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42 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I24-Microfocus Macromolecular Crystallography	Identification of a highly cooperative PROTAC degrader targeting GTP-loaded KRAS(On) alleles Alessio Ciulli , Peter Ettmayer , Kirsten Mcaulay , Vesna Vetma , Ilaria Puoti , Natalia Karolak , Sohini Chakraborti , Emelyne Diers , Enrico Girardi , Shakil Khan , Giorgia Kidd , Katrin G. Kropatsch , Ross Mclennan , Suzanne O’connor , Matthias Samwer , Nicole Trainor , Claire Whitworth , Andre J. Wijaya , Jeff Y. F. Wong , David Zollman , William Farnaby , Johannes Popow Journal Of The American Chemical Society DOI: 10.1021/jacs.5c10354 Diamond Proposal Number(s): [14980] Open Access Show Abstract ▼ Abstract: Kirsten rat sarcoma viral oncogene homologue (KRAS) is a frequently mutated oncogene in multiple types of cancer and is a high priority target for oncology drug development. There are many different KRAS mutations, including mutations that favor the GTP-loaded hydrolysis-incompetent “active” state of KRAS, KRAS(on), that can lead to tumorigenesis. However, small molecule interventions thus far have predominantly targeted single mutations of “inactive” GDP-loaded KRAS, KRAS(off), such as KRASG12C. Here, we address this gap through the development of heterobifunctional VHL-based PROTACs capable of engaging and degrading KRAS(on), thus addressing a wider range of KRAS mutations. By studying ternary complex affinity, stability, and binding modes using SPR and X-ray cocrystal structures, we identified PROTACs that exhibit high positive cooperativity in forming ternary complexes with VHL and GCP-loaded KRAS as representative of KRAS(on) variants. Degrader activity profiling in relevant cancer cells supported the discovery of ACBI4, a PROTAC which forms a highly stable and cooperative ternary complex between VHL and GTP-bound KRAS and which potently degrades KRASG12R, leading to antiproliferative effect in KRAS mutant-driven cancer cells. ACBI4 provides a new chemical tool for studying the impact of degrading KRAS(on) mutants, which is not possible with current pan-KRAS inhibitors or degraders.	Oct 2025
I24-Microfocus Macromolecular Crystallography	Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes Ning Ma , Supriyo Bhattacharya , Sanychen Muk , Zuzana Jandova , Philipp S. Schmalhorst , Soumadwip Ghosh , Keith Le , Emelyne Diers , Nicole Trainor , William Farnaby , Michael J. Roy , Christiane Kofink , Peter Greb , Harald Weinstabl , Alessio Ciulli , Gerd Bader , Kyra Sankar , Andreas Bergner , Nagarajan Vaidehi Nature Communications 16 DOI: 10.1038/s41467-025-63713-7 Open Access Show Abstract ▼ Abstract: Targeted protein degradation using proteolysis-targeting chimeras (PROTACs) offers a promising strategy to eliminate previously undruggable proteins. PROTACs are bifunctional molecules that link a target protein with an E3 ubiquitin ligase, enabling the formation of a ternary complex that promotes ubiquitination and subsequent proteasomal degradation. Although many ternary complex structures are available, understanding how structural features relate to PROTAC function remains challenging due to the dynamic nature of these complexes. Here we show that the interface between the target protein SMARCA2 and the E3 ligase VHL is conformationally flexible and stabilized by interactions involving disordered loops. Using molecular dynamics simulations and X-ray crystallography of SMARCA2–VHL complexes bound to five different PROTACs, we find that interfacial residues often adopt energetically suboptimal, or ‘frustrated,’ configurations. We further show that the degree of frustration correlates with experimentally measured cooperativity for a set of 11 PROTACs. These findings suggest that quantifying interface frustration provides a rational, structure-based approach to guiding PROTAC design.	Sep 2025
	Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open Claudia Tredup , Suzanne Ackloo , Hartmut Beck , Peter J. Brown , Alex N. Bullock , Alessio Ciulli , Ivan Dikic , Kristina Edfeldt , Aled M. Edwards , Jonathan M. Elkins , Henner F. Farin , Edward A. Fon , Matthias Gstaiger , Judith Günther , Anna-Lena Gustavsson , Sandra Häberle , Laura Isigkeit , Kilian V. M. Huber , Andras Kotschy , Oliver Krämer , Andrew R. Leach , Brian D. Marsden , Hisanori Matsui , Daniel Merk , Florian Montel , Monique P. C. Mulder , Susanne Müller , Dafydd R. Owen , Ewgenij Proschak , Sandra Röhm , Alexandra Stolz , Michael Sundström , Frank Von Delft , Timothy M. Willson , Cheryl H. Arrowsmith , Stefan Knapp Rsc Medicinal Chemistry 11 DOI: 10.1039/D4MD00735B Open Access Show Abstract ▼ Abstract: Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public–private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs.	Nov 2024
