1. Publications
  2. Publications

Publications

  1. Tosarini, T., Ramos, P., Profeta, G., Baroni, R., Massirer, K., Couñago, R., & Mondego, J. (2018). Cloning, expression and purification of kinase domains of cacao PR-1 receptor-like kinases. Protein Expression And Purification, 146, 78-84.

  2. Williams, E., & Bullock, A. N. (2018). Structural basis for the potent and selective binding of LDN-212854 to the BMP receptor kinase ALK2. Bone, 109, 251–258.

  3. Han, Z., Wu, H., Kim, S., Yang, X., Li, Q., & Huang, H., ... Zheng, Y. G. (2018). Revealing the protein propionylation activity of the histone acetyltransferase MOF (males absent on the first). Journal Of Biological Chemistry, 293(9), 3410-3420.

  4. Kasinath, V., Faini, M., Poepsel, S., Reif, D., Feng, X., Stjepanovic, G., ... Nogales, E (2018). Structures of human PRC2 with its cofactors AEBP2 and JARID2. Science, 359(6378), 940-944.

  5. Babault, N., Allali-Hassani, A., Li, F., Fan, J., Yue, A., Ju, K., ... Jin, J. (2018). Discovery of Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT). Journal Of Medicinal Chemistry, 61(4), 1541-1551.

  6. Vasta, J. D., Corona, C. R., Wilkinson, J., Zimprich, C. A., Hartnett, J. R., Ingold, M. R., … Robers, M. B. (2018). Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. Cell Chemical Biology, 25(2), 206–214.e11.

  7. Kaniskan, H. Ü., Eram, M. S., Zhao, K., Szewczyk, M. M., Yang, X., Schmidt, K., … Jin, J. (2018). Discovery of Potent and Selective Allosteric Inhibitors of Protein Arginine Methyltransferase 3 (PRMT3). Journal of Medicinal Chemistry, 61(3), 1204–1217.

  8. Clerici, M., Faini, M., Muckenfuss, L., Aebersold, R., & Jinek, M. (2018). Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nature Structural & Molecular Biology, 25(2), 135-138.

  9. Xu, C., Liu, K., Lei, M., Yang, A., Li, Y., Hughes, T., & Min, J. (2018). DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure, 26(1), 85-95.e3.

  10. Shadrick, W., Slavish, P., Chai, S., Waddell, B., Connelly, M., Low, J., ... Potter, P. M. (2018). Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors. Bioorganic & Medicinal Chemistry, 26(1), 25-36.

  11. Houliston, R. S., Lemak, A., Iqbal, A., Ivanochko, D., Duan, S., Kaustov, L., … Arrowsmith, C. H. (2017). Conformational dynamics of the TTD–PHD histone reader module of the UHRF1 epigenetic regulator reveals multiple histone-binding states, allosteric regulation, and druggability. The Journal of Biological Chemistry, 292(51), 20947–20959.

  12. Jurkowska, R. Z., Qin, S., Kungulovski, G., Tempel, W., Liu, Y., Bashtrykov, P., … Jeltsch, A. (2017). H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nature Communications, 8, 2057.

  13. Gerken, P. A., Wolstenhulme, J. R., Tumber, A., Hatch, S. B., Zhang, Y., Müller, S., … Smith, M. D. (2017). Discovery of a Highly Selective Cell‐Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angewandte Chemie (International Ed. in English), 56(49), 15555–15559.

  14. Wu, B., Li, L., Huang, Y., Ma, J., & Min, J. (2017). Readers, writers and erasers of N6 -methylated adenosine modification. Current Opinion In Structural Biology, 47, 67-76.

  15. Zhang, H., Liu, K., Izumi, N., Huang, H., Ding, D., Ni, Z., … Min, J. (2017). Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Proceedings of the National Academy of Sciences of the United States of America, 114(47), 12483–12488.

  16. Fernández-Montalván, A., Berger, M., Kuropka, B., Koo, S., Badock, V., Weiske, J., ... Gorjánácz, M. (2017). Isoform-Selective ATAD2 Chemical Probe with Novel Chemical Structure and Unusual Mode of Action. ACS Chemical Biology, 12(11), 2730-2736.

