APOBEC3 (A3) enzymes are DNA cytosine-to-uracil deaminases that target foreign DNA for destruction as part of innate immunity. A3 enzymes also play integral roles in multiple human diseases. APOBEC3G (A3G) sub-lethally deaminates HIV-1 cDNA during replication, providing a source of genomic mutation that contributes to viral evolution, adaptation, and drug resistance. APOBEC3B (A3B) is overexpressed in at least 6 human cancers, resulting in high levels of C-to-U genomic mutations that drive tumor evolution, heterogeneity, and drug resistance. Therefore, small molecule inhibitors of A3G and A3B may ultimately yield novel therapeutics for applications in infectious disease and cancer. The long-term goal of this project is to develop small molecule inhibitors of A3G and A3B as clinical drugs. The objective in this application is to develop potent chemical probes of A3G and A3B to enable mechanistic studies of both enzymes. High-throughput screening, chemical synthesis, and biochemical testing have been previously employed to identify covalent inhibitors of A3G. The central hypotheses of this application are: 1) Recently published A3G covalent inhibitors have identified a region of the enzyme that is susceptible to small molecule modulation, which can be exploited in probe design, and 2) Recently identified and unpublished non-covalent inhibitors of A3G and A3B can be optimized by computation-based methods to yield potent and selective chemical probes. The rationale for developing A3G and A3B small molecule probes is to enable mechanistic studies of their roles in HIV-1 restriction and cancer evolution, respectively. Furthermore, small molecule A3G and A3B probes will serve as launch points for future drug discovery efforts.
The specific aims of this application are: 1) To develop bifunctiona and reversible covalent A3G inhibitors and 2) To develop non-covalent inhibitors of A3G and A3B. In the first aim, existing small molecules that covalently target A3G will be structurally modified to also engage the zinc atom of A3G, yielding bifunctional inhibitors that are predicted to be more potent than existing compounds. Additionally, existing covalent inhibitors of A3G will be modified to incorporate chemical moieties that can reversibly engage A3G Cys321, yielding molecules that are predicted to be less cross-reactive than the established covalent inhibitors, and therefore, will inhibit A3G in cell lysate and cells. In the second aim, computational modeling based on unpublished non-covalent A3G and A3B inhibitors will be used to guide the development of more selective and more potent non-covalent inhibitors of A3G and A3B. This approach is innovative because the small molecule inhibitors of A3G and A3B described in this proposal represent the first- in-class molecules known to target these enzymes. This work is also innovative due to the unique cross- disciplinary team of scientists, all with expertise in mutation research, that are focused on delivering novel chemical probes of A3 deaminases. The proposed research is significant because it expected to deliver fundamental chemical knowledge of A3 inhibition that will serve as the underpinning for future drugs.

Public Health Relevance

The proposed research will develop small molecule probes of APOBEC3G and APOBEC3B, which are cellular enzymes that deaminate DNA cytosines. APOBEC3G contributes to the high mutation rate of HIV and APOBEC3B is upregulated in human cancers, providing a source of cancer genome mutation. Developed chemical probes of APOBEC3G and APOBEC3B will contribute to the betterment of human health by enabling the characterization of inhibitor binding sites on both enzymes and serving as foundations for future drug development.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Barski, Oleg
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University of Minnesota Twin Cities
Schools of Pharmacy
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Olson, Margaret E; Harris, Reuben S; Harki, Daniel A (2018) APOBEC Enzymes as Targets for Virus and Cancer Therapy. Cell Chem Biol 25:36-49
Passow, Kellan T; Harki, Daniel A (2018) 4-Cyanoindole-2'-deoxyribonucleoside (4CIN): A Universal Fluorescent Nucleoside Analogue. Org Lett 20:4310-4313
Jackson, Paul A; Widen, John C; Harki, Daniel A et al. (2017) Covalent Modifiers: A Chemical Perspective on the Reactivity of ?,?-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions. J Med Chem 60:839-885
Richards, Christopher M; Li, Ming; Perkins, Angela L et al. (2017) Reassessing APOBEC3G Inhibition by HIV-1 Vif-Derived Peptides. J Mol Biol 429:88-96
Shi, Ke; Carpenter, Michael A; Banerjee, Surajit et al. (2017) Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol 24:131-139
Breunig, Stesphanie L; Olson, Margaret E; Harki, Daniel A (2016) Rapid, Microwave Accelerated Synthesis of [1,2,4]Triazolo[3,4-b][1,3,4]oxadiazoles from 4-Acylamino-1,2,4-Triazoles. Tetrahedron Lett 57:4056-4060