I04-Macromolecular Crystallography
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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.
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Nov 2026
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B23-Circular Dichroism
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Xi
Lei
,
Sibo
Peng
,
Nijas
Aliu
,
Rohanah
Hussain
,
Giuliano
Siligardi
,
Tiberiu-Marius
Gianga
,
Xin
Jin
,
Sabrina
Ruggiero
,
Shilpa
Chokshi
,
Luca
Urbani
,
Bernhard F.
Gibbs
,
Elena
Klenova
,
Gurprit S.
Lall
,
Gabriela
Dekany
,
Dietmar
Cholewa
,
Steffen M.
Berger
,
Maryam
Abooali
,
Inna M.
Yasinska
,
Song
Xu
,
Elizaveta
Fasler-Kan
,
Vadim V.
Sumbayev
Diamond Proposal Number(s):
[36941, 38189]
Abstract: Human cancer cells and malignant tumours operate immune evasion machinery, which consists of a set of cross-linked biochemical pathways that suppress the activities of immune cells, such as cytotoxic T cells and natural killer cells. Recent evidence demonstrated that the immune evasion machinery operated by human cancer cells is self-sustaining. However, the mechanisms underlying self-regulation of cancer immune evasion networks remain to be understood. Here we report for the very first time that the cell surface receptor CD44 acts as an enhancer of immune evasion activity in human cancer cells rather than an immune checkpoint per se. Furthermore, upon interaction with galectin-9, CD44 was found to alter cell membrane potential and induce the secretion of TGF-β. Secreted TGF-β displays autocrine and paracrine activities following TGF-β receptor (TGFBR) engagement, which was shown to then activate the Smad3 transcriptional pathway. CD44 complexed to galectin-9 allosterically enhances activity of the TGFBR complex and this was shown to substantially amplify the expression of immune checkpoint proteins crucially associated with suppressing the anti-cancer activities of cytotoxic lymphoid cells. We also demonstrated that this is a fundamental pathway used by human embryos to prevent immune rejection and by innate immune cells to facilitate anti-bacterial innate immune response. Cancer cells and malignant tumours hijack and successfully adapt this fundamental pathway to escape immune surveillance and suppress anti-cancer immune reactions. As such, this autocrine loop allows for the self-regulation of immune evasion networks operated by cancer cells and can be considered as a promising target for highly efficient immunotherapy of cancer.
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Nov 2026
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I04-Macromolecular Crystallography
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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.
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Oct 2026
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Sven
Falke
,
Patrick Y. A.
Reinke
,
Daniel
Rosenberg
,
Pontus
Fischer
,
Jan
Meyer
,
Marina
Galchenkova
,
Alexandra
Tolstikova
,
Valerio
Mariani
,
Johanna M.
Senst
,
Philipp
Lewe
,
Susanne
Witt
,
Armin
Wagner
,
Henry N.
Chapman
,
Mark
Hunter
,
Sebastian
Gunther
,
Alke
Meents
Open Access
Abstract: Emerging human pathogenic RNA viruses such as Lassa virus (LASV) and closely related viruses such as Hantavirus and Andes virus continue to be a major health threat globally. Treatment options for infections are severely limited. The widely conserved cap-snatching endonuclease of LASV (LASVendoN) is therefore used as an interesting drug target for our X-ray compound-screening experiments. Considering recent improvements in instrumentation and serial crystallography method development, different approaches may be used to facilitate pharmaceutical compound screening. Current-generation X-ray free-electron laser (XFEL) sources hold promise for obtaining higher quality diffraction data and achieving a high sample throughput using fixed-target serial femtosecond X-ray crystallography. We collected serial fixed-target X-ray diffraction data at Linac Coherent Light Source and at the synchrotron source PETRA III for comparison and solved the crystal structures of 2,4-dioxo-4-phenylbutanoic acid (DPBA) and baloxavir acid (BXA) binding to the active site of LASVendoN. These solved structures represent a reasonable starting point for drug development. In addition to room-temperature diffraction data, conventional single-crystal diffraction data were recorded at 100 K for comparison. To analyse the sample throughput in a compound-screening experiment at an XFEL, we further present data for the bacterial fosfomycin-resistance protein A with six ligands previously identified in a synchrotron screening experiment. In summary, the XFEL and synchrotron data-collection approaches have proven to be useful for compound screening with minor differences in achievable data quality and resolution. The individual experimental setup, detector and potentially the use of beam sweeping at XFELs at close-to-physiological temperatures combined with reasonable sample consumption and minimized radiation damage are considered to be advantageous for high-throughput drug development.
