1
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Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough. Nat Commun 2024; 15:4446. [PMID: 38789441 PMCID: PMC11126739 DOI: 10.1038/s41467-024-48387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Stop codon readthrough events give rise to longer proteins, which may alter the protein's function, thereby generating short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon readthrough events, we designed a library of reporters. We introduced premature stop codons into mScarlet, which enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon readthrough may occur at rates as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon readthrough events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon readthrough. The RNA polymerase was more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon readthrough by mass spectrometry revealed that temperature regulated the expression of cryptic sequences generated by stop codon readthrough in E. coli. Overall, our findings suggest that the environment affects the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Anastasiia Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Doris Richter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Tobias Jumel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
- Center for Systems Biology Dresden, 01307, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany.
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2
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Perriera R, Vitale E, Pibiri I, Carollo PS, Ricci D, Corrao F, Fiduccia I, Melfi R, Zizzo MG, Tutone M, Pace A, Lentini L. Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression. Int J Mol Sci 2023; 24:15084. [PMID: 37894764 PMCID: PMC10606485 DOI: 10.3390/ijms242015084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.
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Affiliation(s)
| | | | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
| | | | | | | | | | | | | | | | | | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.P.); (E.V.); (P.S.C.); (D.R.); (F.C.); (I.F.); (R.M.); (M.G.Z.); (M.T.); (A.P.)
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3
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Chiavetta RF, Titoli S, Barra V, Cancemi P, Melfi R, Di Leonardo A. Site-Specific RNA Editing of Stop Mutations in the CFTR mRNA of Human Bronchial Cultured Cells. Int J Mol Sci 2023; 24:10940. [PMID: 37446121 DOI: 10.3390/ijms241310940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
It is reported that about 10% of cystic fibrosis (CF) patients worldwide have nonsense (stop) mutations in the CFTR gene, which cause the premature termination of CFTR protein synthesis, leading to a truncated and non-functional protein. To address this issue, we investigated the possibility of rescuing the CFTR nonsense mutation (UGA) by sequence-specific RNA editing in CFTR mutant CFF-16HBEge, W1282X, and G542X human bronchial cells. We used two different base editor tools that take advantage of ADAR enzymes (adenosine deaminase acting on RNA) to edit adenosine to inosine (A-to-I) within the mRNA: the REPAIRv2 (RNA Editing for Programmable A to I Replacement, version 2) and the minixABE (A to I Base Editor). Immunofluorescence experiments show that both approaches were able to recover the CFTR protein in the CFTR mutant cells. In addition, RT-qPCR confirmed the rescue of the CFTR full transcript. These findings suggest that site-specific RNA editing may efficiently correct the UGA premature stop codon in the CFTR transcript in CFF-16HBEge, W1282X, and G542X cells. Thus, this approach, which is safer than acting directly on the mutated DNA, opens up new therapeutic possibilities for CF patients with nonsense mutations.
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Affiliation(s)
- Roberta F Chiavetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Simona Titoli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Patrizia Cancemi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Centro di Oncobiologia Sperimentale (C.O.B.S.), Viale Delle Scienze, 90128 Palermo, Italy
| | - Raffaella Melfi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Centro di Oncobiologia Sperimentale (C.O.B.S.), Viale Delle Scienze, 90128 Palermo, Italy
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4
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Carollo PS, Tutone M, Culletta G, Fiduccia I, Corrao F, Pibiri I, Di Leonardo A, Zizzo MG, Melfi R, Pace A, Almerico AM, Lentini L. Investigating the Inhibition of FTSJ1, a Tryptophan tRNA-Specific 2'-O-Methyltransferase by NV TRIDs, as a Mechanism of Readthrough in Nonsense Mutated CFTR. Int J Mol Sci 2023; 24:9609. [PMID: 37298560 PMCID: PMC10253411 DOI: 10.3390/ijms24119609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations that generate a premature termination codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ribosome's capacity to skip a PTC, thus generating a full-length protein. "TRIDs" are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We investigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their readthrough activity by in silico analysis and in vitro studies. Our results suggest a likely inhibition of FTSJ1, a tryptophan tRNA-specific 2'-O-methyltransferase.