  17. Schuller, M., Riedel, K., Gibbs-Seymour, I., Uth, K., Sieg, C., Gehring, A., ... Knapp, S. (2017). Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Polyadenosine-Diphosphate-Ribose Polymerase 14. ACS Chemical Biology, 12(11), 2866-2874.

  18. Dahlin, J. L., Nelson, K. M., Strasser, J. M., Barsyte-Lovejoy, D., Szewczyk, M. M., Organ, S., … Walters, M. A. (2017). Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors. Nature Communications, 8, 1527.

  19. Zhang, W., Sartori, M., Makhnevych, T., Federowicz, K., Dong, X., Liu, L., ... Sidhu, S. S. (2017). Generation and Validation of Intracellular Ubiquitin Variant Inhibitors for USP7 and USP10. Journal Of Molecular Biology, 429(22), 3546-3560.

  20. Harding, R., Ferreira de Freitas, R., Collins, P., Franzoni, I., Ravichandran, M., Ouyang, H., ... Arrowsmith, C. H. (2017). Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. Journal Of Medicinal Chemistry, 60(21), 9090-9096.

  21. Bradley, A. R., Echalier, A., Fairhead, M., Strain-Damerell, C., Brennan, P., Bullock, A. N., … von Delft, F. (2017). The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery. Essays in Biochemistry, 61(5), 495–503.

  22. Pinkas, D. M., Sanvitale, C. E., Bufton, J. C., Sorrell, F. J., Solcan, N., Chalk, R., … Bullock, A. N. (2017). Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases. Biochemical Journal, 474(22), 3747–3761.

  23. Schapira, M., Tyers, M., Torrent, M., & Arrowsmith, C. (2017). WD40 repeat domain proteins: a novel target class?. Nature Reviews Drug Discovery, 16(11), 773-786.

  24. Foley, D. J., Craven, P. G. E., Collins, P. M., Doveston, R. G., Aimon, A., Talon, R., … Nelson, A. (2017). Synthesis and Demonstration of the Biological Relevance of sp3‐rich Scaffolds Distantly Related to Natural Product Frameworks. Chemistry (Weinheim an Der Bergstrasse, Germany), 23(60), 15227–15232.

  25. Sansook, S., Ocasio, C. A., Day, I. J., Tizzard, G. J., Coles, S. J., Fedorov, O., … Spencer, J. (2017). Synthesis of kinase inhibitors containing a pentafluorosulfanyl moiety †Electronic supplementary information (ESI) available. CCDC 154150–154153. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7ob02289a . Organic & Biomolecular Chemistry, 15(40), 8655–8660.

  26. Song, R., Wang, Z., & Schapira, M. (2017). Disease Association and Druggability of WD40 Repeat Proteins. Journal Of Proteome Research, 16(10), 3766-3773.

  27. Teyra, J., Huang, H., Jain, S., Guan, X., Dong, A., Liu, Y., ... Sidhu, S. S (2017). Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities. Structure, 25(10), 1598-1610.e3.

  28. Ferreira de Freitas, R., & Schapira, M. (2017). A systematic analysis of atomic protein–ligand interactions in the PDB †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7md00381a . Medchemcomm, 8(10), 1970–1981.

  29. Moody, J. D., Levy, S., Mathieu, J., Xing, Y., Kim, W., Dong, C., … Ruohola-Baker, H. (2017). First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 114(38), 10125–10130.

  30. Igoe, N., Bayle, E., Tallant, C., Fedorov, O., Meier, J., Savitsky, P., ... Fish, P. V. (2017). Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins. Journal Of Medicinal Chemistry, 60(16), 6998-7011.

  31. Xiong, Y., Li, F., Babault, N., Wu, H., Dong, A., & Zeng, H., ... Jin, J. (2017). Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorganic & Medicinal Chemistry, 25(16), 4414-4423.

  32. Couñago, R. M., Allerston, C. K., Savitsky, P., Azevedo, H., Godoi, P. H., Wells, C. I., … Gileadi, O. (2017). Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations. Scientific Reports, 7, 7501.

