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bioRxiv · 10.1101/2025.06.18.660085

Leveraging crystallographic fragment screening, algorithmic merging and digital chemistry to target NCS-1 protein-protein interactions for treatment of neurological disorders

Munoz-Reyes, D.·Fieseler, K. K.·Winokan, M.·Golding, M.·Capkin, E.·Ferla, M.·Perez-Suarez, S.·Tomlinson, C. W. E.·Marples, P. G.·Miro-Rodriguez, C.·Aguado, L.·Mansilla, A.·Fearon, D.·Thompson, W.·von Delft, F.·Sanchez-Barrena, M. J.
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Abstract

Efficient drug discovery relies on workflows that integrate structural insights with rapid and cost-effective exploration of chemical space. Here, we present a data-driven fragment-based lead discovery approach to target Neuronal Calcium Sensor 1 (NCS-1) protein-protein interactions (PPIs). This study represents a complete implementation of a single high-value design-make-test-analyze cycle that directly yields compounds with micromolar affinity with the potential to modulate NCS-1 interactions with key targets, including the G-protein chaperone Ric-8A and the dopamine D2 and cannabinoid CB1 receptors. X-ray crystallographic fragment screening (CFS) revealed diverse interaction patterns within the NCS-1 hydrophobic crevice. Algorithmically guided fragment evolution and automated synthesis enabled the rapid generation of over 250 derivatives, with biophysical validation using LC-MS and Grating-coupled interferometry. Structural analyses highlighted key pharmacophores, with selected compounds exhibiting favorable drug-like properties and potential blood-brain barrier penetration, making them promising candidates for neurodegenerative and neurodevelopmental disorders. Our results demonstrate the feasibility of accelerated hit-to-lead development at synchrotrons, demonstrating a robust, scalable platform for PPI-targeting drug discovery. The generated chemically diverse scaffolds provide a strong foundation for future therapeutic optimization.

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Munoz-Reyes, D., Fieseler, K. K., Winokan, M., Golding, M., Capkin, E., Ferla, M., Perez-Suarez, S., Tomlinson, C. W. E., Marples, P. G., Miro-Rodriguez, C., Aguado, L., Mansilla, A., Fearon, D., Thompson, W., von Delft, F., Sanchez-Barrena, M. J.. 2025-06-21. Leveraging crystallographic fragment screening, algorithmic merging and digital chemistry to target NCS-1 protein-protein interactions for treatment of neurological disorders. https://doi.org/10.1101/2025.06.18.660085

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