Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1

Effects of Point Mutations on the Thermal Stability of the NBD1 Domain of hCFTR

Cystic fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. The first nucleotide-binding domain (NBD1) of the CFTR is considered to be a hotspot for CF-causing mutations, and some of these mutations compromise the domain's thermal stability as well as its interactions with other domains. The mechanisms by which such mutations exert their deleterious effects are important in the basic research of this complex disease as well as for the development of mutation-specific therapies. With this in mind, we studied two class-II, severe, CF-causing mutations, L467P and A559T, known to destabilize the domain by 19.3 and 10.7 °C, respectively, and to lead to a misfolded, nonfunctioning CFTR, by conducting microsecond-long molecular dynamics (MD) simulations at an elevated temperature of 410 K on L467P-NBD1 and A559T-NBD1 constructs. For comparison, similar simulations were also performed on the wild-type (WT) construct and on the 6SS-NBD1 and 2PT/M470V-NBD1 constructs, both bearing sets of stabilizing mutations that stabilize the domain by 17.5 and 8.2 °C, respectively. The resulting trajectories were analyzed using multiple metrics, leading to a good correlation between the experimental ΔTm values and the results of the simulations, as well as multiple experimental observations and results of previous modeling efforts. Specifically, our analyses point to specific regions within NBD1 that are substantially affected by the L467P and A559T mutations and, therefore, may play some role in their pathogenesis. Many of these regions are also known to be important for the proper folding and function of the full-length CFTR. Using time-dependent assignment of DSSP elements, we also found that the two mutants follow different disintegration pathways, that of L467P-NBD1 starting in region 464-471 which resides within the F1-like ATP-binding core subdomain and continues in regions 550-562 and 514-523 within the ABCα subdomain whereas that of A559T-NBD1 simultaneously starting at the 550-562 and 514-523 regions. We propose that the analyses presented in this work may pave the way toward the development of L467P and A559T-specific CF therapies and by extension to other mutation-specific therapies for CF and for other diseases involving mutations in NBDs of other proteins.

Trikafta rescues F508del-CFTR by tightening specific phosphorylation-dependent interdomain interactions

Trikafta is well-known for correcting thermal and gating defects caused by the most common cystic fibrosis mutation F508del in the human cystic fibrosis transmembrane conductance regulator even at a physiological temperature. However, the exact correction pathway is still unclear. Here, noncovalent interactions among two transmembrane domains (TMD1 and TMD2), the regulatory (R) domain and two nucleotide binding domains (NBD1 and NBD2) were analyzed. The thermal stability of NBD1 was also evaluated through its tertiary constrained noncovalent interaction networks or thermoring structures. The results demonstrated that Trikafta binding to flexible TMD1 and TMD2 rearranged their interactions with the R domain upon phosphorylation, coupling tightened cytoplasmic TMD1-TMD2 interactions to tightened Mg/ATP-dependent NBD1-NBD2 dimerization, which stabilized NBD1 above human body temperature. Overall, although the deletion of F508 induces the primary thermal defect in NBD1 and then the gating defect at the TMD1-TMD2 interface, Trikafta rescued them in a reverse manner allosterically. These mechanistic insights into the precise correction pathway of this misfolded channel facilitate optimizing cystic fibrosis treatment.

Identification of novel natural compounds against CFTR p.Gly628Arg pathogenic variant

Cystic fibrosis transmembrane conductance regulator (CFTR) protein is an ion channel found in numerous epithelia and controls the flow of water and salt across the epithelium. The aim of our study to find natural compounds that can improve lung function for people with cystic fibrosis (CF) caused by the p.Gly628Arg (rs397508316) mutation of CFTR protein. The sequence of CFTR protein as a target structure was retrieved from UniProt and PDB database. The ligands that included Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and one Trikafta (R*) reference drug were screened out from PubChem database. Autodock vina software carried out docking, and binding energies between the drug and the target were included using docking-score. The following tools examined binding energy, interaction, stability, toxicity, and visualize protein-ligand complexes. The compounds having binding energies of -6.4, -5.1, -6.6, -5.1, and - 6.5 kcal/mol for Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and R*-drug, respectively with mutated CFTR (Gly628Arg) structure were chosen as the most promising ligands. The ligands bind to the mutated CFTR protein structure active sites in hydrophobic bonds, hydrogen bonds, and electrostatic interactions. According to ADMET analyses, the ligands Armepavine and Quercetin also displayed good pharmacokinetic and toxicity characteristics. An MD simulation for 200 ns was also established to ensure that Armepavine and Quercetin ligands attached to the target protein favorably and dynamically, and that protein-ligand complex stability was maintained. It is concluded that Armepavine and Quercetin have stronger capacity to inhibit the effect of mutated CFTR protein through improved trafficking and restoration of original function.

Synthesis and Biological Evaluation of Pyrazole-Pyrimidones as a New Class of Correctors of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)

Cystic fibrosis (CF) is caused by the functional expression defect of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Despite the recent success in CFTR modulator development, the available correctors only partially restore the F508del-CFTR channel function, and several rare CF mutations show resistance to available drugs. We previously identified compound 4172 that synergistically rescued the F508del-CFTR folding defect in combination with the existing corrector drugs VX-809 and VX-661. Here, novel CFTR correctors were designed by applying a classical medicinal chemistry approach on the 4172 scaffold. Molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted to propose a plausible binding site and design more potent and effective analogs. We identified three optimized compounds, which, in combination with VX-809 and the investigational corrector 3151, increased the plasma membrane density and function of F508del-CFTR and other rare CFTR mutants resistant to the currently approved therapies.

Fundamentals of HDX-MS

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.