dong C, Zhang H, Xu C, Arrowsmith CH, Min J

IUCrJ. 1(Pt 6):540-549. doi: 10.1107/S2052252514020922

Publication date: November 1, 2014

PMID: 25485134

X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and QM/MM Study of Hg2+ Transfer between the C-terminal and Buried Catalytic Site Cysteine Pairs.

Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H

Biochemistry. doi: 10.1021/bi500608u

Publication date: October 24, 2014

PMID: 25343681

Inter-Domain Communication Of Human Cystathionine Beta Synthase: Structural Basis Of S-Adenosyl-L-Methionine Activation.

McCorvie TJ, Kopec J, Hyung SJ, Fitzpatrick F, Feng X, Termine D, Strain-Damerell C, Vollmar M, Fleming J, Janz JM, Bulawa C, Yue WW

J. Biol. Chem.. doi: 10.1074/jbc.M114.610782

Publication date: October 21, 2014

PMID: 25336647

Expanding the clinical and molecular spectrum of thiamine pyrophosphokinase deficiency: A treatable neurological disorder caused by TPK1 mutations.

Banka S, de Goede C, Yue WW, Morris AA, von Bremen B, Chandler KE, Feichtinger RG, Hart C, Khan N, Lunzer V, Mataković L, Marquardt T, Makowski C, Prokisch H, Debus O, Nosaka K, Sonwalkar H, Zimmermann FA, Sperl W, Mayr JA

Mol. Genet. Metab.. doi: 10.1016/j.ymgme.2014.09.010

Publication date: October 5, 2014

PMID: 25458521

Kruidenier et al. reply.

Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H, Eberhard D, Hutchinson S, Jones E, Katso R, Leveridge M, Mander PK, Mosley J, Ramirez-Molina C, Rowland P, Schofield CJ, Sheppard RJ, Smith JE, Swales C, Tanner R, Thomas P, Tumber A, Drewes G, Oppermann U, Patel DJ, Lee K, Wilson DM

Nature. 514(7520):E2. doi: 10.1038/nature13689

Publication date: October 1, 2014

PMID: 25279927