Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis (CF). The most prevalent CFTR mutation, ΔF508, blocks folding in the endoplasmic reticulum. Recent work has shown that some ΔF508-CFTR channel activity can be recovered by pharmaceutical modulators (“potentiators” and “correctors”), but ΔF508-CFTR can still be rapidly degraded via a lysosomal pathway involving the CFTR-associated ligand (CAL), which binds CFTR via a PDZ interaction domain. We present a study that goes from theory, to new structure-based computational design algorithms, to computational predictions, to biochemical testing and ultimately to epithelial-cell validation of novel, effective CAL PDZ inhibitors (called “stabilizers”) that rescue ΔF508-CFTR activity. To design the “stabilizers”, we extended our structural ensemble-based computational protein redesign algorithm to encompass protein-protein and protein-peptide interactions. The computational predictions achieved high accuracy: all of the top-predicted peptide inhibitors bound well to CAL. Furthermore, when compared to state-of-the-art CAL inhibitors, our design methodology achieved higher affinity and increased binding efficiency. The designed inhibitor with the highest affinity for CAL (kCAL01) binds six-fold more tightly than the previous best hexamer (iCAL35), and 170-fold more tightly than the CFTR C-terminus. We show that kCAL01 has physiological activity and can rescue chloride efflux in CF patient-derived airway epithelial cells. Since stabilizers address a different cellular CF defect from potentiators and correctors, our inhibitors provide an additional therapeutic pathway that can be used in conjunction with current methods. Author Summary: Cystic fibrosis (CF) is an inherited disease that causes the body to produce thick mucus that clogs the lungs and obstructs the breakdown and absorption of food. The cystic fibrosis transmembrane conductance regulator (CFTR) is mutated in CF patients, and the most common mutation causes three defects in CFTR: misfolding, decreased function, and rapid degradation. Drugs are currently being studied to correct the first two CFTR defects, but the problem of rapid degradation remains. Recently, key protein-protein interactions have been discovered that implicate the protein CAL in CFTR degradation. Here we have developed new computational protein design algorithms and used them to successfully predict peptide inhibitors of the CAL-CFTR interface. Our algorithm uses a structural ensemble-based evaluation of protein sequences and conformations to calculate accurate predictions of protein-peptide binding affinities. The algorithm is general and can be applied to a wide variety of protein-protein interface designs. All of our designed inhibitors bound CAL with high affinity. We tested our top binding peptide and observed that the inhibitor could successfully rescue CFTR function in CF patient-derived epithelial cells. Our designed inhibitors provide a novel therapeutic path which could be used in combination with existing CF therapeutics for additive benefit.