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37 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Structural insights into human brachyury DNA recognition and discovery of progressible binders for cancer therapy Joseph A Newman , Angeline E. Gavard , Nergis Imprachim , Hazel Aitkenhead , Hadley E. Sheppard , Robert Te Poele , Paul A. Clarke , Mohammad Anwar Hossain , Louisa Temme , Hans J. Oh , Carrow I. Wells , Zachary W. Davis-Gilbert , Paul Workman , Opher Gileadi , David H. Drewry Nature Communications 16 DOI: 10.1038/s41467-025-56213-1 Diamond Proposal Number(s): [18145, 19301, 28172] Open Access Show Abstract ▼ Abstract: Brachyury is a transcription factor that plays an essential role in tumour growth of the rare bone cancer chordoma and is implicated in other solid tumours. Brachyury is minimally expressed in healthy tissues, making it a potential therapeutic target. Unfortunately, as a ligandless transcription factor, brachyury has historically been considered undruggable. To investigate direct targeting of brachyury by small molecules, we determine the structure of human brachyury both alone and in complex with DNA. The structures provide insights into DNA binding and the context of the chordoma associated G177D variant. We use crystallographic fragment screening to identify hotspots on numerous pockets on the brachyury surface. Finally, we perform follow-up chemistry on fragment hits and describe the progression of a thiazole chemical series into binders with low µM potency. Thus we show that brachyury is ligandable and provide an example of how crystallographic fragment screening may be used to target protein classes that are difficult to address using other approaches.	Feb 2025
B21-High Throughput SAXS I03-Macromolecular Crystallography	The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures William Bradshaw , Gemma Harris , Opher Gileadi , Vittorio Katis Structure 10 DOI: 10.1016/j.str.2024.09.024 Diamond Proposal Number(s): [19301, 28172, 34598] Open Access Show Abstract ▼ Abstract: Spleen tyrosine kinase (SYK) is central to adaptive and innate immune signaling. It features a regulatory region containing tandem SH2 (tSH2) domains separated by a helical “hinge” segment keeping SYK inactive by associating with the kinase domain. SYK activation is triggered when the tSH2 domains bind to a phosphorylated immunoreceptor tyrosine-based activation motif (ITAM) found on receptor tails. Past mutational studies have indicated that ITAM binding disrupts the hinge-kinase interaction, leading to SYK phosphorylation and activation. However, the mechanism of this process is unclear, as the ITAM interaction occurs far from the hinge region. We have determined crystal structures of three phospho-ITAMs in complex with the tSH2 domains, revealing a highly conserved binding mechanism. These structures, together with mutational studies and biophysical analyses, reveal that phospho-ITAM binding restricts SH2 domain movement and causes allosteric changes in the hinge region. These changes are not compatible with the association of the kinase domain, leading to kinase activation.	Oct 2024
I24-Microfocus Macromolecular Crystallography	Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε Fernando H. De Souza Gama , Luiz A. Dutra , Michael Hawgood , Caio Vinícius Dos Reis , Ricardo A. M. Serafim , Marcos A. Ferreira , Bruno V. M. Teodoro , Jéssica Emi Takarada , André S. Santiago , Dimitrios-Ilias Balourdas , Ann-Sofie Nilsson , Bruno Urien , Vitor M. Almeida , Carina Gileadi , Priscila Z. Ramos , Anita Salmazo , Stanley N. S. Vasconcelos , Micael R. Cunha , Susanne Mueller , Stefan Knapp , Katlin B. Massirer , Jonathan M. Elkins , Opher Gileadi , Alessandra Mascarello , Bennie B. L. G. Lemmens , Cristiano R. W. Guimarães , Hatylas Azevedo , Rafael M. Counago Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.3c02250 Show Abstract ▼ Abstract: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.	May 2024
