Abstract
Cancer-prone alleles exhibit single hotspot mutations. However, the combination of a cancer hotspot and a weak or moderate mutation (the ‘one-two punch’ hypothesis) produces same-allele double variants with a significantly different and potentially graded clinical phenotypic spectrum. Oncogenic PI3Kα variants, which are also associated with benign tumors and neurodevelopmental disorders, offer statistical support for this model. Using atomistic molecular dynamics (MD) simulations, we revealed that PI3Kα variants with single and double mutations exhibit expanded conformational profiles. Double mutations significantly shift the conformational ensembles toward the active form—a more pronounced effect than a single mutation. These double mutants facilitate nSH2 release, iSH2 shift, and A-loop protrusion in solution, promoting PIP2 substrate recruitment at the membrane. Our simulations revealed cryptic pockets within PI3Kα. These pockets are potential drug targets and may exhibit mutation-specific characteristics. A key challenge is that a single drug is often ineffective against PI3Kα variants due to their diverse conformational spectra. To address this, we propose a conformational selection strategy involving a combination of allosteric drugs for variants with graded conformational spectra, particularly those with strong double mutations; we identified such potentially targetable cryptic pockets in double mutants conformers.
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Data availability
Representative structures of PI3Kα variants in solution and their starting points in the membrane, along with PDB trajectories, are available in the GitHub repository: https://github.com/hbj-md/PI3K_variants. The repository also contains the CHARMM topology and parameter of PIP2 for the standard MD simulations performed in this study.
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Acknowledgements
This Research was supported by the Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Intramural Research Program project number ZIA BC 010441 and federal funds from the National Cancer Institute, National Institutes of Health, under contract HHSN261201500003I. The contributions of the NIH authors were made as part of their official duties as NIH federal employees, are in compliance with agency policy requirements, and are considered Works of the United States Government. However, the findings and conclusions presented in this paper are those of the authors and do not necessarily reflect the views of the NIH or the U.S. Department of Health and Human Services. All simulations had been performed using the high-performance computational facilities of the Biowulf PC/Linux cluster at the National Institutes of Health, Bethesda, MD (https://hpc.nih.gov/).
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H.J. and M.Z. built models and ran/analyzed molecular dynamics simulations. B.R.Y. collected genomic data. H.J. wrote the initial draft, and B.R.Y., M.Z., Y.L., and R.N. edited the manuscript. R.N. supervised the project.
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Jang, H., Yavuz, B.R., Zhang, M. et al. Oncogenic PI3Kα variants reveal graded conformational spectrum with mutation-specific cryptic pockets. Commun Chem (2026). https://doi.org/10.1038/s42004-026-01906-x
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DOI: https://doi.org/10.1038/s42004-026-01906-x
