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A team led by David Baker designed a synthetic serine hydrolase from scratch to carry out the successive steps of ester hydrolysis. Chemistry World reported on 25 February 2025 that the best tested designs showed activity it characterized as comparable to natural proteases—a promising laboratory result, not evidence of a commercial enzyme or industrial process.
What the team designed
The target was a serine hydrolase, an enzyme that breaks an ester bond through hydrolysis. The reaction proceeds through four mechanistic steps, so a successful design must support more than a single chemical event: its active site needs to help the substrate and reaction intermediates adopt useful arrangements as the process advances.
The designed active site centers on a catalytic triad of serine, histidine, and aspartate. A nearby oxyanion hole helps orient the substrate in reactive conformations. Rather than adapting a naturally occurring enzyme to perform a new job, the team began with the desired reaction and specified an arrangement of amino acids intended to support it.
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Why a multi-step reaction is a harder design problem
Designing a protein around one favorable arrangement does not guarantee it will support every stage of a reaction. As the chemistry proceeds, the substrate changes into intermediates, and the active site must stabilize the relevant states without trapping the process partway through. Chemistry World explains that designs built around fixed scaffolds can struggle to adapt to these successive stages, leaving a reaction stalled at an intermediate.
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The challenge, then, is not simply to place catalytic amino acids near a substrate. The protein’s structure must hold those amino acids in a useful geometry and accommodate the chemical sequence through its later steps.
How the AI-assisted design pipeline worked
- Specify the catalytic geometry. The team defined the desired active-site arrangement, including the catalytic residues and the geometry needed for the reaction.
- Generate a surrounding protein structure. The researchers used RFdiffusion to generate a protein intended to hold the active site in the specified configuration.
- Find a compatible sequence. A second AI algorithm generated an amino-acid sequence predicted to fold into the proposed structure.
- Assess reaction intermediates. A third program evaluated whether candidate designs could stabilize intermediates across the reaction mechanism.
- Test candidates in the lab. The team reportedly generated close to 1,000 designs, prepared and tested selected candidates predicted to support the complete reaction, and tracked ester hydrolysis with fluorescent markers.
Sam Pellock, a postdoctoral researcher in the Baker lab, described the structure-generation stage to Chemistry World this way: “We take the 3D coordinates of this site and feed it into an AI algorithm called RFdiffusion which generates an entire protein that perfectly holds this active site.”
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What performance was reported
Chemistry World described the best tested enzymes as having activity comparable to natural proteases and called the result a substantial improvement over earlier designed proteins. That is a qualitative characterization in the report: it does not provide an exact activity rate or a numerical comparison with a named natural enzyme, so there is no defensible figure to quote here.
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1Fix the driver behind crashes, sound loss and screen glitches2Repair Windows errors before they cause bigger problems3Scan for outdated or missing drivers - takes under a minuteThe significance is that the researchers reported activity across a multi-step reaction designed from its mechanism, rather than a protein that merely binds a target or supports one isolated stage. The findings are attributed to the team’s laboratory tests as reported by Chemistry World; the available reporting does not establish how the design performs beyond the tested reaction and enzyme class.
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What the result does—and does not—show
- Demonstrated: a designed serine hydrolase was experimentally tested for ester hydrolysis, and the strongest designs were reported to have activity qualitatively comparable to natural proteases.
- Not established by the report: an exact kinetic constant, yield, or quantitative comparison against a particular natural enzyme.
- Still a future direction: extending the approach to other enzyme classes, reactions involving metals or cofactors, and industrial applications.
Victor Guallar, a protein-modelling researcher at the Barcelona Supercomputing Center, called the catalytic efficiencies a “big success” but described extension to additional enzymes and finding an industrial application as next steps. The distinction matters: a laboratory design result can suggest a route toward useful catalysts without demonstrating manufacturing performance, commercial availability, or a ready-to-use product.
Why starting from the reaction matters
Much enzyme engineering begins with a natural enzyme and modifies it to perform a different reaction. Baker described the alternative strategy to Chemistry World as “starting from the reaction,” with amino acids arranged in a desired geometry and generative models used to create proteins containing that active site. This reverses the usual starting point: instead of asking how far an existing protein can be repurposed, the designers specify the chemistry they want and build a protein around it.
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That approach is promising because it treats the reaction mechanism—not just a protein scaffold—as a design constraint. Max Fürst, an enzymologist at the University of Groningen, praised the step-wise pipeline for allowing researchers to dissect what the mechanism requires. He also said the approach could open the door to designing reactions themselves, while describing that prospect as an exciting direction for the field.
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The result was reported by Victoria Atkinson in Chemistry World on 25 February 2025: “Designer protein performs multi-step catalysis with life-like performance”. The University of Groningen research portal’s expert-commentary record cites A. Lauko et al., Science (2025), DOI 10.1126/science.adu2454. This account relies on the accessible reporting and portal record; detailed experimental conditions and quantitative kinetics are not stated in those materials.
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