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

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Covalent inhibitors of S100A4 block the formation of a pro-metastasis non-muscle myosin 2A complex Charline Giroud , Tamas Szommer , Carmen Coxon , Octovia Monteiro , Thomas Grimes , Tryfon Zarganes-Tzitzikas , Thomas Christott , James Bennett , Karly Buchan , Paul E. Brennan , Oleg Fedorov Journal Of Medicinal Chemistry 4 DOI: 10.1021/acs.jmedchem.4c01320 Diamond Proposal Number(s): [19301] Open Access Show Abstract ▼ Abstract: The S100 protein family functions as protein–protein interaction adaptors regulated by Ca2+ binding. Formation of various S100 complexes plays a central role in cell functions, from calcium homeostasis to cell signaling, and is implicated in cell growth, migration, and tumorigenesis. We established a suite of biochemical and cellular assays for small molecule screening based on known S100 protein–protein interactions. From 25 human S100 proteins, we focused our attention on S100A4 because of its well-established role in cancer progression and metastasizes by interacting with nonmuscle myosin II (NMII). We identified several potent and selective inhibitors of this interaction and established the covalent nature of binding, confirmed by mass spectrometry and crystal structures. 5b showed on-target activity in cells and inhibition of cancer cell migration. The identified S100A4 inhibitors can serve as a basis for the discovery of new cancer drugs operating via a novel mode of action.	Oct 2024
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength)	Unexpected noncovalent off-target activity of clinical btk inhibitors leads to discovery of a dual NUDT5/14 antagonist Esra Balikci , Anne-Sophie M. C. Marques , Ludwig G. Bauer , Raina Seupel , James Bennett , Brigitt Raux , Karly Buchan , Klemensas Simelis , Usha Singh , Catherine Rogers , Jennifer Ward , Carol Cheng , Tamas Szommer , Kira Schützenhofer , Jonathan M. Elkins , David L. Sloman , Ivan Ahel , Oleg Fedorov , Paul E. Brennan , Kilian V. M. Huber Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.4c00072 Diamond Proposal Number(s): [19301, 28172] Open Access Show Abstract ▼ Abstract: Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure–activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.	Apr 2024
I04-Macromolecular Crystallography	Discovery of a potent, selective, and cell-active SPIN1 inhibitor Yan Xiong , Holger Greschik , Catrine Johansson , Ludwig Seifert , Vicki Gamble , Kwang-Su Park , Vincent Fagan , Fengling Li , Irene Chau , Masoud Vedadi , Cheryl H. Arrowsmith , Paul Brennan , Oleg Fedorov , Manfred Jung , Gillian Farnie , Jing Liu , Udo Oppermann , Roland Schüle , Jian Jin Journal Of Medicinal Chemistry 9 DOI: 10.1021/acs.jmedchem.4c00121 Show Abstract ▼ Abstract: The methyl-lysine reader protein SPIN1 plays important roles in various human diseases. However, targeting methyl-lysine reader proteins has been challenging. Very few cellularly active SPIN1 inhibitors have been developed. We previously reported that our G9a/GLP inhibitor UNC0638 weakly inhibited SPIN1. Here, we present our comprehensive structure–activity relationship study that led to the discovery of compound 11, a dual SPIN1 and G9a/GLP inhibitor, and compound 18 (MS8535), a SPIN1 selective inhibitor. We solved the cocrystal structure of SPIN1 in complex with 11, confirming that 11 occupied one of the three Tudor domains. Importantly, 18 displayed high selectivity for SPIN1 over 38 epigenetic targets, including G9a/GLP, and concentration dependently disrupted the interactions of SPIN1 and H3 in cells. Furthermore, 18 was bioavailable in mice. We also developed 19 (MS8535N), which was inactive against SPIN1, as a negative control of 18. Collectively, these compounds are useful chemical tools to study biological functions of SPIN1.	Mar 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
I03-Macromolecular Crystallography	Discovery and development strategies for SARS-CoV-2 NSP3 macrodomain inhibitors Marion Schuller , Tryfon Zarganes-Tzitzikas , James Bennett , Stephane De Cesco , Daren Fearon , Frank Von Delft , Oleg Fedorov , Paul E. Brennan , Ivan Ahel Pathogens 12 DOI: 10.3390/pathogens12020324 Diamond Proposal Number(s): [23459] Open Access Show Abstract ▼ Abstract: The worldwide public health and socioeconomic consequences caused by the COVID-19 pandemic highlight the importance of increasing preparedness for viral disease outbreaks by providing rapid disease prevention and treatment strategies. The NSP3 macrodomain of coronaviruses including SARS-CoV-2 is among the viral protein repertoire that was identified as a potential target for the development of antiviral agents, due to its critical role in viral replication and consequent pathogenicity in the host. By combining virtual and biophysical screening efforts, we discovered several experimental small molecules and FDA-approved drugs as inhibitors of the NSP3 macrodomain. Analogue characterisation of the hit matter and crystallographic studies confirming binding modes, including that of the antibiotic compound aztreonam, to the active site of the macrodomain provide valuable structure–activity relationship information that support current approaches and open up new avenues for NSP3 macrodomain inhibitor development.	Feb 2023