B21-High Throughput SAXS I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Alena Kroupova , Valentina A. Spiteri , Zoe J. Rutter , Hirotake Furihata , Darren Darren , Sarath Ramachandran , Sohini Chakraborti , Kevin Haubrich , Julie Pethe , Denzel Gonzales , Andre J. Wijaya , Maria Rodriguez-Rios , Manon Sturbaut , Dylan M. Lynch , William Farnaby , Mark A. Nakasone , David Zollman , Alessio Ciulli Nature Communications 15 DOI: 10.1038/s41467-024-52871-9 Diamond Proposal Number(s): [26793, 35324, 33832, 38813] Open Access Show Abstract ▼ Abstract: The ubiquitin E3 ligase cereblon (CRBN) is the target of therapeutic drugs thalidomide and lenalidomide and is recruited by most targeted protein degraders (PROTACs and molecular glues) in clinical development. Biophysical and structural investigation of CRBN has been limited by current constructs that either require co-expression with the adaptor DDB1 or inadequately represent full-length protein, with high-resolution structures of degrader ternary complexes remaining rare. We present the design of CRBNmidi, a construct that readily expresses from E. coli with high yields as soluble, stable protein without DDB1. We benchmark CRBNmidi for wild-type functionality through a suite of biophysical techniques and solve high-resolution co-crystal structures of its binary and ternary complexes with degraders. We qualify CRBNmidi as an enabling tool to accelerate structure-based discovery of the next generation of CRBN based therapeutics.	Oct 2024
Krios I-Titan Krios I at Diamond	Mechanism of degrader-targeted protein ubiquitinability Charlotte Crowe , Mark A. Nakasone , Sarah Chandler , Conner Craigon , Gajanan Sathe , Michael H. Tatham , Nikolai Makukhin , Ronald T. Hay , Alessio Ciulli Science Advances 10 DOI: 10.1126/sciadv.ado6492 Diamond Proposal Number(s): [31827] Open Access Show Abstract ▼ Abstract: Small-molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and potential to tackle previously undrugged targets. Stable and long-lived degrader-mediated ternary complexes drive fast and profound target degradation; however, the mechanisms by which they affect target ubiquitination remain elusive. Here, we show cryo-EM structures of the VHL Cullin 2 RING E3 ligase with the degrader MZ1 directing target protein Brd4BD2 toward UBE2R1-ubiquitin, and Lys456 at optimal positioning for nucleophilic attack. In vitro ubiquitination and mass spectrometry illuminate a patch of favorably ubiquitinable lysines on one face of Brd4BD2, with cellular degradation and ubiquitinomics confirming the importance of Lys456 and nearby Lys368/Lys445, identifying the “ubiquitination zone.” Our results demonstrate the proficiency of MZ1 in positioning the substrate for catalysis, the favorability of Brd4BD2 for ubiquitination by UBE2R1, and the flexibility of CRL2 for capturing suboptimal lysines. We propose a model for ubiquitinability of degrader-recruited targets, providing a mechanistic blueprint for further rational drug design.	Oct 2024
I24-Microfocus Macromolecular Crystallography	Targeting cancer with small-molecule pan-KRAS degraders Johannes Popow , William Farnaby , Andreas Gollner , Christiane Kofink , Gerhard Fischer , Melanie Wurm , David Zollman , Andre Wijaya , Nikolai Mischerikow , Carina Hasenoehrl , Polina Prokofeva , Heribert Arnhof , Silvia Arce-Solano , Sammy Bell , Georg Boeck , Emelyne Diers , Aileen B. Frost , Jake Goodwin-Tindall , Jale Karolyi-Oezguer , Shakil Khan , Theresa Klawatsch , Manfred Koegl , Roland Kousek , Barbara Kratochvil , Katrin Kropatsch , Arnel A. Lauber , Ross Mclennan , Sabine Olt , Daniel Peter , Oliver Petermann , Vanessa Roessler , Peggy Stolt-Bergner , Patrick Strack , Eva Strauss , Nicole Trainor , Vesna Vetma , Claire Whitworth , Siying Zhong , Jens Quant , Harald Weinstabl , Bernhard Kuster , Peter Ettmayer , Alessio Ciulli Science 385, 1338 - 1347 DOI: 10.1126/science.adm8684 Diamond Proposal Number(s): [14980] Show Abstract ▼ Abstract: Mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) protein are highly prevalent in cancer. However, small-molecule concepts that address oncogenic KRAS alleles remain elusive beyond replacing glycine at position 12 with cysteine (G12C), which is clinically drugged through covalent inhibitors. Guided by biophysical and structural studies of ternary complexes, we designed a heterobifunctional small molecule that potently degrades 13 out of 17 of the most prevalent oncogenic KRAS alleles. Compared with inhibition, KRAS degradation results in more profound and sustained pathway modulation across a broad range of KRAS mutant cell lines, killing cancer cells while sparing models without genetic KRAS aberrations. Pharmacological degradation of oncogenic KRAS was tolerated and led to tumor regression in vivo. Together, these findings unveil a new path toward addressing KRAS-driven cancers with small-molecule degraders.	Sep 2024
