Publications

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2017

Progress towards a public chemogenomic set for protein kinases and a call for contributions.

Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM

PLoS ONE. 12(8):e0181585. doi: 10.1371/journal.pone.0181585

Publication date: August 3, 2017

PMID: 28767711

(19) F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers.

Dalvit C, Knapp S

Magn Reson Chem. doi: 10.1002/mrc.4640

Publication date: August 1, 2017

PMID: 28762528

IDUA mutational profile and genotype-phenotype relationships in UK patients with Mucopolysaccharidosis I.

Ghosh A, Mercer J, Mackinnon S, Yue WW, Church H, Beesley CE, Broomfield A, Jones SA, Tylee K

Hum. Mutat.. doi: 10.1002/humu.23301

Publication date: July 28, 2017

PMID: 28752568

BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis.

Roberts TC, Etxaniz U, Dall'Agnese A, Wu SY, Chiang CM, Brennan PE, Wood MJA, Puri PL

Sci Rep. 7(1):6153. doi: 10.1038/s41598-017-06483-7

Publication date: July 21, 2017

PMID: 28733670

Design of a chemical probe for the Bromodomain and Plant Homeodomain Finger-containing (BRPF) family of proteins.

Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b00611

Publication date: July 17, 2017

PMID: 28714688

Global analysis of protein folding using massively parallel design, synthesis, and testing.

Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D

Science. 357(6347):168-175. doi: 10.1126/science.aan0693

Publication date: July 14, 2017

PMID: 28706065

NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin.

Melo-Hanchuk TD, Slepicka PF, Meirelles GV, Basei FL, Lovato DV, Granato DC, Pauletti BA, Domingues RR, Leme AFP, Pelegrini AL, Lenz G, Knapp S, Elkins JM, Kobarg J

Sci Rep. 7(1):5445. doi: 10.1038/s41598-017-05325-w

Publication date: July 14, 2017

PMID: 28710492

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB

Cell Stem Cell. doi: 10.1016/j.stem.2017.06.004

Publication date: July 11, 2017

PMID: 28712938

Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH

Nat Commun. 8:15921. doi: 10.1038/ncomms15921

Publication date: June 30, 2017

PMID: 28665395

Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.

Xiong Y, Li F, Babault N, Wu H, Dong A, Zeng H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J

Bioorg. Med. Chem.. doi: 10.1016/j.bmc.2017.06.021

Publication date: June 19, 2017

PMID: 28662962

Readers, writers and erasers of N(6)-methylated adenosine modification.

Wu B, Li L, Huang Y, Ma J, Min J

Curr. Opin. Struct. Biol.. 47:67-76. doi: 10.1016/j.sbi.2017.05.011

Publication date: June 15, 2017

PMID: 28624569

Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment.

Aquino B, Couñago RM, Verza N, Ferreira LM, Massirer KB, Gileadi O, Arruda P

Front Plant Sci. 8:852. doi: 10.3389/fpls.2017.00852

Publication date: June 13, 2017

PMID: 28603531

Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.

Chaikuad A, Filippakopoulos P, Marcsisin SR, Picaud S, Schröder M, Sekine S, Ichijo H, Engen JR, Takeda K, Knapp S

Structure. doi: 10.1016/j.str.2017.05.020

Publication date: June 10, 2017

PMID: 28648608

Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10.

Zhang W, Sartori MA, Makhnevych T, Federowicz KE, Dong X, Liu L, Nim S, Dong A, Yang J, Li Y, Haddad D, Ernst A, Heerding D, Tong Y, Moffat J, Sidhu SS

J. Mol. Biol.. doi: 10.1016/j.jmb.2017.05.025

Publication date: June 3, 2017

PMID: 28587923

A trust approach for sharing research reagents.

Edwards A, Morgan M, Al Chawaf A, Andrusiak K, Charney R, Cynader Z, ElDessouki A, Lee Y, Moeser A, Stern S, Zuercher WJ

Sci Transl Med. 9(392):. doi: 10.1126/scitranslmed.aai9055

Publication date: May 31, 2017

PMID: 28566431

Oxalyl Boronates Enable Modular Synthesis of Bioactive Imidazoles.