I04-1-Macromolecular Crystallography (fixed wavelength)	Novel starting points for human glycolate oxidase inhibitors, revealed by crystallography-based fragment screening Sabrina R. Mackinnon , Gustavo A. Bezerra , Tobias Krojer , Tamas Szommer , Frank Von Delft , Paul E. Brennan , Wyatt W. Yue Frontiers In Chemistry 10 DOI: 10.3389/fchem.2022.844598 Diamond Proposal Number(s): [18145] Open Access Show Abstract ▼ Abstract: Primary hyperoxaluria type I (PH1) is caused by AGXT gene mutations that decrease the functional activity of alanine:glyoxylate aminotransferase. A build-up of the enzyme’s substrate, glyoxylate, results in excessive deposition of calcium oxalate crystals in the renal tract, leading to debilitating renal failure. Oxidation of glycolate by glycolate oxidase (or hydroxy acid oxidase 1, HAO1) is a major cellular source of glyoxylate, and siRNA studies have shown phenotypic rescue of PH1 by the knockdown of HAO1, representing a promising inhibitor target. Here, we report the discovery and optimization of six low-molecular-weight fragments, identified by crystallography-based fragment screening, that bind to two different sites on the HAO1 structure: at the active site and an allosteric pocket above the active site. The active site fragments expand known scaffolds for substrate-mimetic inhibitors to include more chemically attractive molecules. The allosteric fragments represent the first report of non-orthosteric inhibition of any hydroxy acid oxidase and hold significant promise for improving inhibitor selectivity. The fragment hits were verified to bind and inhibit HAO1 in solution by fluorescence-based activity assay and surface plasmon resonance. Further optimization cycle by crystallography and biophysical assays have generated two hit compounds of micromolar (44 and 158 µM) potency that do not compete with the substrate and provide attractive starting points for the development of potent and selective HAO1 inhibitors.	May 2022
I14-Hard X-ray Nanoprobe	Imaging articular cartilage in osteoarthritis using targeted peptide radiocontrast agents Milan M. Fowkes , Patricia Das Neves Borges , Fernando Cacho-Nerin , Paul E. Brennan , Tonia L. Vincent , Ngee H. Lim Plos One 17 DOI: 10.1371/journal.pone.0268223 Diamond Proposal Number(s): [22977] Open Access Show Abstract ▼ Abstract: Background: Established MRI and emerging X-ray contrast agents for non-invasive imaging of articular cartilage rely on non-selective electrostatic interactions with negatively charged proteoglycans. These contrast agents have limited prognostic utility in diseases such as osteoarthritis (OA) due to the characteristic high turnover of proteoglycans. To overcome this limitation, we developed a radiocontrast agent that targets the type II collagen macromolecule in cartilage and used it to monitor disease progression in a murine model of OA. Methods: To confer radiopacity to cartilage contrast agents, the naturally occurring tyrosine derivative 3,5-diiodo-L-tyrosine (DIT) was introduced into a selective peptide for type II collagen. Synthetic DIT peptide derivatives were synthesised by Fmoc-based solid-phase peptide synthesis and binding to ex vivo mouse tibial cartilage evaluated by high-resolution micro-CT. Di-Iodotyrosinated Peptide Imaging of Cartilage (DIPIC) was performed ex vivo and in vivo 4, 8 and 12 weeks in mice after induction of OA by destabilisation of the medial meniscus (DMM). Finally, human osteochondral plugs were imaged ex vivo using DIPIC. Results: Fifteen DIT peptides were synthesised and tested, yielding seven leads with varying cartilage binding strengths. DIPIC visualised ex vivo murine articular cartilage comparably to the ex vivo contrast agent phosphotungstic acid. Intra-articular injection of contrast agent followed by in vivo DIPIC enabled delineation of damaged murine articular cartilage. Finally, the translational potential of the contrast agent was confirmed by visualisation of ex vivo human cartilage explants. Conclusion: DIPIC has reduction and refinement implications in OA animal research and potential clinical translation to imaging human disease.	May 2022
