Structure/function & evolution of protein interactions towards drug design

Protein complexation occurs through kinetic processes within the crowded cellular environment. We utilize biophysical tools, protein-engineering techniques, in vitro evolution, and simulations to deepen our understanding of protein interactions and to inform their design.

For instance, we have recently developed a SARS-CoV-2 inhibitor through an innovative yeast display in vitro evolution technique. This inhibitor has been shown in primate studies to effectively block CoV-2 entry, regardless of the variant. Additionally, our use of in vitro evolution mimics the virus's own evolutionary path to its present strains.

In our investigations into protein interactions in crowded environments, we made an unexpected discovery: the association and dissociation rate constants in these conditions are nearly as fast as those in water, likely due to the occluded volume effect. This insight led us to examine enzymatic reactions within living cells, where we observed that the degradation of substrates by beta-lactamase was limited by the substrate availability, despite its apparent abundance. This prompted further study into the diffusion rates of small molecules in crowded environments and within cells.

Our findings indicate that basic substrates diffuse slowly within cells due to sequestration, potentially in lysosomes or other areas. Modifying these small molecules can significantly affect their reactivity, offering crucial insights for drug design, particularly since most drugs are basic in nature. These studies underscore the complex interplay between dynamics and the cellular environment, with important implications for the development and optimization of therapeutic agents.