Ontogeny-based immunogens for the induction of V2-directed HIV broadly neutralizing antibodies

Abstract

The development of a preventative HIV vaccine able to elicit broadly neutralizing antibodies (bNAbs) remains a major challenge. Antibodies that recognize the V2 region at the apex of the HIV envelope trimer are among the most common bNAb specificities during chronic infection and many exhibit remarkable breadth and potency. Understanding the developmental pathway of these antibodies has provided insights into their precursors, and the viral strains that engage them, as well as defined how such antibodies mature to acquire breadth. V2-apex bNAbs are derived from rare precursors with long anionic CDR H3s that are often deleted in the B cell repertoire. However, longitudinal studies suggest that once engaged, these precursors contain many of the structural elements required for neutralization, and can rapidly acquire breadth through moderate levels of somatic hypermutation in response to emerging viral variants. These commonalities in the precursors and mechanism of neutralization have enabled the identification of viral strains that show enhanced reactivity for V2 precursors from multiple donors, and may form the basis of germline targeting approaches. In parallel, new structural insights into the HIV trimer, the target of these quaternary antibodies, has created invaluable new opportunities for ontogeny-based immunogens designed to select for rare V2-bNAb precursors, and drive them toward breadth.

Keywords: HIV; V2-apex; broadly neutralizing antibodies; long CDR H3; ontogeny; trimeric immunogens.

Figure 1

Global alignment and trimeric location of V1V2 within the envelope trimer. (A) Logogram illustrating the amino acid profile of the 2015 version of the LANL premade alignment for Group M V1V2 envelope sequences. The size of each amino acid in the profile indicates prevalence of that amino acid in global sequences. The V1V2 sequence of HXB2 is placed below the profile. Beta strands and strand‐connecting loops (SCL_{A ‐B} and SCL_{C ‐D}) are illustrated by arrows and dashed lines respectively. Modified from 58 (B) Side view ribbon representation of the HIV envelope trimer, highlighting the location of the V1V2 domain at the trimer apex. The five anti‐parallel beta strands (beta‐barrel) are shown in purple, while stick and surface representations of the N156 and N160 glycans are shown in cyan and blue respectively. Key amino acid residues at position 166 and 169 are shown as spheres in green and orange respectively. The approximate position of the viral membrane is indicated. (C) Ribbon representation of the trimer showing the view from the angle of approach by V2‐apex bNAbs. PDB ID: 4TVP. N‐linked glycans were modeled using http://www.glycosciences.de/modeling/glyprot/php/main.php

Figure 2

Broadly neutralizing V1V2‐directed antibodies share common structural features. Fabs for prototypical members of each lineage are presented in cartoon representation. Unusually long CDR H3s protrude beyond the framework region (upper row). The CDR H3 regions are shown close up as cartoon with sulfated tyrosines displayed as sticks. Electrostatic charge is shown depicted on the surface to the right of each cartoon representation (second row). Antibodies are shown in the trimer context with 3D EM reconstructions for PG9 and CAP256.09, 2D EM class average for PGDM1400, and an alignment to trimer model for CH03 (row 3). Lineages from each donor show a binding stoichiometry of one fab per trimer. PGDM1400 engages as a steeper angle down the center of the threefold axis rather than off‐center as observed for other V1V2 bNAbs. Crystal structures of PG9 and CH03 highlight atomic‐level detail of antibody binding. CAP256.25 atomic interactions are modeled based on EM, MD, HDX and paratope mapping. PGT145/PGDM1400 atomic level details are unknown but data suggest binding differs from other members of this extended class (bottom row)

Figure 3

Structural advances in definition of the V1V2 epitope. (A) Crystal structures of monomeric scaffolded‐V1V2 bound by PG9 laid the foundation for the structural definition of the V1V2 domain. PG16 bound to the same scaffold with an alternate glycoform highlighted the specificity of lineage members to heterogeneity in the glycan shield. (B) CH58 and CH59, antibodies isolated from an RV144 vaccine that do not neutralize tier 2 virus, were crystallized with a V2 peptide. These structures, together with Surface Plasmon Resonance data, revealed that the C‐strand of V1V2 adopts multiple conformations on monomeric gp120, masking the broadly neutralized epitope. (C) EM of PG9 in complex with the trimeric BG505 SOSIP.664 together with high‐resolution crystal complexes suggests that the quaternary preference of PG9 is a consequence of binding the N160 glycan of the neighboring protomer. (D) The crystal structure of CH03 bound to a trimeric V1V2 scaffold confirms a strong interaction with the neighboring N160 glycan in addition to the N160 of the primary‐bound protomer. (E) Multiple crystal structures of trimeric Env (SOSIP.664) define the full quaternary epitope of V1V2, which has protective glycans at N156 and N160 and is positively charged

Figure 4

Schematic of B cell ontogeny of the V2‐apex extended class of broadly neutralizing antibodies from four donors. Long, negatively charged CDR H3s are established during immunoglobulin gene recombination, forming progenitor B cells. Unusual viral variants with weak antigen affinity select these rare precursors, which mature to acquire breadth with moderate levels of somatic hypermutation. Mature bNAbs share a common mode of recognition of the HIV‐1 envelope trimer, with many determinants of neutralization present in the unmutated common ancestor. Figure adapted from Zhou et al.90

Figure 5

Antibody maturation pathways and their implications for HIV vaccine design. (A) Schematic depicting how CAP256 viral evolution results in the engagement of the CAP256‐VRC26 UCA (light gray) and the subsequent development of two distinct mAb sublineages. The sublineage with restricted evolution contains dead‐end mAbs (dark gray), which cannot tolerate viral escape mutations. The continually evolving sublineage contains bNAbs (red) and off‐track mAbs (turquoise). Although both bNAbs and off‐track mAbs have high levels of SHM, only the former mature to recognize multiple immunotypes, and thus acquire breadth. Adapted from 69 (B) Schematic depicting a vaccine approach that seeks to recapitulate key viral events that drove neutralization breadth in the CAP256‐VRC26 lineage by the use of sequential or cocktail approaches. Adapted from 69