Publications | Structural Genomics Consortium

Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction.

Bolshan Y, Getlik M, Kuznetsova E, Wasney GA, Hajian T, Poda G, Nguyen KT, Wu H, Dombrovski L, Dong A, Senisterra G, Schapira M, Arrowsmith CH, Brown PJ, Al-Awar R, Vedadi M, Smil D

ACS Med Chem Lett. 4(3):353-7. doi: 10.1021/ml300467n

Publication date: March 14, 2013

PMID: 24900672

Systems approaches to genomic and epigenetic inter-regulation of peptide hormones in stress and reproduction.

Lovejoy DA, Barsyte-Lovejoy D

Prog. Biophys. Mol. Biol.. doi: 10.1016/j.pbiomolbio.2013.02.002

Publication date: March 14, 2013

PMID: 23500148

Crystal structures of the catalytic domain of human soluble guanylate cyclase.

Allerston CK, von Delft F, Gileadi O

PLoS ONE. 8(3):e57644. doi: 10.1371/journal.pone.0057644

Publication date: March 7, 2013

PMID: 23505436

Strategy to Target the Substrate Binding site of SET Domain Protein Methyltransferases.

Nguyen KT, Li F, Poda G, Smil D, Vedadi M, Schapira M

J Chem Inf Model. doi: 10.1021/ci300596x

Publication date: March 1, 2013

PMID: 23410263

Insight into S-adenosyl-L-methionine biosynthesis from crystal structures of human methionine adenosyltransferase catalytic and regulatory subunits.

Shafqat N, Muniz JR, Pilka ES, Paragrigoriou E, von Delft F, Oppermann U, Yue WW

Biochem. J.. doi: 10.1042/BJ20121580

Publication date: February 20, 2013

PMID: 23425511

A structural mapping of mutations causing succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency.

Shafqat N, Kavanagh KL, Sass JO, Christensen E, Fukao T, Lee WH, Oppermann U, Yue WW

J. Inherit. Metab. Dis.. doi: 10.1007/s10545-013-9589-z

Publication date: February 19, 2013

PMID: 23420214

A small molecule inhibitor of the BLM helicase modulates chromosome stability in human cells.

Nguyen GH, Dexheimer TS, Rosenthal AS, Chu WK, Singh DK, Mosedale G, Bachrati CZ, Schultz L, Sakurai M, Savitsky P, Abu M, McHugh PJ, Bohr VA, Harris CC, Jadhav A, Gileadi O, Maloney DJ, Simeonov A, Hickson ID

Chem. Biol.. 20(1):55-62. doi: 10.1016/j.chembiol.2012.10.016

Publication date: January 24, 2013

PMID: 23352139

Solution structure of the Big domain from Streptococcus pneumoniae reveals a novel Ca2+-binding module.

Wang T, Zhang J, Zhang X, Xu C, Tu X

Sci Rep. 3:1079. doi: 10.1038/srep01079

Publication date: January 16, 2013

PMID: 23326635

Novel Inverse Binding Mode of Indirubin Derivatives Yields Improved Selectivity for DYRK Kinases.

Myrianthopoulos V, Kritsanida M, Gaboriaud-Kolar N, Magiatis P, Ferandin Y, Durieu E, Lozach O, Cappel D, Soundararajan M, Filippakopoulos P, Sherman W, Knapp S, Meijer L, Mikros E, Skaltsounis AL

ACS Med Chem Lett. 4(1):22-26. doi: 10.1021/ml300207a

Publication date: January 10, 2013

PMID: 23336033

LRIG2 Mutations Cause Urofacial Syndrome.

Stuart HM, Roberts NA, Burgu B, Daly SB, Urquhart JE, Bhaskar S, Dickerson JE, Mermerkaya M, Silay MS, Lewis MA, Olondriz MB, Gener B, Beetz C, Varga RE, Gülpınar O, Süer E, Soygür T, Ozçakar ZB, Yalçınkaya F, Kavaz A, Bulum B, Gücük A, Yue WW, Erdogan F, Berry A, Hanley NA, McKenzie EA, Hilton EN, Woolf AS, Newman WG

Am. J. Hum. Genet.. doi: 10.1016/j.ajhg.2012.12.002

Publication date: January 9, 2013

PMID: 23313374

Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain.

