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Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, Hunt JF. Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator. J Biol Chem 2018; 293:17685-17704. [PMID: 29903914 PMCID: PMC6240863 DOI: 10.1074/jbc.ra117.000819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/31/2018] [Indexed: 01/07/2023] Open
Abstract
Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.
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Affiliation(s)
- Chi Wang
- From the Departments of Biological Sciences and
| | - Andrei A. Aleksandrov
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Zhengrong Yang
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | | | - Elizabeth A. Proctor
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pradeep Kota
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jianli An
- the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and
| | - Anna Kaplan
- From the Departments of Biological Sciences and
| | - Netaly Khazanov
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Brent R. Stockwell
- From the Departments of Biological Sciences and ,Chemistry, Columbia University, New York, New York 10027
| | - Hanoch Senderowitz
- the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Nikolay V. Dokholyan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R. Riordan
- the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - John F. Hunt
- From the Departments of Biological Sciences and , To whom correspondence should be addressed. Tel.:
212-854-5443; Fax:
212-865-8246; E-mail:
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Hutt DM, Loguercio S, Campos AR, Balch WE. A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease. J Mol Biol 2018; 430:2951-2973. [PMID: 29924966 PMCID: PMC6097907 DOI: 10.1016/j.jmb.2018.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
The advent of precision medicine for genetic diseases has been hampered by the large number of variants that cause familial and somatic disease, a complexity that is further confounded by the impact of genetic modifiers. To begin to understand differences in onset, progression and therapeutic response that exist among disease-causing variants, we present the proteomic variant approach (ProVarA), a proteomic method that integrates mass spectrometry with genomic tools to dissect the etiology of disease. To illustrate its value, we examined the impact of variation in cystic fibrosis (CF), where 2025 disease-associated mutations in the CF transmembrane conductance regulator (CFTR) gene have been annotated and where individual genotypes exhibit phenotypic heterogeneity and response to therapeutic intervention. A comparative analysis of variant-specific proteomics allows us to identify a number of protein interactions contributing to the basic defects associated with F508del- and G551D-CFTR, two of the most common disease-associated variants in the patient population. We demonstrate that a number of these causal interactions are significantly altered in response to treatment with Vx809 and Vx770, small-molecule therapeutics that respectively target the F508del and G551D variants. ProVarA represents the first comparative proteomic analysis among multiple disease-causing mutations, thereby providing a methodological approach that provides a significant advancement to existing proteomic efforts in understanding the impact of variation in CF disease. We posit that the implementation of ProVarA for any familial or somatic mutation will provide a substantial increase in the knowledge base needed to implement a precision medicine-based approach for clinical management of disease.
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Affiliation(s)
- Darren M Hutt
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Salvatore Loguercio
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
| | - Alexandre Rosa Campos
- Sanford Burnham Prebys Medical Discovery Institute Proteomic Core 10901 North Torrey Pines Road, La Jolla CA USA 92037
| | - William E Balch
- The Scripps Research Institute, Department of Molecular Medicine, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- Integrative Structural and Computational Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
- The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Rd, La Jolla CA USA 92037
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53
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Gentzsch M, Mall MA. Ion Channel Modulators in Cystic Fibrosis. Chest 2018; 154:383-393. [PMID: 29750923 PMCID: PMC6113631 DOI: 10.1016/j.chest.2018.04.036] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/15/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and remains one of the most common life-shortening genetic diseases affecting the lung and other organs. CFTR functions as a cyclic adenosine monophosphate-dependent anion channel that transports chloride and bicarbonate across epithelial surfaces, and disruption of these ion transport processes plays a central role in the pathogenesis of CF. These findings provided the rationale for pharmacologic modulation of ion transport, either by targeting mutant CFTR or alternative ion channels that can compensate for CFTR dysfunction, as a promising therapeutic approach. High-throughput screening has supported the development of CFTR modulator compounds. CFTR correctors are designed to improve defective protein processing, trafficking, and cell surface expression, whereas potentiators increase the activity of mutant CFTR at the cell surface. The approval of the first potentiator ivacaftor for the treatment of patients with specific CFTR mutations and, more recently, the corrector lumacaftor in combination with ivacaftor for patients homozygous for the common F508del mutation, were major breakthroughs on the path to causal therapies for all patients with CF. The present review focuses on recent developments and remaining challenges of CFTR-directed therapies, as well as modulators of other ion channels such as alternative chloride channels and the epithelial sodium channel as additional targets in CF lung disease. We further discuss how patient-derived precision medicine models may aid the translation of emerging next-generation ion channel modulators from the laboratory to the clinic and tailor their use for optimal therapeutic benefits in individual patients with CF.
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Affiliation(s)
- Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, NC; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health, Berlin, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research, University of Heidelberg, Heidelberg, Germany.
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54
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Chin S, Hung M, Won A, Wu YS, Ahmadi S, Yang D, Elmallah S, Toutah K, Hamilton CM, Young RN, Viirre RD, Yip CM, Bear CE. Lipophilicity of the Cystic Fibrosis Drug, Ivacaftor (VX-770), and Its Destabilizing Effect on the Major CF-causing Mutation: F508del. Mol Pharmacol 2018; 94:917-925. [PMID: 29903751 DOI: 10.1124/mol.118.112177] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022] Open
Abstract
Deletion of phenylalanine at position 508 (F508del) in cystic fibrosis transmembrane conductance regulator (CFTR) is the most common cystic fibrosis (CF)-causing mutation. Recently, ORKAMBI, a combination therapy that includes a corrector of the processing defect of F508del-CFTR (lumacaftor or VX-809) and a potentiator of channel activity (ivacaftor or VX-770), was approved for CF patients homozygous for this mutation. However, clinical studies revealed that the effect of ORKAMBI on lung function is modest and it was proposed that this modest effect relates to a negative impact of VX-770 on the stability of F508del-CFTR. In the current studies, we showed that this negative effect of VX-770 at 10 μM correlated with its inhibitory effect on VX-809-mediated correction of the interface between the second membrane spanning domain and the first nucleotide binding domain bearing F508del. Interestingly, we found that VX-770 exerted a similar negative effect on the stability of other membrane localized solute carriers (SLC26A3, SLC26A9, and SLC6A14), suggesting that this negative effect is not specific for F508del-CFTR. We determined that the relative destabilizing effect of a panel of VX-770 derivatives on F508del-CFTR correlated with their predicted lipophilicity. Polarized total internal reflection fluorescence microscopy on a supported lipid bilayer model shows that VX-770, and not its less lipophilic derivative, increased the fluidity of and reorganized the membrane. In summary, our findings show that there is a potential for nonspecific effects of VX-770 on the lipid bilayer and suggest that this effect may account for its destabilizing effect on VX-809- rescued F508del-CFTR.
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Affiliation(s)
- Stephanie Chin
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Maurita Hung
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Amy Won
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Yu-Sheng Wu
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Saumel Ahmadi
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Donghe Yang
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Salma Elmallah
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Krimo Toutah
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - C Michael Hamilton
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Robert N Young
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Russell D Viirre
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Christopher M Yip
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
| | - Christine E Bear
- Department of Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (S.C., M.H., Y.-S.W., S.A., D.Y., C.E.B.); Departments of Biochemistry (S.C., C.E.B.) and Physiology (M.H., Y.-S.W., S.A., C.E.B.), and Institute of Biomaterials and Biomedical Engineering (A.W., C.M.Y.), University of Toronto, Toronto, Ontario, Canada; Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada (S.E., K.T., R.D.V.); and Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada (C.M.H., R.N.Y.)
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Tosco A, Villella VR, Castaldo A, Kroemer G, Maiuri L, Raia V. Repurposing therapies for the personalised treatment of cystic fibrosis. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1483231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Antonella Tosco
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Valeria R. Villella
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Alice Castaldo
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Guido Kroemer
- Equipe11 labellisée Ligue Nationale Contrele Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Paris, Sorbonne Paris Cité, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, HôpitalEuropéen Georges Pompidou, AP-HP, Paris, France
| | - Luigi Maiuri
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Valeria Raia
- Regional Cystic Fibrosis Center, Pediatric Unit, Department of Translational Medical Sciences, Federico II University, Naples, Italy
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56
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DeStefano S, Gees M, Hwang TC. Physiological and pharmacological characterization of the N1303K mutant CFTR. J Cyst Fibros 2018; 17:573-581. [PMID: 29887518 DOI: 10.1016/j.jcf.2018.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/13/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND N1303K, one of the common, severe disease-causing mutations in the CFTR gene, causes both defective biogenesis and gating abnormalities of the CFTR protein. The goals of the present study are to quantitatively assess the gating defects associated with the N1303K mutation and its pharmacological response to CFTR modulators including potentiators VX-770 and GLPG1837 and correctors VX-809, and VX-661. METHODS Gating behavior and pharmacological responses to CFTR potentiators were assessed using patch-clamp technique in the excised, inside-out mode. We also examined the effects of GLPG1837, VX-770, VX-809 and VX-661 on N1303K-CFTR surface expression using Western blot analysis. RESULTS Like wild-type (WT) CFTR, N1303K-CFTR channels were activated by protein kinase A-dependent phosphorylation, but the open probability (Po) of phosphorylated N1303K-CFTR was extremely low (~0.03 vs ~0.45 in WT channels). N1303K mutants showed abnormal responses to ATP analogs or mutations that disrupt ATP hydrolysis and/or dimerization of CFTR's two nucleotide-binding domains (NBDs). However, the Po of N1303K-CFTR was dramatically increased by GLPG1837 (~17-fold) and VX-770 (~8-fold). VX-809 or VX-661 enhanced N1303K-CFTR maturation by 2-3 fold, and co-treatment with GLPG1837 or VX-770 did not show any negative drug-drug interaction. CONCLUSION N1303K has a severe gating defect, reduced ATP-dependence and aberrant response to ATP analogs. These results suggest a defective function of the NBDs in N1303K-CFTR. An improvement of channel function by GLPG1837 or VX-770 and an increase of Band C protein by VX-809 or VX-661 support a therapeutic strategy of combining CFTR potentiator and corrector for patients carrying the N1303K mutation.
