I04-Macromolecular Crystallography
|
Stéphane
Bourg
,
Matthieu
Place
,
Chloé
Copin
,
Apirat
Chaikuad
,
Thomas
Robert
,
Hanna
Holzmann
,
Susanne
Müller
,
Stéphane
Bach
,
Sandrine
Ruchaud
,
Stefan
Knapp
,
Frédéric
Buron
,
Sylvain
Routier
,
Pascal
Bonnet
Abstract: CLK1 is one of the four human isoforms of the cdc2-like (CLK) kinases that has been suggested as a therapeutic target in diverse diseases based on its important role regulating mRNA splicing. For example, CLKs and closely related kinases such as DYRK1A have been targeted in Alzheimer’s disease and other diseases in which splice site selection contributes to the disease development. Here we have developed an efficient in silico fragment-based ligand design approach to identify novel CLK1 inhibitors with excellent ligand efficiency based on an imidazo[2,1-b][1,3,4]thiadiazole fragment. More than one million docking poses were generated from 26,225 unique virtual compounds, and after applying several filtering steps, 11 compounds were selected, synthesized and their CLK1 inhibition and cellular potency were evaluated. Gratifyingly, inhibitor potencies were in excellent agreement with predicted values and crystallographic data of an inhibitor bound to CLK1 confirmed the unusual binding mode of the compounds.
|
Oct 2026
|
|
I03-Macromolecular Crystallography
|
Barbara
Forte
,
Fiona
Bellany
,
Peter S.
Campbell
,
Giulia
Chemi
,
Alice
Dawson
,
Mark
Anderson
,
Yaw
Aniweh
,
Anna Y.
Burkhard
,
Anna Caroline Campos
Aguiar
,
Alisje
Churchyard
,
Caitlin A.
Cooper
,
Amália
Dos Santos Ferreira
,
Mufuliat Toyin
Famodimu
,
Francis G.
Fang
,
Xiao
Hu
,
Tonnie
Huijs
,
Delphine
Baud
,
Chimed
Jansen
,
María Belén
Jiménez Díaz
,
Roger
Bonnert
,
Susan
Boyd
,
Benigno
Crespo-Fernández
,
Branko
Mitasev
,
Simone
Montagna
,
Sachel
Mok
,
Dinakaran
Murugesan
,
Sunil K.
Narwal
,
Neil R.
Norcross
,
John
Okombo
,
Heekuk
Park
,
Caroline
Peet
,
Dhelio B.
Pereira
,
John M.
Post
,
Janette
Reader
,
Jennifer
Riley
,
David A.
Robinson
,
Raku
Shinkyo
,
Frederick R. C.
Simeons
,
Laura
Simpson
,
Alasdair
Smith
,
Dennis
Smith
,
Josefine
Striepen
,
Carolina B. G.
Teles
,
Rianne
Van Der Laak
,
Anne-Catrin
Uhlemann
,
Amélie
Vantaux
,
Caroline
Wilson
,
Benoît
Witkowski
,
Gavin
Wood
,
Tomas
Yeo
,
Fabio
Zuccotto
,
Iñigo
Angulo-Barturen
,
Jake
Baum
,
Judith M.
Bolscher
,
Rafael Victorio Carvalho
Guido
,
Lyn-Marié
Birkholtz
,
Michael J.
Delves
,
Laurent
Dembele
,
David A.
Fidock
,
Francisco Javier
Gamo
,
Dennis E.
Kyle
,
Steven P.
Maher
,
Jean
Popovici
,
Chris
Walpole
,
Fabian
Gusovsky
,
Paul A.
Willis
,
Kevin D.
Read
,
Ian H.
Gilbert
,
Beatriz
Baragaña
Diamond Proposal Number(s):
[10071, 26793]
Open Access
Abstract: A fused dihydropyrrolidino-pyrimidine hit with low lipophilicity and excellent ligand efficiency was identified in a biochemical screen of the Global Health Chemical Diversity Library (GHCDL) against Plasmodium lysyl-tRNA synthetase (KRS). Structure-guided lead optimization delivered analogues with potent parasite growth inhibition, excellent biochemical and cellular selectivity (>1000-fold), and oral efficacy in the malaria NOD-scid-IL2Rγnull (SCID) mouse model. Structural information and computational methods were deployed to identify a potent and selective basic KRS inhibitor (30) with an extended half-life to reduce the dose regimen to a single-dose cure. Compound 30 displayed a long half-life across preclinical species, favorable safety, and activity across Plasmodium species as well as against drug-resistant and sensitive P. falciparum strains and field isolates. Unfortunately, 30 lacked oral bioavailability, which could not be mitigated with a prodrug approach. Nevertheless, learnings from this series will assist future KRS programs in delivering a clinical candidate with this novel mode of action.
|
Jun 2026
|
|
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
|
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.
|
Jun 2026
|
|
I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
|
María
Conde-Giménez
,
Sandra
Salillas
,
María
Galiana-Cameo
,
Juan E.
