华盛顿大学David Baker团队取得一项新突破。他们提出了原子精确的RF扩散抗体从头设计。相关论文于2025年11月5日发表于国际顶尖学术期刊《自然》杂志上。

在这里，课题组证明了将计算蛋白设计主题（一个微调的RFdiffthemion网络）与酵母显示筛选相结合，可以以原子水平的精度重新生成抗体可变重链（VHHs）、单链可变片段（scFvs）和与主题指定的表位结合的全抗体。研究小组通过实验表征了VHH结合物的疾病相关表位。冷冻电镜证实了设计的靶向流感血凝素和艰难梭菌毒素B （TcdB）的VHHs的结合姿态。靶向流感的VHH的高分辨率结构证实了所设计的互补性决定区域（CDRs）的原子准确性。虽然最初的计算设计显示出适度的亲和力（数十到数百纳摩尔K_d），但亲和性成熟主题化的OrthoRep能够生产出保持预期表位选择性的个位数纳摩尔结合物。通过结合设计的重链和轻链CDRs，该课题组研究人员进一步展示了针对TcdB和PHOX2B肽-MHC复合物的scFvs的从头设计。低温电子显微镜证实了两个不同的TcdB scFvs的结合姿态，其中一个设计的高分辨率数据验证了所有六个CDR环的原子精确设计构象。他们的方法为计算设计、筛选和表征完全新生抗体建立了一个框架，在结构和表位靶向方面具有原子水平的精度。

据了解，尽管抗体在现代医学中发挥着核心作用，但目前还没有办法完全用计算机设计新颖的表位特异性抗体。相反，抗体的发现目前依赖于免疫、随机文库筛选或直接从患者身上分离抗体。

附：英文原文

Title: Atomically accurate de novo design of antibodies with RFdiffusion

Author: Bennett, Nathaniel R., Watson, Joseph L., Ragotte, Robert J., Borst, Andrew J., See, DJena L., Weidle, Connor, Biswas, Riti, Yu, Yutong, Shrock, Ellen L., Ault, Russell, Leung, Philip J. Y., Huang, Buwei, Goreshnik, Inna, Tam, John, Carr, Kenneth D., Singer, Benedikt, Criswell, Cameron, Wicky, Basile I. M., Vafeados, Dionne, Garcia Sanchez, Mariana, Kim, Ho Min, Vzquez Torres, Susana, Chan, Sidney, Sun, Shirley M., Spear, Timothy T., Sun, Yi, OReilly, Keelan, Maris, John M., Sgourakis, Nikolaos G., Melnyk, Roman A., Liu, Chang C., Baker, David

Issue&Volume: 2025-11-05

Abstract: Despite the central role of antibodies in modern medicine, no method currently exists to design novel, epitope-specific antibodies entirely in silico. Instead, antibody discovery currently relies on immunization, random library screening or the isolation of antibodies directly from patients1. Here we demonstrate that combining computational protein design using a fine-tuned RFdiffusion2 network with yeast display screening enables the de novo generation of antibody variable heavy chains (VHHs), single-chain variable fragments (scFvs) and full antibodies that bind to user-specified epitopes with atomic-level precision. We experimentally characterize VHH binders to four disease-relevant epitopes. Cryo-electron microscopy confirms the binding pose of designed VHHs targeting influenza haemagglutinin and Clostridium difficile toxin B (TcdB). A high-resolution structure of the influenza-targeting VHH confirms atomic accuracy of the designed complementarity-determining regions (CDRs). Although initial computational designs exhibit modest affinity (tens to hundreds of nanomolar Kd), affinity maturation using OrthoRep3 enables production of single-digit nanomolar binders that maintain the intended epitope selectivity. We further demonstrate the de novo design of scFvs to TcdB and a PHOX2B peptide–MHC complex by combining designed heavy-chain and light-chain CDRs. Cryo-electron microscopy confirms the binding pose for two distinct TcdB scFvs, with high-resolution data for one design verifying the atomically accurate design of the conformations of all six CDR loops. Our approach establishes a framework for the computational design, screening and characterization of fully de novo antibodies with atomic-level precision in both structure and epitope targeting.

DOI: 10.1038/s41586-025-09721-5

Source: https://www.nature.com/articles/s41586-025-09721-5