Lee CF, Holownia A, Bennett JM, Elkins JM, St Denis JD, Adachi S, Yudin AK

Angew. Chem. Int. Ed. Engl.. 56(22):6264-6267. doi: 10.1002/anie.201611006

Publication date: May 22, 2017

PMID: 28267269

The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats.

Pascoal CC, Islam Z, Adamoski D, Ferreira IM, Righetto RD, Bettini J, Portugal RV, Yue WW, Gonzalez A, Dias SMG, Ambrosio ALB

J. Biol. Chem.. doi: 10.1074/jbc.M117.787291

Publication date: May 19, 2017

PMID: 28526749

Protein destabilization and loss of protein-protein interaction are fundamental mechanisms in cblA-type methylmalonic aciduria.

Plessl T, Bürer C, Lutz S, Yue WW, Baumgartner MR, Froese DS

Hum. Mutat.. doi: 10.1002/humu.23251

Publication date: May 12, 2017

PMID: 28497574

A specific and covalent JNK-1 ligand selected from an encoded self-assembling chemical library.

Zimmermann G, Rieder U, Bajic D, Vanetti S, Chaikuad A, Knapp S, Scheuermann J, Mattarella M, Neri D

Chemistry. doi: 10.1002/chem.201701644

Publication date: May 9, 2017

PMID: 28485044

In Vivo Biotinylation of Antigens in E. coli.

Gräslund S, Savitsky P, Müller-Knapp S

Methods Mol. Biol.. 1586:337-344. doi: 10.1007/978-1-4939-6887-9_22

Publication date: May 5, 2017

PMID: 28470616

N- and C-Terminal Truncations to Enhance Protein Solubility and Crystallization: Predicting Protein Domain Boundaries with Bioinformatics Tools.

Cooper CDO, Marsden BD

Methods Mol. Biol.. 1586:11-31. doi: 10.1007/978-1-4939-6887-9_2

Publication date: May 5, 2017

PMID: 28470596

Recombinant Protein Expression in E. coli : A Historical Perspective.

Gileadi O

Methods Mol. Biol.. 1586:3-10. doi: 10.1007/978-1-4939-6887-9_1

Publication date: May 5, 2017

PMID: 28470595

Hyperactive locomotion in a Drosophila model is a functional readout for the synaptic abnormalities underlying fragile X syndrome.

Kashima R, Redmond PL, Ghatpande P, Roy S, Kornberg TB, Hanke T, Knapp S, Lagna G, Hata A

Sci Signal. 10(477):. doi: 10.1126/scisignal.aai8133

Publication date: May 2, 2017

PMID: 28465421

Histone lysine methyltransferase structure activity relationships that allow for segregation of G9a inhibition and anti-Plasmodium activity.

Sundriyal S, Chen PB, Lubin AS, Lueg GA, Li F, White AJP, Malmquist NA, Vedadi M, Scherf A, Fuchter MJ

Medchemcomm. 8(5):1069-1092. doi: 10.1039/c7md00052a

Publication date: May 1, 2017

PMID: 29308121

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F

Nat Commun. 8:15123. doi: 10.1038/ncomms15123

Publication date: April 24, 2017

PMID: 28436492

Global survey of the immunomodulatory potential of common drugs.

Vladimer GI, Snijder B, Krall N, Bigenzahn JW, Huber KVM, Lardeau CH, Sanjiv K, Ringler A, Berglund UW, Sabler M, de la Fuente OL, Knöbl P, Kubicek S, Helleday T, Jäger U, Superti-Furga G

Nat. Chem. Biol.. doi: 10.1038/nchembio.2360

Publication date: April 24, 2017

PMID: 28437395

The RNF168 paralog RNF169 defines a new class of ubiquitylated-histone reader involved in the response to DNA damage.

Kitevski-LeBlanc J, Fradet-Turcotte A, Kukic P, Wilson MD, Portella G, Yuwen T, Panier S, Duan S, Canny MD, van Ingen H, Arrowsmith CH, Rubinstein JL, Vendruscolo M, Durocher D, Kay LE

Elife. 6:. doi: 10.7554/eLife.23872

Publication date: April 13, 2017

PMID: 28406400

Benzo-isoquinoline-diones As Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains.