Martínez-Oliván
,
Alejandro
Mahía
,
Manuel
Ledesma
,
Juan José
Galano-Frutos
,
Ritwik
Maity
,
Adrián
Velázquez-Campoy
,
María D.
Díaz-De-Villegas
,
Ramon
Hurtado-Guerrero
,
Javier
Sancho
Diamond Proposal Number(s):
[14739]
Open Access
Abstract: henylketonuria (PKU) is an inherited metabolic disorder caused by pathogenic variants in phenylalanine hydroxylase (PAH), leading to toxic phenylalanine accumulation and severe neurological complications if untreated. Current pharmacological treatment relies on tetrahydrobiopterin (BH4), which benefits only a subset of patients, highlighting a major unmet need for alternative therapies. Here, we combined high-throughput screening, computational modelling, and drug repurposing to identify pharmacological chaperones capable of rescuing PAH function. We evaluated 26 structurally diverse small molecules in HEK293T cells expressing wild-type PAH or one of eight PKU-associated variants spanning phenotypes from mild to classical disease. Chaperoning efficacy was strongly variant-dependent, and for every variant tested at least one compound produced a greater activity increase than BH4 under identical assay conditions. Notably, belinostat, a clinically approved histone deacetylase inhibitor, emerged as the most effective compound for several clinically severe variants. Mechanistically, functional rescue consistently correlated with an increased population of tetrameric, catalytically competent PAH, as quantified by mass photometry. The crystal structure of the PAH–belinostat complex (PDB ID: 9T1O), together with structural models for all compounds, provide a framework for rational optimization. These results establish a preclinical proof-of-concept for genotype-guided pharmacological chaperone therapy in PKU and support the feasibility of personalized, variant-specific treatment strategies.
|
Jun 2026
|
|
Krios IV-Titan Krios IV at Diamond
|
Diamond Proposal Number(s):
[25452, 32707]
Open Access
Abstract: Antimicrobial resistance is driving the search for new antibiotics and a greater understanding of their mechanism of action. Doxycycline is amongst the most-prescribed antimicrobials. It demonstrates a particularly low minimum inhibitory concentration against the zoonotic pathogen Coxiella burnetii. Doxycycline canonically targets the bacterial ribosome by blocking tRNA binding at the decoding centre (A site) of the small subunit. Using cryo-electron microscopy, we analysed doxycycline binding to C. burnetii and Escherichia coli ribosomes. Both structures reveal doxycycline binding at the exit tunnel in the large subunit. In C. burnetii three doxycycline molecules stack to block the tunnel. In E. coli one doxycycline molecule triggers a major change in the conformation of the ribosome. This rearrangement of the peptidyl transferase centre blocks tRNA binding and nascent chain accommodation, abolishing interactions that are fundamental to ribosome function. We identify a distinct ribosomal protein in the C. burnetii large subunit and characterise an additional member of the prokaryotic ribosome hibernation-promoting factor family. These insights into ribosome function and antibiotic action may aid the development of new ribosome inhibitor antibiotics.
|
Jun 2026
|
|
I13-2-Diamond Manchester Imaging
|
Karo
De Rycke
,
Marina
Horvat
,
Lisa
Caboor
,
Petra
Vermassen
,
Griet
De Smet
,
Sophie
Lobbestael
,
Marta
Santana Silva
,
Wouter
Steyaert
,
Matthias
Van Impe
,
Patrick
Segers
,
Julie
De Backer
,
Patrick
Sips
Diamond Proposal Number(s):
[32919]
Open Access
Abstract: Fibrillin defects lead to severe cardiovascular complications in Marfan syndrome (MFS), including aortic dilation, dissection, and rupture. To model MFS, zebrafish mutants lacking various fibrillin genes were generated. Among these mutant lines, only fibrillin-3–deficient zebrafish exhibited cardiovascular phenotypes mimicking human disease. Multimodal imaging revealed early cardiac defects, bulbus arteriosus dilation, and valve abnormalities. Transcriptomic analysis identified altered regulation of pathways related to extracellular matrix homeostasis and immune system activation. This zebrafish model, recapitulating key cardiovascular features of MFS, provides a valuable platform to investigate disease mechanisms and identify novel treatment strategies.
|
May 2026
|
|
I22-Small angle scattering & Diffraction
|
Diamond Proposal Number(s):
[29929]
Abstract: Objectives: Biomimetic hydroxyapatite (HAp)-based composites are promising materials for dental restorations due to their hierarchical structure and similarity to natural dental tissues. This study aims to investigate the three-dimensional crystallographic organization of HAp within nacre-inspired composites and to evaluate how different polymers infiltrations influence the structural orientation.
