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

Area of Science:

• Biochemistry
• Molecular Biology
• Cancer Research

Background:

• APOBEC3A is an enzyme that acts as an endogenous mutagen in human cancers.
• Its DNA C-to-U editing activity leads to mutations, DNA breakage, and chromosomal aberrations.
• Inhibiting APOBEC3A could offer a new anti-cancer strategy by blocking mutagenesis and tumor evolvability.

Purpose of the Study:

• To elucidate the structural basis of APOBEC3A inhibition by modified DNA hairpin structures.
• To understand the molecular basis for APOBEC3A's substrate preference for YTCD motifs.
• To evaluate the potency and cellular activity of novel APOBEC3A inhibitors.

Main Methods:

• X-ray crystallography was used to determine the structure of APOBEC3A in complex with a DNA inhibitor.
• Biochemical assays were performed to assess the inhibitory potency of synthesized compounds.
• Cell-based assays were employed to confirm the inhibition of APOBEC3A activity in human cells.

Main Results:

• The study reveals the structural mechanism of competitive inhibition of APOBEC3A by hairpin DNA containing 2'-deoxy-5-fluorozebularine.
• The structural basis for APOBEC3A's preference for YTCD motifs was elucidated.
• Nuclease-resistant phosphorothioated derivatives of the inhibitors demonstrated nanomolar potency in vitro and effectively blocked APOBEC3A activity in cells.

Conclusions:

• Novel DNA-based inhibitors targeting APOBEC3A have been developed.
• These inhibitors provide structural insights into APOBEC3A function and inhibition.
• The inhibitors show promise as research tools and potential adjuncts for next-generation anti-cancer therapies.