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Affiliation(s)
- Samantha DeStefano
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, United States; Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211, United States
| | | | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, United States; Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211, United States.
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57
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Molinski SV, Ahmadi S, Ip W, Ouyang H, Villella A, Miller JP, Lee PS, Kulleperuma K, Du K, Di Paola M, Eckford PD, Laselva O, Huan LJ, Wellhauser L, Li E, Ray PN, Pomès R, Moraes TJ, Gonska T, Ratjen F, Bear CE. Orkambi® and amplifier co-therapy improves function from a rare CFTR mutation in gene-edited cells and patient tissue. EMBO Mol Med 2018; 9:1224-1243. [PMID: 28667089 PMCID: PMC5582412 DOI: 10.15252/emmm.201607137] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The combination therapy of lumacaftor and ivacaftor (Orkambi®) is approved for patients bearing the major cystic fibrosis (CF) mutation: ΔF508. It has been predicted that Orkambi® could treat patients with rarer mutations of similar “theratype”; however, a standardized approach confirming efficacy in these cohorts has not been reported. Here, we demonstrate that patients bearing the rare mutation: c.3700 A>G, causing protein misprocessing and altered channel function—similar to ΔF508‐CFTR, are unlikely to yield a robust Orkambi® response. While in silico and biochemical studies confirmed that this mutation could be corrected and potentiated by lumacaftor and ivacaftor, respectively, this combination led to a minor in vitro response in patient‐derived tissue. A CRISPR/Cas9‐edited bronchial epithelial cell line bearing this mutation enabled studies showing that an “amplifier” compound, effective in increasing the levels of immature CFTR protein, augmented the Orkambi® response. Importantly, this “amplifier” effect was recapitulated in patient‐derived nasal cultures—providing the first evidence for its efficacy in augmenting Orkambi® in tissues harboring a rare CF‐causing mutation. We propose that this multi‐disciplinary approach, including creation of CRISPR/Cas9‐edited cells to profile modulators together with validation using primary tissue, will facilitate therapy development for patients with rare CF mutations.
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Affiliation(s)
- Steven V Molinski
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Saumel Ahmadi
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Wan Ip
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Hong Ouyang
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | | | | | - Po-Shun Lee
- Proteostasis Therapeutics, Cambridge, MA, USA
| | - Kethika Kulleperuma
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Kai Du
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Michelle Di Paola
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Paul Dw Eckford
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Onofrio Laselva
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Ling Jun Huan
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Leigh Wellhauser
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Ellen Li
- Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Peter N Ray
- Division of Molecular Genetics, Hospital for Sick Children, Toronto, ON, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Theo J Moraes
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Tanja Gonska
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Felix Ratjen
- Division of Respiratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Christine E Bear
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada .,Programme in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
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58
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Hwang TC, Yeh JT, Zhang J, Yu YC, Yeh HI, Destefano S. Structural mechanisms of CFTR function and dysfunction. J Gen Physiol 2018; 150:539-570. [PMID: 29581173 PMCID: PMC5881446 DOI: 10.1085/jgp.201711946] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 12/18/2022] Open
Abstract
Hwang et al. integrate new structural insights with prior functional studies to reveal the functional anatomy of CFTR chloride channels. Cystic fibrosis (CF) transmembrane conductance regulator (CFTR) chloride channel plays a critical role in regulating transepithelial movement of water and electrolyte in exocrine tissues. Malfunction of the channel because of mutations of the cftr gene results in CF, the most prevalent lethal genetic disease among Caucasians. Recently, the publication of atomic structures of CFTR in two distinct conformations provides, for the first time, a clear overview of the protein. However, given the highly dynamic nature of the interactions among CFTR’s various domains, better understanding of the functional significance of these structures requires an integration of these new structural insights with previously established biochemical/biophysical studies, which is the goal of this review.
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Affiliation(s)
- Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO .,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO.,Department of Biological Engineering, University of Missouri, Columbia, MO
| | - Jiunn-Tyng Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO
| | - Jingyao Zhang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Biological Engineering, University of Missouri, Columbia, MO
| | - Ying-Chun Yu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
| | - Han-I Yeh
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
| | - Samantha Destefano
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO.,Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO
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59
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Sites associated with Kalydeco binding on human Cystic Fibrosis Transmembrane Conductance Regulator revealed by Hydrogen/Deuterium Exchange. Sci Rep 2018; 8:4664. [PMID: 29549268 PMCID: PMC5856801 DOI: 10.1038/s41598-018-22959-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Cystic Fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). Mutations associated with CF cause loss-of-function in CFTR leading to salt imbalance in epithelial tissues. Kalydeco (also called VX-770 or ivacaftor) was approved for CF treatment in 2012 but little is known regarding the compound’s interactions with CFTR including the site of binding or mechanisms of action. In this study we use hydrogen/deuterium exchange (HDX) coupled with mass spectrometry to assess the conformational dynamics of a thermostabilized form of CFTR in apo and ligand-bound states. We observe HDX protection at a known binding site for AMPPNP and significant protection for several regions of CFTR in the presence of Kalydeco. The ligand-induced changes of CFTR in the presence of Kalydeco suggest a potential binding site.
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60
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Kym PR, Wang X, Pizzonero M, Van der Plas SE. Recent Progress in the Discovery and Development of Small-Molecule Modulators of CFTR. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:235-276. [PMID: 29680149 DOI: 10.1016/bs.pmch.2018.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cystic fibrosis (CF) is a genetic disorder driven by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. While different mutations lead to varying levels of disease severity, the most common CFTR F508del mutation leads to defects in protein stability, trafficking to the cell membrane and gating of chloride ions. Recently, advances in medicinal chemistry have led to the identification small-molecule drugs that result in significant clinical efficacy in improving lung function in CF patients. Multiple CFTR modulators are required to fix the various defects in the CFTR protein. Small-molecule potentiators increase the open-channel probability and improve the gating of ions through CFTR. Small-molecule correctors stabilize the protein fold of the mutant channel, facilitating protein maturation and translocation to the cellular membrane. Recent data suggest that triple-combination therapy consisting of a potentiator and two correctors that operate through distinct mechanisms will be required to deliver highly significant clinical efficacy for most CF patients. The progress in medicinal chemistry that has led to the identification of novel CFTR potentiators and correctors is presented in this chapter.
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Affiliation(s)
- Phil R Kym
- AbbVie Discovery Chemistry and Technology, North Chicago, IL, United States
| | - Xueqing Wang
- AbbVie Discovery Chemistry and Technology, North Chicago, IL, United States
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61
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Zhang S, Stoll G, Pedro JMBS, Sica V, Sauvat A, Obrist F, Kepp O, Li Y, Maiuri L, Zamzami N, Kroemer G. Evaluation of autophagy inducers in epithelial cells carrying the ΔF508 mutation of the cystic fibrosis transmembrane conductance regulator CFTR. Cell Death Dis 2018; 9:191. [PMID: 29415993 PMCID: PMC5833759 DOI: 10.1038/s41419-017-0235-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022]
Abstract
Cystic Fibrosis (CF) due to the ΔF508 mutation of cystic fibrosis transmembrane conductance regulator (CFTR) can be treated with a combination of cysteamine and Epigallocatechin gallate (EGCG). Since ECGC is not a clinically approved drug, we attempted to identify other compounds that might favourably interact with cysteamine to induce autophagy and thus rescuing the function of ΔF508 CFTR as a chloride channel in the plasma membrane. For this, we screened a compound library composed by chemically diverse autophagy inducers for their ability to enhance autophagic flux in the presence of cysteamine. We identified the antiarrhythmic Ca2+ channel blocker amiodarone, as an FDA-approved drug having the property to cooperate with cysteamine to stimulate autophagy in an additive manner. Amiodarone promoted the re-expression of ΔF508 CFTR protein in the plasma membrane of respiratory epithelial cells. Hence, amiodarone might be yet another compound for the etiological therapy of CF in patients bearing the ΔF508 CFTR mutation.
