Chemical biology and structural studies on the bidirectional allosteric mechanism of regulation of phosphoinositide-dependent protein kinase 1 PDK1 (Póster))

LISSY GROSS; MARIANA SACERDOTI; ALEJANDRO E. LEROUX; ABHIJEET GHODE; GANESH S. ANAND; JÖRG O. SCHULZE; SEBASTIÁN KLINKE; RICARDO M. BIONDI

Evento online debido a la pandemia de coronavirus

Simposio; PDB50: A special symposium celebrating the 50th anniversary of the Protein Data Bank; 2021

American Society for Biochemistry and Molecular Biology (ASBMB)

Phosphoinositide-dependent protein kinase 1 (PDK1) is a master AGC kinase of the PI3K signalling pathway that phosphorylates at least other 23 AGC kinases, being PKB/Akt the most relevant substrate for growth and cell survival, and therefore a potential drug target for cancer treatment. Over the years, our laboratory used a chemical and structural biology approach to study and characterize in detail the allosteric regulation of the catalytic domain of PDK1. We developed small compounds that bind to a regulatory site, termed the PIF-pocket, and activate PDK1, mimicking the mechanism of activation of AGC kinases by phosphorylation. Using an integrative approach between biochemistry, crystallography and molecular dynamics, we first demonstrated an allosteric regulation from a regulatory site to the active site, and the existence of the reverse process. This bidirectional allosteric mechanism of regulation between both pockets can therefore be modulated by small molecules that bind to their specific orthosteric site and either enhance or inhibit interactions at the allosteric site. Taking this into consideration, it is not surprising that while the pharmaceutical industry has been developing compounds that bind at the ATP-binding site of kinases, they unwillingly developed drugs that affect protein kinase-protein interactions. Therefore, two compounds that equally inhibit the activity of a given kinase could have drastic differences in cells and patients if they differentially affect the formation of protein kinase complexes. We now provide further evidence of the bidirectional system using hydrogen/deuterium exchange (HDX) experiments and present a rather complete structural model for a kinase that can be modulated bidirectionally with small compounds. On the other hand, could metabolites bind at the active site of protein kinases and physiologically regulate the formation of protein kinase complexes? We found that adenosine binds at the ATP-binding site and allosterically enhances interactions in the PIF-Pocket regulatory site of PDK1. The findings open the possibility that the physiological regulation of the kinase complexes may be modulated by metabolites and implies that the metabolic state of cells could directly feedback to the regulation of cell signalling.