Engineering Fast-Acting Covalent Protein Therapeutics

A team led by Bobo Dang and Ting Zhou at Westlake University have developed a high-throughput platform for developing fast-acting covalent protein therapeutics. This new platform, described in a Science paper, addresses key limitations in extending covalent strategies to protein therapeutics, particularly engineered miniproteins.

Development has been hindered by a kinetic mismatch: miniproteins clear rapidly in vivo, while covalent bond formation proceeds too slowly. High-throughput platforms for optimizing covalent reactivity have also been absent. The researchers proposed that precise spatial positioning of chemical warheads within protein scaffolds enables molecular preorganization, accelerating covalent bonds without raising intrinsic reactivity.

Their platform merges yeast surface display with chemoselective protein modification to screen diverse crosslinkers and millions of protein variants. Optimizing warhead placement and local chemical environment yields rapid, irreversible target engagement.

Applied to PD-L1, the platform produced IB101, a covalent antagonist. Structural analysis showed IB101 creates a binding pocket positioning the warhead optimally for accelerated covalent formation. IB101 blocks the PD-1/PD-L1 immune checkpoint, delivering strong antitumor activity in mouse models. Despite short in vivo half-life, IB101 ensures durable target engagement and tumor suppression, surpassing conventional antibodies under similar conditions.

The system also engineered IB201, a covalent IL-18 variant. IB201 rapidly forms covalent receptor bonds, boosting signaling strength and duration. In vivo, it triggers potent antitumor immune responses without systemic toxicity, showing covalent engineering's value for cytokine therapies.

Versatility extended to a covalent inhibitor of SARS-CoV-2's receptor-binding domain (RBD), achieving lasting viral neutralization across modalities.

This approach establishes a general strategy for covalent protein therapeutics. It aligns covalent bond formation with fast in vivo clearance timescales, resolving a core field limitation. The findings offer a framework for biologics combining rapid kinetics with sustained engagement, applicable to cancer immunotherapy, antiviral therapy, and more.