Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth
Jordan R. Willis, Gopal Sapparapu, Sasha Murrell, Jean-Philippe Julien, Vidisha Singh, Hannah G. King, Yan Xia, Jennifer A. Pickens, Celia C. LaBranche, James C. Slaughter, David C. Montefiori, Ian A. Wilson, Jens Meiler, James E. Crowe Jr.
Jordan R. Willis, Gopal Sapparapu, Sasha Murrell, Jean-Philippe Julien, Vidisha Singh, Hannah G. King, Yan Xia, Jennifer A. Pickens, Celia C. LaBranche, James C. Slaughter, David C. Montefiori, Ian A. Wilson, Jens Meiler, James E. Crowe Jr.
View: Text | PDF
Research Article AIDS/HIV

Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth

Abstract

Several HIV envelope-targeting (Env-targeting) antibodies with broad and potent neutralizing activity have been identified and shown to have unusual features. Of these, the PG9 antibody has a long heavy chain complementarity determining region 3 (HCDR3) and possesses unique structural elements that interact with protein and glycan features of the HIV Env glycoprotein. Here, we used the Rosetta software suite to design variants of the PG9 antibody HCDR3 loop with the goal of identifying variants with increased potency and breadth of neutralization for diverse HIV strains. One variant, designated PG9_N100FY, possessed increased potency and was able to neutralize a diverse set of PG9-resistant HIV strains, including those lacking the Env N160 glycan, which is critical for PG9 binding. An atomic resolution structure of the PG9_N100FY fragment antigen binding (Fab) confirmed that the mutated residue retains the paratope surface when compared with WT PG9. Differential scanning calorimetry experiments revealed that the mutation caused a modest increase in thermodynamic stability of the Fab, a feature predicted by the computational model. Our findings suggest that thermodynamic stabilization of the long HCDR3 in its active conformation is responsible for the increased potency of PG9_N100FY, and strategies aimed at stabilizing this region in other HIV antibodies could become an important approach to in silico optimization of antibodies.

Authors

Jordan R. Willis, Gopal Sapparapu, Sasha Murrell, Jean-Philippe Julien, Vidisha Singh, Hannah G. King, Yan Xia, Jennifer A. Pickens, Celia C. LaBranche, James C. Slaughter, David C. Montefiori, Ian A. Wilson, Jens Meiler, James E. Crowe Jr.

×

Figure 1

Rosetta predicts mutations that enhance PG9 fitness.

Options: View larger image (or click on image) Download as PowerPoint
Rosetta predicts mutations that enhance PG9 fitness. (A) Redesigned PG9 ...
(A) Redesigned PG9 sequences for the HCDR3 loop are shown as sequence logo. The height of the logo, in bits, indicates how many times an amino acid was preferred at that position in 100 simulations using Rosetta. The WT sequence, with 3 HCDR3 position numbering schemes (top: the sequentially numbered position as each residue appears in the PDB file; middle: IMGT, ref. 47; and bottom: Kabat, ref. 11) is shown on the x-axis. (B) Mutational energy analysis for each residue in the HCDR3, shown using Kabat numbering. Mutational fitness due to stability and binding energy ± STD (y-axis) is shown as a function of individual mutations (x-axis); a more negative fitness energy score is preferred. The mutations are grouped and colored by position. For mutations that were made experimentally, a panel shows the WT PG9 sequence in ball-and-stick representation, where the carbons match the color of the bar in the graph, nitrogens are shown in deep-blue, and oxygens are shown in red. The HCDR3 residues are shown in blue. Residues within 5 Å are shown as stick representation. The V1/V2 scaffold (PDB ID: 3U4E) (2) is shown in yellow with glycans at positions 156 and 160 (HIV strain HXBc2 numbering) shown in surface representation. Non-HCDR3 heavy chain amino acids are shown in white. Light chain amino acids are shown in pink. (C) Alignment of HCDR3 sequences of the 5 PG9 variants that were characterized experimentally. The WT PG9 sequence is shown at the top, with Kabat numbering.