HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope

Abstract

HIV-1 envelope (Env) mimetics are candidate components of prophylactic vaccines and potential therapeutics. Here we use a synthetic V3-glycopeptide ("Man₉-V3") for structural studies of an HIV Env third variable loop (V3)-glycan directed, broadly neutralizing antibody (bnAb) lineage ("DH270"), to visualize the epitope on Env and to study how affinity maturation of the lineage proceeded. Unlike many previous V3 mimetics, Man₉-V3 encompasses two key features of the V3 region recognized by V3-glycan bnAbs-the conserved GDIR motif and the N332 glycan. In our structure of an antibody fragment of a lineage member, DH270.6, in complex with the V3 glycopeptide, the conformation of the antibody-bound glycopeptide conforms closely to that of the corresponding segment in an intact HIV-1 Env trimer. An additional structure identifies roles for two critical mutations in the development of breadth. The results suggest a strategy for use of a V3 glycopeptide as a vaccine immunogen.

Fig. 1

Antibody and virus data. a DH270 clonal lineage tree. b Sequence logo of the V3 region of CH848 autologous viruses. The beginning and end of the GDIR motif are indicated. The frequency of each amino acid at each site is indicated by its height

Fig. 2

DH270.6-Env V3 loop structure. a DH270.6-Man₉-V3 crystal structure. The V3 region of the ³²⁴GDIR³²⁷ motif is labeled, and glycans are shown as green sticks. The two major anchor points are circled. b Secondary structure of Man₉-V3. Each node (.) represents a peptide backbone carbonyl or amide group; dashed lines represent hydrogen bonds; Y represents a side chain; Man₉ glycans are shown as colored forks. A schematic diagram of the Man₉GlcNAc₂ glycan with the glycan moiety nomenclature is also shown. c The antibody-³²⁴GDIR³²⁷ motif hydrogen bonds. d Contacts between the antibody and Man₉ D1 arm

Fig. 3

HIV trimer V3 region compared to V3 glycopeptide. a Superposition of the V3 glycopeptide (red) from the DH270.6-Man₉-V3 complex onto the V3 region (cyan) of the PGT128-BG505 complex (PDB ID: 5ACO). Glycans from the DH270.6-Man₉-V3 complex are shown as green sticks. b Superposition of V3 glycopeptide (red) from the DH270.6-Man₉-V3 complex onto the V3 region of other HIV Envs (both in complex, and unliganded) (PDB ID’s 4ZMJ, 5CEZ, 5I8H, 5FYK, 5FYJ, 5T3S, 5V8L, 5T3Z)

Fig. 4

Binding of DH270.6 and Env. Biolayer interferometry association and dissociation curves are shown for a wild-type (K_D = 2.76 nM) and R327A mutant (K_D = 7.64 nM) forms of 92BR SOSIP.664 Env tested with DH270.6 Fab at the indicated concentrations and b wild-type and mutant forms of DH270.6 Fab binding to wild-type 92BR SOSIP.664

Fig. 5

DH270.3-Man₉ crystal structure. a The structure of DH270.3 (orange) in complex with Man₉ (magenta), superposed on DH270.6 (blue) in complex with Man₉-V3 (red), with glycans shown as green sticks. b Contacts made by DH270.3 and Man₉. c Sequence alignments of DH270 lineage members with glycan and peptide contact sites indicated. CDR loops, framework regions, and improbable mutations are also shown