I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity Martina Pierri , Xingui Liu , Alena Kroupova , Zoe Rutter , Alex J. Hallatt , Alessio Ciulli Bioorganic & Medicinal Chemistry Letters 21 DOI: 10.1016/j.bmcl.2024.129861 Diamond Proposal Number(s): [26793] Open Access Show Abstract ▼ Abstract: Proteolysis targeting chimeras (PROTACs) are heterobifunctional small-molecule degraders made of a linker connecting a target-binding moiety to a ubiquitin E3 ligase-binding moiety. The linker unit is known to influence the physicochemical and pharmacokinetic properties of PROTACs, as well as the properties of ternary complexes, in turn impacting on their degradation activity in cells and in vivo. Our LRRK2 PROTAC XL01126, bearing a trans-cyclohexyl group in the linker, is a better and more cooperative degrader than its corresponding cis- analogue despite its much weaker binary binding affinities. Here, we investigate how this subtle stereocenter alteration in the linker affects the ligand binding affinity to the E3 ligase VHL. We designed a series of molecular matched pairs, truncating from the full PROTACs down to the VHL ligand, and find that across the series the trans-cyclohexyl compounds showed consistently weaker VHL-binding affinity compared to the cis- counterparts. High-resolution co-crystal structures revealed that the trans linker exhibits a rigid stick-out conformation, while the cis linker collapses into a folded-back conformation featuring a network of intramolecular contacts and long-range interactions with VHL. These observations are noteworthy as they reveal how a single stereochemical inversion within a PROTAC linker impacts conformational rigidity and binding mode, in turn fine-tuning differentiated propensity to binary and ternary complex formation, and ultimately cellular degradation activity.	Jun 2024
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2 Sarath Ramachandran , Nikolai Makukhin , Kevin Haubrich , Manjula Nagala , Beth Forrester , Dylan M. Lynch , Ryan Casement , Andrea Testa , Elvira Bruno , Rosaria Gitto , Alessio Ciulli Nature Communications 14 DOI: 10.1038/s41467-023-41894-3 Open Access Show Abstract ▼ Abstract: The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.	Oct 2023
I04-Macromolecular Crystallography	Expanding the structural diversity at the phenylene core of ligands for the von Hippel–Lindau E3 ubiquitin ligase: development of highly potent hypoxia-inducible factor-1α stabilizers Alessio Ciulli , Michael Gütschow , Lan Phuong Vu , Claudia J. Diehl , Ryan Casement , Adam G. Bond , Christian Steinebach , Nika Strašek , Aleša Bricelj , Andrej Perdih , Gregor Schnakenburg , Izidor Sosič Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.3c00434 Diamond Proposal Number(s): [26793] Open Access Show Abstract ▼ Abstract: Hypoxia-inducible factor-1α (HIF-1α) constitutes the principal mediator of cellular adaptation to hypoxia in humans. The HIF-1α protein level and activity are tightly regulated by the ubiquitin E3 ligase von Hippel–Lindau (VHL). Here, we performed a structure-guided and bioactivity-driven design of new VHL inhibitors. Our iterative and combinatorial strategy focused on chemical variability at the phenylene unit and encompassed further points of diversity. The exploitation of tailored phenylene fragments and the stereoselective installation of the benzylic methyl group provided potent VHL ligands. Three high-resolution structures of VHL–ligand complexes were determined, and bioactive conformations of these ligands were explored. The most potent inhibitor (30) exhibited dissociation constants lower than 40 nM, independently determined by fluorescence polarization and surface plasmon resonance and an enhanced cellular potency, as evidenced by its superior ability to induce HIF-1α transcriptional activity. Our work is anticipated to inspire future efforts toward HIF-1α stabilizers and new ligands for proteolysis-targeting chimera (PROTAC) degraders.	Sep 2023
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

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