Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide

Abstract

Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1 fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with substitutions to negatively charged amino acids at residue positions 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV-1; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structural analysis of the naturally elicited ACS202 antibody in complex with the HIV-1 Env trimer with an alanine 517 to glutamine substitution suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence, perhaps reflecting the immunization with fusion peptide of the vaccine-elicited antibodies.

Keywords: HIV-1 vaccine; fusion peptide; naturally elicited; neutralizing antibody; vaccine elicited.

Figure 1

Diverse FP sequences are target sites for naturally elicited antibodies, as revealed by peptide-substitution analysis. (A) Structural reprentation of the HIV-1 Env trimer in complex with naturally elicited FP-targeted antibodies.The angle of approach was calculated using the trimer axis ,and the antibody axis. The antibody axis was calculated by measuring the rotation of the light chain onto the heavy chain during a superposition alignment. (B) Logo plots with peptide substitution scan data from PEPperPRINT with all atom BSA bar plots.The height of each amino acid mutation corresponds to the relative improvement over WT, with positive values improving over WT, negative values decreasing binding over WT.

Figure 2

Peptide-substitution analysis reveals vaccine-elicted antibodies targeting FP site of vulnerability are less permissive to FP variation (A) Overall structure context of vaccine elicited antibodies in complex with HIV-1 Env trimer. The structure from DFPH-a. 15 is displayed for DFPH-a.01. The angle of approach was calculated using the trimer axis, and the antibody axis. The antibody axis was calculated by measuring the rotation of the light chain onto the heavy chain during a superposition alignmnent. (B) Logo plots with peptide substitution scan data from PEPperPRINT with all atom BSA bar plots. The heightof each amino acid mutation corresponds to the relative improvement over WT, with positive values improving over WT, negative values decreasing binding over WT. DFPH-a.01 BSA values were calculated using the closely related DFPH-a.15 structure as the DFPH-a.01 structure was unavailable.

Figure 3

Quantification of FP recognation reveals naturally elicited antibodies bind significantly more diverse FP sequences than those that are vaccine-elicited (A) Top oanels: Count analysis: Number of mutation with higher PEPperPRINT intensity value than WT for positions 512-520. On the left, each point corresponds to a particular position and antibody for n=72 vaccine elicited and n=27 for naturally elicited antibodies. On the right: values are averaged across antibodies for a given position. Bottom panels: Magnitude analysis: Average PEPperPRINT intensity value for entries higher than WT for positions 512-520. Error bars correspond to 95% confidence interval. (B) The intensity values for each position are normalized and used to compute per-position entropies with base=20 to normalize. Entropies for both naturally and vaccine elicited antibodies are correlated with all atom BSA.

Figure 4

Cryo-EM structure of ACS202 in complex with BG505 Env trimer with A517E explains enhanced affinity of A517E substitution (A) Cryo-EM structure of BG505_A517E in complex with ACS202. (B) Electron density at the trimer-antibody interface,contoured at 4 σ The map was from final cryoSPARC non-uniformed refinement,sharpened, at a nominal resolution of 2.3 Å. (C) Structural alignment of BG505_A517E-ACS202 complexes. The structures were aligned by the antibody heavy chain shown. (D) Key residue pair in the BG505_ACS202 complex contributed to enhanced binding affinity.

Figure 5

Atomic level interactions from MD simulation analysis corroborate trends observed by peptide-substitution analysis (A) Diagram for in silico structural analysis pipeline of FP mutants. (B) Overall energies suggest mutations on naturally elicited antibodies improve binding whereas vaccine elicited antibodies do not tolerate those mutations as well (C) Pairwise energy analysis reveals specific interactions responsible for the binding differences observed in PEPperPRINT Numbering of residues is sequential and not in kabat format (D) MD structures of FP mutants in complex with antibodies FP residues are color coded by the energy contributions from (C), with red indicating more favorable energetic interactions and blue indicating unfavorable.