James LI, Barsyte-Lovejoy D, Zhong N, Krichevsky L, Korboukh VK, Herold JM, Macnevin CJ, Norris JL, Sagum CA, Tempel W, Marcon E, Guo H, Gao C, Huang XP, Duan S, Emili A, Greenblatt JF, Kireev DB, Jin J, Janzen WP, Brown PJ, Bedford MT, Arrowsmith CH, Frye SV

Nat. Chem. Biol.. doi: 10.1038/nchembio.1157

Publication date: January 6, 2013

PMID: 23292653

Structural Insights into the Activation of MST3 by MO25.

Mehellou Y, Alessi DR, Macartney TJ, Szklarz M, Knapp S, Elkins JM

Biochem. Biophys. Res. Commun.. doi: 10.1016/j.bbrc.2012.12.113

Publication date: January 4, 2013

PMID: 23296203

A Strategy for Modulation of Enzymes in the Ubiquitin System.

Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P, Persaud A, Walker JR, Neculai AM, Neculai D, Vorobyov A, Garg P, Beatty L, Chan PK, Juang YC, Landry MC, Yeh C, Zeqiraj E, Karamboulas K, Allali-Hassani A, Vedadi M, Tyers M, Moffat J, Sicheri F, Pelletier L, Durocher D, Raught B, Rotin D, Yang J, Moran MF, Dhe-Paganon S, Sidhu SS

Science. doi: 10.1126/science.1230161

Publication date: January 3, 2013

PMID: 23287719

Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5.

Senisterra G, Wu H, Allali-Hassani A, Wasney GA, Barsyte-Lovejoy D, Dombrovski L, Dong A, Nguyen KT, Smil D, Bolshan Y, Hajian T, He H, Seitova A, Chau I, Li F, Poda G, Couture JF, Brown PJ, Al-Awar R, Schapira M, Arrowsmith CH, Vedadi M

Biochem. J.. 449(1):151-9. doi: 10.1042/BJ20121280

Publication date: January 1, 2013

PMID: 22989411

The design and synthesis of 5- and 6-isoxazolylbenzimidazoles as selective inhibitors of the BET bromodomains.

Hay D, Fedorov O, Filippakopoulos P, Martin S, Philpott M, Picaud S, Hewings DS, Uttakar S, Heightman TD, Conway SJ, Knapp S, Brennan PE

Medchemcomm. 4(1):140-144. doi: 10.1039/C2MD20189E

Publication date: January 1, 2013

PMID: 26682033

(R)-β-lysine modified elongation factor P functions in translation elongation.

Bullwinkle TJ, Zou SB, Rajkovic A, Hersch SJ, Elgamal S, Robinson N, Smil D, Bolshan Y, Navarre WW, Ibba M

J. Biol. Chem.. doi: 10.1074/jbc.M112.438879

Publication date: December 31, 2012

PMID: 23277358

Crystal Structure of the Human SUV39H1 Chromodomain and Its Recognition of Histone H3K9me2/3.

Wang T, Xu C, Liu Y, Fan K, Li Z, Sun X, Ouyang H, Zhang X, Zhang J, Li Y, Mackenzie F, Min J, Tu X

PLoS ONE. 7(12):e52977. doi: 10.1371/journal.pone.0052977

Publication date: December 28, 2012

PMID: 23285239

Nahuoic Acid A Produced by a Streptomyces sp. Isolated From a Marine Sediment Is a Selective SAM-Competitive Inhibitor of the Histone Methyltransferase SETD8.

Williams DE, Dalisay DS, Li F, Amphlett J, Maneerat W, Chavez MA, Wang YA, Matainaho T, Yu W, Brown PJ, Arrowsmith CH, Vedadi M, Andersen RJ

Org. Lett.. doi: 10.1021/ol303416k

Publication date: December 28, 2012

PMID: 23272941

Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors.

Yu W, Chory EJ, Wernimont AK, Tempel W, Scopton A, Federation A, Marineau JJ, Qi J, Barsyte-Lovejoy D, Yi J, Marcellus R, Iacob RE, Engen JR, Griffin C, Aman A, Wienholds E, Li F, Pineda J, Estiu G, Shatseva T, Hajian T, Al-Awar R, Dick JE, Vedadi M, Brown PJ, Arrowsmith CH, Bradner JE, Schapira M

Nat Commun. 3:1288. doi: 10.1038/ncomms2304

Publication date: December 18, 2012

PMID: 23250418

A public-private partnership to unlock the untargeted kinome.