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Affiliation(s)
| | - Marco Tutone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
| | | | | | | | | | | | | | | | | | | | - Laura Lentini
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
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5
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Kim YJ, Krainer AR. Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Mol Cells 2023; 46:10-20. [PMID: 36697233 PMCID: PMC9880599 DOI: 10.14348/molcells.2023.2172] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Antisense oligonucleotide (ASO) technology has become an attractive therapeutic modality for various diseases, including Mendelian disorders. ASOs can modulate the expression of a target gene by promoting mRNA degradation or changing pre-mRNA splicing, nonsense-mediated mRNA decay, or translation. Advances in medicinal chemistry and a deeper understanding of post-transcriptional mechanisms have led to the approval of several ASO drugs for diseases that had long lacked therapeutic options. For instance, an ASO drug called nusinersen became the first approved drug for spinal muscular atrophy, improving survival and the overall disease course. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Although Trikafta and other CFTR-modulation therapies benefit most CF patients, there is a significant unmet therapeutic need for a subset of CF patients. In this review, we introduce ASO therapies and their mechanisms of action, describe the opportunities and challenges for ASO therapeutics for CF, and discuss the current state and prospects of ASO therapies for CF.
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Affiliation(s)
- Young Jin Kim
- Department of Pediatrics, Mount Sinai Hospital, New York, NY 10029, USA
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6
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Corrao F, Zizzo MG, Tutone M, Melfi R, Fiduccia I, Carollo PS, Leonardo AD, Caldara G, Perriera R, Pace A, Belmonte B, Sammataro S, Pibiri I, Lentini L. Nonsense codons suppression. An acute toxicity study of three optimized TRIDs in murine model, safety and tolerability evaluation. Biomed Pharmacother 2022; 156:113886. [DOI: 10.1016/j.biopha.2022.113886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/02/2022] Open
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7
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Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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8
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Huang S, Bhattacharya A, Ghelfi MD, Li H, Fritsch C, Chenoweth DM, Goldman YE, Cooperman BS. Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination. Nat Commun 2022; 13:2413. [PMID: 35523781 PMCID: PMC9076611 DOI: 10.1038/s41467-022-30080-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic diseases are often caused by nonsense mutations, but only one TRID (translation readthrough inducing drug), ataluren, has been approved for clinical use. Ataluren inhibits release factor complex (RFC) termination activity, while not affecting productive binding of near-cognate ternary complex (TC, aa-tRNA.eEF1A.GTP). Here we use photoaffinity labeling to identify two sites of ataluren binding within rRNA, proximal to the decoding center (DC) and the peptidyl transfer center (PTC) of the ribosome, which are directly responsible for ataluren inhibition of termination activity. A third site, within the RFC, has as yet unclear functional consequences. Using single molecule and ensemble fluorescence assays we also demonstrate that termination proceeds via rapid RFC-dependent hydrolysis of peptidyl-tRNA followed by slow release of peptide and tRNA from the ribosome. Ataluren is an apparent competitive inhibitor of productive RFC binding, acting at or before the hydrolysis step. We propose that designing more potent TRIDs which retain ataluren's low toxicity should target areas of the RFC binding site proximal to the DC and PTC which do not overlap the TC binding site.
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Affiliation(s)
- Shijie Huang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- GSK, 14200 Shady Grove Rd, Rockville, MD, 20850, USA
| | - Arpan Bhattacharya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mikel D Ghelfi
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hong Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Clark Fritsch
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yale E Goldman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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9
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Bezzerri V, Lentini L, Api M, Busilacchi EM, Cavalieri V, Pomilio A, Diomede F, Pegoraro A, Cesaro S, Poloni A, Pace A, Trubiani O, Lippi G, Pibiri I, Cipolli M. Novel Translational Read-through-Inducing Drugs as a Therapeutic Option for Shwachman-Diamond Syndrome. Biomedicines 2022; 10:biomedicines10040886. [PMID: 35453634 PMCID: PMC9024944 DOI: 10.3390/biomedicines10040886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is one of the most commonly inherited bone marrow failure syndromes (IBMFS). In SDS, bone marrow is hypocellular, with marked neutropenia. Moreover, SDS patients have a high risk of developing myelodysplastic syndrome (MDS), which in turn increases the risk of acute myeloid leukemia (AML) from an early age. Most SDS patients are heterozygous for the c.183-184TA>CT (K62X) SBDS nonsense mutation. Fortunately, a plethora of translational read-through inducing drugs (TRIDs) have been developed and tested for several rare inherited diseases due to nonsense mutations so far. The authors previously demonstrated that ataluren (PTC124) can restore full-length SBDS protein expression in bone marrow stem cells isolated from SDS patients carrying the nonsense mutation K62X. In this study, the authors evaluated the effect of a panel of ataluren analogues in restoring SBDS protein resynthesis and function both in hematological and non-hematological SDS cells. Besides confirming that ataluren can efficiently induce SBDS protein re-expression in SDS cells, the authors found that another analogue, namely NV848, can restore full-length SBDS protein synthesis as well, showing very low toxicity in zebrafish. Furthermore, NV848 can improve myeloid differentiation in bone marrow hematopoietic progenitors, enhancing neutrophil maturation and reducing the number of dysplastic granulocytes in vitro. Therefore, these findings broaden the possibilities of developing novel therapeutic options in terms of nonsense mutation suppression for SDS. Eventually, this study may act as a proof of concept for the development of similar approaches for other IBMFS caused by nonsense mutations.
