I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Julian M.
Ludäscher
,
Emma
Scaletti Hutchinson
,
Guillem
Vila-Julià
,
Ann-Sofie
Jemth
,
Saher
Shahid
,
Elisee
Wiita
,
Israel
Cabeza De Vaca
,
Szymon
Pach
,
Lukas
Gajdos
,
Swati
Aggarwal
,
Ellen
Walse
,
Oliver
Mortusewicz
,
Thomas
Helleday
,
Jens
Carlsson
,
Pal
Stenmark
Diamond Proposal Number(s):
[29948]
Open Access
Abstract: Human single-strand-selective monofunctional uracil DNA glycosylase 1 (hSMUG1) removes uracil, 5-hydroxymethyluracil (5hmU) and 5-fluorouracil (5FU) from DNA, thereby initiating the base excision repair (BER) process. hSMUG1 is important for maintaining genomic integrity and plays a significant role in cancer biology. Here, we present the structures of hSMUG1, including complexes with products (uracil and 5FU) and an enzyme-product complex of hSMUG1 with double-stranded DNA (dsDNA). Analysis of our hSMUG1-dsDNA complex reveals how uracil is flipped out of the dsDNA for excision and identifies key residues that we confirm to be critical for both DNA binding and enzymatic activity. Furthermore, our hSMUG1 substrate complexes, molecular dynamics simulations and neutron diffraction data suggest a mechanism by which the substrate uracil rotates following base excision. The structural and functional information presented here will be highly useful for the future development of inhibitors and/or activators targeting hSMUG1.
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Jun 2026
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Krios II-Titan Krios II at Diamond
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Valentina A.
Spiteri
,
Dmitri
Segal
,
Alejandro
Correa-Sáez
,
Kentaro
Iso
,
Ryan
Casement
,
Miquel
Muñoz I Ordoño
,
Mark A.
Nakasone
,
Gajanan
Sathe
,
Caroline
Schätz
,
Hannah E.
Peters
,
Mark
Doward
,
Lisa
Kainacher
,
Angus D.
Cowan
,
Alessio
Ciulli
,
Georg E.
Winter
Diamond Proposal Number(s):
[37630]
Open Access
Abstract: Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) target proteins for degradation by co-opting an E3 ligase. While heterotrivalent PROTACs that can recruit multiple E3 ligases have been described, all MGDs reported to date depend on a single E3. Using orthogonal genetic screening, biophysical and structural analyses, we show that a monovalent MGD can recruit CUL4DCAF16 and CRL1FBXO22 in parallel to degrade SMARCA2/4. Deep mutational scanning identifies C173 in DCAF16 as essential for degrader activity and intact protein mass spectrometry confirms covalent modification at this site. Elucidating the ternary complex structure reveals a unique binding mode and a distinct interface of neointeractions that underlie degrader specificity. We demonstrate that ligase dependency is chemically and genetically tunable. Minimal compound modifications shift preference from DCAF16 to FBXO22, while a single substitution boosts degrader dependency on DCAF16. These results establish a framework for designing tunable dual E3 ligase degraders to mitigate potential resistance mechanisms.
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May 2026
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I03-Macromolecular Crystallography
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Francesco Aleksy
Greco
,
Kamal Rayees
Abdul Azeez
,
Marko
Mitrović
,
Saran Aswathaman
Sivashanmugam
,
Martin Peter
Schwalm
,
Franziska
Preuss
,
Deep
Chatterjee
,
Viktoria
Morasch
,
Sebastian
Mathea
,
Thomas
Hanke
,
Susanne
Müller
,
Stefan
Knapp
Open Access
Abstract: Integrin-linked kinase (ILK) is a pseudokinase that directly interacts with β-integrins and plays a pivotal role in regulating focal adhesion function. ILK has been implicated in the development of various diseases, particularly cancer. However, currently, no validated ligands for ILK have been reported. Here, we describe the identification of 3-cyano-quinolines that potently bind to ILK (KD = ∼250 nM), and crystallographic studies revealed a type I binding mode. A medicinal chemistry campaign exploring structure–activity relationships (SAR) using a robust parallel synthesis approach provided comprehensive SAR and identified regions amenable to modification. In addition, we demonstrated that the optimized 3-cyano-quinoline 1 (DHP) modulates actin cytoskeletal dynamics. This work highlights the first validated ILK ligands and establishes a foundation for future translational efforts, such as the development of selective PROTACs targeting ILK for degradation by the ubiquitin system.