Methods: Nacre-inspired HAp ceramic scaffolds were fabricated via bidirectional freeze-casting and subsequently infiltrated with different polymers, including Polyurethane (PU), Poly(methyl methacrylate) (PMMA), Epoxy, and Urethane dimethacrylate (UDMA). The three-dimensional structural organization and crystallite orientation of these composites were investigated using synchrotron-based 3D SAXS tensor tomography (3D SASTT), complemented by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX).
Results: The results reveal distinct differences in crystallite alignment among the composites. HAp/PU exhibits the highest degree of preferred orientation (∼0.7–0.8), whereas HAp/PMMA and HAp/Epoxy show lower alignment values (∼0.2–0.4). The HAp/UDMA composite displays heterogeneous orientation with localized regions of moderate alignment. SEM and EDX analyses confirm variations in lamellar morphology, polymer infiltration, and porosity distribution across the composites.
Significance: These findings demonstrate that 3D SASTT enables quantitative mapping of nanoscale crystallite orientation within bulk biomimetic scaffolds and provides new insights into the hierarchical structure of composites, supporting structural design of advanced dental restorative materials.
|
May 2026
|
|
I03-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[39641]
Open Access
Abstract: Nicotinamidases (PncA) catalyze the hydrolysis of nicotinamide to nicotinic acid, a key step in NAD+ salvage pathways. In the Lyme disease spirochete Borrelia burgdorferi, the plasmid-encoded gene bbe22 encodes a PncA enzyme that is essential for survival in both mammalian and tick hosts. Previous genetic and biochemical studies demonstrated that translation of B. burgdorferi PncA initiates from a rare non-canonical AUU start codon, resulting in a protein that is 24 residues longer than the sequence currently annotated in major databases. Despite these findings, public resources such as UniProt and KEGG still list a truncated protein beginning at residue 36, which lacks part of the N-terminal region required for enzymatic activity. Here we report the crystal structure of full-length B. burgdorferi PncA determined at 3.2 Å resolution. The structure reveals the canonical fold of bacterial nicotinamidases and clear electron density for a ligand in the active site consistent with nicotinic acid, the product of the enzymatic reaction. Structural comparison with homologous PncA enzymes demonstrates conservation of the catalytic architecture, including residues involved in substrate binding and catalysis. Importantly, the experimentally determined structure confirms that the longer N-terminal sequence described previously is required for formation of the correct fold and active-site geometry, whereas the truncated annotation is structurally inconsistent with the observed fold and with AlphaFold predictions. Our results provide the first structural characterization of B. burgdorferi PncA and resolve the long-standing annotation discrepancy for bbe22, validating the correct protein sequence and providing the structural basis for nicotinamidase activity in this essential metabolic enzyme.
|
May 2026
|
|
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
|
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.
|
May 2026
|
|
I04-Macromolecular Crystallography
|
Gernot
Langer
,
Nico
Bräuer
,
Daryl
Walter
,
Stuart
Flanagan
,
Olivier Rémi
Barbeau
,
Wei Tsung
Yau
,
James
Jenkins
,
Dennis
Wegener
,
Daren
Fearon
,
Anne-Marie
Coelho
,
Benjamin
Bader
,
Anders
Friberg
,
Hartmut
Beck
,
Vera
Pütter
,
Frank
Sacher
Abstract: Human Phospholipase A2 Group V (hPLA2-G5) is elevated in inflammatory conditions and promotes neutrophil and macrophage recruitment. Its enzymatic activity activates lipid receptors and cytosolic phospholipase A2 (cPLA2), leading to arachidonic acid release and PGE2 production─key mediators of chronic inflammation. Thus, hPLA2-G5 represents a promising therapeutic target for diseases with inflammatory pain, such as in endometriosis─a highly debilitating disease characterized by the ectopic growth of endometriotic cells in the abdominal cavity. High-throughput and fragment-based screening identified structurally related small molecule hits. Optimization of the physicochemical and pharmacokinetic properties of the HTS hit led to the identification of BAY-439, a potent and selective hPLA2-G5 inhibitor with single-digit nanomolar activity. Accepted as a donated chemical probe by the Structural Genomics Consortium, both BAY-439 and the inactive negative probe BAY-163 are freely available as valuable pharmacological tools to investigate the role of hPLA2-G5 both under physiological and pathological conditions.
|
May 2026
|
|
