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Fragment-based lead discovery (FBLD) is an efficient and effective method for identifying novel chemical scaffolds that have advantages in drug development. X-ray crystallography has an inherent advantage in recognizing low-affinity fragments and integrates fragment identification with complex structure determination, making it an increasingly important tool for screening fragment compounds. Here, we introduce a crystallographic fragment-screening platform developed by the biological macromolecular crystallography group at Shanghai Synchrotron Radiation Facility, named the XFBLD-Platform. This platform promotes fragment-based lead discovery through a comprehensive workflow that includes high-throughput complex crystal preparation, crystal harvesting, diffraction data collection and analysis, and fragment-affinity estimation. It integrates advanced hardware, high-performance beamline facilities and specialized experimental design and data-management software. The platform provides a rapid and practical approach for structure-based drug development.
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http://dx.doi.org/10.1107/S2059798325006801 | DOI Listing |
J Comput Chem
September 2025
Johnson & Johnson, Beerse, Belgium.
Herein we report the in silico discovery of 13 novel micromolar potent inhibitors of the SARS-CoV-2 NSP13 helicase validated in cellular antiviral and biophysical ThermoFluor assays. The compounds, discovered using a novel fragment-based pharmacophore virtual screening workflow named FragmentScout, enable the advancement of novel antiviral agents. FragmentScout uses publicly accessible structural data of the SARS-CoV-2 NSP13 helicase, which was previously generated at the Diamond LightSource by XChem high-throughput crystallographic fragment screening.
View Article and Find Full Text PDFJ Med Chem
September 2025
Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States.
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.
View Article and Find Full Text PDFStructure
August 2025
Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, UK; Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcas
Sites of protein-protein interaction (PPI) are potentially more selective binding sites for therapeutics than protein substrate-binding sites. PPIs include distinct regions frequently called "hotspots," sites of key amino acid interactions. Prospective identification of these hotspots through X-ray crystallographic screening could assist in the identification of separation of function mutants for experimental validation, enhance confidence in AI-generated multiprotein complex predictions, and accelerate development of selective chemical probes.
View Article and Find Full Text PDFEur J Med Chem
December 2025
National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People's Republic of China. Electronic address:
Pin1 is a phosphorylation-dependent peptidyl-prolyl isomerase that specifically recognizes and catalyzes the cis-trans isomerization of pSer/Thr-Pro motifs. It plays a pivotal role in cell cycle regulation, signal transduction, and tumorigenesis. Due to its overexpression in many cancer types, Pin1 has emerged as a promising target for the development of anticancer drugs.
View Article and Find Full Text PDFActa Crystallogr D Struct Biol
September 2025
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China.
Fragment-based lead discovery (FBLD) is an efficient and effective method for identifying novel chemical scaffolds that have advantages in drug development. X-ray crystallography has an inherent advantage in recognizing low-affinity fragments and integrates fragment identification with complex structure determination, making it an increasingly important tool for screening fragment compounds. Here, we introduce a crystallographic fragment-screening platform developed by the biological macromolecular crystallography group at Shanghai Synchrotron Radiation Facility, named the XFBLD-Platform.
View Article and Find Full Text PDF