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通过可解释的机器学习优化治疗性抗体以减少自身聚集和非特异性结合。

Optimization of therapeutic antibodies for reduced self-association and non-specific binding via interpretable machine learning.

机构信息

Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.

Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.

出版信息

Nat Biomed Eng. 2024 Jan;8(1):45-56. doi: 10.1038/s41551-023-01074-6. Epub 2023 Sep 4.

Abstract

Antibody development, delivery, and efficacy are influenced by antibody-antigen affinity interactions, off-target interactions that reduce antibody bioavailability and pharmacokinetics, and repulsive self-interactions that increase the stability of concentrated antibody formulations and reduce their corresponding viscosity. Yet identifying antibody variants with optimal combinations of these three types of interactions is challenging. Here we show that interpretable machine-learning classifiers, leveraging antibody structural features descriptive of their variable regions and trained on experimental data for a panel of 80 clinical-stage monoclonal antibodies, can identify antibodies with optimal combinations of low off-target binding in a common physiological-solution condition and low self-association in a common antibody-formulation condition. For three clinical-stage antibodies with suboptimal combinations of off-target binding and self-association, the classifiers predicted variable-region mutations that optimized non-affinity interactions while maintaining high-affinity antibody-antigen interactions. Interpretable machine-learning models may facilitate the optimization of antibody candidates for therapeutic applications.

摘要

抗体的开发、传递和功效受到抗体-抗原亲和力相互作用、降低抗体生物利用度和药代动力学的非靶标相互作用以及增加浓缩抗体制剂稳定性并降低其相应粘度的排斥性自相互作用的影响。然而,确定具有这三种相互作用最佳组合的抗体变体具有挑战性。在这里,我们表明,可解释的机器学习分类器可以利用描述其可变区的抗体结构特征,并利用针对 80 种临床阶段单克隆抗体的实验数据进行训练,从而可以识别出在常见生理溶液条件下具有低非靶标结合和在常见抗体制剂条件下具有低自缔合的最佳组合的抗体。对于三种具有非靶标结合和自缔合组合不理想的临床阶段抗体,分类器预测了可变区突变,这些突变优化了非亲和力相互作用,同时保持了高亲和力的抗体-抗原相互作用。可解释的机器学习模型可能有助于优化抗体候选物用于治疗应用。

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