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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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Peptide binding affinities for human MHC II proteins.IC50 values are plotted as cognate wild type and variant pairs, where lower IC50 values correspond to higher affinity binding with human MHC II. The slope of the connecting lines are a relative measure of deimmunizing efficacy, where larger positive slopes indicate a greater fold decrease in affinity relative to wild type. Lines with negative slopes indicate a mutation that enhanced MHC II binding. Shading indicates binding strength by category: strong (IC50<1 µM, dark grey), moderate (1 µM≤IC50<10 µM, medium grey), weak (10 µM≤IC50<100 µM, light grey), or non-binding (IC50 ≥100 µM, white).
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pcbi-1003988-g005: Peptide binding affinities for human MHC II proteins.IC50 values are plotted as cognate wild type and variant pairs, where lower IC50 values correspond to higher affinity binding with human MHC II. The slope of the connecting lines are a relative measure of deimmunizing efficacy, where larger positive slopes indicate a greater fold decrease in affinity relative to wild type. Lines with negative slopes indicate a mutation that enhanced MHC II binding. Shading indicates binding strength by category: strong (IC50<1 µM, dark grey), moderate (1 µM≤IC50<10 µM, medium grey), weak (10 µM≤IC50<100 µM, light grey), or non-binding (IC50 ≥100 µM, white).

Mentions: The immunoreactivity of various constructs was assessed by measuring the MHC II binding affinity of their corresponding peptide fragments. These competition immunoassays are a widely recognized metric for assessing immunogenic potential and validating computational predictions [22], [25], [33], [35], [36], [37], [38], [39]. Synthetic fragments of wild type P99βL were designed so as to encompass each of the epitopes targeted by the deimmunization algorithm, and corresponding variant peptides were synthesized to represent the deimmunized designs (S2 Table). The affinity of each peptide for human MHC II molecules DRB1*0101, 0401, 0701, and 1501 was measured by competition with known peptide immunogens for each allele. A quantitative comparison of wild type versus variant MHC II binding affinity was used as a proxy measure for the success of epitope deletion (Fig. 5). Peptide affinities are reported as IC50 values, and putative epitopes were classified as strong (IC50<1 µM), moderate (1 µM≤IC50<10 µM), weak (10 µM≤IC50<100 µM), or non-binders (IC50≥100 µM).


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)

Peptide binding affinities for human MHC II proteins.IC50 values are plotted as cognate wild type and variant pairs, where lower IC50 values correspond to higher affinity binding with human MHC II. The slope of the connecting lines are a relative measure of deimmunizing efficacy, where larger positive slopes indicate a greater fold decrease in affinity relative to wild type. Lines with negative slopes indicate a mutation that enhanced MHC II binding. Shading indicates binding strength by category: strong (IC50<1 µM, dark grey), moderate (1 µM≤IC50<10 µM, medium grey), weak (10 µM≤IC50<100 µM, light grey), or non-binding (IC50 ≥100 µM, white).
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1003988-g005: Peptide binding affinities for human MHC II proteins.IC50 values are plotted as cognate wild type and variant pairs, where lower IC50 values correspond to higher affinity binding with human MHC II. The slope of the connecting lines are a relative measure of deimmunizing efficacy, where larger positive slopes indicate a greater fold decrease in affinity relative to wild type. Lines with negative slopes indicate a mutation that enhanced MHC II binding. Shading indicates binding strength by category: strong (IC50<1 µM, dark grey), moderate (1 µM≤IC50<10 µM, medium grey), weak (10 µM≤IC50<100 µM, light grey), or non-binding (IC50 ≥100 µM, white).
Mentions: The immunoreactivity of various constructs was assessed by measuring the MHC II binding affinity of their corresponding peptide fragments. These competition immunoassays are a widely recognized metric for assessing immunogenic potential and validating computational predictions [22], [25], [33], [35], [36], [37], [38], [39]. Synthetic fragments of wild type P99βL were designed so as to encompass each of the epitopes targeted by the deimmunization algorithm, and corresponding variant peptides were synthesized to represent the deimmunized designs (S2 Table). The affinity of each peptide for human MHC II molecules DRB1*0101, 0401, 0701, and 1501 was measured by competition with known peptide immunogens for each allele. A quantitative comparison of wild type versus variant MHC II binding affinity was used as a proxy measure for the success of epitope deletion (Fig. 5). Peptide affinities are reported as IC50 values, and putative epitopes were classified as strong (IC50<1 µM), moderate (1 µM≤IC50<10 µM), weak (10 µM≤IC50<100 µM), or non-binders (IC50≥100 µM).

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