I03-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[39189]
Open Access
Abstract: The enzymes Cannabichromenic Acid Synthase (CBCAS), Cannabidiolic Acid Synthase (CBDAS) and Tetrahydrocannabinolic Acid Synthase (THCAS) are together the major cannabinoid synthase enzymes responsible for the biosynthesis of their respective metabolites from a common precursor Cannabigerolic Acid (CBGA). As the catalysts responsible for generating biological molecules of significant pharmaceutical value, there has been considerable interest in the enzymes with respect to heterologous production, mechanism, and incorporation into synthetic biology pathways for the facile industrial production of these molecules. The enzymes share high degrees of homology, and therefore their distinct specificities are governed by very subtle differences in sequence and therefore structure, although, until now, only a structure for THCAS has been reported. In this report, we present structures of CBCAS, CBDAS and a structure of THCAS at a higher resolution than the known structure, each in complex with their flavin coenzyme FAD. The structures reveal active site differences that may be responsible for the complementary activities observed, in terms of both first-shell amino acid substitutions, but also in more remote residues that influence active site topology through referred effects, or that have effects on substrate access. The structures provide a useful and informative platform for the rational engineering of improved or altered chemoselectivity in these enzymes.
|
Dec 2026
|
|
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[34182]
Open Access
Abstract: Chikungunya virus (CHIKV) outbreaks impose significant burdens on healthcare systems and raise an urgent need for effective antiviral therapies. So far there are no specific drugs against CHIKV infection. CHIKV-encoded macrodomain is critical for virulence and counteracts the host immune response, representing a promising antiviral drug target. Here, we describe small molecule inhibitors targeting the CHIKV macrodomain. Compound 1 (MDOLL-0273) was identified through a high-throughput screening using a fluorescence resonance energy transfer based assay, exhibiting an IC50 of 8.9 μM, and its inhibitory activity was validated through multiple orthogonal assays. The compound features a thiobarbiturate-indole scaffold and shows high selectivity over a panel of human and viral ADP-ribose binding and hydrolyzing proteins. X-ray crystallography revealed that the inhibitor occupies an adenine binding site of the macrodomain and extends into a novel cryptic pocket. Guided by structure-activity relationship studies, compound 11 (MDOLL-0591) of the developed series with similar IC50 of 10 μM but with increased lipophilicity was discovered to have antiviral activity against CHIKV in cell culture, demonstrating that macrodomain could be targeted in virus infections.
|
Nov 2026
|
|
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
Open Access
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
|
|
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Diamond Proposal Number(s):
[36570]
Open Access
Abstract: Leishmaniasis is a neglected disease that affects around two million people every year. Current treatments are often highly toxic or prone to resistance, underscoring the urgent need for new therapeutic strategies. PROTACs may offer a promising alternative, as they can potentially mitigate both toxicity and resistance. However, very little is known about the ubiquitin–proteasome system (UPS) in Leishmania. Notably, only two E3 ligases containing a CULT domain have been identified so far, and none carrying a von Hippel–Lindau (VHL) domain─the classical E3 ligase used by clinically advanced PROTACs. In this work, we take an important step toward understanding the UPS in Leishmania, and we propose that in this organism the UbC4 E2 enzyme, rather than an E3, may be directly exploited to develop a PROTAC able to engage a protein of interest. Here, we report the biochemical and structural characterization of the Leishmania major ubiquitin-conjugating enzyme 4 (UbC4). Through a fragment screening campaign, we identified 10 fragments binding to distinct cavities on UbC4. Among these, five interact with the same noncatalytic pocket that is poorly conserved in humans, while one fragment binds near the catalytic cysteine. Using DeepFrag predictions and molecular docking, we explored fragment elongation strategies to enhance affinity for their respective binding sites, with the goal of guiding the development of E2-recruiting PROTACs or UPS inhibitors for the treatment of leishmaniasis.
|
Sep 2026
|
|
I03-Macromolecular Crystallography
|
Open Access
Abstract: Carbapenem-resistant Enterobacterales (CRE), including Escherichia coli and Klebsiella pneumoniae are increasingly common pathogens. Resistance in CRE is often associated with production of K. pneumoniae (KPC) carbapenemases. We report a structurally modified meropenem derivative, JDB-1-200 (i.e., 8-epi-meropenem, in which the stereochemistry of the C8 hydroxyl is inverted), displaying enhanced activity relative to meropenem against KPC-producing CRE. JDB-1-200 alone displayed superior activity (MICs of 0.5 to 1 mg/L, compared with >8 mg/L for meropenem) against several clinically relevant Enterobacterales, including KPC-producing K. pneumoniae and Citrobacter freundii. Crystallographic analysis of JDB-1-200 complexes with the E166Q deacylation-deficient KPC-2 mutant, compared with an analogous meropenem (8R-hydroxyl) complex, indicates that the improvement arises from the JDB 8S-hydroxyl group acting as a hydrogen-bond donor to the hydrolytic water, slowing acyl-enzyme hydrolysis, with similar interactions observed in a CTX-M-15:JDB-1-200 complex. Kinetic inhibition data for KPC-2 and CTX-M-15 indicate that JDB-1-200 could be used alone or alongside a β-lactamase inhibitor for effective CRE treatment.
|
Sep 2026
|
|
NONE-No attached Diamond beamline
|
Daniel
Muñoz-Reyes
,
Kate K.
