A resource-efficient structure-based workflow for fragment progression enables parallel hit discovery and validation of functionally diverse modulators of NCS-1 protein–protein interactions
8 affiliations
- 1Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Blas Cabrera”, CSIC Serrano 119 Madrid 28006 Spain
- 2Department of Statistics, University of Oxford Oxford OX1 3LB UK
- 3Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
- 4Centre for Medicines Discovery, University of Oxford Oxford OX3 7DQ UK
- 5Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0QX UK
- 6Department of Neurobiology, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y Cajal Madrid Spain
- 7Department of Systems Biology, Universidad de Alcalá Madrid Spain
- 8Department of Biochemistry, University of Johannesburg Johannesburg 2006 South Africa
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 (SARs), 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 grating-coupled interferometry and crystallography, respectively. 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.
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BibTeX
@article{munozreyes2026resourceefficient,
title = {{A resource-efficient structure-based workflow for fragment progression enables parallel hit discovery and validation of functionally diverse modulators of NCS-1 protein–protein interactions}},
author = {Daniel Muñoz-Reyes and Kate K. Fieseler and Max Winokan and Mathew Golding and Eda Capkin and Matteo Ferla and Sara Pérez-Suárez and Charlie W. E. Tomlinson and Peter G. Marples and Celia Miró-Rodríguez and Lorena Aguado and Alicia Mansilla and Daren Fearon and Warren Thompson and Frank von Delft and María José Sánchez-Barrena},
journal = {Chemical Science},
year = {2026},
month = sep,
doi = {10.1039/d6sc02031c},
url = {https://doi.org/10.1039/d6sc02031c},
note = {CC BY 3.0},
}
RIS
TY - JOUR
TI - A resource-efficient structure-based workflow for fragment progression enables parallel hit discovery and validation of functionally diverse modulators of NCS-1 protein–protein interactions
AU - Daniel Muñoz-Reyes
AU - Kate K. Fieseler
AU - Max Winokan
AU - Mathew Golding
AU - Eda Capkin
AU - Matteo Ferla
AU - Sara Pérez-Suárez
AU - Charlie W. E. Tomlinson
AU - Peter G. Marples
AU - Celia Miró-Rodríguez
AU - Lorena Aguado
AU - Alicia Mansilla
AU - Daren Fearon
AU - Warren Thompson
AU - Frank von Delft
AU - María José Sánchez-Barrena
PY - 2026
DA - 2026/09/02
JO - Chemical Science
DO - 10.1039/d6sc02031c
UR - https://doi.org/10.1039/d6sc02031c
AB - Efficient drug discovery workflows ideally generate data that directly address key translational milestones, including confirmation of target engagement and binding pose, structure–activity relationships (SARs), 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 grating-coupled interferometry and crystallography, respectively. 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.
SN - 2041-6520
SN - 2041-6539
ER -