New insights into structure and function of bis-phosphinic acid derivatives and implications for CFTR modulation

Abstract

C407 is a compound that corrects the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein carrying the p.Phe508del (F508del) mutation. We investigated the corrector effect of c407 and its derivatives on F508del-CFTR protein. Molecular docking and dynamics simulations combined with site-directed mutagenesis suggested that c407 stabilizes the F508del-Nucleotide Binding Domain 1 (NBD1) during the co-translational folding process by occupying the position of the p.Phe1068 side chain located at the fourth intracellular loop (ICL4). After CFTR domains assembly, c407 occupies the position of the missing p.Phe508 side chain. C407 alone or in combination with the F508del-CFTR corrector VX-809, increased CFTR activity in cell lines but not in primary respiratory cells carrying the F508del mutation. A structure-based approach resulted in the synthesis of an extended c407 analog G1, designed to improve the interaction with ICL4. G1 significantly increased CFTR activity and response to VX-809 in primary nasal cells of F508del homozygous patients. Our data demonstrate that in-silico optimized c407 derivative G1 acts by a mechanism different from the reference VX-809 corrector and provide insights into its possible molecular mode of action. These results pave the way for novel strategies aiming to optimize the flawed ICL4–NBD1 interface.

One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies

“…One of the first CFTR correctors to be identified, the benzo(c)quinolizinium compounds (MPBs) were thought to bind NBD1 and promote maturation as well as stimulate function [ 161 , 162 , 163 ]. Bis-phosphinic acid derivatives c407 and G1, targeting the NBD1, were recently modeled to fill the cavity left by the missing phenylalanine side chain in F508del, thereby restoring the NBD1:ICL4 interface [ 164 , 165 ]. In cell models, additivity of c407 with VX-809 suggests these compounds might represent a complementary MoA with existing CFTR corrector types.…”

Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing

“…Furthermore, the combination of three modulators (Trikafta) show a synergic effect that is achieved, once again, by the binding of the drugs to different CFTR regions [ 91 ]. Finally, the CFTR-rescuing activity of lumacaftor is increased when it is used in combination with digitoxigenin [ 83 ] and with C407, another corrector that binds the mutated CFTR in the same region here identified for NAM [ 14 ]. Interestingly, two of the three residues interacting with NAM (W496 of NBD1 and R1070 of ICL4) were found to also interact with C407 [ 14 ].…”

“…The second study, based on molecular docking and molecular dynamics, locates the lumacaftor in the first nucleotide-binding domain (NBD1), and reports the drug as able to induce the stabilization of the NBD1:ICL4 (IntraCellular Loop 4) interaction and the stabilization of the already-folded CFTR in its native conformation [ 12 , 13 ]. Similarly, a new low molecular weight (MW) compound (c407) has been recently described to rescue F508del-CFTR activity by binding the protein in a different site from that of lumacaftor, hence exerting a synergic effect when used in combination [ 14 ]. Accordingly, phenylsulfonamide-pyrrolopyridine acts synergistically with VX770 to increase the truncated W1282X-CFTR function [ 15 ].…”

Molecular mechanisms of cystic fibrosis – how mutations lead to misfunction and guide therapy

“…For instance, MCG1516A, a corrector additive to VX-661, was proposed to target the interface between NBD1 and NBD2 principally as it is not additive to the G550E revertant, in contrast to the R1070W one (at the interface between ICL4 and NBD1) [ 106 ]. Other corrector binding sites have been proposed within NBD1 [ 107 ] and at the NBD1:ICL4 interface [ 108–110 ].…”