Knapp S, Arruda P, Blagg J, Burley S, Drewry DH, Edwards A, Fabbro D, Gillespie P, Gray NS, Kuster B, Lackey KE, Mazzafera P, Tomkinson NC, Willson TM, Workman P, Zuercher WJ

Nat. Chem. Biol.. 9(1):3-6. doi: 10.1038/nchembio.1113

Publication date: December 15, 2012

PMID: 23238671

Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells.

Zhang W, Prakash C, Sum C, Gong Y, Li Y, Kwok JJ, Thiessen N, Pettersson S, Jones SJ, Knapp S, Yang H, Chin KC

J. Biol. Chem.. 287(51):43137-55. doi: 10.1074/jbc.M112.413047

Publication date: December 14, 2012

PMID: 23086925

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development.

Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG

Cell. 151(6):1200-13. doi: 10.1016/j.cell.2012.11.014

Publication date: December 7, 2012

PMID: 23217707

Tudor domains of the PRC2 components PHF1 and PHF19 selectively bind to histone H3K36me3.

Qin S, Guo Y, Xu C, Bian C, Fu M, Gong S, Min J

Biochem. Biophys. Res. Commun.. doi: 10.1016/j.bbrc.2012.11.116

Publication date: December 7, 2012

PMID: 23228662

CDR-H3 Diversity Is Not Required for Antigen Recognition by Synthetic Antibodies.

Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS

J. Mol. Biol.. doi: 10.1016/j.jmb.2012.11.037

Publication date: December 3, 2012

PMID: 23219464

Certhrax Toxin, an Anthrax-related ADP-ribosyltransferase from Bacillus cereus.

Visschedyk D, Rochon A, Tempel W, Dimov S, Park HW, Merrill AR

J. Biol. Chem.. 287(49):41089-102. doi: 10.1074/jbc.M112.412809

Publication date: November 30, 2012

PMID: 22992735

Epigallocatechin-3-gallate up-regulates tumor suppressor gene expression via a reactive oxygen species-dependent down-regulation of UHRF1.

Achour M, Mousli M, Alhosin M, Ibrahim A, Peluso J, Muller CD, Schini-Kerth VB, Hamiche A, Dhe-Paganon S, Bronner C

Biochem. Biophys. Res. Commun.. doi: 10.1016/j.bbrc.2012.11.087

Publication date: November 28, 2012

PMID: 23201574

Structural insights into the inactive subunit of the apicoplast-localized caseinolytic protease complex of Plasmodium falciparum.

El Bakkouri M, Rathore S, Calmettes C, Wernimont AK, Liu K, Sinha D, Asad M, Jung P, Hui R, Mohmmed A, Houry WA

J. Biol. Chem.. doi: 10.1074/jbc.M112.416560

Publication date: November 28, 2012

PMID: 23192353

Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit.

Fish PV, Filippakopoulos P, Bish G, Brennan PE, Bunnage ME, Cook AS, Federov O, Gerstenberger BS, Jones H, Knapp S, Marsden B, Nocka K, Owen DR, Philpott M, Picaud S, Primiano MJ, Ralph MJ, Sciammetta N, Trzupek JD

J. Med. Chem.. 55(22):9831-7. doi: 10.1021/jm3010515

Publication date: November 26, 2012

PMID: 23095041

Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-lysine Interactions.

Hewings DS, Rooney TP, Jennings LE, Hay DA, Schofield CJ, Brennan PE, Knapp S, Conway SJ

J. Med. Chem.. 55(22):9393-413. doi: 10.1021/jm300915b

Publication date: November 26, 2012

PMID: 22924434

Histone recognition by human malignant brain tumor domains.

Nady N, Krichevsky L, Zhong N, Duan S, Tempel W, Amaya MF, Ravichandran M, Arrowsmith CH

J. Mol. Biol.. 423(5):702-18. doi: 10.1016/j.jmb.2012.08.022

Publication date: November 9, 2012

PMID: 22954662

Selectivity, cocrystal structures, and neuroprotective properties of leucettines, a family of protein kinase inhibitors derived from the marine sponge alkaloid leucettamine B.

