Transplanting enzyme active site geometry into antibody CDRs for catalytic antibody design

Abstract

Abstract

Antibodies provide programmable molecular recognition, whereas enzymes enable repeated chemical transformation. Catalytic antibodies seek to combine these properties within a single protein scaffold. However, conventional approaches based on transition state analogue immunisation, library screening or local mutagenesis provide limited control over the atomic arrangement of catalytic residues. They also frequently produce antibodies that bind substrates without supporting efficient chemical turnover. Recent advances in generative protein design have enabled the construction of antibody complementarity determining regions and the scaffolding of functional motifs under structural constraints. A systematic strategy for transferring experimentally supported enzyme active site geometry into antibody variable domains is still lacking. Here, we present a computational framework that treats antibody and enzyme structures as distinct but complementary inputs. Developable Fv or VHH structures provide the immunoglobulin scaffold. Enzyme complexes containing substrates, products or transition state analogues provide catalytic residues, ligand conformations, metals, cofactors and key water networks. The selected catalytic atoms are mapped into antibody complementarity determining regions, while the surrounding loops are reconstructed using antibody compatible representations and constrained all atom diffusion. Sequence design and structural back prediction are followed by filters for antibody folding, catalytic geometry, ligand positioning, conformational stability and developability. The framework avoids direct fusion of intact enzymes and antibodies. Instead, it transfers only the local geometry required for catalysis. This separation of scaffold selection from catalytic motif selection creates a testable route for determining whether natural enzyme chemistry can be embedded within antibody formats. It also provides a practical basis for evaluating substrate binding, chemical conversion, product release and catalytic turnover as separate design objectives.