APOBEC Enzymes as Targets for Virus and Cancer Therapy Margaret E. Olson, Reuben S. Harris, Daniel A. Harki  Cell Chemical Biology  Volume 25, Issue 1, Pages 36-49 (January 2018) DOI: 10.1016/j.chembiol.2017.10.007 Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Structure, Organization, and Enzymatic Activity of Human A3 Enzymes (A) The seven human A3 family members are distinguished by their number of structural domains (represented as one or two arrows), the phylogenetic grouping of each domain (Z1, green; Z2, orange; Z3, blue), and subcellular localization. Rendered X-ray structures (PyMOL) depict the catalytic domains of A3B (PDB: 5CQD; Shi et al., 2015), A3F (PDB: 5HX5; Shaban et al., 2016), and A3G (PDB: 3V4K; Li et al., 2012), and the full-length structures of A3A (PDB: 5SWW; Shi et al., 2017), A3C (PDB: 3VM8; Kitamura et al., 2012), and A3H (PDB: 6B0B; Shaban et al., 2017). Structurally, each A3 domain has six α helices (red) and five β strands (yellow). The flexible and variable loops are depicted in green. The active-site coordinates a single zinc ion (gray sphere). (B) The proposed mechanism of A3-mediated ssDNA C-to-U deamination. (C) A3A-ssDNA X-ray co-crystal structure (PDB: 5SWW) shows that the DNA substrate binds in a U-shaped confirmation with the −1 base flipped out of the active site and the target DNA cytosine interacting with the catalytic zinc (Shi et al., 2017). The −1 base forms specificity-conferring H-bonding contacts with residues of A3A. Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Model for A3-Mediated HIV-1 Restriction In an infected cell, a sublethal number of A3s incorporate into budding viral particles and hitch-hike to virus naive cells. HIV-1 modulates A3 expression through Vif, which forms an E3 ubiquitin ligase complex that polyubiquitinates A3s and triggers their degradation at the 26S proteasome. The A3s restrict viral replication through both deamination-dependent mutagenesis and deamination-independent RT inhibition mechanisms. Adapted from Harris and Dudley (2015). Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 Therapeutic Strategies to Target the A3-Vif Interface (A) In a clinical infection, A3-catalyzed restriction is inhibited by Vif-mediated ubiquitylation and proteasomal degradation. Despite this inhibition, a sublethal level of A3 deamination is observed. Thus, the activities of Vif and the A3s are balanced to achieve optimum viral fitness. (B) Therapy by hypermutation: This therapeutic strategy seeks to inhibit Vif and/or block the Vif-A3 interface, thereby reinstating the restrictive capabilities of the A3s (Haché et al., 2006). Upon Vif inhibition, the relevant A3s can lethally mutate the viral genome. (C) Therapy by hypomutation: Inhibition of the A3s may deprive the virus of a needed mutation source. Inhibiting viral fitness may enable immunological or antiretroviral HIV-1 clearance (Harris, 2008). Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 Chemical Structures of Small Molecules that Function through “Therapy by Hypermutation” Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 5 Candidate Inhibitors of Vif Interaction Surfaces (A) X-ray structure of the Vif/CBF-β/CUL5/ELOB/ELOC complex (PDB: 4N9F) (Guo et al., 2014). Color scheme: Vif (magenta), CBF-β (yellow), CUL5 NTD (green), ELOC (orange), ELOB (cyan), Zn (gray). (B) Chemical structures of VEC-5, a putative Vif-ELOC PPI inhibitor, SN-1 and -2 and Baculiferin L and M, Vif-A3 PPI inhibitors. Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 6 HTS for Small Molecules that Function through “Therapy by Hypomutation” (A) Schematic of a fluorescence-based C-to-U deamination assay for high-throughput screening. Uninhibited A3-catalyzed deamination results in a high fluorescence readout, while potent A3 inhibition reads as background fluorescence. (B) Chemical structures of published A3G inhibitors. Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 7 Model Depicting the Impact of A3B-Catalyzed Mutation in Cancer (A) Mutation catalyzed by A3B can accelerate tumor cell growth, metastasis, and the development of therapeutic resistance. A3B preferentially deaminates DNA cytosines in a 5′-TCA context. The resulting uracil templates the insertion of adenine during complementary strand synthesis, and uracil base excision repair will convert the U-A base pair to T-A (a C-to-T transition mutation). (B) Schematic representation of tumor volume during an A3B knockdown study in an ER+ breast cancer xenograft model (Law et al., 2016). At 50 days, mice were injected with tumor cells expressing a shRNA control or a shRNA to knockdown endogenous A3B. At 125 days, TAM treatment was initiated to suppress growth of similarly sized tumors. However, by 300 days, most of the control (A3B-expressing) tumors had become resistant to TAM therapy, whereas the growth of most of the A3B-depleted tumors was still suppressed. This study demonstrates that A3B contributes to the development of tamoxifen resistance. Cell Chemical Biology 2018 25, 36-49DOI: (10.1016/j.chembiol.2017.10.007) Copyright © 2017 Elsevier Ltd Terms and Conditions