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April 12th, 2025
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Novartis Biomedical Research
biochemistry
biorxiv

An analysis of free energy methods to quantify and displace the KRasG12D Thr58 water

Dickson, C. J.Open in Google Scholar

The KRasG12D mutant is an attractive target in oncology and can now be drugged via the switch-II allosteric pocket. Non-covalent ligands typically bind in the presence of a conserved structural water, which interacts with Thr58 and Gly10. In this work, we use a dataset of published non-covalent KRasG12D inhibitors to evaluate free energy methods for the interaction with or displacement of this conserved water molecule. We find that the Thr58 water and a second proximal water site are predicted to be unstable relative to bulk water and that relative binding free energy methods capture suitably well the binding affinities of ligands that disturb or replace these waters.

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