Structure and inhibition of the human SNM1a and SNM1b/Apollo DNA repair exonucleases

The human SNM1A and SNM1B enzymes are 5'-3' exonucleases implicated in DNA interstrand crosslink (ICL) repair. Cells deficient in SNM1A or SNM1B show increased sensitivity to clinically important crosslinking drugs such as mitomycin C (MMC). Moreover, purified SNM1A and SNM1B have been shown to resect cross-linked DNA past the site of cross-links. Consequently, inhibitors of these enzymes may be useful in potentiating the effects of ICL agents in cancer chemotherapy. Since key residues at the active sites of SNM1A and SNM1B are conserved with those on bacterial metallo-β-lactamases (MBLs), compounds that inhibit bacterial MBLs were included in a screen for inhibitors of SNM1A and SNM1B. A real-time fluorescence assay was developed for a high-throughput screen for inhibitors of SNM1A/B. It produced 22 hit compounds with 4 different scaffolds. Since these compounds are either the natural substrates of MBLs or mimics of these substrates, it is not surprising that most of these compounds are reversible competitive inhibitors of hSNM1A and SNM1B. Crystal structures of SNM1A and SNM1B were solved and they show that, while their active sites are near-identical, the charges on the surface of these proteins were very different. Biochemical studies of the putative DNA binding groove identified amino acid residues that could be involved in DNA binding. Therefore, this current study helps elucidate the structural properties of SNM1A and SNM1B, and show that inhibitors to these enzymes can be developed and potentially sensitise cancer cells to ICL-inducing chemotherapeutics.