Bouché L, Christ CD, Siegel S, Fernández-Montalván AE, Holton SJ, Fedorov O, Ter Laak A, Sugawara T, Stöckigt D, Tallant C, Bennett JM, Monteiro OP, Díaz-Sáez L, Siejka P, Meier J, Puetter V, Weiske J, Müller S, Huber KV, Hartung IV, Haendler B

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b00306

Publication date: April 12, 2017

PMID: 28402630

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.

Kawamura A, Münzel M, Kojima T, Yapp C, Bhushan B, Goto Y, Tumber A, Katoh T, King ON, Passioura T, Walport LJ, Hatch SB, Madden S, Müller S, Brennan PE, Chowdhury R, Hopkinson RJ, Suga H, Schofield CJ

Nat Commun. 8:14773. doi: 10.1038/ncomms14773

Publication date: April 6, 2017

PMID: 28382930

Molecular basis for the methylation specificity of ATXR5 for histone H3.

Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF

Nucleic Acids Res.. doi: 10.1093/nar/gkx224

Publication date: April 5, 2017

PMID: 28383693

Structure-based design of highly selective inhibitors of the CREB binding protein bromodomain.

Denny RA, Flick AC, Coe JW, Langille J, Basak A, Liu S, Stock IA, Sahasrabudhe P, Bonin PD, Hay DA, Brennan PE, Pletcher MT, Jones LH, Chekler EL

J. Med. Chem.. doi: 10.1021/acs.jmedchem.6b01839

Publication date: April 4, 2017

PMID: 28375629

MOB1 mediated phospho-recognition in the core mammalian Hippo pathway.

Couzens AL, Xiong S, Knight JD, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, Gingras AC

Mol. Cell Proteomics. doi: 10.1074/mcp.M116.065490

Publication date: April 3, 2017

PMID: 28373298

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.

Pearce NM, Bradley AR, Krojer T, Marsden BD, Deane CM, von Delft F

Struct Dyn. 4(3):032104. doi: 10.1063/1.4974176

Publication date: March 28, 2017

PMID: 28345007

Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.

Aryal P, Jarerattanachat V, Clausen MV, Schewe M, McClenaghan C, Argent L, Conrad LJ, Dong YY, Pike AC, Carpenter EP, Baukrowitz T, Sansom MS, Tucker SJ

Structure. doi: 10.1016/j.str.2017.03.006

Publication date: March 24, 2017

PMID: 28392258

Human apo-SRP72 and SRP68/72 complex structures reveal the molecular basis of protein translocation.

Gao Y, Zhang Q, Lang Y, Liu Y, Dong X, Chen Z, Tian W, Tang J, Wu W, Tong Y, Chen Z

J Mol Cell Biol. doi: 10.1093/jmcb/mjx010

Publication date: March 20, 2017

PMID: 28369529

Development of a monoclonal anti-ADAMTS-5 antibody that specifically blocks the interaction with LRP1.

Santamaria S, Fedorov O, McCafferty J, Murphy G, Dudhia J, Nagase H, Yamamoto K

MAbs. 0. doi: 10.1080/19420862.2017.1304341

Publication date: March 17, 2017

PMID: 28306378

Tetrahydroisoquinoline-7-carboxamide Derivatives as New Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors.

Wang Z, Zhang Y, Bartual SG, Luo J, Xu T, Du W, Xun Q, Tu Z, Brekken RA, Ren X, Bullock AN, Liang G, Lu X, Ding K

ACS Med Chem Lett. 8(3):327-332. doi: 10.1021/acsmedchemlett.6b00497

Publication date: March 9, 2017

PMID: 28337325

Assessing histone demethylase inhibitors in cells: lessons learned.

Hatch SB, Yapp C, Montenegro RC, Savitsky P, Gamble V, Tumber A, Ruda GF, Bavetsias V, Fedorov O, Atrash B, Raynaud F, Lanigan R, Carmichael L, Tomlin K, Burke R, Westaway SM, Brown JA, Prinjha RK, Martinez ED, Oppermann U, Schofield CJ, Bountra C, Kawamura A, Blagg J, Brennan PE, Rossanese O, Müller S

Epigenetics Chromatin. 10:9. doi: 10.1186/s13072-017-0116-6

Publication date: March 8, 2017

PMID: 28265301

Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis.