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Affiliation(s)
- Shaoyi Zhang
- Faculty of Medicine, University of Paris Sud-Saclay, Kremlin-Bicêtre, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France.,Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Gautier Stoll
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - José Manuel Bravo San Pedro
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Valentina Sica
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Allan Sauvat
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Florine Obrist
- Faculty of Medicine, University of Paris Sud-Saclay, Kremlin-Bicêtre, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,Sorbonne Paris Cité, Université Paris Descartes, Paris, France.,Gustave Roussy Comprehensive Cancer Center, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Yousheng Li
- Department of General Surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Luigi Maiuri
- European Institute for Research in Cystic Fibrosis, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy.,SCDU of Pediatrics, Department of Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Naoufal Zamzami
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France. .,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France. .,Sorbonne Paris Cité, Université Paris Descartes, Paris, France. .,Gustave Roussy Comprehensive Cancer Center, Villejuif, France. .,Université Pierre et Marie Curie, Paris, France.
| | - Guido Kroemer
- Faculty of Medicine, University of Paris Sud-Saclay, Kremlin-Bicêtre, France. .,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France. .,Institut National de la Santé et de la Recherche Médicale UMRS1138, Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France. .,Sorbonne Paris Cité, Université Paris Descartes, Paris, France. .,Gustave Roussy Comprehensive Cancer Center, Villejuif, France. .,Université Pierre et Marie Curie, Paris, France. .,Pôle de Biologie, Hôpital Européen Georges Pompidou, APsupp-HP, Paris, France. .,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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62
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Odera M, Furuta T, Sohma Y, Sakurai M. Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR. Biophys Physicobiol 2018; 15:33-44. [PMID: 29607278 PMCID: PMC5873040 DOI: 10.2142/biophysico.15.0_33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/28/2017] [Indexed: 02/03/2023] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that belongs to the ATP binding cassette protein superfamily. Deletion of phenylalanine at position 508 (ΔF508) is the most common CF-associated mutation and is present in nearly 90% of CF patients. Currently, atomistic level studies are insufficient for understanding the mechanism by which the deletion of a single amino acid causes greatly reduced folding as well as trafficking and gating defects. To clarify this mechanism, we first constructed an atomic model of the inward-facing ΔF508-CFTR and performed allatom molecular dynamics (MD) simulations of the protein in a membrane environment. All of the computational methodologies used are based on those developed in our previous study for wild-type CFTR. Two important findings were obtained. First, consistent with several previous computational results, the deletion of F508 causes a disruption of a hydrophobic cluster located at the interface between the nucleotide binding domain 1 (NBD1) and intracellular loop 4 (ICL4). This exerts unfavorable influences on the correlated motion between ICLs and transmembrane domains (TMDs), likely resulting in gating defects. Second, the F508 deletion affected the NBD1-NBD2 interface via allosteric communication originating from the correlated motion between NBDs and ICLs. As a result, several unusual inter-residue interactions are caused at the NBD1-NBD2 interface. In other words, their correct dimerization is impaired. This study provided insight into the atomic-level details of structural and dynamics changes caused by the ΔF508 mutation and thus provides good insight for drug design.
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Affiliation(s)
- Mitsuhiko Odera
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshiro Sohma
- Department of Pharmaceutical Sciences, Graduate School of Pharmacy and Center for Medical Science, International University of Health and Welfare, Ohtawara, Tochigi 324-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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63
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Riquelme SA, Hopkins BD, Wolfe AL, DiMango E, Kitur K, Parsons R, Prince A. Cystic Fibrosis Transmembrane Conductance Regulator Attaches Tumor Suppressor PTEN to the Membrane and Promotes Anti Pseudomonas aeruginosa Immunity. Immunity 2017; 47:1169-1181.e7. [PMID: 29246444 PMCID: PMC5738266 DOI: 10.1016/j.immuni.2017.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/11/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
The tumor suppressor PTEN controls cell proliferation by regulating phosphatidylinositol-3-kinase (PI3K) activity, but the participation of PTEN in host defense against bacterial infection is less well understood. Anti-inflammatory PI3K-Akt signaling is suppressed in patients with cystic fibrosis (CF), a disease characterized by hyper-inflammatory responses to airway infection. We found that Ptenl-/- mice, which lack the NH2-amino terminal splice variant of PTEN, were unable to eradicate Pseudomonas aeruginosa from the airways and could not generate sufficient anti-inflammatory PI3K activity, similar to what is observed in CF. PTEN and the CF transmembrane conductance regulator (CFTR) interacted directly and this interaction was necessary to position PTEN at the membrane. CF patients under corrector-potentiator therapy, which enhances CFTR transport to the membrane, have increased PTEN amounts. These findings suggest that improved CFTR trafficking could enhance P. aeruginosa clearance from the CF airway by activating PTEN-mediated anti-bacterial responses and might represent a therapeutic strategy.
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Affiliation(s)
| | | | - Andrew L Wolfe
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily DiMango
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Kipyegon Kitur
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Ramon Parsons
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY 10032, USA.
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64
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Correcting CFTR folding defects by small-molecule correctors to cure cystic fibrosis. Curr Opin Pharmacol 2017; 34:83-90. [PMID: 29055231 DOI: 10.1016/j.coph.2017.09.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/18/2022]
Abstract
Pharmacological intervention to treat the lethal genetic disease cystic fibrosis has become reality, even for the severe, most common folding mutant F508del CFTR. CFTR defects range from absence of the protein, misfolding that leads to degradation rather than cell-surface localization (such as F508del), to functional chloride-channel defects on the cell surface. Corrector and potentiator drugs improve cell-surface location and channel activity, respectively, and combination therapy of two correctors and a potentiator have shown synergy. Several combinations are in the drug-development pipeline and although the primary defect is not repaired, rescue levels are reaching those resembling a cure for CF. Combination therapy with correctors may also improve functional CFTR mutants and benefit patients on potentiator therapy.
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65
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Gao X, Hwang TC. Spatial positioning of CFTR's pore-lining residues affirms an asymmetrical contribution of transmembrane segments to the anion permeation pathway. J Gen Physiol 2017; 147:407-22. [PMID: 27114613 PMCID: PMC4845689 DOI: 10.1085/jgp.201511557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/28/2016] [Indexed: 12/22/2022] Open
Abstract
CFTR is a chloride channel and a member of the ABC transporter superfamily; however, its structure is unknown. By making a series of cysteine mutants, Gao and Hwang show that CFTR lacks the twofold pseudo-symmetry seen in the permeation pathway of bone fide ABC transporters. The structural composition of CFTR’s anion permeation pathway has been proposed to consist of a short narrow region, flanked by two wide inner and outer vestibules, based on systematic cysteine scanning studies using thiol-reactive probes of various sizes. Although these studies identified several of the transmembrane segments (TMs) as pore lining, the exact spatial relationship between pore-lining elements remains under debate. Here, we introduce cysteine pairs in several key pore-lining positions in TM1, 6, and 12 and use Cd2+ as a probe to gauge the spatial relationship of these residues within the pore. We find that inhibition of single cysteine CFTR mutants, such as 102C in TM1 or 341C in TM6, by intracellular Cd2+ is readily reversible upon removal of the metal ion. However, the inhibitory effect of Cd2+ on the double mutant 102C/341C requires the chelating agent dithiothreitol (DTT) for rapid reversal, indicating that 102C and 341C are close enough to the internal edge of the narrow region to coordinate one Cd2+ ion between them. We observe similar effects of extracellular Cd2+ on TM1/TM6 cysteine pairs 106C/337C, 107C/337C, and 107C/338C, corroborating the idea that these paired residues are physically close to each other at the external edge of the narrow region. Although these data paint a picture of relatively symmetrical contributions to CFTR’s pore by TM1 and TM6, introducing cysteine pairs between TM6 and TM12 (348C/1141C, 348C/1144C, and 348C/1145C) or between TM1 and TM12 (95C/1141C) yields results that contest the long-held principle of twofold pseudo-symmetry in the assembly of ABC transporters’ TMs. Collectively, these findings not only advance our current understanding of the architecture of CFTR’s pore, but could serve as a guide for refining computational models of CFTR by imposing physical constraints among pore-lining residues.
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Affiliation(s)
- Xiaolong Gao
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 Department of Biological Engineering, University of Missouri, Columbia, MO 65211
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 Department of Biological Engineering, University of Missouri, Columbia, MO 65211 Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65211
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66
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Simhaev L, McCarty NA, Ford RC, Senderowitz H. Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane Conductance Regulator Protein. J Chem Inf Model 2017; 57:1932-1946. [DOI: 10.1021/acs.jcim.7b00091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Luba Simhaev
- Department
of Chemistry, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Nael A. McCarty
- Division
of Pulmonology, Allergy/Immunology, Cystic Fibrosis, and Sleep, Department
of Pediatrics, Emory + Children’s Center for Cystic Fibrosis
and Airways Disease Research, Emory University School of Medicine and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, Georgia 30322, United States
| | - Robert C. Ford
- Faculty
of Biology Medicine and Health, University of Manchester, Oxford
Road, Manchester, M13 9PL, U.K
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67
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Musgaard M, Paramo T, Domicevica L, Andersen OJ, Biggin PC. Insights into channel dysfunction from modelling and molecular dynamics simulations. Neuropharmacology 2017; 132:20-30. [PMID: 28669899 DOI: 10.1016/j.neuropharm.2017.06.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/06/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022]
Abstract
Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.'
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Affiliation(s)
- Maria Musgaard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Teresa Paramo
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Laura Domicevica
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Ole Juul Andersen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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68
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Das J, Aleksandrov AA, Cui L, He L, Riordan JR, Dokholyan NV. Transmembrane helical interactions in the CFTR channel pore. PLoS Comput Biol 2017. [PMID: 28640808 PMCID: PMC5501672 DOI: 10.1371/journal.pcbi.1005594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants. Several CFTR homology models have been developed using bacterial ABC transporters as templates but these have low sequence similarity to CFTR and are not ion channels. Here, we refine an earlier model in an outward (OWF) and develop an inward (IWF) facing model employing an integrated experimental-molecular dynamics simulation (200 ns) approach. Our IWF structure agrees well with a recently solved cryo-EM structure of a CFTR IWF state. We utilize cysteine cross-linking to verify positions and orientations of residues within trans-membrane helices (TMHs) of the OWF conformation and to reconstruct a physiologically relevant pore structure. Comparison of pore profiles of the two conformations reveal a radius sufficient to permit passage of hydrated Cl- ions in the OWF but not the IWF model. To identify structural determinants that distinguish the two conformations and possible rearrangements of TMHs within them responsible for channel gating, we perform cross-linking by bifunctional reagents of multiple predicted pairs of cysteines in TMH 6 and 12 and 6 and 9. To determine whether the effects of cross-linking on gating observed are the result of switching of the channel from open to close state, we also treat the same residue pairs with monofunctional reagents in separate experiments. Both types of reagents prevent ion currents indicating that pore blockage is primarily responsible.
