Protein protein interactions are always a challenge to optimise and it looks like the latest offering from Google DeepMind may be of significant help.

Protein binders that can bind tightly to a target protein are hard to design. Traditional methods are time intensive, requiring multiple rounds of extensive lab work. After the binders are created, they undergo additional experimental rounds to optimize binding affinity, so they bind tightly enough to be usefu

AlphaProteo generates novel proteins that bind to other proteins. Given the structure of a target molecule and a set of preferred binding locations on that molecule, AlphaProteo generates a candidate protein that binds to the target at those locations.

Whilst code is not available, note

If you’re a biologist, whose research could benefit from target-specific protein binding, and you’d like to register interest in being a trusted tester for AlphaProteo, please reach out to us on alphaproteo@google.com.

I've been working with the BioFocus group at Chesterford Park (now part of Charles River) thinking about ligands for Protein Protein Interactions, some of the work was described on a poster at the 18th Cambridge Medicinal Chemistry Meeting held in Cambridge in September this year. The poster is now available online http://www.criver.com/files/pdfs/nonsource/do-privileged-ppi-scaffolds-exist.aspx

Protein-protein interactions (PPIs) are ubiquitous in cellular biochemistry; however they are often difficult drug targets to interrogate due to their unique molecular topologies. A consequence is that low hit rates are frequently observed in PPI HTS campaigns and there remains an unmet need for innovative small molecule PPI inhibitors (SMPPIIs). The term "privileged scaffold" was coined in 1988 when core structures were found to bind to more than one receptor with high affinity. This led us to pose the question: “Do privileged PPI scaffolds exist?”

A brilliant group of scientists to work with, many stimulating discussions in a very important area.

I’ve just added a section on Protein-Protein interactions.

These seem to be an increasingly popular target class and I’ hope to expand on it as we find out more.