BindCraft generates novel peptides to improve gene therapy vectors

© 2025 EPFL

© 2025 EPFL

The group of Bruno Correia at EPFL reported in the journal Nature a new open-source AI platform called ‘BindCraft’ for the discovery of protein binders. As an evolution of AlfaFold2 for protein structure prediction, this user-friendly tool offers unprecedented efficacy for de novo design of protein-protein interactors, with many foreseen applications. In collaboration with Christian Schellhaas and Lennart Nickel from the Correia Lab, the EPFL Bertarelli Platform for Gene Therapy (PTBTG) explored a novel important application of this technology, using protein binders designed with BindCraft to engineer the surface of the adeno-associated viral (AAV) vectors.

AAV vectors have been successfully applied for several therapeutic applications, reaching clinical practice during the past few years. However, the natural serotypes that are typically used for gene therapy have the disadvantage to target a broad range of different cells and tissues. Because of this, high vector doses need to be injected into patients and there is an increased risk of side effects as the vector also targets cells or tissues that are not primarily involved in the disease.

To address this problem, we generated a ‘de-targeted’ AAV vector no more able to transduce cells in the dish by mutating key amino acids responsible for its primary interaction with glycans. Next, miniproteins were designed using BindCraft to bind a selected receptor on the cell surface. When modified by incorporating these peptides into the capsid, AAV gained the ability to transduce only the cells expressing the targeted receptor. We are currently further harnessing this approach to generate novel, more specific AAV vectors either as research tool or for ‘precision’ gene therapy.

References

Pacesa, M., Nickel, L., Schellhaas, C. et al. One-shot design of functional protein binders with BindCraft. Nature (2025). https://doi.org/10.1038/s41586-025-09429-6