Comparative Magnitude of Cross-Strain Conservation of HIV Variable Loop Neutralization Epitopes

Abstract

Although the sequence variable loops of the human immunodeficiency virus' (HIV-1) surface envelope glycoprotein (gp120) can exhibit good immunogenicity, characterizing conserved (invariant) cross-strain neutralization epitopes within these loops has proven difficult. We recently developed a method to derive sensitive and specific signature motifs for the three-dimensional (3D) shapes of the HIV-1 neutralization epitopes in the third variable (V3) loop of gp120 that are recognized by human monoclonal antibodies (mAbs). We used the signature motif method to estimate the conservation of these epitopes across circulating worldwide HIV-1 strains. The epitope targeted by the anti-V3 loop neutralizing mAb 3074 is present in 87% of circulating strains, distributed nearly evenly among all subtypes. The results for other anti-V3 Abs are: 3791, present in 63% of primarily non-B subtypes; 2219, present in 56% of strains across all subtypes; 2557, present in 52% across all subtypes; 447-52D, present in 11% of primarily subtype B strains; 537-10D, present in 9% of primarily subtype B strains; and 268-D, present in 5% of primarily subtype B strains. The estimates correlate with in vitro tests of these mAbs against diverse viral panels. The mAb 3074 thus targets an epitope that is nearly completely conserved among circulating HIV-1 strains, demonstrating the presence of an invariant structure hidden in the dynamic and sequence-variable V3 loop in gp120. Since some variable loop regions are naturally immunogenic, designing immunogens to mimic their conserved epitopes may be a promising vaccine discovery approach. Our results suggest one way to quantify and compare the magnitude of the conservation.

Immunogenicity of a Prefusion HIV-1 Envelope Trimer in Complex with a Quaternary-Structure-Specific Antibody

“…3 and 4), suggesting its greater stability in the closed conformation. We also tested an expanded panel of V3 MAbs, including 2219, 2557, 2558, 3037, 1006-15D, and 3074 (24,25), targeting regions of the V3 peptide, by MSD-ECLIA (Fig. 4B) and lectin-capture ELISA (Fig.…”

Visualization of Retroviral Envelope Spikes in Complex with the V3 Loop Antibody 447-52D on Intact Viruses by Cryo-Electron Tomography

“…The V3 loop plays an important role in the function of the Env spike by serving as part of the coreceptor binding site following CD4 ligation (20,65) and provides a key target of the humoral immunity (66)(67)(68). The crystal structure of the CD4-liganded gp120 core with an intact V3 loop shows the loop protruding about 30 Å above the core and, presumably, toward the target cell (58).…”

Cross-Clade HIV-1 Neutralizing Antibodies Induced with V3-Scaffold Protein Immunogens following Priming with gp120 DNA

“…The final two V3 inserts, V3 2219 and V3 3074 , were designed by making appropriate mutations in the consensus C V3 crown in the critical residues of the "signature motifs." Signature motifs were derived previously based on the 3D shapes of epitopes in V3 that are recognized by human MAbs which are able to neutralize diverse strains of viruses from multiple clades (3,14,64). Briefly, by studying the crystal structures of MAb/epitope complexes (13,36,60,61), identifying the key V3 residues that are recognized by the MAb, and determining the stringency with which these residues are required for neutralization by that MAb, a signature motif for the epitope recognized by that MAb can be defined.…”

“…Briefly, by studying the crystal structures of MAb/epitope complexes (13,36,60,61), identifying the key V3 residues that are recognized by the MAb, and determining the stringency with which these residues are required for neutralization by that MAb, a signature motif for the epitope recognized by that MAb can be defined. For example, the signature motif for the relatively clade B-restricted anti-V3 MAb 447-52D is P 16 R 18 , where proline is required at position 16 in the V3 loop and arginine is required at position 18 (14,64). The only V3 insert that bears this motif of the five used in this study was the V3 B insert ( Table 1).…”

“…The V3-scaffold immunogens used here were rationally designed using a large body of structural data derived from crystals of V3 peptides complexed to V3-specific MAbs (13,18,36,60,61), bioinformatics analyses, and molecular modeling studies (3,14,36,64,71). This resulted in V3 epitopes which captured conserved V3 structures shared between the various viral subtypes and which were spliced into a structurally compatible region of a protein scaffold, cholera toxin B (66).…”