Design of High Affinity Binders to Convex Protein Target Sites

Baker, D.; Yang, W.; Hicks, D. R.; Ghosh, A.; Schwartze, T. A.; Coventry, B.; Goreshnik, I.; Allen, A.; Halabiya, S.; Kim, C.; Hinck, C. S.; Lee, D. S.; Bera, A.; Li, Z.; Wang, Y.; Schlichthaerle, T.; Cao, L.; Huang, B.; Garrett, S.; Gerben, S. R.; Rettie, S.; Heine, P.; Edman, N.; Murray, A. N.; Carter, L. P.; Stewart, L.; Almo, S.; Hinck, A. P.

doi:10.1101/2024.05.01.592114

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bioRxiv · 10.1101/2024.05.01.592114

Design of High Affinity Binders to Convex Protein Target Sites

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Abstract

While there has been progress in the de novo design of small globular miniproteins (50-65 residues) to bind to primarily concave regions of a target protein surface, computational design of minibinders to convex binding sites remains an outstanding challenge due to low level of overall shape complementarity. Here, we describe a general approach to generate computationally designed proteins which bind to convex target sites that employ geometrically matching concave scaffolds. We used this approach to design proteins binding to TGF{beta}RII, CTLA-4 and PD-L1 which following experimental optimization have low nanomolar to picomolar affinities and potent biological activity. Co-crystal structures of the TGF{beta}RII and CTLA-4 binders in complex with the receptors are in close agreement with the design models. Our approach provides a general route to generating very high affinity binders to convex protein target sites.

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Baker, D., Yang, W., Hicks, D. R., Ghosh, A., Schwartze, T. A., Coventry, B., Goreshnik, I., Allen, A., Halabiya, S., Kim, C., Hinck, C. S., Lee, D. S., Bera, A., Li, Z., Wang, Y., Schlichthaerle, T., Cao, L., Huang, B., Garrett, S., Gerben, S. R., Rettie, S., Heine, P., Edman, N., Murray, A. N., Carter, L. P., Stewart, L., Almo, S., Hinck, A. P.. 2024-05-03. Design of High Affinity Binders to Convex Protein Target Sites. https://doi.org/10.1101/2024.05.01.592114

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