Machine-learning-assisted universal protein activation in living mice.

Journal: Cell
Published Date: May 20, 2025

Abstract

A universal strategy to precisely control protein activation in living animals is crucial for gain-of-function study of proteins under in vivo settings. We herein report CAGE-Prox, a computer-aided proximal decaging strategy for on-demand protein activation as well as protein-protein interaction modulations in living mice. Through machine-learning-assisted evolution of desired aminoacyl-tRNA synthetases (aaRSs), we successfully incorporated chemically caged amino acids into rationally designed "decaging sites" to transiently block target proteins' function, which can be restored in situ via a small-molecule-triggered bioorthogonal cleavage reaction. This method demonstrates broad applicability ranging from activating proteins of interest to cell-type-specific modulation of distinct phenotypes in living systems. Beyond the active-pocket decaging, CAGE-Prox also enables precise control of protein-protein interactions, as exemplified by a "gated" anti-CD3 antibody that permits chemically regulated T cell recruitment and activation at tumor sites. Overall, CAGE-Prox offers a universal platform for time-resolved biological studies and on-demand therapeutic interventions under living conditions.

Authors

  • Xin Wang
    Key Laboratory of Bio-based Material Science & Technology (Northeast Forestry University), Ministry of Education, Harbin 150040, China.
  • Yuan Liu
    Department of General Surgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China.
  • Zhenchao Wang
    College of Pharmacy, Guizhou University, Guiyang, China.
  • Xiangmei Zeng
    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.
  • William Shu Ching Ngai
    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
  • Jie Wang
  • Heng Zhang
    Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Xiao Xie
    Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.
  • Rongfeng Zhu
    Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
  • Xinyuan Fan
    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.
  • Chu Wang
    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University , Beijing 100871, China.
  • Peng R Chen
    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China. Electronic address: pengchen@pku.edu.cn.

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