	Target 2035 – update on the quest for a probe for every protein Susanne Müller , Suzanne Ackloo , Arij Al Chawaf , Bissan Al-Lazikani , Albert Antolin , Jonathan B. Baell , Hartmut Beck , Shaunna Beedie , Ulrich A. K. Betz , Gustavo Arruda Bezerra , Paul E. Brennan , David Brown , Peter J. Brown , Alex N. Bullock , Adrian J. Carter , Apirat Chaikuad , Mathilde Chaineau , Alessio Ciulli , Ian Collins , Jan Dreher , David Drewry , Kristina Edfeldt , Aled M. Edwards , Ursula Egner , Stephen V. Frye , Stephen M. Fuchs , Matthew D. Hall , Ingo V. Hartung , Alexander Hillisch , Stephen H. Hitchcock , Evert Homan , Natarajan Kannan , James R. Kiefer , Stefan Knapp , Milka Kostic , Stefan Kubicek , Andrew S. Leach , Sven Lindemann , Brian D. Marsden , Hisanori Matsui , Jordan L. Meier , Daniel Merk , Maurice Michel , Maxwell R. Morgan , Anke Mueller-Fahrnow , Dafydd R. Owen , Benjamin G. Perry , Saul H. Rosenberg , Kumar Singh Saikatendu , Matthieu Schapira , Cora Scholten , Sujata Sharma , Anton Simeonov , Michael Sundström , Giulio Superti-Furga , Matthew H. Todd , Claudia Tredup , Masoud Vedadi , Frank Von Delft , Timothy M. Willson , Georg E. Winter , Paul Workman , Cheryl H. Arrowsmith Rsc Medicinal Chemistry 17 DOI: 10.1039/D1MD00228G Open Access Show Abstract ▼ Abstract: Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.	Dec 2021
I24-Microfocus Macromolecular Crystallography	The structural basis of fatty acid elongation by the ELOVL elongases Laiyin Nie , Tomas C. Pascoa , Ashley C. W. Pike , Simon R. Bushell , Andrew Quigley , Gian Filippo Ruda , Amy Chu , Victoria Cole , David Speedman , Tiago Moreira , Leela Shrestha , Shubhashish M. M. Mukhopadhyay , Nicola A. Burgess-Brown , James D. Love , Paul E. Brennan , Elisabeth P. Carpenter Nature Structural & Molecular Biology 28, 512 - 520 DOI: 10.1038/s41594-021-00605-6 Diamond Proposal Number(s): [19301] Show Abstract ▼ Abstract: Very long chain fatty acids (VLCFAs) are essential building blocks for the synthesis of ceramides and sphingolipids. The first step in the fatty acid elongation cycle is catalyzed by the 3-keto acyl-coenzyme A (CoA) synthases (in mammals, ELOVL elongases). Although ELOVLs are implicated in common diseases, including insulin resistance, hepatic steatosis and Parkinson’s, their underlying molecular mechanisms are unknown. Here we report the structure of the human ELOVL7 elongase, which comprises an inverted transmembrane barrel surrounding a 35-Å long tunnel containing a covalently attached product analogue. The structure reveals the substrate-binding sites in the narrow tunnel and an active site deep in the membrane. We demonstrate that chain elongation proceeds via an acyl-enzyme intermediate involving the second histidine in the canonical HxxHH motif. The unusual substrate-binding arrangement and chemistry suggest mechanisms for selective ELOVL inhibition, relevant for diseases where VLCFAs accumulate, such as X-linked adrenoleukodystrophy.	Jun 2021
I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Fragment screening reveals starting points for rational design of galactokinase 1 inhibitors to treat classic galactosemia Sabrina R. Mackinnon , Tobias Krojer , William R. Foster , Laura Diaz-Saez , Manshu Tang , Kilian V. M. Huber , Frank Von Delft , Kent Lai , Paul Brennan , Gustavo Arruda Bezerra , Wyatt W. Yue Acs Chemical Biology 152 DOI: 10.1021/acschembio.0c00498 Diamond Proposal Number(s): [18145] Open Access Show Abstract ▼ Abstract: Classic galactosemia is caused by loss-of-function mutations in galactose-1-phosphate uridylyltransferase (GALT) that lead to toxic accumulation of its substrate, galactose-1-phosphate. One proposed therapy is to inhibit the biosynthesis of galactose-1-phosphate, catalyzed by galactokinase 1 (GALK1). Existing inhibitors of human GALK1 (hGALK1) are primarily ATP-competitive with limited clinical utility to date. Here, we determined crystal structures of hGALK1 bound with reported ATP- competitive inhibitors of the spiro-benzoxazole series, to reveal their binding mode in the active site. Spurred by the need for additional chemotypes of hGALK1 inhibitors, desirably targeting a nonorthosteric site, we also performed crystallography-based screening by soaking hundreds of hGALK1 crystals, already containing active site ligands, with fragments from a custom library. Two fragments were found to bind close to the ATP binding site, and a further eight were found in a hotspot distal from the active site, highlighting the strength of this method in identifying previously uncharacterized allosteric sites. To generate inhibitors of improved potency and selectivity targeting the newly identified binding hotspot, new compounds were designed by merging overlapping fragments. This yielded two micromolar inhibitors of hGALK1 that were not competitive with respect to either substrate (ATP or galactose) and demonstrated good selectivity over hGALK1 homologues, galactokinase 2 and mevalonate kinase. Our findings are therefore the first to demonstrate inhibition of hGALK1 from an allosteric site, with potential for further development of potent and selective inhibitors to provide novel therapeutics for classic galactosemia.	Mar 2021

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