Fieseler
,
Max
Winokan
,
Mathew
Golding
,
Eda
Capkin
,
Matteo
Ferla
,
Sara
Pérez-Suárez
,
Charles W. E.
Tomlinson
,
Peter G.
Marples
,
Celia
Miró-Rodríguez
,
Lorena
Aguado
,
Alicia
Mansilla
,
Daren
Fearon
,
Warren A.
Thompson
,
Frank
Von Delft
,
Maria Jose
Sanchez Barrena
Diamond Proposal Number(s):
[31306]
Open Access
Abstract: Efficient drug discovery workflows ideally generate data that directly address key translational milestones, including confirmation of target engagement and binding pose, structure-activity relationships (SAR), and biological relevance, within rapid and resource-efficient experimental cycles. Here, we describe a data-driven, automation-assisted, customizable framework for fragment-to-hit progression that directly delivers structurally validated hit series primed for rapid SAR exploration, by exploiting the high-throughput crystallography available at synchrotrons. This recently evolved direct-to-biology approach combines X-ray crystallographic fragment screening with algorithmically-guided fragment merging and reagent prioritization; low-cost robotic array synthesis and reaction production assessment by LC-MS; and finally orthogonal biophysical evaluation of crude reaction mixtures for binding assessment and 3D binding pose using respectively grating-coupled interferometry and crystallography. We demonstrated the effectiveness of the strategy on a challenging target class, by collectively progressing a large set of fragment hits through a single DMTA cycle comprising over 250 synthetically diverse compounds, enabling rapid, resource- and cost-effective exploration of the off-catalogue chemical space. This led to the discovery of protein-protein interaction modulators of Neuronal Calcium Sensor 1 (NCS-1), a key regulator in the central nervous system with therapeutic relevance, which contains a large interaction pocket capable of accommodating multiple protein partners. We advanced fragments into scaffold series that selectively engage biologically validated subpockets and, importantly, revealed allosteric and cryptic binding sites, critical for achieving specificity in target modulation and subsequent hit-to-lead generation. The approach is general, engineerable and scalable, and provides proof-of-principle for how to expand the scope of fragment-based hit discovery.
|
Sep 2026
|
|
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
|
Hyunsoo
Kim
,
Beatriz
Romartinez-Alonso
,
Xu
Xiao
,
Yajing
Gao
,
John Paul
Kennelly
,
Alessandra
Ferrari
,
Rui
Li
,
Liujuan
Cui
,
Emily
Whang
,
John W. R.
Schwabe
,
Michael E.
Jung
,
Peter
Tontonoz
Diamond Proposal Number(s):
[34438]
Open Access
Abstract: Aster proteins (Aster-A, -B, and -C) are crucial for transporting cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER). Asters are expressed in a cell type–specific manner across tissues. Their global disruption leads to varied physiological outcomes given the diverse roles of cholesterol throughout the body. We previously identified sterol analogs, such AI-3d, that inhibit all three Aster proteins. However, their utility is limited by toxicity and off-target effects. Here, we report the development of nonsteroidal Aster inhibitors that are active in cells and in vivo, using binding-guided design to generate compounds with isoform-selective affinities. We found that YKJ-124 is a low-toxicity, Aster-A–preferring inhibitor that elevates PM-accessible cholesterol in primary T cells and potentiates store-operated Ca2+ entry in Th17 cells, phenocopying Aster-A deficiency. YKJ-300 and YKJ-305 selectively target Aster-C; cocrystal structures and point mutation studies reveal a Ser477-dependent hydrogen bond (Gly in Aster-A/B) that underlies this specificity. We also explored the in vivo consequences of pharmacologic Aster-C inhibition. YKJ-305 treatment of mice blunted fasting-induced hepatic cholesterol transport and cholesterol ester formation, accompanied by compensatory activation of the SREBP2 pathway. Last, we also identify broader-spectrum inhibitors (YKJ-86) and dual Aster-A/C inhibitors (YKJ-262) that drive PM cholesterol accumulation in fibroblasts and human intestinal enteroids. Together, these chemical probes enable isoform-resolved manipulation of Aster-dependent cholesterol trafficking and provide a foundation for developing Aster-targeted therapies for cholesterol dysregulation.
|
Sep 2026
|
|
I03-Macromolecular Crystallography
|
Dawn
Mulligan
,
Selyna
Mai
,
Kriti
Acharya
,
Jaclyn
Robustelli
,
Christina
Cuttitta
,
Réginald
Ambroise
,
Jeffrey
Tredup
,
Chunhong
Yan
,
Nicolas
Szapiel
,
Joseph
Yanchunas
,
John A.
Newitt
,
Brian P.
