Chemically Programmed Antibodies As HIV‑1 Attachment Inhibitors

Herein, we describe the design and application of two small-molecule anti-HIV compounds for the creation of chemically programmed antibodies. <i>N</i>-Acyl-β-lactam derivatives of two previously described molecules BMS-378806 and BMS-488043 that inhibit the interaction between HIV-1 gp120 and T-cells were synthesized and used to program the binding activity of aldolase antibody 38C2. Discovery of a successful linkage site to BMS-488043 allowed for the synthesis of chemically programmed antibodies with affinity for HIV-1 gp120 and potent HIV-1 neutralization activity. Derivation of a successful conjugation strategy for this family of HIV-1 entry inhibitors enables its application in chemically programmed antibodies and vaccines and may facilitate the development of novel bispecific antibodies and topical microbicides

Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 123, 123, 125, and 126.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: For each of the ten HIV-1 broadly neutralizing monoclonal antibodies (bnMAb) considered in this study, we report the residues identified by the compressed sensing (CS) classifier, positions identified by the mutual information (MI) classifier, and positions identified by the ensemble classifier (formed by combining the CS and MI predictions) predicted to lie within the bnMAb epitope. The number of residues identified by the CS classifier, <i>n_CS</i>, number of positions identified by the MI classifier, <i>n_MI</i>, number of positions predicted by the ensemble classifier, <i>n_ENS</i>, and number of positions identified by alanine scans, <i>n_EXPT</i>, may differ between bnMAbs.</p

Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 135, 143, and 145.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: See footnote to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>.</p

Mutual information (MI) selection of PGT-123 epitope positions.

<p>The redundancy spectrum produced by application of the mutual information classification algorithm to the neutralization activity of bnMAb PGT-123 against a panel of 141 HIV-1 pseudoviruses (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562.s001" target="_blank">Table S1</a>) using an IC₅₀ cutoff of 10 µg/ml. The ordinate records the computed redundancy of the residue identity in each position with the observed neutralization activity. The abscissa lists the positions of the protein in decreasing order of redundancy. The dashed line indicates the cutoff computed by the shuffling procedure described in Materials and Methods, <i>R_cutoff</i> = 0.15, above which redundancy values should be considered statistically significant. These results suggest that the three top ranked positions – respectively, 332, 334 and 330– be retained in the model (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>). For clarity of viewing, plots are terminated at the 100-component model.</p

Compressed sensing (CS) selection of PGT-123 epitope residues.

<p>Results of the application of the compressed sensing classification algorithm to the neutralization activity of bnMAb PGT-123 against a panel of 141 HIV-1 pseudoviruses (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562.s001" target="_blank">Table S1</a>). In each panel, the abscissa indicates the number of non-zero elements in the signal vector computed by the LASSO algorithm, and therefore the number of residues incorporated into the regularized least squares fit of the neutralization data (Eqn. 3). For clarity of viewing, plots are terminated at the 100-component model. As indicated by the arrows, knees in the (a) mean squared error (MSE) over the complete data set and (b) leave-one-out cross-validation mean squared error (LOOCV-MSE) curves were identified using the L method at 11 and 9 residues, respectively <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Salvador1" target="_blank">[77]</a>. The mean of these values motivated the selection of the ten residues constituting this model: I323, H330, N332, N334, S334, S612, N671, Q740, V815, and V843 (c.f. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>).</p

Logo plot of the variability of selected positions in HIV-1 Env within the 141-strain pseudovirus panel.

<p>We present data for all positions identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Tables 1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t003" target="_blank">3</a> as significant determinants of bnMAb neutralization activity by either the ensemble classifier or experimental alanine scan data.</p

Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 127, 128, and 130.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: See footnote to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>.</p

Plasma concentration of CD4-IgG2 in treated animals.

<p>Animals administered 200 mg of CD4-IgG2 showed plasma concentrations in the range of 500 to 1400 ng/ml at the time of challenge. No apparent correlation between plasma concentration and protection was observed. The CD4-IgG2 concentration at the time of challenge in animals administered 20 mg was 100 ng/ml for 1 animal and below the limit of detection (8 ng/ml) for 2 animals. Serum samples from the remaining 3 animals administered 20 mg were unavailable for this analysis.</p

Protection of CD4-IgG2-treated rhesus macaques in a high-dose SIVmac239 challenge experiment.

<p>To maintain serum concentrations, CD4-IgG2 (or control human polyclonal IgG) was administered subcutaneously over a two-week period by an ALZET osmotic pump. Animals were challenged intrarectally with a single high dose inoculum (3–5×10³ TCID₅₀) of SIVmac239 3-days after initiation of CD4-IgG2 administration. (<b>A</b>) Viral loads for animals treated with 200 mg of control polyclonal human IgG as a function of time following SIVmac239 challenge. All control animals became infected. (<b>B</b>) Viral loads for animals administered 20 mg CD4-IgG2 as a function of time following SIVmac239 challenge. Three out of 6 animals were fully protected and one infected animal showed delayed primary viremia. Due to a technical problem with the ALZET osmotic pump, one of the protected animals (98045) did not receive the full dose of 20 mg but this animal did not become infected. (<b>C</b>) Viral loads for animals administered 200 mg CD4-IgG2 as a function of time following SIVmac239 challenge. Five out of 7 animals were protected and showed no sign of infection at any time point. The minimum detection level was 125 SIV RNA copies/ml with a 95% confidence level. Open symbol indicates protected animal, closed symbol indicates infected animal.</p

Anti-human CD4 response in animals treated with CD4-IgG2.

<p>Animal sera were tested in a human CD4-specific ELISA to detect macaque antibody responses against CD4-IgG2. Serum samples were tested up to 23 days post-viral challenge and no responses were detected before day 15, indicating that the animal protection outcome was independent of a response against human CD4. Serum samples from 3 animals administered 20 mg CD4-IgG2 were unavailable for this analysis.</p