Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A

• Published in: Nature communications Vol. 14; no. 1; pp. 6382 - 13
• Main Authors: Harjes, Stefan, Kurup, Harikrishnan M., Rieffer, Amanda E., Bayarjargal, Maitsetseg, Filitcheva, Jana, Su, Yongdong, Hale, Tracy K., Filichev, Vyacheslav V., Harjes, Elena, Harris, Reuben S., Jameson, Geoffrey B.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11-10-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 14; 14/19; 14/35; 140/131; 631/45/147; 631/45/173; 631/535/1266; 631/67; 82/80; 82/83; Anticancer properties; Antitumor agents; Blocking; Cancer therapies; Chromosome aberrations; Combinatorial analysis; Cytidine Deaminase - chemistry; Cytidine Deaminase - genetics; Deoxyribonucleic acid; DNA; DNA damage; DNA probes; Drug resistance; Enzymes; Humanities and Social Sciences; Humans; Inhibitors; Metastases; multidisciplinary; Mutagenesis; Neoplasms - drug therapy; Neoplasms - genetics; Neoplasms - pathology; Nuclease; Nucleotides; Proteins - chemistry; Science; Science (multidisciplinary); Single-stranded DNA; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-42174-w

The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2′-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A’s preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.
APOBEC3A mutates its host DNA in human cancers to evolve drug resistance. Modified-DNA inhibitors suppress this mutagenic activity in cells, suggesting use as conjuvants in anti-cancer therapies. Here the authors reveal structural insights into how these inhibitors bind APOBEC3A.