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target Marcin Bielinski , Lucy R. Henderson , Yuliana Yosaatmadja , Lonnie P. Swift , Hannah T. Baddock , Matthew J. Bowen , Jurgen Brem , Philip S. Jones , Stuart P. Mcelroy , Angus Morrison , Michael Speake , Stan Van Boeckel , Els Van Doornmalen , Jan Van Groningen , Helma Van Den Hurk , Opher Gileadi , Joseph A Newman , Peter J. Mchugh , Christopher J. Schofield Chemical Science 60 DOI: 10.1039/D4SC00367E Diamond Proposal Number(s): [19301] Open Access Show Abstract ▼ Abstract: The three human SNM1 metallo-β-lactamase fold nucleases (SNM1A–C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline–hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.	Apr 2024
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2 William J. Bradshaw , Emma C. Kennedy , Tiago Moreira , Luke A. Smith , Rod Chalk , Vittorio L. Katis , Justin L. P. Benesch , Paul E. Brennan , Emma J. Murphy , Opher Gileadi Structure 44 DOI: 10.1016/j.str.2024.01.005 Diamond Proposal Number(s): [22717, 15433, 19301] Open Access Show Abstract ▼ Abstract: SHIP1, an inositol 5-phosphatase, plays a central role in cellular signaling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.	Feb 2024
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer’s disease Yuhong Du , William J. Bradshaw , Tina M. Leisner , Joel K. Annor-Gyamfi , Kun Qian , Frances M. Bashore , Arunima Sikdar , Felix O. Nwogbo , Andrey A. Ivanov , Stephen V. Frye , Opher Gileadi , Paul E. Brennan , Allan I. Levey , Alison D. Axtman , Kenneth H. Pearce , Haian Fu , Vittorio L. Katis , Ishita Ajith , Jeff Aube , Ranjita S. Betarbet , Juan Botas , Peter J. Brown , Robert R. Butler , Jacob L. Capener , Gregory W. Carter , Gregory A. Cary , Catherine Chen , Rachel Commander , Sabrina Daglish , Suzanne Doolen , Aled M. Edwards , Michelle E. Etoundi , Kevin J. Frankowski , Marta Glavatshikh , Jake Gockley , Katerina Gospodinova , Anna K. Greenwood , Peter A. Greer , Lea T. Grinberg , Shiva Guduru , Levon Halabelian , Crystal Han , Brian Hardy , Laura M. Heath , Stephanie Howell , Suman Jayadev , Stephen Keegan , May Khanna , Dmitri Kireev , Carl Laflamme , Karina Leal , Tom V. Lee , Qianjin Li , David Li-Kroeger , Zhandong Liu , Benjamin A. Logsdon , Frank M. Longo , Lara M. Mangravite , Peter S. Mcpherson , Richard M. Nwakamma , Carolyn A. Paisie , Arti Parihar , Min Qui , Stacey J. Sukoff Rizzo , Karolina A. Rygiel , Julie Schumacher , David D. Scott , Nicholas T. Seyfried , Joshua M. Shulman , Ben Siciliano , Nathaniel Smith , Michael Stashko , Judith A. Tello Vega , Dilipkumar Uredi , Dongxue Wang , Jianjun Wang , Xiaodong Wang , Zhexing Wen , Jesse C. Wiley , Alexander Wilkes , Charles A. Williams , Timothy M. Willson , Aliza Wingo , Thomas S. Wingo , Novak Yang , Jessica E. Young , Miao Yu , Elizabeth L. Zoeller Journal Of Biological Chemistry 20 DOI: 10.1016/j.jbc.2023.105382 Diamond Proposal Number(s): [19301, 19301] Open Access	Oct 2023
	Characterization of the SARS-CoV-2 ExoN (nsp14ExoN–nsp10) complex: implications for its role in viral genome stability and inhibitor identification Hannah T. Baddock , Sanja Brolih , Yuliana Yosaatmadja , Malitha Ratnaweera , Marcin Bielinski , Lonnie p. Swift , Abimael Cruz-Migoni , Haitian Fan , Jeremy R. Keown , Alexander P. Walker , Garrett m. Morris , Jonathan M. Grimes , Ervin Fodor , Christopher J. Schofield , Opher Gileadi , Peter J. Mchugh Nucleic Acids Research 73 DOI: 10.1093/nar/gkab1303 Open Access Show Abstract ▼ Abstract: The SARS-CoV-2 coronavirus is the causal agent of the current global pandemic. SARS-CoV-2 belongs to an order, Nidovirales, with very large RNA genomes. It is proposed that the fidelity of coronavirus (CoV) genome replication is aided by an RNA nuclease complex, comprising the non-structural proteins 14 and 10 (nsp14–nsp10), an attractive target for antiviral inhibition. Our results validate reports that the SARS-CoV-2 nsp14–nsp10 complex has RNase activity. Detailed functional characterization reveals nsp14–nsp10 is a versatile nuclease capable of digesting a wide variety of RNA structures, including those with a blocked 3′-terminus. Consistent with a role in maintaining viral genome integrity during replication, we find that nsp14–nsp10 activity is enhanced by the viral RNA-dependent RNA polymerase complex (RdRp) consisting of nsp12–nsp7–nsp8 (nsp12–7–8) and demonstrate that this stimulation is mediated by nsp8. We propose that the role of nsp14–nsp10 in maintaining replication fidelity goes beyond classical proofreading by purging the nascent replicating RNA strand of a range of potentially replication-terminating aberrations. Using our developed assays, we identify drug and drug-like molecules that inhibit nsp14–nsp10, including the known SARS-CoV-2 major protease (Mpro) inhibitor ebselen and the HIV integrase inhibitor raltegravir, revealing the potential for multifunctional inhibitors in COVID-19 treatment.	Jan 2022
