Structure-function analysis of PI3K signalling cascade base editing screens in cancer cells
- 1Wellcome Sanger Institute
Abstract
Knowledge of protein structure and function underpins rational drug discovery, yet many targets lack known selectively druggable sites. Furthermore, the identification of secondary druggable sites offers a strategy to overcome drug resistance. Fragment-based drug discovery (FBDD) can identify new ligandable binding pockets, though how to triage those with the ability to exert biologically relevant effects can be unclear. Systematic approaches to identify novel functionally-important protein sites for therapeutic intervention, such as allosteric pockets or protein-protein interaction (PPI) interfaces, has the potential to accelerate drug discovery, particularly when combined with structure-based hit-finding modalities. The phosphoinositide-3 kinase (PI3K) signalling pathway is frequently altered in human cancer and resistance to approved inhibitors is an ongoing challenge. Here, we performed large-scale CRISPR base editing mutagenesis screens across 30 PI3K pathway proteins in three disease-relevant cancer cell models to systematically map functional residues. Integration of base editing data with structural information identified residues corresponding to known catalytic sites, fragment-binding pockets and PPI interfaces, providing validation for the approach. Additionally, we identified putative allosteric pockets near regions of undefined function. Together, these findings establish high-throughput base editing mutagenesis combined with structural analysis as a scalable strategy to delineate structure-function relationships and inform drug development.
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BibTeX
@misc{mccarten2026structurefunction,
title = {{Structure-function analysis of PI3K signalling cascade base editing screens in cancer cells}},
author = {K. Mccarten and B. Abreu and B. Baillif and L. Koob and J. S. Ahn and C. Dincer and J. Esselborn and E. Karakoc and R. F. Ludlow and J. Lyons and G. Picco and M. Sharma and M. L. Verdonk and M. Wade and S. Walker and A. Watterson and M. A. Coelho and T. G. Davies and M. J. Garnett},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.08.748517},
url = {https://www.biorxiv.org/content/10.64898/2026.09.08.748517v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Structure-function analysis of PI3K signalling cascade base editing screens in cancer cells
AU - K. Mccarten
AU - B. Abreu
AU - B. Baillif
AU - L. Koob
AU - J. S. Ahn
AU - C. Dincer
AU - J. Esselborn
AU - E. Karakoc
AU - R. F. Ludlow
AU - J. Lyons
AU - G. Picco
AU - M. Sharma
AU - M. L. Verdonk
AU - M. Wade
AU - S. Walker
AU - A. Watterson
AU - M. A. Coelho
AU - T. G. Davies
AU - M. J. Garnett
PY - 2026
DA - 2026/09/08
PB - bioRxiv
DO - 10.64898/2026.09.08.748517
UR - https://www.biorxiv.org/content/10.64898/2026.09.08.748517v1
AB - Knowledge of protein structure and function underpins rational drug discovery, yet many targets lack known selectively druggable sites. Furthermore, the identification of secondary druggable sites offers a strategy to overcome drug resistance. Fragment-based drug discovery (FBDD) can identify new ligandable binding pockets, though how to triage those with the ability to exert biologically relevant effects can be unclear. Systematic approaches to identify novel functionally-important protein sites for therapeutic intervention, such as allosteric pockets or protein-protein interaction (PPI) interfaces, has the potential to accelerate drug discovery, particularly when combined with structure-based hit-finding modalities. The phosphoinositide-3 kinase (PI3K) signalling pathway is frequently altered in human cancer and resistance to approved inhibitors is an ongoing challenge. Here, we performed large-scale CRISPR base editing mutagenesis screens across 30 PI3K pathway proteins in three disease-relevant cancer cell models to systematically map functional residues. Integration of base editing data with structural information identified residues corresponding to known catalytic sites, fragment-binding pockets and PPI interfaces, providing validation for the approach. Additionally, we identified putative allosteric pockets near regions of undefined function. Together, these findings establish high-throughput base editing mutagenesis combined with structural analysis as a scalable strategy to delineate structure-function relationships and inform drug development.
ER -