Monoclonal antibodies (ca. 150 kDa) and downsized variants such as Nanobodies (ca. 15 kDa) display remarkable specificity and high affinity binding capabilities. However, their therapeutic application is associated with some limitations, including limited in cellulo access and high therapeutic costs. These drawbacks entailed the development of smaller synthetic peptides (ca. 1-3 kDa) based on the paratopes of antibodies or Nanobodies, which so far only met limited success.1
In this context, we explored the feasibility of developing Nanobody-based peptide mimetics of limited molecular weight. Using a structure-based design strategy, several peptidomimetics were developed from the complementarity-determining regions (CDR) of a Nanobody. This Nanobody modulates the nucleotide exchange activity on RAS proteins by interaction with the intracellular RAS:SOS1 complex. Activating mutations in RAS proteins play a crucial role in the development of multiple human cancer types and developmental disorders,2 for which the regulatory guanine exchange factor (GEF) SOS1 represents an attractive therapeutic target.
Guided by a biochemical GEF assay, efficacious CDR3 loop mimetics were developed within a few rounds of optimization by substitution with some (un)natural amino acids and introduction of cyclization tethers. In addition, selected peptidomimetics were found to structurally mimic the native Nanobody CDR3 loop, presenting similar binding poses upon interaction with the RAS:SOS1 complex (as demonstrated by X-ray analysis). Altogether, we provided the first solid proof-of-principle that small peptidomimetics can be developed which mimic both structurally and functionally protein-protein modulatory Nanobodies.