  33. Drewry, D. H., Wells, C. I., Andrews, D. M., Angell, R., Al-Ali, H., Axtman, A. D., … Willson, T. M. (2017). Progress towards a public chemogenomic set for protein kinases and a call for contributions. PLoS ONE, 12(8), e0181585.

  34. Roberts, T. C., Etxaniz, U., Dall’Agnese, A., Wu, S.-Y., Chiang, C.-M., Brennan, P. E., … Puri, P. L. (2017). BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis. Scientific Reports, 7, 6153.

  35. Rocklin, G. J., Chidyausiku, T. M., Goreshnik, I., Ford, A., Houliston, S., Lemak, A., … Baker, D. (2017). Global analysis of protein folding using massively parallel design, synthesis and testing. Science (New York, N.Y.), 357(6347), 168–175.

  36. Denny, R., Flick, A., Coe, J., Langille, J., Basak, A., Liu, S., ... Chekler, E. L. P. (2017). Structure-Based Design of Highly Selective Inhibitors of the CREB Binding Protein Bromodomain. Journal Of Medicinal Chemistry, 60(13), 5349-5363.

  37. Chaikuad, A., Filippakopoulos, P., Marcsisin, S. R., Picaud, S., Schröder, M., Sekine, S., … Knapp, S. (2017). Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly. Structure(London, England:1993), 25(7), 1089–1099.e3.

  38. Banerjee, J. J., Aerne, B. L., Holder, M. V., Hauri, S., Gstaiger, M., & Tapon, N. (2017). Meru couples planar cell polarity with apical-basal polarity during asymmetric cell division. eLife, 6, e25014.

  39. Bergamin, E., Sarvan, S., Malette, J., Eram, M. S., Yeung, S., Mongeon, V., … Couture, J.-F. (2017). Molecular basis for the methylation specificity of ATXR5 for histone H3. Nucleic Acids Research, 45(11), 6375–6387.

  40. Edwards, A., Morgan, M., Al Chawaf, A., Andrusiak, K., Charney, R., Cynader, Z., ... Zuercher, W. J. (2017). A trust approach for sharing research reagents. Science Translational Medicine, 9(392), eaai9055.

  41. Aquino, B., Couñago, R. M., Verza, N., Ferreira, L. M., Massirer, K. B., Gileadi, O., & Arruda, P. (2017). Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment. Frontiers in Plant Science, 8, 852.

  42. Lines, K. E., Stevenson, M., Filippakopoulos, P., Müller, S., Lockstone, H. E., Wright, B., … Thakker, R. V. (2017). Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors. Oncogenesis, 6(5), e332.

  43. Plessl, T., Bürer, C., Lutz, S., Yue, W., Baumgartner, M., Froese, D. (2017). Protein destabilization and loss of protein-protein interaction are fundamental mechanisms in cblA-type methylmalonic aciduria. Human Mutation, 38(8), 988-1001.

  44. Bouché, L., Christ, C. D., Siegel, S., Fernández-Montalván, A. E., Holton, S. J., Fedorov, O., … Haendler, B. (2017). Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains. Journal of Medicinal Chemistry, 60(9), 4002–4022.

  45. Gräslund, S., Savitsky, P., Müller-Knapp, S. (2017). In Vivo Biotinylation of Antigens in E. coli. Methods In Molecular Biology, 1586, 337-344.

  46. Cooper, C. D. O., Marsden, B. D., (2017). N- and C-Terminal Truncations to Enhance Protein Solubility and Crystallization: Predicting Protein Domain Boundaries with Bioinformatics Tools. Methods In Molecular Biology, 1586, 11-31.

  47. Bataille, C., Brennan, M., Byrne, S., Davies, S., Durbin, M., Fedorov, O., … Wynne, G. M. (2017). Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family. Bioorganic & Medicinal Chemistry, 25(9), 2657-2665.

  48. Newman, J. A., Aitkenhead, H., Savitsky, P., Gileadi, O. (2017). Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5. Nucleic Acids Research, 45(7), 4231–4243.