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Oct 2026
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I03-Macromolecular Crystallography
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Maeve
Long
,
James
Tribble
,
Rahul
Upadhyay
,
Alice
Eddershaw
,
Nicholas D.
D'Arcy-Evans
,
Alan
Nicol
,
Sara
Cano
,
Emma
Scaletti Hutchinson
,
Alicia Del
Prado
,
Hannah
Stigsdotter
,
Natálie
Rudolfová
,
Dinesh
Nirmalan
,
Elisée
Wiita
,
Ingrid
Almlöf
,
Richard
Svensson
,
Andreas
Kramer
,
Anas
Bitar
,
Oryn
Purewal-Sidhu
,
Oliver
Mortusewicz
,
Olov
Wallner
,
Opher
Gileadi
,
Evert J.
Homan
,
Stefan
Knapp
,
Pawel
Baranczewski
,
Laurie H.
Sanders
,
Miguel
De Vega
,
Pal
Stenmark
,
Alexandra
Stolz
,
Thomas
Helleday
,
Michael
Sundström
,
Pete
Williams
,
Maurice
Michel
Diamond Proposal Number(s):
[29948]
Open Access
Abstract: Mitochondrial dysfunction is a major component of neurodegeneration. The mitochondrial genome is prone to oxidative damage, and repair proteins are important to maintain mitochondrial DNA integrity. OGG1 initiates base excision repair of oxidative DNA lesions in both nuclear and mitochondrial genomes. While inhibitors of OGG1 have been extensively explored, pharmacological activation of OGG1 through catalytic reprogramming remains underdeveloped. Herein, we report the discovery of mitochondrial enriched organocatalytic switches of OGG1. Biochemical analysis, mutational profiling, and X-ray crystallography confirmed active-site binding and preferential stimulation of β-elimination over glycosylase turnover, effectively reprogramming OGG1. We demonstrate that ORCAs protect mitochondrial function and morphology under oxidative stress, specifically affecting mitochondrial membrane potential and fragment number while attenuating metabolic stress. Mechanistically, ORCAs improved NAD levels in mouse dissociated cortical neurons and provided neuroprotection in a retina axotomy model. Together, the findings position OGG1-ORCAs as potential novel therapies for the treatment of age-related diseases and neurodegeneration.
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Oct 2026
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I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[21673]
Open Access
Abstract: Quatsomes (QS) are highly stable unilamellar nanovesicles formed by the self-assembly of quaternary ammonium surfactants and sterols. Despite their growing potential as nanocarriers, the molecular determinants of QS membrane structure and mechanics remain poorly understood, limiting the rational design of optimized formulations. Here, we investigate the effect of surfactant chain length, counterion identity, and solution ionic content on the structural and nanomechanical properties of cholesterol-based QS membranes assembled from alkyltrimethylammonium (CnTA+) salts. Supported bilayers and multilamellar membrane stacks were characterized under varying ionic conditions using atomic force microscopy (AFM), AFM-force spectroscopy, X-ray reflectivity, and molecular dynamics simulations. While surfactant chain length (C14 vs C16) had only minor effects on membrane stiffness and negligible influence on fluidity, counterion identity emerged as the dominant factor governing membrane behavior. Smaller chaotropic tendence, as provided by Cl- compared to Br-, promoted tighter molecular packing, resulting in more compact, stiffer membranes with reduced fluidity and greater resistance to AFM tip penetration, an effect that was further enhanced by increasing the ionic concentration of the surrounding environment. These findings highlight the critical role of ionic composition in regulating QS membrane organization and mechanics, providing a framework for the rational design of QS-based nanomaterials.
