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119 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I04-1-Macromolecular Crystallography (fixed wavelength)	Workflow for crystallographic fragment screening by crystal soaking for protein targets: a case study on thioredoxin glutathione reductase from Schistosoma mansoni Lauro Neto , Bogar Montoya , Jose Brandao-Neto , Kelly Parker , Frank Von Delft , Nicholas Furnham , Raymond Owens , Floriano Silva-Jr Bio-Protocol 16 DOI: 10.21769/BioProtoc.5651 Open Access Show Abstract ▼ Abstract: Among the biophysical techniques used in fragment-based drug discovery (FBDD) campaigns, crystallography is the most sensitive, allowing for the identification of low-affinity ligands and the characterization of protein–ligand complexes at atomic resolution. Although powerful, the proper application of this technique depends on obtaining crystals capable of diffracting X-rays at high resolution. Additionally, in crystallographic compound screening, the crystals must be resistant to multiple organic solvents used in chemical libraries, such as DMSO. In this protocol, we describe recombinant protein production suitable for crystallization and procedures for X-ray crystallographic screening of a library of 768 fragments. As a case study, we used the Schistosoma mansoni thioredoxin glutathione reductase (SmTGR), a redox enzyme with a key role in controlling oxidative stress in parasites of the Schistosoma genus, which causes schistosomiasis. As a validated pharmacological target, SmTGR is used in the development of new schistosomicidal drugs. The experimental pipeline includes SmTGR expression, purification, and crystallization, crystal soaking, diffraction data collection, and refinement. The 768 fragments from the Diamond-SGC Poised Library (DSPL) were individually soaked onto the crystals, and diffraction data were collected and processed at the I04-1 beamline of the Diamond Light Source synchrotron. Diffraction data were subsequently analyzed using PanDDA to identify fragment-binding events and to enable reliable detection of low-occupancy ligands within the protein crystal structures. In addition to the core experimental steps, this protocol incorporates systematic approaches to overcome limitations frequently encountered in crystallographic screening campaigns, including assessment of crystal solvent tolerance, acceleration of crystal mounting through the use of auxiliary devices, acoustic dispensing–based soaking of hundreds of fragments for low material consumption and high throughput, automated data collection, and efficient data analysis pipeline for the detection of weakly bound ligand. This protocol can be broadly applied to screen diverse compound sets against multiple targets amenable to crystallization.	Mar 2026
	A computational community blind challenge on pan-coronavirus drug discovery data Hugo Macdermott-Opeskin , Jenke Scheen , Cas Wognum , Joshua T. Horton , Devany West , Alexander M. Payne , Maria A. Castellanos , Sean Colby , Edward Griffen , David Cousins , Jessica Stacey , Lauren Reid , Jasmin Cara Aschenbrenner , Daren Fearon , Blake H. Balcomb , Peter Marples , Charles W. E. Tomlinson , Ryan Lithgo , Andre S. Godoy , Max Winokan , Noa Lahav , Shirley Duberstein , Honore Etsmoberg , Lu Zhu , Andrew Quirke , Mohamed Iliyas Abdul Haleem , Irfan Alibay , Gunjan Baid , Benjamin Birnbaum , Kevin P. Bishop , Hugo Bohorquez , Ashmita Bose , C. J. Brown , Jackson Burns , Lianjin Cai , Ruel Cedeno , Stephane De Cesco , Vladimir Chupakhin , Finlay Clark , Daniel J. Cole , Carles Corbi-Verge , Muhammad Danial , Alec Davi , Wim Dehaen , Niklas Piet Doering , Alexis Dougha , Marie-Pierre Dréanic , Bryce Eakin , Anatol Ehrlich , Rokas Elijosius , Jozef Fülöp , Anthony Gitter , Kenneth Goossens , Yaowen Gu , Teresa Head-Gordon , Laurent Hoffer , Johan Hofmans , Ellena Jiang , Benjamin Kaminow , Sina Khosravi , Asma Feriel Khoualdi , Eelke Bart Lenselink , Zhirong Liu , Yue Liu , Sijie Liu , Yizhou Ma , Patrick Maher , Imke Mayer , Oscar Mendez-Lucio , Antonia S. J. S. Mey , Julien Michel , Floriane Montanari , Taoyu Niu , Ryusei Ogino , Ashok Palaniappan , Xiaolin Pan , Auro Patnaik , Long-Hung Pham , Luis Pinto , Justin Purnomo , Alex Rich , Lars Schaaf , Christoph Schran , Rajeev Kumar Singh , Mounika Srilakshmi , Satya Pratik Srivastava , Kunyang Sun , Zhaoxi Sun , Valerij Talagayev , Balamurugan Thirukonda Subramanian Balakrishnan , Ida Titus , Alexandre Tkatchenko , Wojtek Treyde , Giovanni Tricarico , Austin Tripp , Nopsinth Vithayapalert , Yingze Wang , Azmine Toushik Wasi , Steffen Wedig , Gerhard Wolber , Bofei Xu , Weijun Zhou , Frank Von Delft , John D. Chodera Journal Of Chemical Information And Modeling 40 DOI: 10.1021/acs.jcim.5c02106 Show Abstract ▼ Abstract: Computational blind challenges offer critical, unbiased opportunities to assess and accelerate scientific progress, as demonstrated by a breadth of breakthroughs over the past decade. We report the outcomes and key insights from an open science community blind challenge focused on computational methods in drug discovery, using lead optimization data from the AI-driven Structure-enabled Antiviral Platform Discovery Consortium’s pan-coronavirus antiviral discovery program, in partnership with Polaris and the OpenADMET project. This collaborative initiative invited global participants from both academia and industry to develop and apply computational methods to predict the biochemical potency and crystallographic ligand poses of small molecules against key coronavirus targets, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) main protease (Mpro), as well as multiple ADMET assay end points, using previously undisclosed comprehensive experimental drug discovery data sets as benchmarks. By evaluating submissions across multiple tasks and compounds, we established performance leaderboards and conducted meta-analyses to assess methodological strengths, common pitfalls, and areas for improvement. This analysis provides a foundation for best practices in real-world machine learning evaluation, grounded in community-driven benchmarking. We also highlight how next-generation platforms, such as Polaris, enable rigorous challenge design, embedded evaluation frameworks, and broad community engagement. This paper reports the collective findings of the challenge, offering a high-level overview of the data, evaluation infrastructure, and top-performing strategies. We further provide context and support for the accompanying papers authored by the challenge participants in this special issue, which explore individual approaches in greater depth. Together, these contributions aim to advance reproducible, trustworthy, and high-impact computational methods in drug discovery, and to explore best practices and pitfalls in future blind challenge design and execution, including planned initiatives for the OpenADMET project.	Feb 2026
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength)	Structure-activity-relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures Harold Grosjean , Kate K Fieseler , Ruben Sanchez-Garcia , Warren A. Thompson , Charlotte M. Deane , Frank Von Delft , Philip Biggin Chemical Science DOI: 10.1039/D5SC04919A Diamond Proposal Number(s): [30602] Open Access Show Abstract ▼ Abstract: Fragment-based drug design offers multiple routes to advance from fragments. One approach is to build structure-activity relationships (SAR) from analogue series in direct-to-biology workflows. Analogues can be prepared by automated chemistry and tested as crude reaction mixtures (CRMs) without purification, but assay noise often leads to hit resynthesis, potentially discarding false negatives and reducing SAR dataset size. High-throughput (HT) X-ray crystallography has the potential to address these issues by resolving hits directly from 100s–1000s of CRMs. However, no systematic analytics exist for extracting SAR models from HT crystallographic evaluation of CRMs. Here, we demonstrate that crystallographic SAR (xSAR) can be extracted from CRMs evaluated via HT X-ray crystallography. We developed a simple rule-based ligand scoring scheme that identifies conserved chemical features associated with crystallographic binding and non-binding. Applied to a crystallographic dataset of 957 fragment elaborations in CRMs targeting PHIP(2), a therapeutically relevant bromodomain, our xSAR model demonstrated effectiveness in two proof-of-concept experiments. First, it recovered 26 missed binders in the initial dataset (false negatives), doubling the hit rate and denoising the dataset. Second, it enabled a prospective virtual screen that identified novel hits with informative chemistries and measurable binding affinities. This work establishes a proof-of-concept that xSAR models can be directly extracted from large-scale crystallographic readouts of CRMs, offering a valuable methodology to build SAR models and accelerate design-make-test iterations without requiring CRM hit resynthesis and confirmation. This invites future work to utilise advanced analytics and modelling techniques to further strengthen purification-agnostic workflows.	Dec 2025
