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Recent Strategic Advances in CFTR Drug Discovery: An Overview. Int J Mol Sci 2020; 21:ijms21072407. [PMID: 32244346 PMCID: PMC7177952 DOI: 10.3390/ijms21072407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR)-rescuing drugs have already transformed cystic fibrosis (CF) from a fatal disease to a treatable chronic condition. However, new-generation drugs able to bind CFTR with higher specificity/affinity and to exert stronger therapeutic benefits and fewer side effects are still awaited. Computational methods and biosensors have become indispensable tools in the process of drug discovery for many important human pathologies. Instead, they have been used only piecemeal in CF so far, calling for their appropriate integration with well-tried CF biochemical and cell-based models to speed up the discovery of new CFTR-rescuing drugs. This review will give an overview of the available structures and computational models of CFTR and of the biosensors, biochemical and cell-based assays already used in CF-oriented studies. It will also give the reader some insights about how to integrate these tools as to improve the efficiency of the drug discovery process targeted to CFTR.
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Abreu B, Lopes EF, Oliveira ASF, Soares CM. F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis. Proteins 2019; 88:113-126. [PMID: 31298435 DOI: 10.1002/prot.25776] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/17/2019] [Accepted: 07/06/2019] [Indexed: 12/20/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) channel is an ion channel responsible for chloride transport in epithelia and it belongs to the class of ABC transporters. The deletion of phenylalanine 508 (F508del) in CFTR is the most common mutation responsible for cystic fibrosis. Little is known about the effect of the mutation in the isolated nucleotide binding domains (NBDs), on dimer dynamics, ATP hydrolysis and even on nucleotide binding. Using molecular dynamics simulations of the human CFTR NBD dimer, we showed that F508del increases, in the prehydrolysis state, the inter-motif distance in both ATP binding sites (ABP) when ATP is bound. Additionally, a decrease in the number of catalytically competent conformations was observed in the presence of F508del. We used the subtraction technique to study the first 300 ps after ATP hydrolysis in the catalytic competent site and found that the F508del dimer evidences lower conformational changes than the wild type. Using longer simulation times, the magnitude of the conformational changes in both forms increases. Nonetheless, the F508del dimer shows lower C-α RMS values in comparison to the wild-type, on the F508del loop, on the residues surrounding the catalytic site and the portion of NBD2 adjacent to ABP1. These results provide evidence that F508del interferes with the NBD dynamics before and after ATP hydrolysis. These findings shed a new light on the effect of F508del on NBD dynamics and reveal a novel mechanism for the influence of F508del on CFTR.
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Affiliation(s)
- Bárbara Abreu
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Emanuel F Lopes
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A S F Oliveira
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal.,School of Biochemistry & Center for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M Soares
- Protein Modelling Lab, ITQB-NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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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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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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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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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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Pollock NL, Satriano L, Zegarra-Moran O, Ford RC, Moran O. Structure of wild type and mutant F508del CFTR: A small-angle X-ray scattering study of the protein–detergent complexes. J Struct Biol 2016; 194:102-11. [DOI: 10.1016/j.jsb.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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