A matrix of structure-based designs yields improved VRC01-class antibodies for HIV-1 therapy and prevention

Young D Kwon, Mangaiarkarasi Asokan, Jason Gorman, Baoshan Zhang, Qingbo Liu, Mark K Louder, Bob C Lin, Krisha McKee, Amarendra Pegu, Raffaello Verardi, Eun Sung Yang, Vrc Production Program, Kevin Carlton, Nicole A Doria-Rose, Paolo Lusso, John R Mascola, Peter D Kwong, Young D Kwon, Mangaiarkarasi Asokan, Jason Gorman, Baoshan Zhang, Qingbo Liu, Mark K Louder, Bob C Lin, Krisha McKee, Amarendra Pegu, Raffaello Verardi, Eun Sung Yang, Vrc Production Program, Kevin Carlton, Nicole A Doria-Rose, Paolo Lusso, John R Mascola, Peter D Kwong

Abstract

Passive transfer of broadly neutralizing antibodies is showing promise in the treatment and prevention of HIV-1. One class of antibodies, the VRC01 class, appears especially promising. To improve VRC01-class antibodies, we combined structure-based design with a matrix-based approach to generate VRC01-class variants that filled an interfacial cavity, used diverse third-complementarity-determining regions, reduced potential steric clashes, or exploited extended contacts to a neighboring protomer within the envelope trimer. On a 208-strain panel, variant VRC01.23LS neutralized 90% of the panel at a geometric mean IC80 less than 1 μg/ml, and in transgenic mice with human neonatal-Fc receptor, the serum half-life of VRC01.23LS was indistinguishable from that of the parent VRC01LS, which has a half-life of 71 d in humans. A cryo-electron microscopy structure of VRC01.23 Fab in complex with BG505 DS-SOSIP.664 Env trimer determined at 3.4-Å resolution confirmed the structural basis for its ~10-fold improved potency relative to VRC01. Another variant, VRC07-523-F54-LS.v3, neutralized 95% of the 208-isolated panel at a geometric mean IC80 of less than 1 μg/ml, with a half-life comparable to that of the parental VRC07-523LS. Our matrix-based structural approach thus enables the engineering of VRC01 variants for HIV-1 therapy and prevention with improved potency, breadth, and pharmacokinetics.

Keywords: Antibody VRC01; HIV-1 envelope trimer; broadly neutralizing antibody; matrix-based design; polyreactivity; prophylaxis; treatment.

Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Structure-based approach focuses on recognition hotspots for VRC01-class antibodies. (a) Heavy-chain Gly54 to Trp mutation to mimic Phe43CD4 occupying a hydrophobic pocket on gp120. (b) Swap of VRC01 CDR H3 with VRC07 CDR H3 to increase binding surface between gp120 and the CDR H3. (c) Deletion of three residues of N-terminal light chain to better accommodate various lengths and conformations of the V5 region of gp120. (d) Replacement of framework region 3 with VRC03 framework region 3 (03FR3) to extend its interaction to the neighboring protomer. The structure of core gp120 in complex with VRC07-G54W (PDB ID: 4OLZ) is shown, superimposed on the structure of BG505 DS-SOSIP in complex with VRC01 Fab (PDB ID: 6NNF)
Figure 1.
Figure 1.
Structure-based approach focuses on recognition hotspots for VRC01-class antibodies. (a) Heavy-chain Gly54 to Trp mutation to mimic Phe43CD4 occupying a hydrophobic pocket on gp120. (b) Swap of VRC01 CDR H3 with VRC07 CDR H3 to increase binding surface between gp120 and the CDR H3. (c) Deletion of three residues of N-terminal light chain to better accommodate various lengths and conformations of the V5 region of gp120. (d) Replacement of framework region 3 with VRC03 framework region 3 (03FR3) to extend its interaction to the neighboring protomer. The structure of core gp120 in complex with VRC07-G54W (PDB ID: 4OLZ) is shown, superimposed on the structure of BG505 DS-SOSIP in complex with VRC01 Fab (PDB ID: 6NNF)
Figure 2.
Figure 2.
A matrix of structure-based designs identifies a variant, VRC01.23LS, with improved potency and low HEp-2 reactivity. (a) Four different VRC01LS heavy chain variants were paired with three different VRC01LS light chains to generate 12 VRC01LS variants. (b) Neutralization IC50 values of 12 VRC01LS variants assessed on 12 diverse strains of HIV-1. Variant VRC01.23LS neutralized 11 out of 12 viruses with median IC50 of 0.34 μg/ml. (c) HEp-2 cell staining assay against VRC01LS variants was performed at a concentration of 25 μg/ml along with control antibodies, VRC01LS, 4E10, VRC07-523LS, and VRC07-G54W. Control antibodies were assigned a score between 0 and 3. Antibodies scored greater than 1 at 25 µg/ml were considered polyreactive
Figure 2.
Figure 2.
A matrix of structure-based designs identifies a variant, VRC01.23LS, with improved potency and low HEp-2 reactivity. (a) Four different VRC01LS heavy chain variants were paired with three different VRC01LS light chains to generate 12 VRC01LS variants. (b) Neutralization IC50 values of 12 VRC01LS variants assessed on 12 diverse strains of HIV-1. Variant VRC01.23LS neutralized 11 out of 12 viruses with median IC50 of 0.34 μg/ml. (c) HEp-2 cell staining assay against VRC01LS variants was performed at a concentration of 25 μg/ml along with control antibodies, VRC01LS, 4E10, VRC07-523LS, and VRC07-G54W. Control antibodies were assigned a score between 0 and 3. Antibodies scored greater than 1 at 25 µg/ml were considered polyreactive
Figure 3.
Figure 3.
N49P7 and VRC07-523LS variants with improved potency and some HEp-2 reactivity. (a) Matrix of VRC01-class antibody variants. (b) Neutralization IC50 values of N49P7 variants and VRC07-523LS variants against a 12-virus panel. (c) HEp-2 cell staining assay against N49P7 and VRC07 variants was performed in the concentration of 25 μg/ml along with control antibodies, VRC01LS, 4E10, VRC07-523LS, and VRC07-G54W. Control antibodies were assigned a score between 0 and 3. Test antibodies scored greater than 1 at 25 µg/ml were considered polyreactive
Figure 3.
Figure 3.
N49P7 and VRC07-523LS variants with improved potency and some HEp-2 reactivity. (a) Matrix of VRC01-class antibody variants. (b) Neutralization IC50 values of N49P7 variants and VRC07-523LS variants against a 12-virus panel. (c) HEp-2 cell staining assay against N49P7 and VRC07 variants was performed in the concentration of 25 μg/ml along with control antibodies, VRC01LS, 4E10, VRC07-523LS, and VRC07-G54W. Control antibodies were assigned a score between 0 and 3. Test antibodies scored greater than 1 at 25 µg/ml were considered polyreactive
Figure 4.
Figure 4.
Truncation of disordered N-termini of VRC01-class light chains increased potency, while truncation of ordered light chains impaired potency. The N-termini of VRC01-class antibody light chains were shown in purple with 2fo-fc electron density maps in blue mesh contoured at 1 σ
Figure 4.
Figure 4.
Truncation of disordered N-termini of VRC01-class light chains increased potency, while truncation of ordered light chains impaired potency. The N-termini of VRC01-class antibody light chains were shown in purple with 2fo-fc electron density maps in blue mesh contoured at 1 σ
Figure 5.
Figure 5.
VRC01-class antibodies: neutralization potency and breadth against multiclade panel of viruses and serum half-life in human FcRn transgenic mice. (a) Summary of neutralization potency and breadth of VRC01-class antibodies against a panel of 208 pseudoviruses (b) Scattered plots of neutralization potency and breadth with black bars representing median IC50s. A horizontal dotted line extending from the median IC50 of VRC07-523-W54-LS.v3 was drawn as a reference for comparison. (c) Pharmacokinetics of VRC01-class antibodies in human FcRn transgenic mice. Error bars represent SD
Figure 5.
Figure 5.
VRC01-class antibodies: neutralization potency and breadth against multiclade panel of viruses and serum half-life in human FcRn transgenic mice. (a) Summary of neutralization potency and breadth of VRC01-class antibodies against a panel of 208 pseudoviruses (b) Scattered plots of neutralization potency and breadth with black bars representing median IC50s. A horizontal dotted line extending from the median IC50 of VRC07-523-W54-LS.v3 was drawn as a reference for comparison. (c) Pharmacokinetics of VRC01-class antibodies in human FcRn transgenic mice. Error bars represent SD
Figure 6.
Figure 6.
Cryo-EM structure of VRC01.23 Fab in complex with BG505 DS-SOSIP trimer at 3.4-Å resolution. (a) Heavy-chain Gly54 to Trp in its electron density map (b) The N-terminus of light chain VRC01.23LS starting at Leu4 in its electron density map. Cα-Cα distance of 9.5 Å between Leu4 and Thr461 in gp120 was shown in a dotted line. (c) The protruding loop region of the 03FR3 was shown in stick representation. (d) The hydrogen bonding networks between glycan at position 276 of gp120 and Arg66 of VRC01.23 light chain were shown in red dotted lines
Figure 6.
Figure 6.
Cryo-EM structure of VRC01.23 Fab in complex with BG505 DS-SOSIP trimer at 3.4-Å resolution. (a) Heavy-chain Gly54 to Trp in its electron density map (b) The N-terminus of light chain VRC01.23LS starting at Leu4 in its electron density map. Cα-Cα distance of 9.5 Å between Leu4 and Thr461 in gp120 was shown in a dotted line. (c) The protruding loop region of the 03FR3 was shown in stick representation. (d) The hydrogen bonding networks between glycan at position 276 of gp120 and Arg66 of VRC01.23 light chain were shown in red dotted lines

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