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Sep 2026
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Open Access
Abstract: Fragment screens provide an information-rich starting point for designing derivative compounds in structure-based drug discovery. However, derivatives in the fragment-to-hit stage are typically designed from only one or a few fragments, risking premature convergence on an unproductive series and dramatically limiting exploration of the binding site's interaction opportunities. This is avoidable by exploring a broad, chemically diverse set of scaffolds and elaborations spanning interactions revealed across many fragments, as well as those not yet observed. Conventional catalog procurement makes this breadth of testing prohibitively expensive for early discovery. In-house high-throughput (HT) synthesis can raise interaction productivity, the number of unique predicted protein–ligand interactions achievable within a given budget, by lowering the cost per compound, including labor and consumables, yet no design tool exists for this purpose. We introduce Syndirella (Synthesis Directed Elaborations), which presents a candidate elaboration space around input fragment-derived scaffolds, constrained to HT-compatible reactions and catalog reactants, for cost-effective sampling of many scaffolds' elaborations in a single experimental cycle. Applied to three viral protein targets, Syndirella designs demonstrated pharmacophore diversity, recapitulating known fragment interactions, identifying novel functionally relevant ones, and accessing chemical space absent from commercial catalogs. A companion paper details validation on a calcium-binding protein, yielding crystallographic structures and measurable binding, with in-house synthesis achieving a 71% cost reduction over catalog purchasing, labor and consumables included. Reactant rather than product procurement gives potentially 2.5 times as many accessible compounds and higher interaction productivity for the same budget. Syndirella is most impactful for structure-enabled campaigns with fragment-bound crystal structures, robust HT chemistry, and assays compatible with crude reaction mixtures, and is available at https://github.com/oxpig/syndirella.
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Sep 2026
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Abstract: Redox-active transition metal ions, such as Fe and Cu, are critical to support healthy brain function. Unfortunately, Fe and Cu homeostasis is a double-edged sword in the brain, where disturbed amounts or changes in their distribution or chemical form can drive oxidative stress and tissue damage. Characterising the chemical form of Fe and Cu in situ in brain tissue has historically been difficult because few analytical methods are sensitive to the different oxidation states and bonding environments in which Fe and Cu can exist. Recently, XANES spectroscopy has become a popular method for studying Fe and Cu speciation in situ in biological systems. However, one unanswered question in using XANES spectroscopy to study Fe and Cu speciation in situ is how sample preparation affects metal oxidation state and coordination environment. This investigation has therefore compared XANES spectra collected from air-dried brain tissue with spectra from frozen-hydrated brain tissue. The results highlight that to prevent artificial sample-preparation-induced oxidation and detect Fe and Cu as close as possible to in vivo conditions, analysis should be performed on frozen-hydrated tissues.
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Sep 2026
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Open Access
Abstract: The Fc region of immunoglobulin E (IgE-Fc) is an important therapeutic target due to the antibody’s critical role in allergic disorders through interactions with high-affinity (FcεRI) and low-affinity (CD23) receptors. IgE-Fc is known to be conformationally flexible, undergoing large-scale structural changes that modulate receptor binding and downstream biological functions. The mechanistic basis for how ligands induce these allosteric changes is not fully understood. In this study, we investigate structure–function relationships of IgE by characterizing four closely related anti-IgE-Fc Fab fragments with highly conserved sequences that recognize a shared epitope at the base of the Cε2 domain. Despite their sequence similarity, these Fabs exhibit markedly different binding characteristics, stoichiometries, and functional activities. Furthermore, the crystal structures of these four Fab complexes reveal that the bound IgE-Fc adopts a wide range of conformations. These structural differences directly dictate the functional outcomes, ranging from conformations that facilitate FcεRI binding to those that prevent or destabilize receptor interaction. Our findings demonstrate that highly similar antibodies binding to the same epitope on a protein that exhibits significant conformational plasticity can elicit distinct and divergent functional outcomes. This work challenges the conventional antibody discovery paradigm, i.e., “same epitope, same functional outcome,” and highlights the importance of accounting for both the target’s structural flexibility and the resulting functional diversity within antibody selection strategies. This is especially critical when targeting dynamic proteins where allosteric mechanisms are fundamental to function.
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Sep 2026
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I03-Macromolecular Crystallography
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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.
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Sep 2026
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