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

Instruments / Technical Area	Publication Details	Published
I24-Microfocus Macromolecular Crystallography	Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders Alexander Hanzl , Ryan Casement , Hana Imrichova , Scott J. Hughes , Eleonora Barone , Andrea Testa , Sophie Bauer , Jane Wright , Matthias Brand , Alessio Ciulli , Georg E. Winter Nature Chemical Biology 580 DOI: 10.1038/s41589-022-01177-2 Diamond Proposal Number(s): [14980] Show Abstract ▼ Abstract: Targeted protein degradation is a novel pharmacology established by drugs that recruit target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target, different E3 interfaces are critically involved, thus forming defined ‘functional hotspots’. Understanding disruptive mutations in functional hotspots informs on the architecture of the assembly, and highlights residues susceptible to acquire resistance phenotypes. Here we employ haploid genetics to show that hotspot mutations cluster in substrate receptors of hijacked ligases, where mutation type and frequency correlate with gene essentiality. Intersection with deep mutational scanning revealed hotspots that are conserved or specific for chemically distinct degraders and targets. Biophysical and structural validation suggests that hotspot mutations frequently converge on altered ternary complex assembly. Moreover, we validated hotspots mutated in patients that relapse from degrader treatment. In sum, we present a fast and widely accessible methodology to characterize small-molecule degraders and associated resistance mechanisms.	Nov 2022
I24-Microfocus Macromolecular Crystallography	A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo Christiane Kofink , Nicole Trainor , Barbara Mair , Simon Wöhrle , Melanie Wurm , Nikolai Mischerikow , Michael J. Roy , Gerd Bader , Peter Greb , Géraldine Garavel , Emelyne Diers , Ross Mclennan , Claire Whitworth , Vesna Vetma , Klaus Rumpel , Maximilian Scharnweber , Julian E. Fuchs , Thomas Gerstberger , Yunhai Cui , Gabriela Gremel , Paolo Chetta , Stefan Hopf , Nicole Budano , Joerg Rinnenthal , Gerhard Gmaschitz , Moriz Mayer , Manfred Koegl , Alessio Ciulli , Harald Weinstabl , William Farnaby Nature Communications 13 DOI: 10.1038/s41467-022-33430-6 Diamond Proposal Number(s): [14980] Open Access Show Abstract ▼ Abstract: Targeted protein degradation offers an alternative modality to classical inhibition and holds the promise of addressing previously undruggable targets to provide novel therapeutic options for patients. Heterobifunctional molecules co-recruit a target protein and an E3 ligase, resulting in ubiquitylation and proteosome-dependent degradation of the target. In the clinic, the oral route of administration is the option of choice but has only been achieved so far by CRBN- recruiting bifunctional degrader molecules. We aimed to achieve orally bioavailable molecules that selectively degrade the BAF Chromatin Remodelling complex ATPase SMARCA2 over its closely related paralogue SMARCA4, to allow in vivo evaluation of the synthetic lethality concept of SMARCA2 dependency in SMARCA4-deficient cancers. Here we outline structure- and property-guided approaches that led to orally bioavailable VHL-recruiting degraders. Our tool compound, ACBI2, shows selective degradation of SMARCA2 over SMARCA4 in ex vivo human whole blood assays and in vivo efficacy in SMARCA4-deficient cancer models. This study demonstrates the feasibility for broadening the E3 ligase and physicochemical space that can be utilised for achieving oral efficacy with bifunctional molecules.	Oct 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	Stereoselective synthesis of allele-specific BET inhibitors Adam G. Bond , Andrea Testa , Alessio Ciulli Organic & Biomolecular Chemistry 2 DOI: 10.1039/D0OB01165G Diamond Proposal Number(s): [19844] Open Access Show Abstract ▼ Abstract: Developing stereoselective synthetic routes that are efficient and cost-effective allows easy access to biologically active molecules. Our previous syntheses of allele-selective bumped inhibitors of the Bromo and Extra-Terminal (BET) domain proteins, Brd2, Brd3, Brd4 and BrdT, required a wasteful, late-stage alkylation step and expensive chiral separation. To circumvent these limitations, we developed a route based on stereocontrolled alkylation of an N-Pf protected aspartic acid derivative that was used in a divergent, racemisation-free protocol to yield structurally diverse and enantiopure triazolodiazepines. With this approach, we synthesized bumped thienodiazepine-based BET inhibitor, ET-JQ1-OMe, in five steps and 99% ee without the need for chiral chromatography. Exquisite selectivity of ET-JQ1-OMe for Leu-Ala and Leu-Val mutants over wild-type bromodomain was established by isothermal titration calorimetry and X-ray crystallography. Our new approach provides unambiguous chemical evidence for the absolute stereochemistry of the active, allele-specific BET inhibitors and a viable route that will open wider access to this compound class.	Aug 2020
