Speeding Up the Identification of Cystic Fibrosis Transmembrane Conductance Regulator-Targeted Drugs: An Approach Based on Bioinformatics Strategies and Surface Plasmon Resonance

Abstract

Cystic fibrosis (CF) is mainly caused by the deletion of Phe 508 (ΔF508) in the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. New drugs able to rescue ΔF508-CFTR trafficking are eagerly awaited. An integrated bioinformatics and surface plasmon resonance (SPR) approach was here applied to investigate the rescue mechanism(s) of a series of CFTR-ligands including VX809, VX770 and some aminoarylthiazole derivatives (AAT). Computational studies tentatively identified a large binding pocket in the ΔF508-CFTR nucleotide binding domain-1 (NBD1) and predicted all the tested compounds to bind to three sub-regions of this main pocket. Noticeably, the known CFTR chaperone keratin-8 (K8) seems to interact with some residues located in one of these sub-pockets, potentially interfering with the binding of some ligands. SPR results corroborated all these computational findings. Moreover, for all the considered ligands, a statistically significant correlation was determined between their binding capability to ΔF508-NBD1 measured by SPR and the pockets availability measured by computational studies. Taken together, these results demonstrate a strong agreement between the in silico prediction and the SPR-generated binding data, suggesting a path to speed up the identification of new drugs for the treatment of cystic fibrosis.

Structural mechanisms of CFTR function and dysfunction

“…Furthermore, evidence also showed that TMD1 is the shortest-length fragment of CFTR required for the action of VX-809 ( Ren et al, 2013 ), arguing against a role of NBD1–ICL4 interface in forming the binding site for VX-809. A different binding site for VX-809 was lately proposed ( Rusnati et al, 2018 ). Using molecular dynamic simulation and surface Plasmon resonance, they showed that three residues in the NBD1, Y577, V580, and E655, anchored VX-809 through hydrogen bonds.…”

Virtual Screening of Marine Natural Compounds by Means of Chemoinformatics and CDFT-Based Computational Peptidology

“…Drug design can be pursued following a methodology driven by advancement and innovation breakthroughs including a combination of experimental and computational strategies. Computational strategies play a pivotal part in advanced therapeutic chemistry, displaying a special potential for changing the early stages in the process of drug discovery, especially in terms of time and cost savings [1,2].…”

Recent Strategic Advances in CFTR Drug Discovery: An Overview

“…Important to note, the validity of the proposed pipeline can be already assessed retrospectively, by evaluating the degree of consensus of the prediction and results obtained with the various techniques employed. In effect, already reported cases of this consensus are: computational predictions vs. SPR [52] or vs. cell-based assays [49], immunoprecipitation vs. overlay assays or vs. SPR [70], SPR vs. thermostability assays or vs. cell-based assays [48].…”

“…Among the computational models listed above, only a few have been used to better characterize the binding mode of known F508del-CFTR-rescuing drugs, to virtually screen libraries of molecules aimed at the identification of new putative F508del-CFTR-binding compounds or to design new CFTR-targeted drugs [48,49]. On the contrary, a huge amount of computational studies has been developed in the attempt of clarifying at a molecular level the mechanism of action of F508del-CFTR-ligands, using several NBDs RX data [23,[50][51][52] or the more recent cryo EM structures [53].…”

“…(ii) SPR has been used to the study of the direct interaction with mutated CFTR of correctors VRT-325 and Corr-4a [14] and of either F508del-NBD1 [52] or intact F508del-CFTR [48] with a panel of AAT derivatives. Additionally, the pyrazole compound 4172 was demonstrated to bind F508del-CFTR with an affinity that is 25 times higher than that of the first identified type III corrector BIA [73].…”