Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth
Jordan R. Willis, … , Jens Meiler, James E. Crowe Jr.
Jordan R. Willis, … , Jens Meiler, James E. Crowe Jr.
Published May 18, 2015
Citation Information: J Clin Invest. 2015;125(6):2523-2531. https://doi.org/10.1172/JCI80693.
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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.

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Figure 3

PG9_N100FY Fab crystal structure and Rosetta models.

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PG9_N100FY Fab crystal structure and Rosetta models. (A) Unliganded PG9...
(A) Unliganded PG9_N100FY HCDR3 crystal structure. 2Fo – Fc electron density is shown as a mesh grid contoured at 1σ. Electron density shows tyrosine sulfation at YS100G and YS100H but not at N100FY. N100FY stacks against P99 and Y100A, thereby providing increased stability. (B) Unliganded crystal structure aligned with Rosetta complexed model has an all-atom RMSD of 0.68 Å. Rosetta top-scoring model modeled from PDB ID: 3U4E complex is shown in orange. V1/V2 antigen from the model is shown as a gray surface. Crystal structure of the HCDR3 loop of PG9_N100FY is shown in pink. The N100FY mutation, highlighted in red, adopts the same conformation in the crystal structure as in the Rosetta model. (C) Rosetta scores for HCDR3 binding, total binding, HCDR3 stabilization, or total stabilization (scores shown as REU for 1000 simulations ± STD). Only significant differences where the means were below that of WT PG9 are shown. All other comparisons were not significant with a confidence of 0.05 or the means were above that of WT PG9 using a Student’s 2-sided t test. (D) Models for WT PG9 and the top scoring variants N100FL and N100FY are shown in a sphere and surface representation. The atom types are colored for carbon (gray), oxygen (red), or nitrogen (blue). The V1/V2 epitope is indicated in green, the antibody HCDR3 loop in dark blue, the N160 complex glycan in dark green, and non-HCDR3 portions of the antibody heavy chain in black.