I03-Macromolecular Crystallography I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition Yuliana Yosaatmadja , Hannah T. Baddock , Joseph A. Newman , Marcin Bielinski , Angeline E. Gavard , Shubhashish M. M. Mukhopadhyay , Adam a. Dannerfjord , Christopher J. Schofield , Peter j. Mchugh , Opher Gileadi Nucleic Acids Research 44 DOI: 10.1093/nar/gkab693 Diamond Proposal Number(s): [19301] Open Access Show Abstract ▼ Abstract: Artemis (SNM1C/DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in dsDNA break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Artemis deficiency leads to congenital radiosensitive severe acquired immune deficiency (RS-SCID). Artemis belongs to a superfamily of nucleases containing metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. We present crystal structures of the catalytic domain of wildtype and variant forms of Artemis, including one causing RS-SCID Omenn syndrome. The catalytic domain of the Artemis has similar endonuclease activity to the phosphorylated full-length protein. Our structures help explain the predominantly endonucleolytic activity of Artemis, which contrasts with the predominantly exonuclease activity of the closely related SNM1A and SNM1B MBL fold nucleases. The structures reveal a second metal binding site in its β-CASP domain unique to Artemis, which is amenable to inhibition by compounds including ebselen. By combining our structural data with that from a recently reported Artemis structure, we were able model the interaction of Artemis with DNA substrates. The structures, including one of Artemis with the cephalosporin ceftriaxone, will help enable the rational development of selective SNM1 nuclease inhibitors.	Aug 2021
I02-Macromolecular Crystallography I04-Macromolecular Crystallography	A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family Hannah T. Baddock , Joseph A. Newman , Yuliana Yosaatmadja , Marcin Bielinski , Christopher J. Schofield , Opher Gileadi , Peter j. Mchugh Nucleic Acids Research 461 DOI: 10.1093/nar/gkab692 Diamond Proposal Number(s): [15433] Open Access Show Abstract ▼ Abstract: The SNM1 nucleases which help maintain genome integrity are members of the metallo-β-lactamase (MBL) structural superfamily. Their conserved MBL-β-CASP-fold SNM1 core provides a molecular scaffold forming an active site which coordinates the metal ions required for catalysis. The features that determine SNM1 endo- versus exonuclease activity, and which control substrate selectivity and binding are poorly understood. We describe a structure of SNM1B/Apollo with two nucleotides bound to its active site, resembling the product state of its exonuclease reaction. The structure enables definition of key SNM1B residues that form contacts with DNA and identifies a 5′ phosphate binding pocket, which we demonstrate is important in catalysis and which has a key role in determining endo- versus exonucleolytic activity across the SNM1 family. We probed the capacity of SNM1B to digest past sites of common endogenous DNA lesions and find that base modifications planar to the nucleobase can be accommodated due to the open architecture of the active site, but lesions axial to the plane of the nucleobase are not well tolerated due to constriction around the altered base. We propose that SNM1B/Apollo might employ its activity to help remove common oxidative lesions from telomeres.	Aug 2021
I04-1-Macromolecular Crystallography (fixed wavelength)	Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase Joseph A. Newman , Alice Douangamath , Setayesh Yadzani , Yuliana Yosaatmadja , Anthony Aimon , Jose Brandao-Neto , Louise Dunnett , Tyler Gorrie-Stone , Rachael Skyner , Daren Fearon , Matthieu Schapira , Frank Von Delft , Opher Gileadi Nature Communications 12 DOI: 10.1038/s41467-021-25166-6 Diamond Proposal Number(s): [26998] Open Access Show Abstract ▼ Abstract: There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two “druggable” pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.	Aug 2021

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