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Affiliation(s)
- Jhuma Das
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Andrei A. Aleksandrov
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Liying Cui
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lihua He
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John R. Riordan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (JRR); (NVD)
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Cystic Fibrosis Treatment and Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (JRR); (NVD)
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69
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Hudson RP, Dawson JE, Chong PA, Yang Z, Millen L, Thomas PJ, Brouillette CG, Forman-Kay JD. Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface. Mol Pharmacol 2017; 92:124-135. [PMID: 28546419 DOI: 10.1124/mol.117.108373] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanism of action of modulator compounds for the cystic fibrosis transmembrane conductance regulator (CFTR) is key for the optimization of therapeutics as well as obtaining insights into the molecular mechanisms of CFTR function. We demonstrate the direct binding of VX-809 to the first nucleotide-binding domain (NBD1) of human CFTR. Disruption of the interaction between C-terminal helices and the NBD1 core upon VX-809 binding is observed from chemical shift changes in the NMR spectra of residues in the helices and on the surface of β-strands S3, S9, and S10. Binding to VX-809 leads to a significant negative shift in NBD1 thermal melting temperature (Tm), pointing to direct VX-809 interaction shifting the NBD1 conformational equilibrium. An inter-residue correlation analysis of the chemical shift changes provides evidence of allosteric coupling between the direct binding site and the NBD1:CL4 interface, thus enabling effects on the interface in the absence of direct binding in that location. These NMR binding data and the negative Tm shifts are very similar to those previously reported by us for binding of the dual corrector-potentiator CFFT-001 to NBD1 (Hudson et al., 2012), suggesting that the two compounds may share some aspects of their mechanisms of action. Although previous studies have shown an important role for VX-809 in modulating the conformation of the first membrane spanning domain (Aleksandrov et al., 2012; Ren et al., 2013), this additional mode of VX-809 binding provides insight into conformational dynamics and allostery within CFTR.
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Affiliation(s)
- Rhea P Hudson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Jennifer E Dawson
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - P Andrew Chong
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Zhengrong Yang
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Linda Millen
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Philip J Thomas
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Christie G Brouillette
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.)
| | - Julie D Forman-Kay
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, Canada (R.P.H, J.E.D., P.A.C., J.D.F.-K.); Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada (J.D.F.-K.); Center for Structural Biology (Z.Y., C.G.B.) and Department of Chemistry (C.G.B.), University of Alabama at Birmingham, Birmingham, Alabama; and Department of Physiology, UT Southwestern Medical Center, Dallas, Texas (L.M., P.J.T.).
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70
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Zhang Z, Chen J. Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. Cell 2017; 167:1586-1597.e9. [PMID: 27912062 DOI: 10.1016/j.cell.2016.11.014] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.
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Affiliation(s)
- Zhe Zhang
- The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA
| | - Jue Chen
- The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
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71
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Lopes-Pacheco M, Boinot C, Sabirzhanova I, Rapino D, Cebotaru L. Combination of Correctors Rescues CFTR Transmembrane-Domain Mutants by Mitigating their Interactions with Proteostasis. Cell Physiol Biochem 2017; 41:2194-2210. [PMID: 28448979 PMCID: PMC7082854 DOI: 10.1159/000475578] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/15/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND/AIMS Premature degradation of mutated cystic fibrosis transmembrane conductance regulator (CFTR) protein causes cystic fibrosis (CF), the commonest Mendelian disease in Caucasians. Despite recent advances in precision medicines for CF patients, many CFTR mutants have not been characterized and the effects of these new therapeutic approaches are still unclear for those mutants. METHODS Cells transfected or stably expressing four CFTR transmembrane-domain mutants (G85E, E92K, L1077P, and M1101K) were used to: 1) characterize the mutants according to their protein expression, thermal sensitivity, and degradation pathways; 2) evaluate the effects of correctors in rescuing them; and 3) explore the effects of correctors on CFTR interactions with proteostasis components. RESULTS All four mutants exhibited lower protein expression than did wild type-CFTR, and they were degraded by proteasomes and aggresomes. At low temperature, only cells expressing the mutants L1077P and M1101K exhibited increased CFTR maturation. Co-administration of C4 and C18 showed the greatest effect, restoring functional expression and partial stability of CFTR bearing E92K, L1077P, or M1101K at the cell surface. However, this treatment was inefficient in rectifying the defect of CFTR bearing G85E. Correctors rescued CFTR mutants by reducing their interactions with proteostasis components associated with protein retention in the endoplasmic reticulum and ubiquitination. CONCLUSION Co-administration of C4 and C18 rescued CFTR transmembrane-domain mutants by remodeling the CFTR interactome.
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72
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Loo TW, Clarke DM. Corrector VX-809 promotes interactions between cytoplasmic loop one and the first nucleotide-binding domain of CFTR. Biochem Pharmacol 2017; 136:24-31. [PMID: 28366727 DOI: 10.1016/j.bcp.2017.03.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
Abstract
A large number of correctors have been identified that can partially repair defects in folding, stability and trafficking of CFTR processing mutants that cause cystic fibrosis (CF). The best corrector, VX-809 (Lumacaftor), has shown some promise when used in combination with a potentiator (Ivacaftor). Understanding the mechanism of VX-809 is essential for development of better correctors. Here, we tested our prediction that VX-809 repairs folding and processing defects of CFTR by promoting interactions between the first cytoplasmic loop (CL1) of transmembrane domain 1 (TMD1) and the first nucleotide-binding domain (NBD1). To investigate whether VX-809 promoted CL1/NBD1 interactions, we performed cysteine mutagenesis and disulfide cross-linking analysis of Cys-less TMD1 (residues 1-436) and ΔTMD1 (residues 437-1480; NBD1-R-TMD2-NBD2) truncation mutants. It was found that VX-809, but not bithiazole correctors, promoted maturation (exited endoplasmic reticulum for addition of complex carbohydrate in the Golgi) of the ΔTMD1 truncation mutant only when it was co-expressed in the presence of TMD1. Expression in the presence of VX-809 also promoted cross-linking between R170C (in CL1 of TMD1 protein) and L475C (in NBD1 of the ΔTMD1 truncation protein). Expression of the ΔTMD1 truncation mutant in the presence of TMD1 and VX-809 also increased the half-life of the mature protein in cells. The results suggest that the mechanism by which VX-809 promotes maturation and stability of CFTR is by promoting CL1/NBD1 interactions.
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Affiliation(s)
- Tip W Loo
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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73
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Biophysical Approaches Facilitate Computational Drug Discovery for ATP-Binding Cassette Proteins. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2017; 2017:1529402. [PMID: 28409029 PMCID: PMC5376479 DOI: 10.1155/2017/1529402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/27/2017] [Indexed: 12/12/2022]
Abstract
Although membrane proteins represent most therapeutically relevant drug targets, the availability of atomic resolution structures for this class of proteins has been limited. Structural characterization has been hampered by the biophysical nature of these polytopic transporters, receptors, and channels, and recent innovations to in vitro techniques aim to mitigate these challenges. One such class of membrane proteins, the ATP-binding cassette (ABC) superfamily, are broadly expressed throughout the human body, required for normal physiology and disease-causing when mutated, yet lacks sufficient structural representation in the Protein Data Bank. However, recent improvements to biophysical techniques (e.g., cryo-electron microscopy) have allowed for previously “hard-to-study” ABC proteins to be characterized at high resolution, providing insight into molecular mechanisms-of-action as well as revealing novel druggable sites for therapy design. These new advances provide ample opportunity for computational methods (e.g., virtual screening, molecular dynamics simulations, and structure-based drug design) to catalyze the discovery of novel small molecule therapeutics that can be easily translated from computer to bench and subsequently to the patient's bedside. In this review, we explore the utility of recent advances in biophysical methods coupled with well-established in silico techniques towards drug development for diseases caused by dysfunctional ABC proteins.
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74
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Villate-Beitia I, Zarate J, Puras G, Pedraz JL. Gene delivery to the lungs: pulmonary gene therapy for cystic fibrosis. Drug Dev Ind Pharm 2017; 43:1071-1081. [PMID: 28270008 DOI: 10.1080/03639045.2017.1298122] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disorder where the defective gene, the cystic fibrosis transmembrane conductance regulator (CFTR), is well identified. Moreover, the respiratory tract can be targeted through noninvasive aerosolized formulations for inhalation. Therefore, gene therapy is considered a plausible strategy to address this disease. Conventional gene therapy strategies rely on the addition of a correct copy of the CFTR gene into affected cells in order to restore the channel activity. In recent years, genome correction strategies have emerged, such as zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats associated to Cas9 nucleases. These gene editing tools aim to repair the mutated gene at its original genomic locus with high specificity. Besides, the success of gene therapy critically depends on the nucleic acids carriers. To date, several clinical studies have been carried out to add corrected copies of the CFTR gene into target cells using viral and non-viral vectors, some of them with encouraging results. Regarding genome editing systems, preliminary in vitro studies have been performed in order to repair the CFTR gene. In this review, after briefly introducing the basis of CF, we discuss the up-to-date gene therapy strategies to address the disease. The review focuses on the main factors to take into consideration when developing gene delivery strategies, such as the design of vectors and plasmid DNA, in vitro/in vivo tests, translation to human use, administration methods, manufacturing conditions and regulatory issues.
