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

• Type of Material: Article
• Authors: Stefan Harjes, Massey University; Harikrishnan M. Kurup, Massey University; Amanda E. Rieffer, University of Minnesota-Twin Cities; Maitsetseg Mayarjargal, Massey University; Jana Filitcheva, Massey University; Yongdong Su, Emory University; Tray K. Hale, Massey University; Vyacheslav Filichev, Massey University; Elena Harjes, Massey University; Reuben S. Harris, University of Texas, San Antonio; Geoffrey B. Jameson, Massey University
• Language: English
• Date: 2023-10-11
• Publisher: Springer Nature
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2023
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): https://doi.org/10.1038/s41467-023-42174-w
• Title of Journal or Parent Work: Nature Communications
• Volume: 14
• Start Page: 6382
• Grant/Funding Information: Financial support of the Health Research Council of New Zealand in partnership with Breast Cancer Cure, and Breast Cancer Foundation NZ (grant 20/1355) and Kiwi Innovation Network with Massey Ventures Limited (grant MU002391), as well as the support of the School of Natural Sciences, Massey University is gratefully acknowledged. Access to the MX2 Beam Line of the Australian Synchrotron was facilitated by the NZ Synchrotron Group Ltd financially supported by the Ministry of Business Innovation and Enterprise (MBIE) and a consortium of New Zealand universities, including Massey University. Cancer studies in the Harris lab are supported by NCI P01-CA234228 and a Recruitment of Established Investigators Award from the Cancer Prevention and Research Institute of Texas (CPRIT RR220053).
• Keywords: Enzyme mechanisms; Cancer; X-ray crystallography; DNA
• Research Categories: Biology, Molecular; Health Sciences, Oncology

Abstract

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.