Interactions of host APOBEC3 restriction factors with HIV-1 in vivo: implications for therapeutics

Abstract

Restriction factors are natural cellular proteins that defend individual cells from viral infection. These factors include the APOBEC3 family of DNA cytidine deaminases, which restrict the infectivity of HIV-1 by hypermutating viral cDNA and inhibiting reverse transcription and integration. HIV-1 thwarts this restriction activity through its accessory protein virion infectivity factor (Vif), which uses multiple mechanisms to prevent APOBEC3 proteins such as APOBEC3G and APOBEC3F from entering viral particles. Here, we review the basic biology of the interactions between human APOBEC3 proteins and HIV-1 Vif. We also summarise, for the first time, current clinical data on the in vivo effects of APOBEC3 proteins, and survey strategies and progress towards developing therapeutics aimed at the APOBEC3-Vif axis.

Fig. 1. APOBEC3 and Vif function

Viral gene expression proceeds normally. During assembly, however, A3G present in a nonpermissive producer cell (white circles) is encapsidated along with normal virion components. To prevent encapsidation, Vif (yellow circle) expressed from a Vif-proficient virus links A3G to an E3 ligase complex (gray circle), which results in the ubiquitination of A3G and its eventual degradation in the proteasome (26S gray capped cylinder). Alternatively, Vif may directly inhibit encapsidation, lower A3G expression and/or inhibit A3G catalytic activity (not shown). Virions with encapsidated A3G bud from a producer cell and enter a target cell normally. Reverse transcription, however, is blocked by the presence of A3G, either by the direct inhibition of cDNA synthesis or the degradation of uridine-containing cDNA. Uridine-containing cDNA templates A on the viral plus-strand, resulting in G-to-A hypermutation. A direct A3G-mediated block to integration has also been proposed (not shown).

Fig. 2. Methods of enhancing APOBEC3-mediated restriction

Methods of enhancing restriction by APOBEC3 proteins are united in the common goal of delivering more APOBEC3 proteins to the viral core. Strategies, as discussed in the main text, include i) Indirectly increasing APOBEC3 encapsidation by protecting APOBEC3 proteins from degradation. This may occur by chemically shielding APOBEC3 proteins. Alternatively, it may be possible to target inhibitors to a Vif surface that interacts with APOBEC3 proteins or with cellular proteins involved Vif-mediated degradation. Finally, a degradation-resistant variant of an APOBEC3 protein such as A3G D128K may be employed. ii) Directly increasing the encapsidation of APOBEC3 proteins. This may occur by increasing the expression of APOBEC3 proteins, particularly through interferon (orange octagon) upregulation. Alternatively, fusion to a privileged molecule with core access (white circle labeled “Help”) may shuttle APOBEC3 proteins to the viral core with great enough efficiency to overcome Vif-mediated degradation. All methods will theoretically result in greater APOBEC3 encapsidation (white circles) and restriction of HIV-1, even in the presence of Vif.

Fig. 3. Important domains in Vif and A3G

While many papers have identified residues critical to Vif function, only putative continuous interaction domains in Vif (A) and A3G (B) are depicted here for the sake of clarity. Exceptions are made for two important lysines in Vif, K22 and K26, as well as the C-terminal zinc-binding domain of Vif. Vif and A3G are internally to scale, but Vif is depicted at twice its actual size relative to A3G. HIV-1 Vif residues shown are those found in HIV IIIB (EU541617.1). A3G corresponds to reference sequence NP_068594. Note that K26 and ²³SLV²⁵ of Vif are required for neutralization of A3G and A3F, but these residues may not mediate direct interaction with A3F or A3G. Similarly, one group finds that while A3G D128 is important in permitting the degradation of A3G, it does not mediate direct binding to Vif. See main text for references and discussion.

Fig. 4. Important domains of A3G on a full-length model structure

Important domains of A3G identified by genetic analysis are highlighted on a full-length model structure of A3G (Ref. 134) with coloration carried out in Pymol. See main text for references and discussion. Sidechains are shown for key regions, and the right panel represents a rotation of 180 degrees about the y-axis. Red Spheres = Active site zinc. Green Sidechains = ¹²⁴YYFW¹²⁷, multimerization/encapsidation determinant (overlaps 126–127 start of Vif binding region ¹²⁶FWDPDYQ¹³²); Red Sidechain = D¹²⁸, a key residue for Vif sensitivity; Blue Sidechains = ¹²⁹PDYQ¹³², the remainder of the putative Vif binding site. Yellow Sidechains = Residues H⁶⁵ & E⁶⁷ and H²⁵⁷ & E²⁵⁹, the HxE of the pseudocatalytic and catalytic N- and C-terminal domains, respectively. Orange Sidechains = ⁹⁶PC⁹⁷ & C¹⁰⁰ and ²⁸⁷PC²⁸⁸ & C²⁹¹, the PCxxC of the active and pseudoactive N- and C-terminal domains, respectively.