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May 2026
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I04-Macromolecular Crystallography
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Philipp
Münick
,
Dimitrios-Ilias
Balourdas
,
Julianne S.
Funk
,
Büşra
Yüksel
,
Danai
Mavridi
,
Justin
Heftel
,
Birgit
Dreier
,
Jonas V.
Schaefer
,
Birgit
Schäfer
,
Stefan
Knapp
,
Tümay
Telatar
,
Baki
Akgül
,
Andreas
Plückthun
,
Thorsten
Stiewe
,
Andreas C.
Joerger
,
Volker
Dötsch
Abstract: The tumor suppressor p53 is the most frequently mutated protein in tumors and a target for drug development. More than 2000 cancer-associated p53 missense mutations have been reported, most of them located in the DNA-binding domain (DBD). Due to the low intrinsic thermostability of the latter, they often lead to unfolding at physiological temperature. Stabilizing the DBD with small molecules has been shown to be effective in reactivating the cavity-creating cancer mutant Y220C. Unfortunately, the majority of p53 mutants seem to lack druggable binding pockets for small molecules. Here we show that a designed ankyrin repeat protein (DARPin) that binds to the p53 DBD stabilizes temperature-sensitive (TS) p53 cancer mutants, thereby compensating for mutation-induced loss of stability. We determined high-resolution crystal structures of multiple DARPin–mutant p53 complexes, providing mechanistic insights into this mode of stabilization. Reporter gene assays across a comprehensive panel of cancer-associated mutants revealed reactivation of the majority of TS mutants, whereas DNA-contact mutants and those with local misfolding of the DNA-binding surface remained inactive, as expected. We demonstrate that this reactivation induces the transcription of canonical p53 target genes and elicits antiproliferative effects in cancer cell lines. A combination of this DARPin with an mRNA/lipid nanoparticle-based transfection approach may have the potential to reactivate most TS p53 mutants and resensitize cancer cells to chemotherapy.
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May 2026
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I03-Macromolecular Crystallography
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Michael J.
Lambrecht
,
Jun
Liang
,
Peter Man-Un
Ung
,
Malcolm P.
Huestis
,
Bing-Yan
Zhu
,
Lisa M.
Barton
,
Georgette M.
Castanedo
,
Jason R.
Zbieg
,
Robin
Larouche-Gauthier
,
Araz
Jakalian
,
Jean-Philippe
Leclerc
,
Arun
Yadav
,
Pouyan
Haghshenas
,
Samuel
Aubert-Nicol
,
Hossein
Ismaili
,
Liang
Zhao
,
Mélissa
Leblanc
,
Jian
Wang
,
Shouliang
Wang
,
Qiuyue
Wang
,
Thomas
Garner
,
Sophia
Tan
,
Madeleine
Prangley
,
Fabio
Broccatelli
,
Jodie
Pang
,
Jeremy
Murray
,
Christine
Yu
,
Peter
Hsu
,
Sascha
Rutz
,
Satoko
Kakiuchi-Kiyota
,
Isabel
Ishizuka
,
Dennis H.
Leung
,
Ponien
Kou
,
Linda
Bao
,
Xiaojing
Wang
Abstract: Casitas B-lineage lymphoma-b (Cbl-b), an E3 ubiquitin ligase, is a key negative regulator of immune function, and its inhibition is a promising strategy for cancer immunotherapy. Here, we show the optimization of a series of inactive-state Cbl-b inhibitors to improve their potency and pharmacokinetic properties. Through systematic modification of a benzylic amine and a linker region, compound 16 was identified, which demonstrates a favorable balance of biochemical potency, cellular activity, and in vitro ADME properties. Despite exhibiting high IV clearance in vivo, compound 16 achieved oral exposures sufficient to demonstrate significant tumor growth inhibition in a murine CT26 colon-cancer model.