  49. Kitevski-LeBlanc, J., Fradet-Turcotte, A., Kukic, P., Wilson, M. D., Portella, G., Yuwen, T., … Kay, L. E. (2017). The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage. eLife, 6, e23872.

  50. Caron, E., Roncagalli, R., Hase, T., Wolski, W. E., Choi, M., Menoita, M. G., … Gstaiger, M. (2017). Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports, 18(13), 3219–3226.

  51. Batson, J., Toop, H. D., Redondo, C., Babaei-Jadidi, R., Chaikuad, A., Wearmouth, S. F., … Morris, J. C. (2017). Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease. ACS Chemical Biology, 12(3), 825-832.

  52. Tumber, A., Nuzzi, A., Hookway, E. S., Hatch, S. B., Velupillai, S., Johansson, C., … Brennan, P. E. (2017). Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chemical Biology, 24(3), 371–380.

  53. Persson, H., Preger, C., Marcon, E., Lengqvist, J., Gräslund, S. (2017). Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis. Methods In Molecular Biology, 1575, 175-187.

  54. Hatch, S. B., Yapp, C., Montenegro, R. C., Savitsky, P., Gamble, V., Tumber, A., … Müller, S. (2017). Assessing histone demethylase inhibitors in cells: lessons learned. Epigenetics & Chromatin, 10, 9.

  55. Pearce, N. M., Bradley, A. R., Krojer, T., Marsden, B. D., Deane, C. M., & von Delft, F. (2017). Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites. Structural Dynamics, 4(3), 032104.

  56. Carter, A. J., Donner, A., Lee, W. H., Bountra, C. (2017). Establishing a reliable framework for harnessing the creative power of the scientific crowd. PLoS Biology, 15(2), e2001387.

  57. Wang, Z., Zhang, Y., Bartual, S. G., Luo, J., Xu, T., Du, W., … Ding, K. (2017). Tetrahydroisoquinoline-7-carboxamide Derivatives as New Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors. ACS Medicinal Chemistry Letters, 8(3), 327–332.

  58. Grieben, M., Pike, A. C., Shintre, C. A., Venturi, E., El-Ajouz, S., Tessitore, A., … Carpenter, E. P. (2016). Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2). Nature Structural & Molecular Biology, 24(2), 114-122.

  59. Wilkes, M., Madej, M. G., Kreuter, L., Rhinow, D., Heinz, V., De Sanctis, S., … Ziegler, C. (2017). Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2. Nature Structural & Molecular Biology, 24(2), 123-130.

  60. Igoe, N., Bayle, E. D., Fedorov, O., Tallant, C., Savitsky, P., Rogers, C., … Fish, P. V. (2017). Design of a Biased Potent Small Molecule Inhibitor of the Bromodomain and PHD Finger-Containing (BRPF) Proteins Suitable for Cellular and in Vivo Studies. Journal of Medicinal Chemistry, 60(2), 668-680.

  61. Olzscha, H., Fedorov, O., Kessler, B. M., Knapp, S., La Thangue, N. B. (2017). CBP/p300 Bromodomains Regulate Amyloid-like Protein Aggregation upon Aberrant Lysine Acetylation. Cell Chemical Biology, 24(1), 9–23.

  62. Moustakim, M., Clark, P. G. K., Trulli, L., Fuentes de Arriba, A. L., Ehebauer, M. T., Chaikuad, A., … Brennan, P. E. (2017). Discovery of a PCAF Bromodomain Chemical Probe. Angewandte Chemie (International Ed. in English), 56(3), 827–831.

  63. Ciuffa, R., Caron, E., Leitner, A., Uliana, F., Gstaiger, M., Aebersold, R. (2017). Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling. Journal of Proteome Research, 16(1), 14-33.

  64. Fang, H., Knezevic, B., Burnham, K. L., Knight, J. C. (2016). XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits. Genome Medicine, 8, 129.

  65. Popp, T. A., Tallant, C., Rogers, C., Fedorov, O., Brennan, P. E., Müller, S., … Bracher, F. (2016). Development of Selective CBP/P300 Benzoxazepine Bromodomain Inhibitors. Journal of Medicinal Chemistry, 59(19), 8889-8912.