I04-1-Macromolecular Crystallography (fixed wavelength)	Water networks as hydrophobic recognition motifs in proteins Serena G. Piticchio , Miriam Martinez-Cartro , Salvatore Scaffidi , Sergio Rodríguez-Arévalo , Andrea Bagán , Ainoa Sánchez-Arfelis , Sarah Picaud , Tobias Krojer , Panagis Filippakopoulos , Carmen Escolano , Xavier Barril , Frank Von Delft Angewandte Chemie International Edition DOI: 10.1002/anie.202521138 Diamond Proposal Number(s): [19301] Open Access Show Abstract ▼ Abstract: The hydrophobic effect is a central force in molecular recognition, typically attributed to the ordering of water molecules around apolar groups. Hydrophobic interaction sites on proteins are therefore readily predicted based on surface polarity. Yet, in the bromodomain-containing protein 4 (BRD4), a well-known hydrophobic hot spot is paradoxically lined by a network of water molecules. Here we combine binding assays, structural data, molecular dynamics, and free-energy calculations to resolve this apparent contradiction. We show that the water network functions as a hydrophobic recognition motif that cannot accommodate polar groups without disruption. Instead, as the protein pre-organizes the water network, apolar groups can bind with minimal entropic cost. In turn, they reinforce the surrounding hydrogen-bond network, limiting the mobility of the entire protein–water assembly. With this perspective, we identify water networks potentially functioning as hydrophobic motifs in other pharmacological targets, revealing a general but overlooked recognition element with broad implications in drug discovery and protein design.	Nov 2025
I04-1-Macromolecular Crystallography (fixed wavelength)	Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors Xiaomin Ni , R. Blake Richardson , Andre Schutzer Godoy , Matteo P. Ferla , Caroline Kikawa , Jenke Scheen , William W. Hannon , Eda Capkin , Noa Lahav , Blake H. Balcomb , Peter G. Marples , Michael Fairhead , Siyi Wang , Eleanor P. Williams , Charles W. E. Tomlinson , Jasmin C. Aschenbrenner , Ryan Lithgo , Max Winokan , Charline Giroud , Isabela Dolci , Rafaela Sachetto Fernandes , Glaucius Oliva , Anu V. Chandran , Mary-Ann Xavier , Martin A. Walsh , Warren Thompson , Jesse D. Bloom , Nathaniel T. Kenton , Alpha A. Lee , Annette Von Delft , Haim Barr , Karla Kirkegaard , Lizbe Koekemoer , Daren Fearon , Matthew J. Evans , Frank Von Delft Nature Communications 16 DOI: 10.1038/s41467-025-63602-z Diamond Proposal Number(s): [32627] Open Access Show Abstract ▼ Abstract: The Zika viral protease NS2B-NS3 is essential for the cleavage of viral polyprotein precursor into individual structural and non-structural (NS) proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 46 fragments with diverse scaffolds are identified to bind in the active site of the protease, with another 6 fragments observed in a potential allosteric site. To identify binding sites that are intolerant to mutation and thus suppress the outgrowth of viruses resistant to inhibitors developed from bound fragments, we perform deep mutational scanning of the NS2B-NS3 protease. Merging fragment hits yields an extensive set of ‘mergers’, defined as synthetically accessible compounds that recapitulate constellations of observed fragment-protein interactions. In addition, the highly sociable fragment hits enable rapid exploration of chemical space via algorithmic calculation and thus yield diverse possible starting points. In this work, we maximally explore the binding opportunities to NS2B-NS3 protease, facilitating its resistance-resilient antiviral development.	Oct 2025