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May 2026
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Holger
Greschik
,
Florian
Friedrich
,
Ludwig
Seifert
,
Farnoush
Mousavizadeh
,
Francesco
Fiorentino
,
Johannes
Walz
,
Lin
Zhang
,
Jianyu
Li
,
Emanuele
Fabbrizi
,
Stefano
Tomassi
,
Farhad
Panahi
,
Niklas
Papenkordt
,
Silas L.
Wurnig
,
Johannes
Osterroth
,
Anna M.
Strasser
,
Jan
Ruprecht
,
Aurélien F. A.
Moumbock
,
Martin
Hügle
,
Manuela
Sum
,
Ling
Peng
,
Sheng
Wang
,
Adina A.
Baniahmad
,
Laura
Pulido-Cortés
,
H. Th. Marc
Timmers
,
Ralf
Flaig
,
Eric
Metzger
,
Bernhard
Breit
,
Oliver
Einsle
,
Stefan
Günther
,
Dante
Rotili
,
Antonello
Mai
,
Roland
Schüle
,
Manfred
Jung
Open Access
Abstract: The chromatin remodeler CHD1, a regulator of gene activity and potential drug target in prostate cancer (PCa), contains a tandem chromodomain (tCD) binding histone H3 trimethylated at lysine 4 (H3K4me3). We developed the first submicromolar inhibitors (2n and 2s) that target the H3K4me3 binding site of the CHD1 tCD with Kd values of 0.15 μM and 0.14 μM, respectively. Co-crystal structures of these quinoline-based compounds revealed aromatic cage interactions and extended ligand contacts in other parts of the H3K4me3 peptide pocket as the main determinants of high-affinity ligand binding. 2n and 2s engage endogenous CHD1 in cell lysates or the exogenous CHD1 tCD in cells. Furthermore, we provide evidence for selectivity against a panel of methyl-lysine readers and epigenetic enzymes as well as impairment of PCa cell viability. Due to their high potency and defined binding mode, our ligands offer new directions for further optimization.
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May 2026
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I04-Macromolecular Crystallography
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James M.
Smith
,
Bernard
Barlaam
,
David
Beattie
,
Lauren
Bradshaw
,
Ho Man
Chan
,
Sophie L.
Cooke
,
Anna
Cronin
,
Iain
Cumming
,
Emma
Dean
,
Judit É.
Debreczeni
,
Iván
Del Barco Barrantes
,
Douglas
Ferguson
,
Davide
Gianni
,
Michael
Grondine
,
James T.
Lynch
,
Lisa
Mcwilliams
,
Shaun
Moore
,
Piotr
Raubo
,
Yang
Qu
,
Graeme R.
Robb
,
Lixiang
Tan
,
Jelena
Urosevic
,
Mercedes
Vazquez-Chantada
,
Pingping
Wang
Diamond Proposal Number(s):
[20015]
Abstract: Inhibition of the arginine methyltransferase protein arginine methyltransferase 5 (PRMT5) has emerged as a key target for cancer therapy. Leveraging the MTAP synthetic lethality mechanism, MTA-cooperative PRMT5 inhibitors are showing promising potential as precision cancer treatments with a high therapeutic index. Herein, we report our efforts to further optimize our previously reported in vivo tool compound 1 (“AZ-PRMT5i-1”) toward a clinical candidate–quality profile, by addressing key shortcomings of this compound─limited aqueous solubility, low hERG receptor activity, and an unfavorable predicted human dose. Exploration of the terminal lactam substitution group and the central aromatic group of the isindolinone scaffold provided the key structure–activity relationship insights to meet these goals. The highest quality compounds in this series were identified by the use of a dose-to-human (D2H) automated model. These efforts resulted in the identification of 14, which shows the appropriate physicochemical properties, DMPK characteristics, and PRMT5-driven activity to be selected for progression into clinical studies.