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Affiliation(s)
- Valentino Bezzerri
- Cystic Fibrosis Center of Verona, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy; (V.B.); (A.P.)
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90128 Palermo, Italy; (L.L.); (V.C.); (A.P.); (I.P.)
| | - Martina Api
- Cystic Fibrosis Center of Ancona, Azienda Ospedaliero Universitaria Ospedali Riuniti, 60126 Ancona, Italy;
| | - Elena Marinelli Busilacchi
- Hematology Clinic, Università Politecnica delle Marche, AOU Ospedali Riuniti, 60126 Ancona, Italy; (E.M.B.); (A.P.)
| | - Vincenzo Cavalieri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90128 Palermo, Italy; (L.L.); (V.C.); (A.P.); (I.P.)
- Zebrafish Laboratory, Advanced Technologies Network (ATeN) Center, University of Palermo, 90128 Palermo, Italy
| | - Antonella Pomilio
- Department of Medical, Oral and Biotechnological Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy;
| | - Francesca Diomede
- Dipartimento di Tecnologie Innovative in Medicina e Odontoiatria, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.); (O.T.)
| | - Anna Pegoraro
- Cystic Fibrosis Center of Verona, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy; (V.B.); (A.P.)
| | - Simone Cesaro
- Unit of Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy;
| | - Antonella Poloni
- Hematology Clinic, Università Politecnica delle Marche, AOU Ospedali Riuniti, 60126 Ancona, Italy; (E.M.B.); (A.P.)
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90128 Palermo, Italy; (L.L.); (V.C.); (A.P.); (I.P.)
| | - Oriana Trubiani
- Dipartimento di Tecnologie Innovative in Medicina e Odontoiatria, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.); (O.T.)
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, 37126 Verona, Italy;
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, 90128 Palermo, Italy; (L.L.); (V.C.); (A.P.); (I.P.)
| | - Marco Cipolli
- Cystic Fibrosis Center of Verona, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy; (V.B.); (A.P.)
- Correspondence: ; Tel.: +39-045-812-2293
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10
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Yu J, Tang B, He X, Zou P, Zeng Z, Xiao R. Nonsense Suppression Therapy: An Emerging Treatment for Hereditary Skin Diseases. Acta Derm Venereol 2022; 102:adv00658. [DOI: 10.2340/actadv.v102.353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nonsense mutations cause the premature termination of protein translation via premature termination codons (PTCs), leading to the synthesis of incomplete functional proteins and causing large numbers of genetic disorders. The emergence of nonsense suppression therapy is considered to be an effective method for the treatment of hereditary diseases, but its application in hereditary skin diseases is relatively limited. This review summarizes the current research status of nonsense suppression therapy for hereditary skin diseases, and discusses the potential opportunities and challenges of applying new technologies related to nonsense suppression therapy to dermatology. Further research is needed into the possible use of nonsense suppression therapy as a strategy for the safer and specific treatment of hereditary skin diseases.
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11
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Jiang C, Li M, Xu L, Yi Y, Ye J, Hu A. Electrochemical synthesis of 1,2,4-oxadiazoles from amidoximes through dehydrogenative cyclization. Org Biomol Chem 2021; 19:10611-10616. [PMID: 34854450 DOI: 10.1039/d1ob02040d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient and efficient method for the generation of the iminoxy radical through anodic oxidation was developed for the synthesis of 3,5-disubstituted 1,2,4-oxadiazoles from N-benzyl amidoximes. The transformation proceeds through 1.5-Hydrogen Atom Transfer (1,5-HAT) and intramolecular cyclization. The process features simple operation, mild conditions, broad substrate scope and high functional group compatibility, and provides a facile and practical way for the preparation of 1,2,4-oxadiazoles.