Mahon
Abstract: UFMylation is an important biological process where proteins are post-translationally modified via the covalent attachment of the ubiquitin-like modifier (UBL), ubiquitin-fold modifier-1 (UFM1). UFMylation is analogous to ubiquitination, occurring via the transfer of UFM1 across E1-, E2-, and E3-like enzymes, represented by ubiquitin-like modifier-activating enzyme 5 (UBA5), ubiquitin-fold modifier conjugating enzyme 1 (UFC1), and UFM1-specific ligase 1 (UFL1), respectively. Recent work has shown that dysregulation of UFMylation is associated with several diseases, sparking interest in characterizing its enzymes as potential drug targets. To date, only inhibitors targeting UBA5 have been identified, but no such ligands exist for UFC1. In this study, we present the structure of UFC1 in complex with the sulfonic acid CAPS, which revealed a novel ligand-binding pocket in UFC1. Using biophysical assays, coupled with X-ray crystallographic studies of UFC1 variants, we show that binding of CAPS to UFC1 appears pH-dependent and is enhanced by Tyr42. Further, our TSA data show that other sulfa- and sulfonate-based compounds induce dose-dependent destabilization of UFC1, consistent with weak but direct interactions with the enzyme. Lastly, using a UFMylation assay, we show that CAPS, along with Tyr42, may have a limited influence on UFM1 transfer to UFC1 and, consequently, downstream UFMylation of protein substrates. Nevertheless, our data indicate that the CAPS-binding pocket may serve as a design scaffold for the development of UFC1 modulators. With UFC1 emerging as a drug target, our study provides a possible avenue for the design and development of novel UFC1-specific modulators with therapeutic potential.
|
Sep 2026
|
|
B21-High Throughput SAXS
|
Diamond Proposal Number(s):
[36130]
Open Access
Abstract: Nakaseomyces glabratus is an opportunistic pathogen of humans, causing invasive candidiasis (IC). Among the risk factors that favor IC are various host-specific factors. Although drugs are available to treat candidiasis, their clinical application remains limited. Therefore, it is necessary to identify therapeutic targets that will enable the development of new antifungals. In this regard, our research group has identified enzymes as potential therapeutic targets in N. glabratus, including fructose-1,6-bisphosphate aldolase (Fba1) and pyruvate kinase (Pk). Enzyme activity studies on these two enzymes have shown that they are important therapeutic targets against this pathogen. However, their three-dimensional structure has not yet been elucidated, an essential requirement for designating an enzyme as a therapeutic target. To propose Fba1 and Pk of N. glabratus as potential therapeutic targets, we investigated the solution structure and oligomeric state of N. glabratus Fba1 and Pk for the first time by combining Small-Angle X-ray Scattering (SAXS) with AlphaFold3 modeling. SAXS data were collected on the B21 beamline at Diamond Light Source (Didcot, UK), providing solution-scattering profiles, molecular-weight estimates, and low-resolution molecular envelopes. These data indicate that Pk is monomeric and Fba1 homodimeric in solution were used to evaluate and refine the corresponding AlphaFold3 atomic models by molecular dynamics. These structural findings for Fba1 and Pk from N. glabratus open the door to understanding these enzymes as potential therapeutic targets against this pathogen and, at the same time, a basis for future comparative studies.
|
Sep 2026
|
|
Krios III-Titan Krios III at Diamond
|
Jesper S.
Hansen
,
Ashley C. W.
Pike
,
Gamma
Chi
,
Gernot
Wolf
,
Jeppe
Tranberg-Jensen
,
Hannah
Lichtmannegger
,
David
Speedman
,
Alvaro
Ingles-Prieto
,
Fabian
Goericke
,
Helena
Batoulis
,
Hartmut
Beck
,
Rajini
Rao
,
Tooraj
Mirshahi
,
David B.
Sauer
,
Giulio
Superti-Furga
,
Kilian V. M.
Huber
Diamond Proposal Number(s):
[28713]
Open Access
Abstract: Endosomal NHE6 (SLC9A6) and NHE9 (SLC9A9) transporters are essential for maintaining pH homeostasis within endosomes and their dysfunction has been linked to neurological and neurodegenerative disorders. NHE6 and NHE9 are widely considered to function as electroneutral exchangers that couple the export of protons to the import of sodium or potassium ions across cellular membranes, thereby forming the basis of proton leak pathways for internal pH balancing and fine-tuning. Among the 13 identified SLC9 family members, only NHE6 and NHE9 are targeted to endosomes. Despite their biological importance and therapeutic potential, the structural basis for their activity and regulation remains elusive. Here, we present the cryo-EM structures of human NHE9 and two splice variants of NHE6 that differ by alternative inclusion of the β-hairpin motif-containing loop domain located between transmembrane helices 2 and 3, showcasing structural diversity within the organellar NHE subfamily. By mapping the sodium-binding site, our results provide mechanistic insights into ion transport, and for NHE6 we provide evidence for a conserved PIP2-mediated regulatory mechanism. These findings provide a framework for understanding endosomal NHE function with implications for disorders such as Alzheimer’s disease and glioblastoma.
|
Sep 2026
|
|
