Beyond evolution: De novo designed protein toolkit rewriting the rules of synthetic biology

Artificial intelligence (AI)-driven de novo protein design is revolutionizing synthetic biology by facilitating the first-principle rational engineering of protein-based functional modules unbound by known structural templates and evolutionary constraints, enabling a diverse range of applications. Expressing these novel, structurally unprecedented proteins within cellular systems inherently adds complexity to their functional unpredictability. Robust biosafety and bioethics evaluations are therefore required to address potential risks such as immune reactions, cellular pathway disruptions, and environmental persistence. We systematically analyse the computational frameworks underpinning this revolution and highlight the capability of de novo proteins to act as a modular toolkit for synthetic biology. Looking forward, we envision integrating closed-loop validation with multi-omics profiling for comprehensive risk assessments along with a hierarchical design framework for advancing the future of synthetic biology - from the creation of tailored de novo functional protein modules and structure-guided rational genetic circuits design to the development of full-synthetic cellular systems, thereby establishing a scalable path from protein design to system-level implementation.