用结构和序列联合生成抗体,加速优化过程。
Guided Sequence-Structure Generative Modeling for Iterative Antibody Optimization
- 基于抗体-抗原复合物的扩散模型生成新抗体序列。
- 结合实验数据引导生成,实现多轮优化中高亲和力抗体产出。
- 适合需要快速迭代优化抗体的药物研发团队使用。
治疗性抗体候选物常需经过多轮体外实验以改善关键功能与可开发性。这一过程依赖迭代设计,但因难以获取不断演化的先导分子的结构数据,蛋白结构在设计中极少被利用。本文提出一种基于序列与结构的迭代抗体优化策略,融合累积的结合力与可开发性实验数据。首先训练一个作用于抗体-抗原复合物的序列-结构扩散生成模型;随后,利用该模型与预测的复合物结构,在迭代设计中持续优化先导分子。进一步提出一种引导采样方法,通过整合从迭代实验中训练出的模型,使生成偏向理想性质。我们在多个体外与体内实验中验证了该方法,证明其可在抗体优化的不同阶段持续生成高亲和力结合物。
原文摘要 · Abstract (English)
Therapeutic antibody candidates often require extensive engineering to improve key functional and developability properties before clinical development. This can be achieved through iterative design, where starting molecules are optimized over several rounds of in vitro experiments. While protein structure can provide a strong inductive bias, it is rarely used in iterative design due to the lack of structural data for continually evolving lead molecules over the course of optimization. In this work, we propose a strategy for iterative antibody optimization that leverages both sequence and structure as well as accumulating lab measurements of binding and developability. Building on prior work, we first train a sequence-structure diffusion generative model that operates on antibody-antigen complexes. We then outline an approach to use this model, together with carefully predicted antibody-antigen complexes, to optimize lead candidates throughout the iterative design process. Further, we describe a guided sampling approach that biases generation toward desirable properties by integrating models trained on experimental data from iterative design. We evaluate our approach in multiple in silico and in vitro experiments, demonstrating that it produces high-affinity binders at multiple stages of an active antibody optimization campaign.
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