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Synthesis and biological investigation of (+)-JD1, an organometallic BET bromodomain inhibitor Storm Hassell-Hart , Andrew Runcie , Tobias Krojer , Jordan Doyle , Ella Lineham , Cory A. Ocasio , Brenno A. D. Neto , Oleg Fedorov , Graham Marsh , Hannah Maple , Robert Felix , Rebecca Banks , Alessio Ciulli , Sarah Picaud , Panagis Filippakopoulos , Frank Von Delft , Paul Brennan , Helen J. S. Stewart , Timothy J. Chevassut , Martin Walker , Carol Austin , Simon Morley , John Spencer Organometallics DOI: 10.1021/acs.organomet.9b00750 Diamond Proposal Number(s): [19301] Show Abstract ▼ Abstract: (+)-JD1, a rationally designed ferrocene analogue of the BET bromodomain (BRD) probe molecule (+)-JQ1, has been synthesized and evaluated in biophysical, cell-based assays as well as in pharmacokinetic studies. It displays nanomolar activity against BRD isoforms, and its cocrystal structure was determined in complex with the first bromodomain of BRD4 and compared with that of (+)-JQ1, a known BRD4 small-molecule probe. At 1 μM concentration, (+)-JD1 was able to inhibit c-Myc, a key driver in cancer and an indirect target of BRD4.	Dec 2019
I04-Macromolecular Crystallography	Structure-based design of a macrocyclic PROTAC Alessio Ciulli , Andrea Testa , Scott J. Hughes , Xavier Lucas , Jane E. Wright Angewandte Chemie International Edition DOI: 10.1002/anie.201914396 Diamond Proposal Number(s): [14980] Open Access Show Abstract ▼ Abstract: Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Here, we report the design and synthesis of a first macrocyclic PROTAC by adding a second cyclizing linker to the BET degrader MZ1. A co‐crystal structure of macroPROTAC‐1 bound in a ternary complex with VHL and the second Brd4 bromodomain validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12‐fold loss of binary binding affinity for Brd4, macroPROTAC‐1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets.	Nov 2019
I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase Wei-Wei Kung , Sarath Ramachandran , Nikolai Makukhin , Elvira Bruno , Alessio Ciulli Nature Communications 10, 2534 DOI: 10.1038/s41467-019-10190-4 Diamond Proposal Number(s): [14980] Open Access Show Abstract ▼ Abstract: The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.	Jun 2019
I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design William Farnaby , Manfred Koegl , Michael J. Roy , Claire Whitworth , Emelyne Diers , Nicole Trainor , David Zollman , Steffen Steurer , Jale Karolyi-Oezguer , Carina Riedmueller , Teresa Gmaschitz , Johannes Wachter , Christian Dank , Michael Galant , Bernadette Sharps , Klaus Rumpel , Elisabeth Traxler , Thomas Gerstberger , Renate Schnitzer , Oliver Petermann , Peter Greb , Harald Weinstabl , Gerd Bader , Andreas Zoephel , Alexander Weiss-Puxbaum , Katharina Ehrenhöfer-Wölfer , Simon Wöhrle , Guido Boehmelt , Joerg Rinnenthal , Heribert Arnhof , Nicola Wiechens , Meng-Ying Wu , Tom Owen-Hughes , Peter Ettmayer , Mark Pearson , Darryl B. Mcconnell , Alessio Ciulli Nature Chemical Biology DOI: 10.1038/s41589-019-0294-6 Diamond Proposal Number(s): [14980] Show Abstract ▼ Abstract: Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here, we develop proteolysis targeting chimera (PROTAC) degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization toward ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced anti-proliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets, and pave the way toward new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.	Jun 2019
I24-Microfocus Macromolecular Crystallography	Iterative design and optimization of initially inactive Proteolysis Targeting Chimeras (PROTACs) identify VZ185 as a potent, fast and selective von Hippel-Lindau (VHL)-based dual degrader probe of BRD9 and BRD7 Vittoria Zoppi , Scott J. Hughes , Chiara Maniaci , Andrea Testa , Teresa Gmaschitz , Corinna Wieshofer , Manfred Koegl , Kristin Riching , Danette L. Daniels , Andrea Spallarossa , Alessio Ciulli Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.8b01413 Diamond Proposal Number(s): [14980] Open Access Show Abstract ▼ Abstract: Developing PROTACs to redirect the ubiquitination activity of E3 ligases and potently degrade a target protein within cells can be a lengthy and unpredictable process, and it remains unclear whether any combination of E3 and target might be productive for degradation. We describe a probe-quality degrader for a ligase-target pair deemed unsuitable: the von Hippel-Lindau (VHL) and BRD9, a bromodomain-containing subunit of the SWI/SNF chromatin remodeling complex BAF. VHL-based degraders could be optimized from suboptimal compounds in two rounds by systematically varying conjugation patterns and linkers, and monitoring cellular degradation activities, kinetic profiles, and ubiquitination, as well as ternary complex formation thermodynamics. The emerged structure-activity relationships guided the discovery of VZ185, a potent, fast and selective degrader of BRD9 and of its close homolog BRD7. Our findings qualify a new chemical tool for BRD7/9 knockdown, and provide a roadmap for PROTAC development against seemingly incompatible target-ligase combinations.	Dec 2018
I03-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Surface probing by fragment-based screening and computational methods identifies ligandable pockets on the von Hippel-Lindau (VHL) E3 ubiquitin ligase Xavier Lucas , Inge Van Molle , Alessio Ciulli Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.8b00842 Diamond Proposal Number(s): [5841, 7141] Open Access Show Abstract ▼ Abstract: Beyond the targeting of E3 ubiquitin ligases to inhibit protein homeostasis, E3 ligase binders can be converted into targeted protein degraders. We sought to identify new binders of the VHL E3 ligase by biophysical fragment-based screening followed by X-ray crystallographic soaking. We identified fragments binding at the ElonginC:Cullin2 interface and a new cryptic pocket in VHL, along with other potential ligandable sites predicted computationally. The elucidated interactions provide starting points for future ligand development.	Jul 2018

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