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Affiliation(s)
- Ilia Villate-Beitia
- a NanoBioCel Group, University of the Basque Country (UPV/EHU) , Vitoria-Gasteiz , Spain.,b Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Vitoria-Gasteiz , Spain
| | - Jon Zarate
- a NanoBioCel Group, University of the Basque Country (UPV/EHU) , Vitoria-Gasteiz , Spain.,b Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Vitoria-Gasteiz , Spain
| | - Gustavo Puras
- a NanoBioCel Group, University of the Basque Country (UPV/EHU) , Vitoria-Gasteiz , Spain.,b Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Vitoria-Gasteiz , Spain
| | - José Luis Pedraz
- a NanoBioCel Group, University of the Basque Country (UPV/EHU) , Vitoria-Gasteiz , Spain.,b Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Vitoria-Gasteiz , Spain
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75
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Hegde RN, Subramanian A, Pothukuchi P, Parashuraman S, Luini A. Rare ER protein misfolding-mistrafficking disorders: Therapeutic developments. Tissue Cell 2017; 49:175-185. [PMID: 28222887 DOI: 10.1016/j.tice.2017.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022]
Abstract
The presence of a functional protein at the appropriate location in the cell is the result of the processes of transcription, translation, folding and trafficking to the correct destination. There are numerous diseases that are caused by protein misfolding, mainly due to mutations in the respective gene. The consequences of this misfolding may be that proteins effectively lose their function, either by being removed by the cellular quality control machinery or by accumulating at the incorrect intracellular or extracellular location. A number of mutations that lead to protein misfolding and affect trafficking to the final destination, e.g. Cystic fibrosis, Wilson's disease, and Progressive Familial Intrahepatic 1 cholestasis, result in proteins that retain partial function if their folding and trafficking is restored either by molecular or pharmacological means. In this review, we discuss several mutant proteins within this class of misfolding diseases and provide an update on the status of molecular and therapeutic developments and potential therapeutic strategies being developed to counter these diseases.
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Affiliation(s)
| | - Advait Subramanian
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | | | | | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Naples, Italy; Istituto di Ricovero e Cura a Carattere Scientifico SDN, Naples, Italy
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76
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Meng X, Wang Y, Wang X, Wrennall JA, Rimington TL, Li H, Cai Z, Ford RC, Sheppard DN. Two Small Molecules Restore Stability to a Subpopulation of the Cystic Fibrosis Transmembrane Conductance Regulator with the Predominant Disease-causing Mutation. J Biol Chem 2017; 292:3706-3719. [PMID: 28087700 PMCID: PMC5339754 DOI: 10.1074/jbc.m116.751537] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/12/2017] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations that disrupt the plasma membrane expression, stability, and function of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel. Two small molecules, the CFTR corrector lumacaftor and the potentiator ivacaftor, are now used clinically to treat CF, although some studies suggest that they have counteracting effects on CFTR stability. Here, we investigated the impact of these compounds on the instability of F508del-CFTR, the most common CF mutation. To study individual CFTR Cl- channels, we performed single-channel recording, whereas to assess entire CFTR populations, we used purified CFTR proteins and macroscopic CFTR Cl- currents. At 37 °C, low temperature-rescued F508del-CFTR more rapidly lost function in cell-free membrane patches and showed altered channel gating and current flow through open channels. Compared with purified wild-type CFTR, the full-length F508del-CFTR was about 10 °C less thermostable. Lumacaftor partially stabilized purified full-length F508del-CFTR and slightly delayed deactivation of individual F508del-CFTR Cl- channels. By contrast, ivacaftor further destabilized full-length F508del-CFTR and accelerated channel deactivation. Chronic (prolonged) co-incubation of F508del-CFTR-expressing cells with lumacaftor and ivacaftor deactivated macroscopic F508del-CFTR Cl- currents. However, at the single-channel level, chronic co-incubation greatly increased F508del-CFTR channel activity and temporal stability in most, but not all, cell-free membrane patches. We conclude that chronic lumacaftor and ivacaftor co-treatment restores stability in a small subpopulation of F508del-CFTR Cl- channels but that the majority remain destabilized. A fuller understanding of these effects and the characterization of the small F508del-CFTR subpopulation might be crucial for CF therapy development.
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Affiliation(s)
- Xin Meng
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Yiting Wang
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Xiaomeng Wang
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Joe A Wrennall
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Tracy L Rimington
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - Hongyu Li
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Zhiwei Cai
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Robert C Ford
- From the Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom and
| | - David N Sheppard
- the School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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77
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Chen JH, Xu W, Sheppard DN. Altering intracellular pH reveals the kinetic basis of intraburst gating in the CFTR Cl - channel. J Physiol 2017; 595:1059-1076. [PMID: 27779763 DOI: 10.1113/jp273205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/21/2016] [Indexed: 01/14/2023] Open
Abstract
KEY POINTS The cystic fibrosis transmembrane conductance regulator (CFTR), which is defective in the genetic disease cystic fibrosis (CF), forms a gated pathway for chloride movement regulated by intracellular ATP. To understand better CFTR function, we investigated the regulation of channel openings by intracellular pH. We found that short-lived channel closures during channel openings represent subtle changes in the structure of CFTR that are regulated by intracellular pH, in part, at ATP-binding site 1 formed by the nucleotide-binding domains. Our results provide a framework for future studies to understand better the regulation of channel openings, the dysfunction of CFTR in CF and the action of drugs that repair CFTR gating defects. ABSTRACT Cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-gated Cl- channel defective in the genetic disease cystic fibrosis (CF). The gating behaviour of CFTR is characterized by bursts of channel openings interrupted by brief, flickery closures, separated by long closures between bursts. Entry to and exit from an open burst is controlled by the interaction of ATP with two ATP-binding sites, sites 1 and 2, in CFTR. To understand better the kinetic basis of CFTR intraburst gating, we investigated the single-channel activity of human CFTR at different intracellular pH (pHi ) values. When compared with the control (pHi 7.3), acidifying pHi to 6.3 or alkalinizing pHi to 8.3 and 8.8 caused small reductions in the open-time constant (τo ) of wild-type CFTR. By contrast, the fast closed-time constant (τcf ), which describes the short-lived closures that interrupt open bursts, was greatly increased at pHi 5.8 and 6.3. To analyse intraburst kinetics, we used linear three-state gating schemes. All data were satisfactorily modelled by the C1 ↔ O ↔ C2 kinetic scheme. Changing the intracellular ATP concentration was without effect on τo , τcf and their responses to pHi changes. However, mutations that disrupt the interaction of ATP with ATP-binding site 1, including K464A, D572N and the CF-associated mutation G1349D all abolished the prolongation of τcf at pHi 6.3. Taken together, our data suggest that the regulation of CFTR intraburst gating is distinct from the ATP-dependent mechanism that controls channel opening and closing. However, our data also suggest that ATP-binding site 1 modulates intraburst gating.
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Affiliation(s)
- Jeng-Haur Chen
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China.,School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Weiyi Xu
- School of Biomedical Sciences, University of Hong Kong, Hong Kong.,The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
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78
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Chin S, Hung M, Bear CE. Current insights into the role of PKA phosphorylation in CFTR channel activity and the pharmacological rescue of cystic fibrosis disease-causing mutants. Cell Mol Life Sci 2017; 74:57-66. [PMID: 27722768 PMCID: PMC11107731 DOI: 10.1007/s00018-016-2388-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/21/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) channel gating is predominantly regulated by protein kinase A (PKA)-dependent phosphorylation. In addition to regulating CFTR channel activity, PKA phosphorylation is also involved in enhancing CFTR trafficking and mediating conformational changes at the interdomain interfaces of the protein. The major cystic fibrosis (CF)-causing mutation is the deletion of phenylalanine at position 508 (F508del); it causes many defects that affect CFTR trafficking, stability, and gating at the cell surface. Due to the multiple roles of PKA phosphorylation, there is growing interest in targeting PKA-dependent signaling for rescuing the trafficking and functional defects of F508del-CFTR. This review will discuss the effects of PKA phosphorylation on wild-type CFTR, the consequences of CF mutations on PKA phosphorylation, and the development of therapies that target PKA-mediated signaling.
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Affiliation(s)
- Stephanie Chin
- Programme of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Maurita Hung
- Programme of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Christine E Bear
- Programme of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Canada.
- Department of Physiology, University of Toronto, Toronto, Canada.
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79
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Farinha CM, Canato S. From the endoplasmic reticulum to the plasma membrane: mechanisms of CFTR folding and trafficking. Cell Mol Life Sci 2017; 74:39-55. [PMID: 27699454 PMCID: PMC11107782 DOI: 10.1007/s00018-016-2387-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 01/10/2023]
Abstract
CFTR biogenesis starts with its co-translational insertion into the membrane of endoplasmic reticulum and folding of the cytosolic domains, towards the acquisition of a fully folded compact native structure. Efficiency of this process is assessed by the ER quality control system that allows the exit of folded proteins but targets unfolded/misfolded CFTR to degradation. If allowed to leave the ER, CFTR is modified at the Golgi and reaches the post-Golgi compartments to be delivered to the plasma membrane where it functions as a cAMP- and phosphorylation-regulated chloride/bicarbonate channel. CFTR residence at the membrane is a balance of membrane delivery, endocytosis, and recycling. Several adaptors, motor, and scaffold proteins contribute to the regulation of CFTR stability and are involved in continuously assessing its structure through peripheral quality control systems. Regulation of CFTR biogenesis and traffic (and its dysregulation by mutations, such as the most common F508del) determine its overall activity and thus contribute to the fine modulation of chloride secretion and hydration of epithelial surfaces. This review covers old and recent knowledge on CFTR folding and trafficking from its synthesis to the regulation of its stability at the plasma membrane and highlights how several of these steps can be modulated to promote the rescue of mutant CFTR.