I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	Gluebodies offer a route to improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive close contacts Mingda Ye , Mpho Makola , Mark W. Richards , Joseph A. Newman , Michael Fairhead , Selena G. Burgess , Zhihuang Wu , Elizabeth Maclean , Nathan D. Wright , Lizbe Koekemoer , Andrew Thompson , Gustavo Arruda Bezerra , Gangshun Yi , Huanyu Li , Victor Rangel , Dimitrios Mamalis , Hazel Aitkenhead , Benjamin G. Davis , Robert J. C. Gilbert , Katharina L. Duerr , Richard Bayliss , Opher Gileadi , Frank Von Delft Acs Central Science DOI: 10.1021/acscentsci.5c00937 Diamond Proposal Number(s): [26998] Open Access Show Abstract ▼ Abstract: Design of modular, transferable protein assemblies has broad applicability and in structural biology could help with the ever-troublesome crystallization bottleneck, including finding robustly behaved protein crystals for rapidly characterizing ligands or drug candidates or generating multiple polymorphs to illuminate diverse conformations. Nanobodies as crystallization chaperones are well-established but still unreliable, as we show here. Instead, we show an exemplar of how robust crystallization behavior can be engineered by exploring many combinations (>200) of nanobody surface mutations over several iterations. Critically, what needed testing was crystallization and diffraction quality, since target–nanobody binding affinity is decoupled from crystallizability enhancement. Our study yielded multiple polymorphs, all mediated by the same interface, with dramatically improved resolution and diffraction reliability for some mutants; we thus name them ‘Gluebodies’ (Gbs). We further demonstrate that these Gb mutations do transfer to some other targets, both for achieving robust crystallization in alternative packing forms and for establishing the ability to crystallize a key early stage readout. Since the Gb interface is evidently a favored interaction, it may be broadly applicable for modular assembly; more specifically, this work suggests that Gbs should be routinely attempted for crystallization whenever nanobodies are available.	Oct 2025
I04-1-Macromolecular Crystallography (fixed wavelength)	Crystallographic fragment screening of the Dengue virus polymerase reveals multiple binding sites for the development of non-nucleoside antiflavivirals Manisha Saini , Jasmin C. Aschenbrenner , Francesc Xavier Ruiz , Ashima Chopra , Anu V. Chandran , Peter G. Marples , Blake H. Balcomb , Daren Fearon , Frank Von Delft , Eddy Arnold Journal Of Medicinal Chemistry 276 DOI: 10.1021/acs.jmedchem.5c01014 Diamond Proposal Number(s): [32633] Open Access Show Abstract ▼ Abstract: Dengue viruses (DENVs) infect approximately 400 million people each year, and currently, there are no effective therapeutics available. To explore potential starting points for antiviral drug development, we conducted a large-scale crystallographic fragment screen targeting the RNA-dependent RNA polymerase (RdRp) domain of the nonstructural protein 5 (NS5) from DENV serotype 2. Our screening, which involved 1108 fragments, identified 60 hit compounds across various known binding sites, including the active site, N pocket, and RNA tunnel. Additionally, we discovered a novel binding site and a fragment-binding hot spot in thumb site II. These structural findings open amenable avenues for developing non-nucleoside inhibitors and offer valuable insights for future structure-based drug design aimed at DENV and other flaviviral RdRps.	Sep 2025
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Crystal structure of fatty acid thioesterase A bound by 129 fragments provides diverse development opportunities Ekaterina Kot , Matteo P. Ferla , Patricia H. Hollinshead , Charles W. E. Tomlinson , Daren Fearon , Jasmin C. Aschenbrenner , Lizbe Koekemoer , Max Winokan , Michael Fairhead , Xiaomin Ni , Rod Chalk , Katherine S. England , Laura Ortega Varga , Mark Greer Montgomery , Nicholas P. Mulholland , Frank Von Delft Pest Management Science 148 DOI: 10.1002/ps.70199 Diamond Proposal Number(s): [28172, 34598, 30602, 36049] Open Access Show Abstract ▼ Abstract: BACKGROUND: In order to alleviate the growing issue of herbicide resistance, diversification of the herbicide portfolio is necessary. A promising yet underutilized mode-of-action is the inhibition of fatty acid thioesterases (FATs), which terminate de novo fatty acid (FA) biosynthesis by releasing FAs from acyl carrier protein (ACP) cofactors. These enzymes impact plant growth and sterility by determining the amount and length of FAs present. In this study we report a crystallographic fragment screening approach for the identification of novel chemical matter targeting FATs. RESULTS: We have solved the crystal structure of Arabidopsis thaliana FatA to 1.5 Å and conducted a crystallographic fragment screen which identified 129 unique fragments bound in 141 different poses. Ten fragments demonstrated on-scale potency, two