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Affiliation(s)
- Chan Jiang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Mingfang Li
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Leitao Xu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Yangjie Yi
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Jiao Ye
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Aixi Hu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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12
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Bayat F, Homami SS, Monzavi A, Talei Bavil Olyai MR. A combined molecular docking and molecular dynamics simulation approach to probing the host–guest interactions of Ataluren with natural and modified cyclodextrins. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1991921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Farhad Bayat
- Deptartment of Applied Chemistry, Faculty of Science, South Tehran Branch, Islamic Azad University, Tehran, Iran
- Department of Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Saied Homami
- Deptartment of Applied Chemistry, Faculty of Science, South Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Amirhossein Monzavi
- Deptartment of Polymer and Textile Engineering, South Tehran Branch, Islamic Azad University, Tehran, Iran
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Ataluren-Promising Therapeutic Premature Termination Codon Readthrough Frontrunner. Pharmaceuticals (Basel) 2021; 14:ph14080785. [PMID: 34451881 PMCID: PMC8398184 DOI: 10.3390/ph14080785] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/08/2023] Open
Abstract
Around 12% of hereditary disease-causing mutations are in-frame nonsense mutations. The expression of genes containing nonsense mutations potentially leads to the production of truncated proteins with residual or virtually no function. However, the translation of transcripts containing premature stop codons resulting in full-length protein expression can be achieved using readthrough agents. Among them, only ataluren was approved in several countries to treat nonsense mutation Duchenne muscular dystrophy (DMD) patients. This review summarizes ataluren’s journey from its identification, via first in vitro activity experiments, to clinical trials in DMD, cystic fibrosis, and aniridia. Additionally, data on its pharmacokinetics and mechanism of action are presented. The range of diseases with underlying nonsense mutations is described for which ataluren therapy seems to be promising. What is more, experiments in which ataluren did not show its readthrough activity are also included, and reasons for their failures are discussed.
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14
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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15
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Abstract
Inhibiting eukaryotic protein translation with small molecules is emerging as a powerful therapeutic strategy. The advantage of targeting cellular translational machinery is that it is required for the highly proliferative state of many neoplastic cells, replication of certain viruses, and ultimately the expression of a wide variety of protein targets. Although, this approach has been exploited to develop clinical agents, such as homoharringtonine (HHT, 1), used to treat chronic myeloid leukemia (CML), inhibiting components of the translational machinery is often associated with cytotoxic phenotypes. However, recent studies have demonstrated that certain small molecules can inhibit the translation of specific subsets of proteins, leading to lower cytotoxicity, and opening-up therapeutic opportunities for translation inhibitors to be deployed in indications beyond oncology and infectious disease. This review summarizes efforts to develop inhibitors of the eukaryotic translational machinery as therapeutic agents and highlights emerging opportunities for translation inhibitors in the future.
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Affiliation(s)
- Angela Fan
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Phillip P Sharp
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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Pibiri I, Melfi R, Tutone M, Di Leonardo A, Pace A, Lentini L. Targeting Nonsense: Optimization of 1,2,4-Oxadiazole TRIDs to Rescue CFTR Expression and Functionality in Cystic Fibrosis Cell Model Systems. Int J Mol Sci 2020; 21:ijms21176420. [PMID: 32899265 PMCID: PMC7504161 DOI: 10.3390/ijms21176420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) patients develop a severe form of the disease when the cystic fibrosis transmembrane conductance regulator (CFTR) gene is affected by nonsense mutations. Nonsense mutations are responsible for the presence of a premature termination codon (PTC) in the mRNA, creating a lack of functional protein. In this context, translational readthrough-inducing drugs (TRIDs) represent a promising approach to correct the basic defect caused by PTCs. By using computational optimization and biological screening, we identified three new small molecules showing high readthrough activity. The activity of these compounds has been verified by evaluating CFTR expression and functionality after treatment with the selected molecules in cells expressing nonsense–CFTR–mRNA. Additionally, the channel functionality was measured by the halide sensitive yellow fluorescent protein (YFP) quenching assay. All three of the new TRIDs displayed high readthrough activity and low toxicity and can be considered for further evaluation as a therapeutic approach toward the second major cause of CF.
