Transcriptomic and Proteostasis Networks of CFTR and the Development of Small Molecule Modulators for the Treatment of Cystic Fibrosis Lung Disease

Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The diversity of mutations and the multiple ways by which the protein is affected present challenges for therapeutic development. The observation that the Phe508del-CFTR mutant protein is temperature sensitive provided proof of principle that mutant CFTR could escape proteosomal degradation and retain partial function. Several specific protein interactors and quality control checkpoints encountered by CFTR during its proteostasis have been investigated for therapeutic purposes, but remain incompletely understood. Furthermore, pharmacological manipulation of many CFTR interactors has not been thoroughly investigated for the rescue of Phe508del-CFTR. However, high-throughput screening technologies helped identify several small molecule modulators that rescue CFTR from proteosomal degradation and restore partial function to the protein. Here, we discuss the current state of CFTR transcriptomic and biogenesis research and small molecule therapy development. We also review recent progress in CFTR proteostasis modulators and discuss how such treatments could complement current FDA-approved small molecules.

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Characterization of Small Molecule Modulators of the Cystic Fibrosis Transmembrane Conductance Regulator using Backscattering Interferometry

Biophysical Journal ◽

10.1016/j.bpj.2014.11.3193 ◽

2015 ◽

Vol 108 (2) ◽

pp. 585a

Author(s):

Ashley Lockwood ◽

David Heidary ◽

Christopher Richards ◽

Michael Baksh ◽

M.G. Finn

Keyword(s):

Cystic Fibrosis ◽

Small Molecule ◽

Transmembrane Conductance Regulator ◽

Transmembrane Conductance ◽

Backscattering Interferometry ◽

Small Molecule Modulators ◽

Cystic Fibrosis Transmembrane

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Identification of Small Molecule Modulators of Diguanylate Cyclase by FRET-based High-Throughput-Screening

10.1101/402909 ◽

2018 ◽

Author(s):

Matthias Christen ◽

Cassandra Kamischke ◽

Hemantha D. Kulasekara ◽

Kathleen C. Olivas ◽

Bridget R. Kulasekara ◽

...

Keyword(s):

Small Molecules ◽

Small Molecule ◽

High Throughput ◽

Biofilm Formation ◽

High Throughput Screening ◽

Diguanylate Cyclase ◽

Chronic Infections ◽

Structure Activity ◽

Diguanylate Cyclases ◽

Small Molecule Modulators

The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) is a key regulator of cellular motility, the cell cycle, and biofilm formation with its resultant antibiotic tolerance, which may make chronic infections difficult to treat. Therefore, diguanylate cyclases, which regulate the spatiotemporal production of c-di-GMP, may be attractive drug targets to control biofilm formation that is part of chronic infections. In this paper, we present a FRET-based biochemical high-throughput screening approach coupled with detailed structure-activity studies to identify synthetic small molecule modulators of the diguanylate cyclase, DgcA, from Caulobacter crescentus. We identified a set of 7 small molecules that in the low µM range regulate DgcA enzymatic activity. Subsequent structure activity studies on selected scaffolds revealed a remarkable diversity of modulatory behaviors, including slight chemical substitutions that revert the effects from allosteric enzyme inhibition to activation. The compounds identified represent novel chemotypes and are potentially developable into chemical genetic tools for the dissection of c-di-GMP signaling networks and alteration of c-di-GMP associated phenotypes. In sum, our studies underline the importance for detailed mechanism of action studies for inhibitors of c-di-GMP signaling and demonstrate the complex interplay between synthetic small molecules and the regulatory mechanisms that control the activity of diguanylate cyclases.