Tahtouh T, Elkins JM, Filippakopoulos P, Soundararajan M, Burgy G, Durieu E, Cochet C, Schmid RS, Lo DC, Delhommel F, Oberholzer AE, Pearl LH, Carreaux F, Bazureau JP, Knapp S, Meijer L

J. Med. Chem.. 55(21):9312-30. doi: 10.1021/jm301034u

Publication date: November 8, 2012

PMID: 22998443

Mutations in multidomain protein MEGF8 identify a Carpenter syndrome subtype associated with defective lateralization.

Twigg SR, Lloyd D, Jenkins D, Elçioglu NE, Cooper CD, Al-Sannaa N, Annagür A, Gillessen-Kaesbach G, Hüning I, Knight SJ, Goodship JA, Keavney BD, Beales PL, Gileadi O, McGowan SJ, Wilkie AO

Am. J. Hum. Genet.. 91(5):897-905. doi: 10.1016/j.ajhg.2012.08.027

Publication date: November 2, 2012

PMID: 23063620

Structural basis for ASPP2 recognition by the tumor suppressor p73.

Canning P, von Delft F, Bullock AN

J. Mol. Biol.. 423(4):515-27. doi: 10.1016/j.jmb.2012.08.005

Publication date: November 2, 2012

PMID: 22917970

Sinefungin derivatives as inhibitors and structure probes of protein lysine methyltransferase SETD2.

Zheng W, Ibáñez G, Wu H, Blum G, Zeng H, Dong A, Li F, Hajian T, Allali-Hassani A, Amaya MF, Siarheyeva A, Yu W, Brown PJ, Schapira M, Vedadi M, Min J, Luo M

J. Am. Chem. Soc.. 134(43):18004-14. doi: 10.1021/ja307060p

Publication date: October 31, 2012

PMID: 23043551

Structure of the bone morphogenetic protein receptor ALK2 and implications for fibrodysplasia ossificans progressiva.

Chaikuad A, Alfano I, Kerr G, Sanvitale CE, Boergermann JH, Triffitt JT, von Delft F, Knapp S, Knaus P, Bullock AN

J. Biol. Chem.. 287(44):36990-8. doi: 10.1074/jbc.M112.365932

Publication date: October 26, 2012

PMID: 22977237

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.

Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS

Proc. Natl. Acad. Sci. U.S.A.. 109(42):16852-7. doi: 10.1073/pnas.1206563109

Publication date: October 16, 2012

PMID: 23035246

A small-molecule inhibitor of Haspin alters the kinetochore functions of Aurora B.

De Antoni A, Maffini S, Knapp S, Musacchio A, Santaguida S

J. Cell Biol.. 199(2):269-84. doi: 10.1083/jcb.201205119

Publication date: October 15, 2012

PMID: 23071153

Crystal structure of human multiple copies in T-cell lymphoma-1 oncoprotein.

Tempel W, Dimov S, Tong Y, Park HW, Hong BS

Proteins. doi: 10.1002/prot.24198

Publication date: October 8, 2012

PMID: 23042581

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation.

Rothbart SB, Krajewski K, Nady N, Tempel W, Xue S, Badeaux AI, Barsyte-Lovejoy D, Martinez JY, Bedford MT, Fuchs SM, Arrowsmith CH, Strahl BD

Nat. Struct. Mol. Biol.. 19(11):1155-60. doi: 10.1038/nsmb.2391

Publication date: September 30, 2012

PMID: 23022729

C-terminal processing of the teneurin proteins: Independent actions of a teneurin C-terminal associated peptide in hippocampal cells.

Chand D, Casatti CA, de Lannoy L, Song L, Kollara A, Barsyte-Lovejoy D, Brown TJ, Lovejoy DA

Mol. Cell. Neurosci.. 52:38-50. doi: 10.1016/j.mcn.2012.09.006

Publication date: September 28, 2012

PMID: 23026563

Crystal structure of human aurora B in complex with INCENP and VX-680.

Elkins JM, Santaguida S, Musacchio A, Knapp S

J. Med. Chem.. 55(17):7841-8. doi: 10.1021/jm3008954

Publication date: September 13, 2012

PMID: 22920039

Discovery of ligands for ADP-ribosyltransferases via docking-based virtual screening.