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Affiliation(s)
- Carlos M Farinha
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Sara Canato
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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80
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Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel expressed in the apical membrane of epithelia. Mutations in the CFTR gene are the cause of cystsic fibrosis. CFTR is the only ABC-protein that constitutes an ion channel pore forming subunit. CFTR gating is regulated in complex manner as phosphorylation is mandatory for channel activity and gating is directly regulated by binding of ATP to specific intracellular sites on the CFTR protein. This review covers our current understanding on the gating mechanism in CFTR and illustrates the relevance of alteration of these mechanisms in the onset of cystic fibrosis.
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Affiliation(s)
- Oscar Moran
- Istituto di Biofisica, CNR. Via De Marini, 6, 16149, Genoa, Italy.
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81
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Callebaut I, Hoffmann B, Lehn P, Mornon JP. Molecular modelling and molecular dynamics of CFTR. Cell Mol Life Sci 2017; 74:3-22. [PMID: 27717958 PMCID: PMC11107702 DOI: 10.1007/s00018-016-2385-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
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Affiliation(s)
- Isabelle Callebaut
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France.
| | - Brice Hoffmann
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France
| | - Pierre Lehn
- INSERM U1078, SFR ScInBioS, Université de Bretagne Occidentale, Brest, France
| | - Jean-Paul Mornon
- UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Case 115, IMPMC, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris Cedex 05, France
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82
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Chin S, Yang D, Miles AJ, Eckford PDW, Molinski S, Wallace BA, Bear CE. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface. J Biol Chem 2016; 292:1988-1999. [PMID: 28003367 PMCID: PMC5290968 DOI: 10.1074/jbc.m116.762633] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation.
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Affiliation(s)
- Stephanie Chin
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Donghe Yang
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Andrew J Miles
- the Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Paul D W Eckford
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Steven Molinski
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada
| | - B A Wallace
- the Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Christine E Bear
- From the Programme of Molecular Structure and Function, Hospital for Sick Children, Toronto M5G 0A4, Canada; the Department of Biochemistry, University of Toronto, Toronto, Canada; the Department of Physiology, University of Toronto, Toronto, Canada.
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83
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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84
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Bartoszewski R, Króliczewski J, Piotrowski A, Jasiecka AJ, Bartoszewska S, Vecchio-Pagan B, Fu L, Sobolewska A, Matalon S, Cutting GR, Rowe SM, Collawn JF. Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator. Cell Mol Biol Lett 2016; 21:23. [PMID: 28536625 PMCID: PMC5415761 DOI: 10.1186/s11658-016-0025-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Synonymous or silent mutations are often overlooked in genetic analyses for disease-causing mutations unless they are directly associated with potential splicing defects. More recent studies, however, indicate that some synonymous single polynucleotide polymorphisms (sSNPs) are associated with changes in protein expression, and in some cases, protein folding and function. The impact of codon usage and mRNA structural changes on protein translation rates and how they can affect protein structure and function is just beginning to be appreciated. Examples are given here that demonstrate how synonymous mutations alter the translational kinetics and protein folding and/or function. The mechanism for how this occurs is based on a model in which codon usage modulates the translational rate by introducing pauses caused by nonoptimal or rare codons or by introducing changes in the mRNA structure, and this in turn influences co-translational folding. Two examples of this include the multidrug resistance protein (p-glycoprotein) and the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is also used here as a model to illustrate how synonymous mutations can be examined using in silico predictive methods to identify which sSNPs have the potential to change protein structure. The methodology described here can be used to help identify "non-silent" synonymous mutations in other genes.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Jaroslaw Króliczewski
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Anna Janaszak Jasiecka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Briana Vecchio-Pagan
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Lianwu Fu
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Aleksandra Sobolewska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sadis Matalon
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, USA.,Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Garry R Cutting
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Steven M Rowe
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Departments of Medicine and Pediatrics, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
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85
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László L, Sarkadi B, Hegedűs T. Jump into a New Fold-A Homology Based Model for the ABCG2/BCRP Multidrug Transporter. PLoS One 2016; 11:e0164426. [PMID: 27741279 PMCID: PMC5065228 DOI: 10.1371/journal.pone.0164426] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/23/2016] [Indexed: 12/03/2022] Open
Abstract
ABCG2/BCRP is a membrane protein, involved in xenobiotic and endobiotic transport in key pharmacological barriers and drug metabolizing organs, in the protection of stem cells, and in multidrug resistance of cancer. Pharmacogenetic studies implicated the role of ABCG2 in response to widely used medicines and anticancer agents, as well as in gout. Its Q141K variant exhibits decreased functional expression thus increased drug accumulation and decreased urate secretion. Still, there has been no reliable molecular model available for this protein, as the published structures of other ABC transporters could not be properly fitted to the ABCG2 topology and experimental data. The recently published high resolution structure of a close homologue, the ABCG5-ABCG8 heterodimer, revealed a new ABC transporter fold, unique for ABCG proteins. Here we present a structural model of the ABCG2 homodimer based on this fold and detail the experimental results supporting this model. In order to describe the effect of mutations on structure and dynamics, and characterize substrate recognition and cholesterol regulation we performed molecular dynamics simulations using full length ABCG2 protein embedded in a membrane bilayer and in silico docking simulations. Our results show that in the Q141K variant the introduced positive charge diminishes the interaction between the nucleotide binding and transmembrane domains and the R482G variation alters the orientation of transmembrane helices. Moreover, the R482 position, which plays a role the substrate specificity of the transporter, is located in one of the substrate binding pockets identified by the in silico docking calculations. In summary, the ABCG2 model and in silico simulations presented here may have significant impact on understanding drug distribution and toxicity, as well as drug development against cancer chemotherapy resistance or gout.
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Affiliation(s)
- Laura László
- Molecular Biophysics Research Group and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Balázs Sarkadi
- Molecular Biophysics Research Group and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Hegedűs
- Molecular Biophysics Research Group and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail:
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86
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The cystic fibrosis transmembrane conductance regulator (CFTR) and its stability. Cell Mol Life Sci 2016; 74:23-38. [PMID: 27734094 PMCID: PMC5209436 DOI: 10.1007/s00018-016-2386-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is responsible for the disease cystic fibrosis (CF). It is a membrane protein belonging to the ABC transporter family functioning as a chloride/anion channel in epithelial cells around the body. There are over 1500 mutations that have been characterised as CF-causing; the most common of these, accounting for ~70 % of CF cases, is the deletion of a phenylalanine at position 508. This leads to instability of the nascent protein and the modified structure is recognised and then degraded by the ER quality control mechanism. However, even pharmacologically ‘rescued’ F508del CFTR displays instability at the cell’s surface, losing its channel function rapidly and it is rapidly removed from the plasma membrane for lysosomal degradation. This review will, therefore, explore the link between stability and structure/function relationships of membrane proteins and CFTR in particular and how approaches to study CFTR structure depend on its stability. We will also review the application of a fluorescence labelling method for the assessment of the thermostability and the tertiary structure of CFTR.
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87
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Lopes-Pacheco M. CFTR Modulators: Shedding Light on Precision Medicine for Cystic Fibrosis. Front Pharmacol 2016; 7:275. [PMID: 27656143 PMCID: PMC5011145 DOI: 10.3389/fphar.2016.00275] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/11/2016] [Indexed: 12/15/2022] Open
Abstract
Cystic fibrosis (CF) is the most common life-threatening monogenic disease afflicting Caucasian people. It affects the respiratory, gastrointestinal, glandular and reproductive systems. The major cause of morbidity and mortality in CF is the respiratory disorder caused by a vicious cycle of obstruction of the airways, inflammation and infection that leads to epithelial damage, tissue remodeling and end-stage lung disease. Over the past decades, life expectancy of CF patients has increased due to early diagnosis and improved treatments; however, these patients still present limited quality of life. Many attempts have been made to rescue CF transmembrane conductance regulator (CFTR) expression, function and stability, thereby overcoming the molecular basis of CF. Gene and protein variances caused by CFTR mutants lead to different CF phenotypes, which then require different treatments to quell the patients' debilitating symptoms. In order to seek better approaches to treat CF patients and maximize therapeutic effects, CFTR mutants have been stratified into six groups (although several of these mutations present pleiotropic defects). The research with CFTR modulators (read-through agents, correctors, potentiators, stabilizers and amplifiers) has achieved remarkable progress, and these drugs are translating into pharmaceuticals and personalized treatments for CF patients. This review summarizes the main molecular and clinical features of CF, emphasizes the latest clinical trials using CFTR modulators, sheds light on the molecular mechanisms underlying these new and emerging treatments, and discusses the major breakthroughs and challenges to treating all CF patients.
