Disruption of protein–protein interaction hotspots in the C-terminal domain of MLH1 confers mismatch repair deficiency

MutLα, a heterodimer of MLH1 and PMS2, plays a key role in DNA mismatch repair (MMR), which maintains genomic stability by correcting replication errors. Loss of MLH1 function causes MMR deficiency (MMRd), leading to elevated mutation rates and increased cancer susceptibility. However, MMRd can offer a therapeutic advantage, as high tumour mutational burden enhances the efficacy of immune checkpoint inhibition. MMR also drives somatic expansion of CAG repeats linked to Huntington's disease (HD) pathogenesis. The C-terminal domain (CTD) of MLH1 contains at least two distinct protein-protein interaction (PPI) sites. The S1 site supports heterodimerization with the PMS2 endonuclease, whereas the S2 site interacts with MIP-boxes present in MMR-associated factors (EXO1, MSH3) and in the DNA repair nuclease FAN1. Here, using MLH1-S2 mutant cell models and synthetic FAN1-derived peptides containing two adjacent MLH1-binding motifs (MIP and MIM), we demonstrate that selective disruption of MLH1 PPIs impairs MMR <i>in vitro</i>. We further reveal that the peptide is able to inhibit the latent endonuclease activity of recombinant MutLα, possibly via competing with a putative MIM within PMS2. Our findings define key PPI interfaces within the MLH1(CTD) that govern MMR activity and may offer novel therapeutic opportunities to exploit MMRd in cancer and HD.