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Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
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Investigating REPAIRv2 as a Tool to Edit CFTR mRNA with Premature Stop Codons. Int J Mol Sci 2020; 21:ijms21134781. [PMID: 32640650 PMCID: PMC7369808 DOI: 10.3390/ijms21134781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the gene encoding the transmembrane conductance regulator (CFTR) protein. Some CF patients are compound heterozygous or homozygous for nonsense mutations in the CFTR gene. This implies the presence in the transcript of premature termination codons (PTCs) responsible for a truncated CFTR protein and a more severe form of the disease. Aminoglycoside and PTC124 derivatives have been used for the read-through of PTCs to restore the full-length CFTR protein. However, in a precision medicine framework, the CRISPR/dCas13b-based molecular tool “REPAIRv2” (RNA Editing for Programmable A to I Replacement, version 2) could be a good alternative to restore the full-length CFTR protein. This RNA editing approach is based on the targeting of the deaminase domain of the hADAR2 enzyme fused to the dCas13b protein to a specific adenosine to be edited to inosine in the mutant mRNA. Targeting specificity is allowed by a guide RNA (gRNA) complementarily to the target region and recognized by the dCas13b protein. Here, we used the REPAIRv2 platform to edit the UGA PTC to UGG in different cell types, namely IB3-1 cells, HeLa, and FRT cells engineered to express H2BGFPopal and CFTRW1282X, respectively.
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Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes. Int J Mol Sci 2020; 21:ijms21134672. [PMID: 32630050 PMCID: PMC7369780 DOI: 10.3390/ijms21134672] [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: 05/30/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman–Diamond syndrome (SDS), Diamond–Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.
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Morais P, Adachi H, Yu YT. Suppression of Nonsense Mutations by New Emerging Technologies. Int J Mol Sci 2020; 21:ijms21124394. [PMID: 32575694 PMCID: PMC7352488 DOI: 10.3390/ijms21124394] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
Nonsense mutations often result from single nucleotide substitutions that change a sense codon (coding for an amino acid) to a nonsense or premature termination codon (PTC) within the coding region of a gene. The impact of nonsense mutations is two-fold: (1) the PTC-containing mRNA is degraded by a surveillance pathway called nonsense-mediated mRNA decay (NMD) and (2) protein translation stops prematurely at the PTC codon, and thus no functional full-length protein is produced. As such, nonsense mutations result in a large number of human diseases. Nonsense suppression is a strategy that aims to correct the defects of hundreds of genetic disorders and reverse disease phenotypes and conditions. While most clinical trials have been performed with small molecules, there is an increasing need for sequence-specific repair approaches that are safer and adaptable to personalized medicine. Here, we discuss recent advances in both conventional strategies as well as new technologies. Several of these will soon be tested in clinical trials as nonsense therapies, even if they still have some limitations and challenges to overcome.
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Affiliation(s)
- Pedro Morais
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, The Netherlands;
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
- Correspondence: ; Tel.: +1-(585)-275-1271; Fax: +1-(585)-275-6007
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20
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Gogou M, Pavlou E, Haidopoulou K. Therapies that are available and under development for Duchenne muscular dystrophy: What about lung function? Pediatr Pulmonol 2020; 55:300-315. [PMID: 31834673 DOI: 10.1002/ppul.24605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Respiratory failure is the principal source of morbidity and mortality among patients with Duchenne muscular dystrophy exerting a negative influence on their total quality of life. The aim of this review is to provide systematically current literature evidence about the effects of different treatment options (available or under development) for Duchenne muscular dystrophy on the pulmonary function of these patients. METHODS A comprehensive search was undertaken using multiple health-related databases, while two independent reviewers assessed the eligibility of studies. A third person addressed any disagreements between reviewers. The quality of the methodology of the included studies was also assessed. RESULTS A total of 19 original research papers (nine evaluating the role of steroids, six idebenone, three eteplirsen, one stem-cell therapy, and one ataluren) were found to fulfill our selection criteria with the majority of them (14 of 19) being prospective studies, not always including a control group. Endpoints mainly used in these studies were values of pulmonary function tests. Current and under development treatments proved to be safe and no significant adverse events were reported. A beneficial impact on pulmonary function was described by authors in the majority of these studies. The principal effect was slowing of lung disease progress, as expressed by spirometric values. However, the risk of bias was introduced in many of the above studies, while high heterogeneity in terms of treatment protocols and outcome measures limits the comparability of the results. CONCLUSION Glucocorticoids remain the best-studied pharmacologic therapy for Duchenne muscular dystrophy and very likely delay the expected decline in lung function. With regard to new therapeutic agents, initial study results are encouraging. However, larger clinical trials are needed that minimize the risk of study bias, optimize the comparability of treatment groups, examine clinically meaningful pulmonary outcome measures, and include long-term follow up.
