Computational design of metalloproteases

De novo design of enzymes that cleave amide bonds represents a major challenge1,2. Here we use RFdiffusion methods3,4 to de novo design proteins with water-activating zinc-based active sites adjacent to a peptide substrate binding pocket. Of 135 designs tested, 36% catalyse cleavage of their cognate peptide substrates at the targeted scissile bond. The best design accelerates peptide-bond hydrolys