Towards the Targeting of Self-Assembling Proteins in Drug Design

The last decade has seen the targeting of protein-protein interactions (PPIs) emerging as a new strategy of drug design. This strategy allowed to tackle challenging drug targets – sometimes referred as undruggable – whose active site cannot usually be drugged. The originality of the present project is to extend the methodology of PPI targeting to homomeric interfaces, i.e. targeting PPIs between monomers of the same drug target in order to disrupt its quaternary structure. These numerous PPIs constitute an underexplored pool of potential targets for therapeutic interventions.
Our working hypothesis is that targeting the self-assembly of homomeric enzymes should provide a novel drug design approach. Our main goals are to develop a robust analytical/biophysical platform to characterize and assess homomeric protein-protein interactions (PPIs) and to identify new hit compounds (peptides and/or irreversible inhibitors) able to target these PPIs.
In previous and ongoing works, two case studies involving two different oligomeric disruption strategies were investigated: (i) the design of (stapled)peptides to target the lactate dehydrogenase (LDH) tetrameric form and (ii) the design of allosteric covalent drugs targeting the phosphoglycerate dehydrogenase (PHGDH) tetramer. Based on these strong preliminary results, we will tailor our collaborative platform and network to tackle challenging targets through the self-association process. To extend the developed tools and strategies made on PHGDH and LDH, two other drug targets active as homomer will be introduced, the phosphoserine phosphatase (Ser B), a validated target in the search of antitubercular antibiotics, and arginase, an arginine-catabolizing enzyme notably involved in the phenomenon of tumoral immune escape.
Developing homomeric disruptors involves several technical challenges and we will thus rely on the use of specific experimental tools to monitor protein self-association and protein-drug interactions. A combined use of analytical instrumentations will be necessary to tackle the conformational dynamics of the systems, the conformation-driven aspects of protein: ligand interactions and the unbiased screening for modulators of protein-protein interactions. With those aims in view, orthogonal approaches will be used, namely thermophoresis, nuclear magnetic resonance, chromatography, electrophoresis, mass spectrometry, crystallography, and immuno-based assays.
Ultimately, the present project could thus inspire the elaboration of a repertoire of targets that are usually qualified as undruggable, but that could potentially be drugged at their oligomeric interfaces. Hence, our collaborative project not only aims at establishing new fundamental knowledge’s on protein self-assembly and their targeting but also at the setting up of experimental and modeling methodologies to interrogate the self-assembly.