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Affiliation(s)
- Maria Gogou
- Second Department of Pediatrics, University General Hospital AHEPA, Thessaloniki, Greece
| | - Evangelos Pavlou
- Second Department of Pediatrics, University General Hospital AHEPA, Thessaloniki, Greece
| | - Katerina Haidopoulou
- Second Department of Pediatrics, University General Hospital AHEPA, Thessaloniki, Greece
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21
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Tarrasó G, Real-Martinez A, Parés M, Romero-Cortadellas L, Puigros L, Moya L, de Luna N, Brull A, Martín MA, Arenas J, Lucia A, Andreu AL, Barquinero J, Vissing J, Krag TO, Pinós T. Absence of p.R50X Pygm read-through in McArdle disease cellular models. Dis Model Mech 2020; 13:dmm.043281. [PMID: 31848135 PMCID: PMC6994938 DOI: 10.1242/dmm.043281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022] Open
Abstract
McArdle disease is an autosomal recessive disorder caused by the absence of muscle glycogen phosphorylase, which leads to blocked muscle glycogen breakdown. We used three different cellular models to evaluate the efficiency of different read-through agents (including amlexanox, Ataluren, RTC13 and G418) in McArdle disease. The first model consisted of HeLa cells transfected with two different GFP-PYGM constructs presenting the Pygm p.R50X mutation (GFP-PYGM p.R50X and PYGM Ex1-GFP p.R50X). The second cellular model was based on the creation of HEK293T cell lines stably expressing the PYGM Ex1-GFP p.R50X construct. As these plasmids encode murine Pygm cDNA without any intron sequence, their transfection in cells would allow for analysis of the efficacy of read-through agents with no concomitant nonsense-mediated decay interference. The third model consisted of skeletal muscle cultures derived from the McArdle mouse model (knock-in for the p.R50X mutation in the Pygm gene). We found no evidence of read-through at detectable levels in any of the models evaluated. We performed a literature search and compared the premature termination codon context sequences with reported positive and negative read-through induction, identifying a potential role for nucleotide positions −9, −8, −3, −2, +13 and +14 (the first nucleotide of the stop codon is assigned as +1). The Pygm p.R50X mutation presents TGA as a stop codon, G nucleotides at positions −1 and −9, and a C nucleotide at −3, which potentially generate a good context for read-through induction, counteracted by the presence of C at −2 and its absence at +4. Summary: Here, we evaluated the efficiency of different read-through agents in McArdle disease cell culture models, revealing that read-through compounds do not restore full-length muscle glycogen phosphorylase.
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Affiliation(s)
- Guillermo Tarrasó
- Mitochondrial and Neuromuscular Disorders Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Alberto Real-Martinez
- Mitochondrial and Neuromuscular Disorders Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Marta Parés
- Gene and Cell Therapy Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Lídia Romero-Cortadellas
- Gene and Cell Therapy Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Laura Puigros
- Gene and Cell Therapy Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Laura Moya
- Gene and Cell Therapy Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Noemí de Luna
- Laboratori de Malalties Neuromusculars, Institut de Recerca Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona 08041, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Astrid Brull
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Miguel Angel Martín
- Mitochondrial and Neuromuscular Diseases Laboratory, 12 de Octubre Hospital Research Institute (i+12), Madrid 28041, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Joaquin Arenas
- Mitochondrial and Neuromuscular Diseases Laboratory, 12 de Octubre Hospital Research Institute (i+12), Madrid 28041, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Alejandro Lucia
- Mitochondrial and Neuromuscular Diseases Laboratory, 12 de Octubre Hospital Research Institute (i+12), Madrid 28041, Spain.,Faculty of Sport Sciences, European University, Madrid 28670, Spain
| | - Antoni L Andreu
- Mitochondrial and Neuromuscular Disorders Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Jordi Barquinero
- Gene and Cell Therapy Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Thomas O Krag
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Tomàs Pinós
- Mitochondrial and Neuromuscular Disorders Unit, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
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Campofelice A, Lentini L, Di Leonardo A, Melfi R, Tutone M, Pace A, Pibiri I. Strategies against Nonsense: Oxadiazoles as Translational Readthrough-Inducing Drugs (TRIDs). Int J Mol Sci 2019; 20:ijms20133329. [PMID: 31284579 PMCID: PMC6651739 DOI: 10.3390/ijms20133329] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/24/2022] Open
Abstract
This review focuses on the use of oxadiazoles as translational readthrough-inducing drugs (TRIDs) to rescue the functional full-length protein expression in mendelian genetic diseases caused by nonsense mutations. These mutations in specific genes generate premature termination codons (PTCs) responsible for the translation of truncated proteins. After a brief introduction on nonsense mutations and their pathological effects, the features of various classes of TRIDs will be described discussing differences or similarities in their mechanisms of action. Strategies to correct the PTCs will be presented, particularly focusing on a new class of Ataluren-like oxadiazole derivatives in comparison to aminoglycosides. Additionally, recent results on the efficiency of new candidate TRIDs in restoring the production of the cystic fibrosis transmembrane regulator (CFTR) protein will be presented. Finally, a prospectus on complementary strategies to enhance the effect of TRIDs will be illustrated together with a conclusive paragraph about perspectives, opportunities, and caveats in developing small molecules as TRIDs.
