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Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate.

Salvat RS, Parker AS, Choi Y, Bailey-Kellogg C, Griswold KE - PLoS Comput. Biol. (2015)

Bottom Line: As a result, there is a growing need for improved deimmunization technologies.Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions.These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates.

View Article: PubMed Central - PubMed

Affiliation: Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America.

ABSTRACT
The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts.

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Epitope predictions, measured IC50 values, and correlations by individual peptide.For each MHC allele, the number of predicted epitopes within a given synthetic peptide is shown on the left, and the measured IC50 values are shown on the right. Peptides were categorized as strong (IC50<1 µM, red), moderate (1 µM≤IC50<10 µM, orange), weak (10 µM≤IC50<100 µM, yellow), or non-binding (IC50 ≥100 µM, white). Positive correlations between epitope prediction and experimental measurements (binding cutoff at 100 µM) are highlighted in blue on the left.
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pcbi-1003988-g006: Epitope predictions, measured IC50 values, and correlations by individual peptide.For each MHC allele, the number of predicted epitopes within a given synthetic peptide is shown on the left, and the measured IC50 values are shown on the right. Peptides were categorized as strong (IC50<1 µM, red), moderate (1 µM≤IC50<10 µM, orange), weak (10 µM≤IC50<100 µM, yellow), or non-binding (IC50 ≥100 µM, white). Positive correlations between epitope prediction and experimental measurements (binding cutoff at 100 µM) are highlighted in blue on the left.

Mentions: High affinity interaction between peptide antigens and class II MHC is a key determinant of subsequent T cell immunogenicity [40], [41], [42], and a total of four wild type P99βL peptides were found to possess sub-micromolar IC50's for one or more of the tested alleles. The wild type A13+N14 peptide was a high affinity binder of DRB1*0701 (IC50 = 800 nM), and both A13D and A13E successfully converted this to a weak binding interaction with N14R yielding a moderate binding interaction (Fig. 6). As found in prior studies [25], wild type peptide L149 was bound by all four alleles, and here it was a particularly strong binder of 1501 (IC50 = 300 nM). The L149Q mutation reduced 1501 affinity by 40-fold, converting this strong binding interaction to a weak interaction. Wild type peptide I262 also bound all four alleles, and it possessed sub-micromolar affinity for both 0401 and 1501. The I262V mutation yielded a 6-fold reduction in 1501 affinity, thereby converting a strong binder to a moderate binder. In contrast, I262V did not substantially alter affinity for allele 0401, although this outcome was predicted during the design process (Fig. 3). The only other high affinity binding of a wild type peptide was 0101 binding of I48, which, contrary to predictions, was unaffected by the I48V mutation.


Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate.

Salvat RS, Parker AS, Choi Y, Bailey-Kellogg C, Griswold KE - PLoS Comput. Biol. (2015)

Epitope predictions, measured IC50 values, and correlations by individual peptide.For each MHC allele, the number of predicted epitopes within a given synthetic peptide is shown on the left, and the measured IC50 values are shown on the right. Peptides were categorized as strong (IC50<1 µM, red), moderate (1 µM≤IC50<10 µM, orange), weak (10 µM≤IC50<100 µM, yellow), or non-binding (IC50 ≥100 µM, white). Positive correlations between epitope prediction and experimental measurements (binding cutoff at 100 µM) are highlighted in blue on the left.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4288714&req=5

pcbi-1003988-g006: Epitope predictions, measured IC50 values, and correlations by individual peptide.For each MHC allele, the number of predicted epitopes within a given synthetic peptide is shown on the left, and the measured IC50 values are shown on the right. Peptides were categorized as strong (IC50<1 µM, red), moderate (1 µM≤IC50<10 µM, orange), weak (10 µM≤IC50<100 µM, yellow), or non-binding (IC50 ≥100 µM, white). Positive correlations between epitope prediction and experimental measurements (binding cutoff at 100 µM) are highlighted in blue on the left.
Mentions: High affinity interaction between peptide antigens and class II MHC is a key determinant of subsequent T cell immunogenicity [40], [41], [42], and a total of four wild type P99βL peptides were found to possess sub-micromolar IC50's for one or more of the tested alleles. The wild type A13+N14 peptide was a high affinity binder of DRB1*0701 (IC50 = 800 nM), and both A13D and A13E successfully converted this to a weak binding interaction with N14R yielding a moderate binding interaction (Fig. 6). As found in prior studies [25], wild type peptide L149 was bound by all four alleles, and here it was a particularly strong binder of 1501 (IC50 = 300 nM). The L149Q mutation reduced 1501 affinity by 40-fold, converting this strong binding interaction to a weak interaction. Wild type peptide I262 also bound all four alleles, and it possessed sub-micromolar affinity for both 0401 and 1501. The I262V mutation yielded a 6-fold reduction in 1501 affinity, thereby converting a strong binder to a moderate binder. In contrast, I262V did not substantially alter affinity for allele 0401, although this outcome was predicted during the design process (Fig. 3). The only other high affinity binding of a wild type peptide was 0101 binding of I48, which, contrary to predictions, was unaffected by the I48V mutation.

Bottom Line: As a result, there is a growing need for improved deimmunization technologies.Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions.These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates.

View Article: PubMed Central - PubMed

Affiliation: Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America.

ABSTRACT
The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts.

Show MeSH