Cross-linked DNA with carbazole pseudo-nucleoside enables potent inhibition of the cancer DNA- and RNA-mutating enzyme APOBEC3A

The human antiviral enzyme APOBEC3A has mutagenic activity in many human cancers, where it is used to fuel tumour evolution. Its single-stranded DNA and RNA C-to-U editing activities contribute to undesirable mutagenic outcomes in cancers. Inhibitors of APOBEC3A may therefore block mutagenesis and prevent tumour evolution and thus reduce detrimental outcomes such as drug resistance and metastasis. Here we demonstrate that use of a carbazole pseudo-nucleoside as a part of a covalent cross-link between distant nucleotides in DNA leads to a faster deaminating substrate and upon changing of dC to 2'-deoxy-5-fluorozebularine to a more potent inhibitor of APOBEC3A (Ki = 29 ± 5 nM) in comparison with a DNA hairpin and previously described cross-linked DNAs. Truncation of the DNA sequence led to the first 4-mer cross-linked DNA inhibitor of APOBEC3A with nanomolar potency that is also stable against digestion by a phosphodiesterase. This provides a platform for a rational design of competitive inhibitors of APOBEC3 with properties of small-molecule drugs.