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May 2026
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14043, 25402, 33658, 40158]
Open Access
Abstract: Bruton’s Tyrosine Kinase (BTK) is a validated target for hematological malignancies, with numerous FDA-approved inhibitors on the market. Current therapies target the highly conserved ATP binding site and hence limit the therapeutic index given the site’s highly conserved nature across the kinome. We explore a novel approach for BTK inhibition by targeting the PH domain-mediated membrane recruitment and activation of BTK. We have identified a fragment which covalently modifies a lysine in the inositol phosphate (PIP3) binding site and inhibits the binding of a soluble PIP3 headgroup analog to the PH domain. Fragment growth and an extensive structure-binding relationship study uncovered 27 crystal structures and a best-in-class analog, 24. Evaluation of pKa values of the targeted lysine in BTK and other PH domains suggests this as a more general approach to PH domain inhibition.
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May 2026
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Michael
Berlin
,
Jennifer
Cantley
,
Fabio
Broccatelli
,
Lin
Cao
,
Huifen
Chen
,
Tommy K.
Cheung
,
Andrew P.
Crew
,
Dean
Dinicola
,
Hanqing
Dong
,
Matthew
Grimmer
,
Brian D.
Hamman
,
Alicia
Harbin
,
Mingtao
He
,
Xiuxian
Hu
,
Alison J.
Hole
,
Thomas
Januario
,
Philip S.
Kerry
,
Xiangjia
Liu
,
Connor
Quinn
,
Christopher M.
Rose
,
Emma
Rousseau
,
Lawrence B.
Snyder
,
Leanna R.
Staben
,
Gan
Wang
,
Jing
Wang
,
Xiaofen
Ye
,
Robert L.
Yauch
,
Peter S.
Dragovich
Diamond Proposal Number(s):
[23279]
Open Access
Abstract: Modification of the VHL-binding fragments contained in proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) improved degradation selectivity over the closely-related paralog protein BRG1 (SMARCA4). In particular, replacement of the phenyl-thiazole entity commonly employed in the generation of VHL-dependent PROTACs with pyridyl-thiazole, phenyl imidazole, and phenyl-nitrile moieties consistently improved the BRG1/BRM degradation selectivity ratios of multiple, structurally-diverse degrader compounds. Crystal structures of these new VHL-binding fragments in complex with the VHL protein were obtained to better understand their interactions. Some of these VHL alterations, the phenyl-nitrile substitution in particular, afforded molecules that displayed strong antiproliferative activities against BRM-dependent (BRG1-mutant) cancers but minimal potency toward wild-type cell lines. One such compound (21, G-9293) was profiled in detailed broad proteomics and chromatin accessibility experiments, and its biological properties were clearly differentiated from a less-selective BRM-degrader (5, A947) in the latter assessment. The highly selective molecule (21, G-9293) was also extensively profiled in vitro using a panel of lung cancer cell lines (defined by BRG1 or BRM status) along with several prostate cancer lines. It exhibited similar antiproliferation activity relative to the less-selective BRM-degrader (5, A947) against the lung lines but significantly diminished potency toward the prostate cancer cells.
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May 2026
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[21035]
Open Access
Abstract: The protein kinase C-related kinase (PKN) family of serine/threonine kinases consists of PKN1, PKN2 and PKN3, all of which are Rho family GTPase effectors. PKNs have three N-terminal Homology Region 1 (HR1) domains (HR1a, HR1b and HR1c), which form antiparallel coiled coils, which in two cases interact with Rho family GTPases, activating the kinase. The PKNs are implicated in several important cellular processes, including cytoskeletal regulation, cell adhesion, gene expression and cell cycle progression, and are also implicated in cancer. Here we have investigated the roles of the HR1 domains in PKN oligomerisation. We show that PKN1 HR1a is a dimer and that the HR1c domain drives further oligomerization. We have mapped the interactions between the HR1 domains and used an integrative approach to model HR1-containing PKN1 dimers. Biophysical analysis shows that RhoA forms a 1:2 complex with HR1a, resulting in a rearrangement of the HR1a dimer, an outcome supported by SAXS models. In contrast, Rac1 binds to monomeric HR1a, suggesting that this GTPase activates PKN1 via a different mechanism. These data provide structural insight into interactions between HR1 domains and the Rho family proteins and their potential consequences for PKN1 activation.
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Apr 2026
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