De novo design of epitope-specific antibodies via a structure-driven computational workflow
Accurate modeling of antibody-antigen complex structures holds significant potential for advancing biomedical research and the design of therapeutic antibodies. Compared to general proteins, progress in antibody structure prediction and design has been slow, and antibody discovery is still based on time-consuming animal immunization or library screening methods. Here, we present tFold System, a high-throughput computational workflow that integrates antibody structure prediction (tFold-Ab), antibody-antigen complex modeling (tFold-Ag), structure-guided virtual screening, and de novo epitope-specific antibody design. Using this system, we de novo design monoclonal antibodies (mAbs) against four therapeutically relevant antigens: influenza hemagglutinin (Flu A), PD-1, PD-L1, and SARS-CoV-2 RBD (SC2RBD). Experimental validation by surface plasmon resonance (SPR) following high-throughput screening via phage display shows the designed antibodies achieve nanomolar binding affinities and precise epitope targeting, demonstrating the efficiency of the integrated computational-experimental pipeline. Our results demonstrate that tFold System overcomes key limitations of existing methods by enabling rapid, high-throughput antibody discovery against user-defined epitopes.
Authors
- Houtim Lai
- Long-Kai Huang (ORCID: https://orcid.org/0000-0001-5263-1443)
- Tingyang Xu (ORCID: https://orcid.org/0000-0002-8487-9045)
- Zihan Wu (ORCID: https://orcid.org/0000-0001-6342-9881)
- Huaxian Jia (ORCID: https://orcid.org/0000-0002-3586-0225)
- Jiaxiang Wu (ORCID: https://orcid.org/0000-0001-9132-5625)
- Peilin Zhao (ORCID: https://orcid.org/0000-0001-8543-3953)
- Rubo Wang (ORCID: https://orcid.org/0000-0002-6514-975X)
- Biaobin Jiang (ORCID: https://orcid.org/0000-0002-9995-4925)
- Yiran Song (ORCID: https://orcid.org/0009-0000-6683-3337)
- Chenchen Qin (ORCID: https://orcid.org/0009-0009-8763-8616)
- Ningqiao Huang (ORCID: https://orcid.org/0000-0001-6566-5140)
- Yu Zhao (ORCID: https://orcid.org/0000-0001-8179-4903)
- Fandi Wu (ORCID: https://orcid.org/0000-0003-1615-3004)
- Shaoning Li
- Fan Yang (ORCID: https://orcid.org/0000-0002-1245-1197)
- Fang Wang (ORCID: https://orcid.org/0000-0002-1491-5207)
- Wei Liu (ORCID: https://orcid.org/0000-0001-7285-0520)
- Yang Xiao
- Bing He (ORCID: https://orcid.org/0000-0003-1719-9290)
- Jianhua Yao (ORCID: https://orcid.org/0000-0001-9157-9596)
- Yu Rong (ORCID: https://orcid.org/0000-0001-7387-302X)
- Yuyi Liu (ORCID: https://orcid.org/0000-0002-9114-4071)
Institutions
- Tencent (China) (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-12-10
- DOI
- https://doi.org/10.1038/s41467-025-67361-9
- Citations
- 1
- Primary Topic
- Monoclonal and Polyclonal Antibodies Research
- Type
- article
- Field-Weighted Citation Impact
- 1.36