Andersson CD, Karlberg T, Ekblad T, Lindgren AE, Thorsell AG, Spjut S, Uciechowska U, Niemiec MS, Wittung-Stafshede P, Weigelt J, Elofsson M, Schüler H, Linusson A

J. Med. Chem.. 55(17):7706-18. doi: 10.1021/jm300746d

Publication date: September 13, 2012

PMID: 22823910

Druggability analysis and structural classification of bromodomain acetyl-lysine binding sites.

Vidler LR, Brown N, Knapp S, Hoelder S

J. Med. Chem.. 55(17):7346-59. doi: 10.1021/jm300346w

Publication date: September 13, 2012

PMID: 22788793

Structural determination of the phosphorylation domain of the ryanodine receptor.

Sharma P, Ishiyama N, Nair U, Li W, Dong A, Miyake T, Wilson A, Ryan T, MacLennan DH, Kislinger T, Ikura M, Dhe-Paganon S, Gramolini AO

FEBS J.. 279(20):3952-64. doi: 10.1111/j.1742-4658.2012.08755.x

Publication date: September 11, 2012

PMID: 22913516

Structure and mechanism of human UDP-xylose synthase: evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid.

Eixelsberger T, Sykora S, Egger S, Brunsteiner M, Kavanagh KL, Oppermann U, Brecker L, Nidetzky B

J. Biol. Chem.. 287(37):31349-58. doi: 10.1074/jbc.M112.386706

Publication date: September 7, 2012

PMID: 22810237

The PHD and chromo domains regulate the ATPase activity of the human chromatin remodeler CHD4.

Watson AA, Mahajan P, Mertens HD, Deery MJ, Zhang W, Pham P, Du X, Bartke T, Zhang W, Edlich C, Berridge G, Chen Y, Burgess-Brown NA, Kouzarides T, Wiechens N, Owen-Hughes T, Svergun DI, Gileadi O, Laue ED

J. Mol. Biol.. 422(1):3-17. doi: 10.1016/j.jmb.2012.04.031

Publication date: September 7, 2012

PMID: 22575888

C-Terminal region of teneurin-1 co-localizes with dystroglycan and modulates cytoskeletal organization through an extracellular signal-regulated kinase-dependent stathmin- and filamin A-mediated mechanism in hippocampal cells.

Chand D, Song L, deLannoy L, Barsyte-Lovejoy D, Ackloo S, Boutros PC, Evans K, Belsham DD, Lovejoy DA

Neuroscience. 219:255-70. doi: 10.1016/j.neuroscience.2012.05.069

Publication date: September 6, 2012

PMID: 22698694

Pharmacological inhibition of LIM kinase stabilizes microtubules and inhibits neoplastic growth.

Prudent R, Vassal-Stermann E, Nguyen CH, Pillet C, Martinez A, Prunier C, Barette C, Soleilhac E, Filhol O, Beghin A, Valdameri G, Honoré S, Aci-Sèche S, Grierson D, Antonipillai J, Li R, Di Pietro A, Dumontet C, Braguer D, Florent JC, Knapp S, Bernard O, Lafanechère L

Cancer Res.. 72(17):4429-39. doi: 10.1158/0008-5472.CAN-11-3342

Publication date: September 1, 2012

PMID: 22761334

The corky root rot pathogen Pyrenochaeta lycopersici secretes a proteinaceous inducer of cell death affecting host plants differentially.

Clergeot PH, Schuler H, Mørtz E, Brus M, Vintila S, Ekengren S

Phytopathology. 102(9):878-91. doi: 10.1094/PHYTO-01-12-0004

Publication date: September 1, 2012

PMID: 22708726

Structures of human DPP7 reveal the molecular basis of specific inhibition and the architectural diversity of proline-specific peptidases.

Bezerra GA, Dobrovetsky E, Dong A, Seitova A, Crombett L, Shewchuk LM, Hassell AM, Sweitzer SM, Sweitzer TD, McDevitt PJ, Johanson KO, Kennedy-Wilson KM, Cossar D, Bochkarev A, Gruber K, Dhe-Paganon S

PLoS ONE. 7(8):e43019. doi: 10.1371/journal.pone.0043019

Publication date: August 29, 2012

PMID: 22952628