Persson H, Preger C, Marcon E, Lengqvist J, Gräslund S

Methods Mol. Biol.. 1575:175-187. doi: 10.1007/978-1-4939-6857-2_10

Publication date: March 4, 2017

PMID: 28255880

Gentle, fast and effective crystal soaking by acoustic dispensing.

Collins PM, Ng JT, Talon R, Nekrosiute K, Krojer T, Douangamath A, Brandao-Neto J, Wright N, Pearce NM, von Delft F

Acta Crystallogr D Struct Biol. 73(Pt 3):246-255. doi: 10.1107/S205979831700331X

Publication date: March 1, 2017

PMID: 28291760

Proper modelling of ligand binding requires an ensemble of bound and unbound states.

Pearce NM, Krojer T, von Delft F

Acta Crystallogr D Struct Biol. 73(Pt 3):256-266. doi: 10.1107/S2059798317003412

Publication date: March 1, 2017

PMID: 28291761

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

Krojer T, Talon R, Pearce N, Collins P, Douangamath A, Brandao-Neto J, Dias A, Marsden B, von Delft F

Acta Crystallogr D Struct Biol. 73(Pt 3):267-278. doi: 10.1107/S2059798316020234

Publication date: March 1, 2017

PMID: 28291762

WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design.

Deane CM, Wall ID, Green DV, Marsden BD, Bradley AR

Acta Crystallogr D Struct Biol. 73(Pt 3):279-285. doi: 10.1107/S2059798316009529

Publication date: March 1, 2017

PMID: 28291763

Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family.

Bataille CJ, Brennan MB, Byrne S, Davies SG, Durbin M, Fedorov O, Huber KV, Jones AM, Knapp S, Liu G, Nadali A, Quevedo CE, Russell AJ, Walker RG, Westwood R, Wynne GM

Bioorg. Med. Chem.. doi: 10.1016/j.bmc.2017.02.056

Publication date: February 28, 2017

PMID: 28341403

Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells.

Tumber A, Nuzzi A, Hookway ES, Hatch SB, Velupillai S, Johansson C, Kawamura A, Savitsky P, Yapp C, Szykowska A, Wu N, Bountra C, Strain-Damerell C, Burgess-Brown NA, Ruda GF, Fedorov O, Munro S, England KS, Nowak RP, Schofield CJ, La Thangue NB, Pawlyn C, Davies F, Morgan G, Athanasou N, Müller S, Oppermann U, Brennan PE

Cell Chem Biol. doi: 10.1016/j.chembiol.2017.02.006

Publication date: February 27, 2017

PMID: 28262558

Peptide recognition by HP1 chromoshadow domains revisited: plasticity in the pseudosymmetric histone binding site of human HP1.

Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J

J. Biol. Chem.. doi: 10.1074/jbc.M116.768374

Publication date: February 21, 2017

PMID: 28223359

Establishing a reliable framework for harnessing the creative power of the scientific crowd.

Carter AJ, Donner A, Lee WH, Bountra C

PLoS Biol.. 15(2):e2001387. doi: 10.1371/journal.pbio.2001387

Publication date: February 16, 2017

PMID: 28199324

Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2.

Barnash KD, The J, Norris-Drouin JL, Cholensky SH, Worley BM, Li F, Stuckey JI, Brown PJ, Vedadi M, Arrowsmith CH, Frye SV, James LI

ACS Comb Sci. doi: 10.1021/acscombsci.6b00174

Publication date: February 6, 2017

PMID: 28165227

Targeting human SET1/MLL family of proteins.

Vedadi M, Blazer L, Eram MS, Barsyte-Lovejoy D, Arrowsmith CH, Hajian T

Protein Sci.. doi: 10.1002/pro.3129

Publication date: February 4, 2017

PMID: 28160335

Development of potent, selective SRPK1 inhibitors as potential topical therapeutics for neovascular eye disease.

Batson J, Toop HD, Redondo C, Babaei-Jadidi R, Chaikuad A, Wearmouth SF, Gibbons B, Allen C, Tallant C, Zhang J, Du C, Hancox J, Hawtrey T, Da Rocha J, Griffith R, Knapp S, Bates DO, Morris JC

ACS Chem. Biol.. doi: 10.1021/acschembio.6b01048

Publication date: January 30, 2017

PMID: 28135068

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