  66. Myrianthopoulos, V., Gaboriaud-Kolar, N., Tallant, C., Hall, M.-L., Grigoriou, S., Brownlee, P. M., … Mikros, E. (2016). Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis. Journal of Medicinal Chemistry, 59(19), 8787–8803.

  67. Picaud, S., Leonards, K., Lambert, J.-P., Dovey, O., Wells, C., Fedorov, O., … Filippakopoulos, P. (2016). Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Science Advances, 2(10), e1600760.

  68. Hauri, S., Comoglio, F., Seimiya, M., Gerstung, M., Glatter, T., Hansen, K., … Beisel, C. (2016). A High-Density Map for Navigating the Human Polycomb Complexome. Cell Reports, 17(2), 583-595.

  69. Milhas, S., Raux, B., Betzi, S., Derviaux, C., Roche, P., Restouin, A., … Morelli, X. (2016). Protein–Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery. ACS Chemical Biology, 11(8), 2140-2148.

  70. Nowak, R., Tumber, A., Johansson, C., Che, K., Brennan, P., Owen, D., Oppermann, U. (2016). Advances and challenges in understanding histone demethylase biology. Current Opinion In Chemical Biology, 33, 151-159.

  71. Montenegro, R. C., Clark, P. G. K., Howarth, A., Wan, X., Ceroni, A., Siejka, P., … Müller, S. (2016). BET inhibition as a new strategy for the treatment of gastric cancer. Oncotarget, 7(28), 43997–44012.

  72. Sdelci, S., Lardeau, C., Tallant, C., Klepsch, F., Klaiber, B., Bennett, J., … Kubicek, S. (2016). Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nature Chemical Biology, 12(7), 504-510.

  73. Johansson, C., Velupillai, S., Tumber, A., Szykowska, A., Hookway, E. S., Nowak, R. P., … Oppermann, U. (2016). Structural analysis of human KDM5B guides histone demethylase inhibitor development. Nature Chemical Biology, 12(7), 539-545.

  74. Mathea, S., Abdul Azeez, K. R., Salah, E., Tallant, C., Wolfreys, F., Konietzny, R., … Knapp, S. (2016). Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS Chemical Biology, 11(6), 1595–1602.

  75. Sutherell, C. L., Tallant, C., Monteiro, O. P., Yapp, C., Fuchs, J. E., Fedorov, O., … Ley, S. V. (2016). Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex. Journal of Medicinal Chemistry, 59(10), 5095–5101.

  76. Martin, L. J., Koegl, M., Bader, G., Cockcroft, X.-L., Fedorov, O., Fiegen, D., … McConnell, D. (2016). Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. Journal of Medicinal Chemistry, 59(10), 4462–4475.

  77. Gerstenberger, B. S., Trzupek, J. D., Tallant, C., Fedorov, O., Filippakopoulos, P., Brennan, P. E., … Owen, D. R. (2016). Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit. Journal of Medicinal Chemistry, 59(10), 4800–4811.

  78. Arshad, Z., Smith, J., Roberts, M., Lee, W. H., Davies, B., Bure, K., … Brindley, D. (2016). Open Access Could Transform Drug Discovery: A Case Study of JQ1. Expert Opinion on Drug Discovery, 11(3), 321-332.

  79. Hammitzsch, A., Tallant, C., Fedorov, O., O’Mahony, A., Brennan, P. E., Hay, D. A., … Bowness, P. (2015). CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses. Proceedings of the National Academy of Sciences of the United States of America, 112(34), 10768–10773.

  80. Edwards, A., Arrowsmith, C., Bountra, C., Bunnage, M., Feldmann, M., Knight, J., ... Young, L. (2015). Preclinical target validation using patient-derived cells. Nature Reviews Drug Discovery, 14(3), 149-150.

  81. Knapp, S., Sundström, M. (2014). Recently targeted kinases and their inhibitors—the path to clinical trials. Current Opinion in Pharmacology, 17, 58-63.