of these exploiting different interactions to known herbicides. Elaboration of one of the fragments resulted in an improvement of affinity from ~20 μm to ~90 nm KD. Finally, superposition of our crystal structures revealed that some fragments exploit large conformational changes in the substrate binding site. CONCLUSION: We have fully enabled FatA as a target for rapid, rational hit-to-lead development, with robust structural, biophysical and biochemical assays. We provide a set of fragment hits which represent diverse, novel scaffolds that both recapitulate interactions made by current herbicides, and also target novel regions within the active and dimer sites. Our fragments can be readily merged and allow for effective catalogue-based structure–activity relationship (SAR) exploration. Together these data will accelerate the development of novel, alternative herbicides to combat herbicide resistance.	Sep 2025
Krios I-Titan Krios I at Diamond	Covalently constrained 'Di-Gembodies' enable parallel structure solutions by cryo-EM Gangshun Yi , Dimitrios Mamalis , Mingda Ye , Loic Carrique , Michael Fairhead , Huanyu Li , Katharina L. Duerr , Peijun Zhang , David B. Sauer , Frank Von Delft , Benjamin G. Davis , Robert J. C. Gilbert Nature Chemical Biology 52 DOI: 10.1038/s41589-025-01972-7 Diamond Proposal Number(s): [20223, 21004] Open Access Show Abstract ▼ Abstract: Whilst cryo-electron microscopy(cryo-EM) has become a routine methodology in structural biology, obtaining high-resolution cryo-EM structures of small proteins (<100 kDa) and increasing overall throughput remain challenging. One approach to augment protein size and improve particle alignment involves the use of binding proteins or protein-based scaffolds. However, a given imaging scaffold or linking module may prove inadequate for structure solution and availability of such scaffolds remains limited. Here, we describe a strategy that exploits covalent dimerization of nanobodies to trap an engineered, predisposed nanobody-to-nanobody interface, giving Di-Gembodies as modular constructs created in homomeric and heteromeric forms. By exploiting side-chain-to-side-chain assembly, they can simultaneously display two copies of the same or two distinct proteins through a subunit interface that provides sufficient constraint required for cryo-EM structure determination. We validate this method with multiple soluble and membrane structural targets, down to 14 kDa, demonstrating a flexible and scalable platform for expanded protein structure determination.	Aug 2025
I04-1-Macromolecular Crystallography (fixed wavelength)	Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain Yeojin Kim , Aleksandar Lučić , Christopher Lenz , Frederic Farges , Martin P. Schwalm , Krishna Saxena , Thomas Hanke , Peter G. Marples , Jasmin C. Aschenbrenner , Daren Fearon , Frank Von Delft , Andreas Kramer , Stefan Knapp Communications Chemistry 8 DOI: 10.1038/s42004-025-01574-3 Diamond Proposal Number(s): [29658] Open Access Show Abstract ▼ Abstract: Tripartite motif-containing protein 21 (TRIM21), and particularly its PRY-SPRY protein interaction domain, plays a critical role in the immune response by recognizing intracellular antibodies targeting them for degradation. In this study, we performed a crystallographic fragment screening (CFS) campaign to identify potential small molecule binders targeting the PRY-SPRY domain of TRIM21. Our screen identified a total of 109 fragments binding to TRIM21 that were distributed across five distinct binding sites. These fragments have been designed to facilitate straightforward follow-up chemistry, making them ideal starting points for further chemical optimization. A subsequent fragment merging approach demonstrated improved activity. To enable functional validation of compounds with full length human TRIM21, we established a NanoBRET assay suitable for measuring target engagement to the main Fc binding site in life cells. The high-resolution structural data and observed binding modes across the different sites highlight the versatility of the PRY-SPRY domain as a target for small-molecule intervention. The presented data provide a solid foundation for structure-guided ligand design, enabling the rational design of more potent and selective compounds, with the goal to develop bivalent molecules such as Proteolysis Targeting Chimeras (PROTACs).	Jun 2025

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