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Affiliation(s)
- Miquéias Lopes-Pacheco
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
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88
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Abstract
The anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is a unique ATP-binding cassette (ABC) transporter. CFTR plays a pivotal role in transepithelial ion transport as its dysfunction in the genetic disease cystic fibrosis (CF) dramatically demonstrates. Phylogenetic analysis suggests that CFTR first appeared in aquatic vertebrates fulfilling important roles in osmosensing and organ development. Here, we review selectively, knowledge of CFTR structure, function and pharmacology, gleaned from cross-species comparative studies of recombinant CFTR proteins, including CFTR chimeras. The data argue that subtle changes in CFTR structure can affect strongly channel function and the action of CF mutations.
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89
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Gentzsch M, Ren HY, Houck SA, Quinney NL, Cholon DM, Sopha P, Chaudhry IG, Das J, Dokholyan NV, Randell SH, Cyr DM. Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770. Am J Physiol Lung Cell Mol Physiol 2016; 311:L550-9. [PMID: 27402691 DOI: 10.1152/ajplung.00186.2016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/24/2016] [Indexed: 01/06/2023] Open
Abstract
Cystic fibrosis (CF) is a lethal recessive genetic disease caused primarily by the F508del mutation in the CF transmembrane conductance regulator (CFTR). The potentiator VX-770 was the first CFTR modulator approved by the FDA for treatment of CF patients with the gating mutation G551D. Orkambi is a drug containing VX-770 and corrector VX809 and is approved for treatment of CF patients homozygous for F508del, which has folding and gating defects. At least 30% of CF patients are heterozygous for the F508del mutation with the other allele encoding for one of many different rare CFTR mutations. Treatment of heterozygous F508del patients with VX-809 and VX-770 has had limited success, so it is important to identify heterozygous patients that respond to CFTR modulator therapy. R117H is a more prevalent rare mutation found in over 2,000 CF patients. In this study we investigated the effectiveness of VX-809/VX-770 therapy on restoring CFTR function in human bronchial epithelial (HBE) cells from R117H/F508del CF patients. We found that VX-809 stimulated more CFTR activity in R117H/F508del HBEs than in F508del/F508del HBEs. R117H expressed exclusively in immortalized HBEs exhibited a folding defect, was retained in the ER, and degraded prematurely. VX-809 corrected the R117H folding defect and restored channel function. Because R117 is involved in ion conductance, VX-770 acted additively with VX-809 to restore CFTR function in chronically treated R117H/F508del cells. Although treatment of R117H patients with VX-770 has been approved, our studies indicate that Orkambi may be more beneficial for rescue of CFTR function in these patients.
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Affiliation(s)
- Martina Gentzsch
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Hong Y Ren
- Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Scott A Houck
- Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Nancy L Quinney
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina
| | - Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina
| | - Pattarawut Sopha
- Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Imron G Chaudhry
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Jhuma Das
- Department of Biochemistry, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Nikolay V Dokholyan
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
| | - Douglas M Cyr
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina, Chapel Hill, North Carolina; Department of Cell Biology and Physiology. University of North Carolina, Chapel Hill, North Carolina; and
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90
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Convertino M, Das J, Dokholyan NV. Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases. ACS Chem Biol 2016; 11:1471-89. [PMID: 27097127 DOI: 10.1021/acschembio.6b00195] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Errors in protein folding may result in premature clearance of structurally aberrant proteins, or in the accumulation of toxic misfolded species or protein aggregates. These pathological events lead to a large range of conditions known as conformational diseases. Several research groups have presented possible therapeutic solutions for their treatment by developing novel compounds, known as pharmacological chaperones. These cell-permeable molecules selectively provide a molecular scaffold around which misfolded proteins can recover their native folding and, thus, their biological activities. Here, we review therapeutic strategies, clinical potentials, and cost-benefit impacts of several classes of pharmacological chaperones for the treatment of a series of conformational diseases.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Jhuma Das
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
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91
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Wang G, Linsley R, Norimatsu Y. External Zn2+binding to cysteine-substituted cystic fibrosis transmembrane conductance regulator constructs regulates channel gating and curcumin potentiation. FEBS J 2016; 283:2458-75. [DOI: 10.1111/febs.13752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 05/02/2016] [Accepted: 05/11/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Guangyu Wang
- Department of Physiology and Pharmacology; Oregon Health & Sciences University; Portland OR USA
- Department of Drug Research and Development; Institute of Biophysical Medico-chemistry; Reno NV USA
- Department of Physiology and Membrane Biology; University of California School of Medicine; Davis CA USA
| | | | - Yohei Norimatsu
- Department of Physiology; Kirksville College of Osteopathic Medicine; A.T. Still University; Kirksville MO USA
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92
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Faure G, Bakouh N, Lourdel S, Odolczyk N, Premchandar A, Servel N, Hatton A, Ostrowski MK, Xu H, Saul FA, Moquereau C, Bitam S, Pranke I, Planelles G, Teulon J, Herrmann H, Roldan A, Zielenkiewicz P, Dadlez M, Lukacs GL, Sermet-Gaudelus I, Ollero M, Corringer PJ, Edelman A. Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis. J Mol Biol 2016; 428:2898-915. [PMID: 27241308 DOI: 10.1016/j.jmb.2016.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 01/26/2023]
Abstract
Deletion of Phe508 in the nucleotide binding domain (∆F508-NBD1) of the cystic fibrosis transmembrane regulator (CFTR; a cyclic AMP-regulated chloride channel) is the most frequent mutation associated with cystic fibrosis. This mutation affects the maturation and gating of CFTR protein. The search for new high-affinity ligands of CFTR acting as dual modulators (correctors/activators) presents a major challenge in the pharmacology of cystic fibrosis. Snake venoms are a rich source of natural multifunctional proteins, potential binders of ion channels. In this study, we identified the CB subunit of crotoxin from Crotalus durissus terrificus as a new ligand and allosteric modulator of CFTR. We showed that CB interacts with NBD1 of both wild type and ∆F508CFTR and increases their chloride channel currents. The potentiating effect of CB on CFTR activity was demonstrated using electrophysiological techniques in Xenopus laevis oocytes, in CFTR-HeLa cells, and ex vivo in mouse colon tissue. The correcting effect of CB was shown by functional rescue of CFTR activity after 24-h ΔF508CFTR treatments with CB. Moreover, the presence of fully glycosylated CFTR was observed. Molecular docking allowed us to propose a model of the complex involving of the ABCβ and F1-like ATP-binding subdomains of ΔF508-NBD1. Hydrogen-deuterium exchange analysis confirmed stabilization in these regions, also showing allosteric stabilization in two other distal regions. Surface plasmon resonance competition studies showed that CB disrupts the ∆F508CFTR-cytokeratin 8 complex, allowing for the escape of ∆F508CFTR from degradation. Therefore CB, as a dual modulator of ΔF508CFTR, constitutes a template for the development of new anti-CF agents.
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Affiliation(s)
- Grazyna Faure
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France.
| | - Naziha Bakouh
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Stéphane Lourdel
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Norbert Odolczyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Aiswarya Premchandar
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Nathalie Servel
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Aurélie Hatton
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Maciej K Ostrowski
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Haijin Xu
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Frederick A Saul
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Christelle Moquereau
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Sara Bitam
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Iwona Pranke
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Gabrielle Planelles
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Jacques Teulon
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Harald Herrmann
- Department of Molecular Genetics, German Cancer Research Center, D-69120 Heidelberg, Germany; Institute of Neuropathology, University Hospital Erlangen, D-91054 Erlangen, Germany
| | - Ariel Roldan
- Department of Physiology, McGill University, Montreal, Canada
| | - Piotr Zielenkiewicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Michal Dadlez
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | | | - Isabelle Sermet-Gaudelus
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Mario Ollero
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Aleksander Edelman
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
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93
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Gakhal AK, Jensen TJ, Bozoky Z, Roldan A, Lukacs GL, Forman-Kay J, Riordan JR, Sidhu SS. Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs 2016; 8:1167-76. [PMID: 27185291 DOI: 10.1080/19420862.2016.1186320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel in the apical surface of epithelial cells in the airway and gastrointestinal tract, and mutation of CFTR is the underlying cause of cystic fibrosis. However, the precise molecular details of the structure and function of CFTR in native and disease states remains elusive and cystic fibrosis researchers are hindered by a lack of high specificity, high affinity binding reagents for use in structural and biological studies. Here, we describe a panel of synthetic antigen-binding fragments (Fabs) isolated from a phage-displayed library that are specific for intracellular domains of CFTR that include the nucleotide-binding domains (NBD1 and NBD2), the R-region, and the regulatory insertion loop of NBD1. Binding assays performed under conditions that promote the native fold of the protein demonstrated that all Fabs recognized full-length CFTR. However, only the NBD1-specific Fab recognized denatured CFTR by western blot, suggesting a conformational epitope requirement for the other Fabs. Surface plasmon resonance experiments showed that the R-region Fab binds with high affinity to both the phosphorylated and unphosphorylated R-region. In addition, NMR analysis of bound versus unbound R-region revealed a distinct conformational effect upon Fab binding. We further defined residues involved with antibody recognition using an overlapping peptide array. In summary, we describe methodology complementary to previous hybridoma-based efforts to develop antibody reagents to CFTR, and introduce a synthetic antibody panel to aid structural and biological studies.