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Affiliation(s)
- Ambra Campofelice
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università Degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy.
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23
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Lentini L, Melfi R, Cancemi P, Pibiri I, Di Leonardo A. Caffeine boosts Ataluren's readthrough activity. Heliyon 2019; 5:e01963. [PMID: 31294114 PMCID: PMC6595402 DOI: 10.1016/j.heliyon.2019.e01963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/31/2019] [Accepted: 06/12/2019] [Indexed: 01/19/2023] Open
Abstract
The readthrough of nonsense mutations by small molecules like Ataluren is considered a novel therapeutic approach to overcome the gene defect in several genetic diseases as cystic fibrosis (CF). This pharmacological approach suppresses translation termination at premature termination codons (PTCs readthrough) thus restoring the expression of a functional protein. However, readthrough might be limited by the nonsense-mediated mRNA decay (NMD), a cell process that reduces the amount/level of PTCs containing mRNAs. Here we investigate the combined action of Ataluren and caffeine to enhance the readthrough of PTCs. IB3.1 CF cells with a nonsense mutation were treated with caffeine to attenuate the Nonsense-Mediated mRNA Decay (NMD) activity and thus enhance the stability of the nonsense (ns)-CFTR-mRNA to be targeted by Ataluren. Our results show that NMD attenuation by caffeine enhances mRNA stability and more importantly when combined with Ataluren increase the recovery of the full-length CFTR protein.
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Affiliation(s)
- Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
- Corresponding author.
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Patrizia Cancemi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
- Centro di OncoBiologia Sperimentale (COBS) via San Lorenzo Colli 90145 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
- Centro di OncoBiologia Sperimentale (COBS) via San Lorenzo Colli 90145 Palermo, Italy
- Corresponding author.
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Tutone M, Pibiri I, Lentini L, Pace A, Almerico AM. Deciphering the Nonsense Readthrough Mechanism of Action of Ataluren: An in Silico Compared Study. ACS Med Chem Lett 2019; 10:522-527. [PMID: 30996790 DOI: 10.1021/acsmedchemlett.8b00558] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/07/2019] [Indexed: 12/26/2022] Open
Abstract
Ataluren was reported to suppress nonsense mutations by promoting the readthrough of premature stop codons, although its mechanism of action (MOA) is still debated. The likely interaction of Ataluren with CFTR-mRNA has been previously studied by molecular dynamics. In this work we extended the modeling of Ataluren's MOA by complementary computational approaches such as induced fit docking (IFD), quantum polarized ligand docking (QPLD), MM-GBSA free-energy calculations, and computational mutagenesis. In addition to CFTR-mRNA, this study considered other model targets implicated in the translation process, such as eukaryotic rRNA 18S, prokaryotic rRNA 16S, and eukaryotic Release Factor 1 (eRF1), and we performed a comparison with a new promising Ataluren analogue (NV2445) and with a series of aminoglycosides, known to suppress the normal proofreading function of the ribosome. Results confirmed mRNA as the most likely candidate target for Ataluren and its analogue, and binding energies calculated after computational mutagenesis highlighted how Ataluren's interaction with the premature stop codon could be affected by ancillary nucleotides in the genetic context.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo, via Archirafi 28 - viale delle Scienze, Edificio 16 & 17, 90100-Palermo-Italy
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25
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Froux L, Billet A, Becq F. Modulating the cystic fibrosis transmembrane regulator and the development of new precision drugs. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1547109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Lionel Froux
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers, Poitiers, France
| | - Arnaud Billet
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers, Poitiers, France
| | - Frédéric Becq
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers, Poitiers, France
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26
