Differential Inhibition of APOBEC3 DNA‐Mutator Isozymes by Fluoro‐ and Non‐Fluoro‐Substituted 2′‐Deoxyzebularine Embedded in Single‐Stranded DNA

Abstract

The APOBEC3 (APOBEC3A‐H) enzyme family is part of the human innate immune system that restricts pathogens by scrambling pathogenic single‐stranded (ss) DNA by deamination of cytosines to produce uracil residues. However, APOBEC3‐mediated mutagenesis of viral and cancer DNA promotes its evolution, thus enabling disease progression and the development of drug resistance. Therefore, APOBEC3 inhibition offers a new strategy to complement existing antiviral and anticancer therapies by making such therapies effective for longer periods of time, thereby preventing the emergence of drug resistance. Here, we have synthesised 2′‐deoxynucleoside forms of several known inhibitors of cytidine deaminase (CDA), incorporated them into oligodeoxynucleotides (oligos) in place of 2′‐deoxycytidine in the preferred substrates of APOBEC3A, APOBEC3B, and APOBEC3G, and evaluated their inhibitory potential against these enzymes. An oligo containing a 5‐fluoro‐2′‐deoxyzebularine (5FdZ) motif exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable 2′‐deoxyzebularine‐containing (dZ‐containing) oligo. A similar inhibition trend was observed for wild‐type APOBEC3A. In contrast, use of the 5FdZ motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ‐containing oligo both in the case of APOBEC3GCTD and in that of full‐length wild‐type APOBEC3G.

Small-Angle X-ray Scattering Models of APOBEC3B Catalytic Domain in a Complex with a Single-Stranded DNA Inhibitor

“…Based on the position of the SEC elution profile, we conclude that peak 1 corresponds to homo-dimeric A3B CTD * (with a molecular weight of ~44 kDa, referred to as ‘A3B CTD * dimer’). This contrasts with the other A3B CTD variants we reported in previous studies [ 59 , 61 , 80 ], A3B CTD -QM-ΔL3, A3B CTD -QM-ΔL3-E255A, and A3B CTD -DM, which eluted only as monomeric species. Previous reports have suggested that A3A exists as both a monomer and a dimer in vitro [ 52 , 53 ].…”

Inhibition of base editors with anti-deaminases derived from viruses

“…Further exploration is necessary to find efficient and specific Ades in addition to those tested in this study. In addition to virus-derived Ades, it has been reported that single-stranded binding proteins, small-molecule inhibitors and chemically modified oligonucleotides can suppress the cytosine deaminase activity of APOBEC deaminases 60 – 65 . These potential antagonists of deaminases merit further exploration to develop new inhibitors of CBEs in the future.…”

Aberrantly Activated APOBEC3B Is Associated With Mutant p53-Driven Refractory/Relapsed Diffuse Large B-Cell Lymphoma

“…As APOBEC3B has been shown to be associated with mutations in genomic DNA, tumorigenesis, and drug resistance, it is a potential therapeutic target for cancer treatment. Inhibiting APOBEC3B via modified single-stranded DNA and thereby reducing the risk of genomic mutations ( 43 – 45 ) and targeting uracil DNA glycosylases to selectively inhibit tumor cells with high APOBEC3B expression ( 46 ) have been described as possible strategies. However, it is unclear whether the former can reduce the frequency of TP53 mutations in DLBCL and the latter can prevent R/R in DLBCL.…”