Combining deep mutational scanning and Next-Generation Protein Sequencing to harness dominant protein variants to develop DNA repair inhibitors

AACR 2026 Poster – The most clinically effective DNA repair enzyme inhibitors convert the protein target itself into a therapeutic agent. Topoisomerase poisons block the completion of the topoisomerase reaction resulting in a genotoxic DNA-protein adduct. Similar mechanisms underlie clinically relevant PARP inhibitors and other emerging therapeutics targeting DNA Damage Response proteins.

Which repair proteins can be converted into gain-of-function therapeutic agents?

How can we elicit this gain-of-function phenotype with a therapeutic?

We developed an approach, Mutational Target Mapping (MTM), that uses deep mutational scanning to identify dominant missense variants that define structure-function relationships in drug targets.

Dominant missense protein variants can model the behavior of a potential drug to discover and validate mechanisms of action and define genetic dependencies.

Combining this approach with benchtop protein sequencing on the Quantum-Si Platinum® instrument, we can identify, track, and characterize the phenotypic effects of dominant missense variants in cells and biochemical assays.

We applied this approach to several therapeutic targets discovering key residues in orthosteric and allosteric sites that can be mutated to elicit a dominant phenotype.