Partial filling capillary electrophoretic mobility shift competition assay: a versatile and reliable tool for the assessment of weak biomolecular interactions

Fragment-based drug discovery (FBDD) proved its efficacy in the past 20 years, due to its ability to perform efficient and fruitful optimization campaigns, and is now a well recognized strategy for both academia and pharmaceutical industry. FBDD detects low molecular-weight (MW) ligands (fragments) that bind to biologically important targets, then a structure-guided fragment growing or merging approach is performed giving rise to potent molecules with drug-like properties.
However, the analytical arsenal able to point out weak interactions is rather expensive, time consuming or unable to reflect the physiological environment. In this framework, we developed a generic, fully automated, microscale electrophoretic mobility shift competition assay that can be used for primary screening of weak biomolecular interactions between fragments and the target of interest.
The affinity capillary electrophoresis (ACE) competitive approach is based on the monitoring of the competition of fragments with a known target inhibitor (PL) for the same active site. The consequence of the competition is a modification of PL electrophoretic mobility, modification that can be measured and used for ligand screening and/or IC50 determination.
To achieve our goal, particular attention has been paid to the optimization of the binding environment parameters: an optimal buffer was used for the binding measurements, a partial filling approach was considered to gain sensitivity and to reduce protein consumption and a neutral dynamic coating was performed to reduce protein adsorption to the capillary wall. Moreover, the binding partners concentrations and the electrophoretic conditions were carefully optimized. It is noteworthy that the interactions occur in solution, using the protein in its native form, thus mimicking the physiological environment.The accuracy and reliability of the proposed method was demonstrated by monitoring the competition of two known fragments inhibiting thrombin, namely benzamidine and p-aminobenzamidine and a relatively weak inhibitor, nafamostat with a known thrombin inhibitor, pefabloc (PEFA). The measured IC50 were found to be in good accordance with the previously reported ones. Additionally, a small chemical library was built to evaluate the performance of the newly developed screening-bioassay. The optimized method proved to be remarkably reproducible (migration time RSDs < 1.2%) and selective. The results prove the high discriminatory potency of the method and its ability to screen neutral, negatively or positively charged molecules, as well as molecules that have no or low UV-VIS absorbance, significantly expanding the applicability of the assay compared to a direct approach [1].
Finally, the ability of this approach to discriminate between competitive and irreversible thrombin binders was also demonstrated.References
[1] E. Farcas, C. Bouckaert, A.-C. Servais, J. Hanson, L. Pochet, M. Fillet, Analytica Chimica Acta, 2017, 984, 211-222