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The Druggable Genome as Seen from the Protein Data Bank

10.1101/2020.02.06.937730 ◽

2020 ◽

Author(s):

Jiayan Wang ◽

Setayesh Yazdani ◽

Ana Han ◽

Matthieu Schapira

Keyword(s):

Human Genome ◽

Small Molecule ◽

Data Bank ◽

Specific Protein ◽

Genome Project ◽

Protein Families ◽

Small Molecule Ligands ◽

Human Proteins ◽

Small Molecule Modulators ◽

Druggable Genome

AbstractAlmost twenty years after the human genome was sequenced, the wealth of data produced by the international human genome project has not translated into a significantly improved drug discovery enterprise. This is in part because small molecule modulators that could be used to explore the cellular function of their target proteins and to discover new therapeutic opportunities are only available for a limited portion of the human proteome. International efforts are underway to develop such chemical tools for a few, specific protein families, and a “Target 2035” call to enable, expand and federate these efforts towards a comprehensive chemical coverage of the druggable genome was recently announced. But what is the druggable genome? Here, we systematically review structures of human proteins bound to drug-like ligands available from the protein databank (PDB) and use ligand desolvation upon binding as a druggability metric to draw a landscape of the human druggable genome. We show that the vast majority of druggable protein families, including some highly populated and deeply associated with cancer according to genomic screens, are almost orphan of small molecule ligands, and propose a list of 46 druggable domains representing 3440 human proteins that could be the focus of large chemical probe discovery efforts.

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Identification of Small‐Molecule Modulators of Diguanylate Cyclase by FRET‐Based High‐Throughput Screening

ChemBioChem ◽

10.1002/cbic.201800593 ◽

2018 ◽

Vol 20 (3) ◽

pp. 394-407 ◽

Cited By ~ 5

Author(s):

Matthias Christen ◽

Cassandra Kamischke ◽

Hemantha D. Kulasekara ◽

Kathleen C. Olivas ◽

Bridget R. Kulasekara ◽

...

Keyword(s):

Small Molecule ◽

High Throughput ◽

High Throughput Screening ◽

Diguanylate Cyclase ◽

Small Molecule Modulators

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Insights into the mechanisms underlying CFTR channel activity, the molecular basis for cystic fibrosis and strategies for therapy

Essays in Biochemistry ◽

10.1042/bse0500233 ◽

2011 ◽

Vol 50 ◽

pp. 233-248 ◽

Cited By ~ 30

Author(s):

Patrick Kim Chiaw ◽

Paul D.W. Eckford ◽

Christine E. Bear

Keyword(s):

Cystic Fibrosis ◽

Small Molecule ◽

Molecular Basis ◽

Structural Changes ◽

Common Mutation ◽

Channel Activity ◽

Wild Type ◽

In The Wild ◽

Cftr Protein ◽

Small Molecule Modulators

Mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) cause CF (cystic fibrosis), a fatal genetic disease commonly leading to airway obstruction with recurrent airway inflammation and infection. Pulmonary obstruction in CF has been linked to the loss of CFTR function as a regulated Cl− channel on the lumen-facing membrane of the epithelium lining the airways. We have learned much about the molecular basis for nucleotide- and phosphorylation-dependent regulation of channel activity of the normal (wild-type) version of the CFTR protein through electrophysiological studies. The major CF-causing mutation, F508del-CFTR, causes the protein to misfold and be retained in the ER (endoplasmic reticulum). Importantly, recent studies in cell culture have shown that retention in the ER can be ‘corrected’ through the application of certain small-molecule modulators and, once at the surface, the altered channel function of the major mutant can be ‘potentiated’, pharmacologically. Importantly, two such small molecules, a ‘corrector’ (VX-809) and a ‘potentiator’ (VX-770) compound are undergoing clinical trial for the treatment of CF. In this chapter, we describe recent discoveries regarding the wild-type CFTR and F508del-CFTR protein, in the context of molecular models based on X-ray structures of prokaryotic ABC (ATP-binding cassette) proteins. Finally, we discuss the promise of small-molecule modulators to probe the relationship between structure and function in the wild-type protein, the molecular defects caused by the most common mutation and the structural changes required to correct these defects.

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