Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking

E- and VE-cadherins are among proteins forming intercellular junctions that are a crucial component of cell-cell adhesion in the intercellular junctions of the biological barriers (i.e., blood-brain barrier (BBB) and intestinal mucosa barrier). The BBB prevents the delivery of large therapeutic molecules from the systemic circulation to the central nervous system. Previously, HAV and ADT peptides that were identified from the extracellular-1 domain (EC1 domain) of E-cadherin successfully modulated the BBB intercellular junctions to improve the permeation of molecules across the BBB both in vivo and in vitro. Here, we use computational methods to perform a more exhaustive and systematic search for novel peptides that can effectively interfere with E-cadherin interactions to enhance the permeability of the BBB. In the first stage, computational protein-protein docking was employed to explore possible interactions between the first two extracellular domains of human E-cadherin (EC12). Based on the predicted model of binding interfaces, 115 different peptide sequences were proposed as candidates for disrupting cadherin-cadherin interactions in the BBB intercellular junctions. Next, the discovered peptides were redocked to E-cadherin, and the binding modes and affinities of peptide-protein complexes were analyzed. Using different protein-peptide docking methods, several peptides were identified as exhibiting a strong binding affinity for EC12, which were selected for future experimental validation and further sequence optimization. One initial peptide with a sequence of WVIPPIS was involved in a domain-swapping interaction; this peptide was synthesized, and its binding affinity to the recombinant EC1 domain was tested with surface plasmon resonance, yielding a dissociation constant <i>K</i>_D of 239 nM, corresponding to a binding free energy of -9.07 kcal/mol at 25 °C. Overall, our results present a systematic approach for generating novel peptides with high potential to disrupt the BBB for improving drug delivery to the brain.