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Affiliation(s)
- Amandeep K Gakhal
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
| | - Timothy J Jensen
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Zoltan Bozoky
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - Ariel Roldan
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Gergely L Lukacs
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Julie Forman-Kay
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - John R Riordan
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Sachdev S Sidhu
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
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94
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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95
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Lopes-Pacheco M, Sabirzhanova I, Rapino D, Morales MM, Guggino WB, Cebotaru L. Correctors Rescue CFTR Mutations in Nucleotide-Binding Domain 1 (NBD1) by Modulating Proteostasis. Chembiochem 2016; 17:493-505. [PMID: 26864378 DOI: 10.1002/cbic.201500620] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 11/12/2022]
Abstract
We evaluated whether small molecule correctors could rescue four nucleotide-binding domain 1 (NBD1) mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (A455E, S492F, ΔI507, and R560T). We first transfected Cos-7 cells (green monkey kidney cells) with A455E, S492F, ΔI507, or R560T and created HEK-293 (human embryonic kidney cells) cell lines stably expressing these CFTR mutations. The mutants showed lowered protein expression, instability at physiological temperature, and rapid degradation. After treatment with correctors CFFT-002, CFFT-003, C3, C4, and/or C18, the combination of C18+C4 showed the most correction and resulted in increased CFTR residing in the plasma membrane. We found a profound decrease in binding of CFTR to histone deacetylases (HDAC) 6 and 7 and heat shock proteins (Hsps) 27 and 40. Silencing Hsp27 or 40 rescued the mutants, but no additional amount of CFTR was rescued when both proteins were knocked down simultaneously. Thus, CFTR mutations in NBD1 can be rescued by a combination of correctors, and the treatment alters the interaction between mutated CFTR and the endoplasmic reticulum machinery.
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Affiliation(s)
- Miquéias Lopes-Pacheco
- Departments of Medicine and Physiology, Division of Gastroenterology and Hepatology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA.,Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 303 CCS/Bloco G/Sala G2-055, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Inna Sabirzhanova
- Departments of Medicine and Physiology, Division of Gastroenterology and Hepatology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Daniele Rapino
- Departments of Medicine and Physiology, Division of Gastroenterology and Hepatology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Marcelo M Morales
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 303 CCS/Bloco G/Sala G2-055, Rio de Janeiro, RJ, 21941-902, Brazil
| | - William B Guggino
- Departments of Medicine and Physiology, Division of Gastroenterology and Hepatology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Liudmila Cebotaru
- Departments of Medicine and Physiology, Division of Gastroenterology and Hepatology, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA.
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96
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Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:13-32. [PMID: 27311317 DOI: 10.1007/5584_2016_33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.
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97
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Estácio SG, Martiniano HFMC, Faísca PFN. Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR. MOLECULAR BIOSYSTEMS 2016; 12:2834-48. [DOI: 10.1039/c6mb00193a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The deletion of phenylalanine 508 reshapes the conformational space of the NBD1 domain that populates unique intermediate states that provide insights into the molecular events that underlie the impaired folding of F508del-NBD1.
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Affiliation(s)
- Sílvia G. Estácio
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Hugo F. M. C. Martiniano
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Patrícia F. N. Faísca
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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98
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Ehrhardt A, Chung WJ, Pyle LC, Wang W, Nowotarski K, Mulvihill CM, Ramjeesingh M, Hong J, Velu SE, Lewis HA, Atwell S, Aller S, Bear CE, Lukacs GL, Kirk KL, Sorscher EJ. Channel Gating Regulation by the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) First Cytosolic Loop. J Biol Chem 2015; 291:1854-1865. [PMID: 26627831 DOI: 10.1074/jbc.m115.704809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/06/2022] Open
Abstract
In this study, we present data indicating a robust and specific domain interaction between the cystic fibrosis transmembrane conductance regulator (CFTR) first cytosolic loop (CL1) and nucleotide binding domain 1 (NBD1) that allows ion transport to proceed in a regulated fashion. We used co-precipitation and ELISA to establish the molecular contact and showed that binding kinetics were not altered by the common clinical mutation F508del. Both intrinsic ATPase activity and CFTR channel gating were inhibited severely by CL1 peptide, suggesting that NBD1/CL1 binding is a crucial requirement for ATP hydrolysis and channel function. In addition to cystic fibrosis, CFTR dysregulation has been implicated in the pathogenesis of prevalent diseases such as chronic obstructive pulmonary disease, acquired rhinosinusitis, pancreatitis, and lethal secretory diarrhea (e.g. cholera). On the basis of clinical relevance of the CFTR as a therapeutic target, a cell-free drug screen was established to identify modulators of NBD1/CL1 channel activity independent of F508del CFTR and pharmacologic rescue. Our findings support a targetable mechanism of CFTR regulation in which conformational changes in the NBDs cause reorientation of transmembrane domains via interactions with CL1 and result in channel gating.
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Affiliation(s)
- Annette Ehrhardt
- From the Gregory Fleming James Cystic Fibrosis Research Center and; the Department of Pediatrics, Emory University, Atlanta, Georgia 30322
| | - W Joon Chung
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Departments of Neurobiology
| | - Louise C Pyle
- From the Gregory Fleming James Cystic Fibrosis Research Center and
| | - Wei Wang
- Cellular, Integrative, and Developmental Biology
| | | | - Cory M Mulvihill
- the Hospital for Sick Children Research Institute, Toronto M5G 1X8, Canada
| | | | - Jeong Hong
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Cellular, Integrative, and Developmental Biology
| | - Sadanandan E Velu
- Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Hal A Lewis
- Bristol-Myers Squibb, Princeton, New Jersey 08543
| | | | - Steve Aller
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Pharmacology, and
| | - Christine E Bear
- the Hospital for Sick Children Research Institute, Toronto M5G 1X8, Canada,; the Departments of Biochemistry and; Physiology, University of Toronto, Toronto M5G 1X8, Canada, and
| | - Gergely L Lukacs
- the Department of Physiology, McGill University, Montreal H3G 1Y6, Canada
| | - Kevin L Kirk
- From the Gregory Fleming James Cystic Fibrosis Research Center and; Cellular, Integrative, and Developmental Biology
| | - Eric J Sorscher
- the Department of Pediatrics, Emory University, Atlanta, Georgia 30322,.
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99
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Gong X, Ahner A, Roldan A, Lukacs GL, Thibodeau PH, Frizzell RA. Non-native Conformers of Cystic Fibrosis Transmembrane Conductance Regulator NBD1 Are Recognized by Hsp27 and Conjugated to SUMO-2 for Degradation. J Biol Chem 2015; 291:2004-2017. [PMID: 26627832 DOI: 10.1074/jbc.m115.685628] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 12/24/2022] Open
Abstract
A newly identified pathway for selective degradation of the common mutant of the cystic fibrosis transmembrane conductance regulator (CFTR), F508del, is initiated by binding of the small heat shock protein, Hsp27. Hsp27 collaborates with Ubc9, the E2 enzyme for protein SUMOylation, to selectively degrade F508del CFTR via the SUMO-targeted ubiquitin E3 ligase, RNF4 (RING finger protein 4) (1). Here, we ask what properties of CFTR are sensed by the Hsp27-Ubc9 pathway by examining the ability of NBD1 (locus of the F508del mutation) to mimic the disposal of full-length (FL) CFTR. Similar to FL CFTR, F508del NBD1 expression was reduced 50-60% by Hsp27; it interacted preferentially with the mutant and was modified primarily by SUMO-2. Mutation of the consensus SUMOylation site, Lys(447), obviated Hsp27-mediated F508del NBD1 SUMOylation and degradation. As for FL CFTR and NBD1 in vivo, SUMO modification using purified components in vitro was greater for F508del NBD1 versus WT and for the SUMO-2 paralog. Several findings indicated that Hsp27-Ubc9 targets the SUMOylation of a transitional, non-native conformation of F508del NBD1: (a) its modification decreased as [ATP] increased, reflecting stabilization of the nucleotide-binding domain by ligand binding; (b) a temperature-induced increase in intrinsic fluorescence, which reflects formation of a transitional NBD1 conformation, was followed by its SUMO modification; and (c) introduction of solubilizing or revertant mutations to stabilize F508del NBD1 reduced its SUMO modification. These findings indicate that the Hsp27-Ubc9 pathway recognizes a non-native conformation of mutant NBD1, which leads to its SUMO-2 conjugation and degradation by the ubiquitin-proteasome system.
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Affiliation(s)
| | | | - Ariel Roldan
- the Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Gergely L Lukacs
- the Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Patrick H Thibodeau
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 and
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100
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Solomon GM, Marshall SG, Ramsey BW, Rowe SM. Breakthrough therapies: Cystic fibrosis (CF) potentiators and correctors. Pediatr Pulmonol 2015; 50 Suppl 40:S3-S13. [PMID: 26097168 PMCID: PMC4620567 DOI: 10.1002/ppul.23240] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 12/28/2022]
Abstract
Cystic Fibrosis is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene resulting in abnormal protein function. Recent advances of targeted molecular therapies and high throughput screening have resulted in multiple drug therapies that target many important mutations in the CFTR protein. In this review, we provide the latest results and current progress of CFTR modulators for the treatment of cystic fibrosis, focusing on potentiators of CFTR channel gating and Phe508del processing correctors for the Phe508del CFTR mutation. Special emphasis is placed on the molecular basis underlying these new therapies and emerging results from the latest clinical trials. The future directions for augmenting the rescue of Phe508del with CFTR modulators are also emphasized.
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Affiliation(s)
- George M Solomon
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, Alabama
| | - Susan G Marshall
- Division of Pulmonary Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - Bonnie W Ramsey
- Division of Pulmonary Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington
| | - Steven M Rowe
- Department of Medicine and the Gregory Fleming James Cystic Fibrosis Research Center, Birmingham, Alabama.,Departments of Medicine, Pediatrics, Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
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