Designing de novo binders to TNFα

Obtain experimentally verified de novo designed protein binders to human tumor necrosis factor alpha (TNFα), specifically targeting the polar interface between two subunits of the TNFα homotrimer, with measurable binding affinity.

Background

TNFα is a pro-inflammatory cytokine and a major therapeutic target in inflammatory disease. The authors selected TNFα as a highly challenging target based on in silico analysis and attempted de novo binder design using AlphaProteo, focusing on a polar region at the interface between two subunits of the homotrimer.

Despite successes across seven other targets, the authors were unable to obtain binding hits for TNFα. They suggest this difficulty may be due to the flat, highly polar binding site, highlighting an unresolved design challenge for this target and similar interfaces.

References

Given TNFα's unusual in silico difficulty and high biomedical importance, we designed and experimentally tested binders to this target, but failed to obtain hits.

— De novo design of high-affinity protein binders with AlphaProteo (2409.08022 - Zambaldi et al., 12 Sep 2024) in Section 2.1, Subsubsection “Multiple binding hits within one 96-well plate of designs per target”