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Rubino S, Pibiri I, Minacori C, Alduina R, Di Stefano V, Orecchio S, Buscemi S, Girasolo MA, Tesoriere L, Attanzio A. Synthesis, structural characterization, anti-proliferative and antimicrobial activity of binuclear and mononuclear Pt(II) complexes with perfluoroalkyl-heterocyclic ligands. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.07.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Pibiri I, Lentini L, Melfi R, Tutone M, Baldassano S, Ricco Galluzzo P, Di Leonardo A, Pace A. Rescuing the CFTR protein function: Introducing 1,3,4-oxadiazoles as translational readthrough inducing drugs. Eur J Med Chem 2018; 159:126-142. [PMID: 30278331 DOI: 10.1016/j.ejmech.2018.09.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Nonsense mutations in the CFTR gene prematurely terminate translation of the CFTR mRNA leading to the production of a truncated protein that lacks normal function causing a more severe form of the cystic fibrosis (CF) disease. About 10% of patients affected by CF show a nonsense mutation. A potential treatment of this alteration is to promote translational readthrough of premature termination codons (PTCs) by Translational Readthrough Inducing Drugs (TRIDs) such as PTC124. In this context we aimed to compare the activity of PTC124 with analogues differing in the heteroatoms position in the central heterocyclic core. By a validated protocol consisting of computational screening, synthesis and biological tests we identified a new small molecule (NV2445) with 1,3,4-oxadiazole core showing a high readthrough activity. Moreover, we evaluated the CFTR functionality after NV2445 treatment in CF model systems and in cells expressing a nonsense-CFTR-mRNA. Finally, we studied the supramolecular interactions between TRIDs and CFTR-mRNA to assess the biological target/mechanism and compared the predicted ADME properties of NV2445 and PTC124.
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Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Sara Baldassano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Paola Ricco Galluzzo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy; Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145, Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
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28
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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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29
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Affiliation(s)
- Brian Raymer
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Samit K. Bhattacharya
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
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30
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Dabrowski M, Bukowy-Bieryllo Z, Zietkiewicz E. Advances in therapeutic use of a drug-stimulated translational readthrough of premature termination codons. Mol Med 2018; 24:25. [PMID: 30134808 PMCID: PMC6016875 DOI: 10.1186/s10020-018-0024-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/31/2022] Open
Abstract
Premature termination codons (PTCs) in the coding regions of mRNA lead to the incorrect termination of translation and generation of non-functional, truncated proteins. Translational readthrough of PTCs induced by pharmaceutical compounds is a promising way of restoring functional protein expression and reducing disease symptoms, without affecting the genome or transcriptome of the patient. While in some cases proven effective, the clinical use of readthrough-inducing compounds is still associated with many risks and difficulties. This review focuses on problems directly associated with compounds used to stimulate PTC readthrough, such as their interactions with the cell and organism, their toxicity and bioavailability (cell permeability; tissue deposition etc.). Various strategies designed to overcome these problems are presented.
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Affiliation(s)
- Maciej Dabrowski
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland
| | | | - Ewa Zietkiewicz
- Institute of Human Genetics; Polish Academy of Sciences, Poznan, Poland.
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31
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32
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Bai L, Gao C, Liu Q, Yu C, Zhang Z, Cai L, Yang B, Qian Y, Yang J, Liao X. Research progress in modern structure of platinum complexes. Eur J Med Chem 2017; 140:349-382. [PMID: 28985575 DOI: 10.1016/j.ejmech.2017.09.034] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
Since the antitumor activity of cisplatin was discovered in 1967 by Rosenberg, platinum-based anticancer drugs have played an important role in chemotherapy in clinic. Nevertheless, platinum anticancer drugs also have caused severe side effects and cross drug resistance which limited their applications. Therefore, a significant amount of efforts have been devoted to developing new platinum-based anticancer agents with equal or higher antitumor activity but lower toxicity. Until now, a large number of platinum-based complexes have been prepared and extensively investigated in vitro and in vivo. Among them, some platinum-based complexes revealing excellent anticancer activity showed the potential to be developed as novel type of anticancer agents. In this account, we present such platinum-based anticancer complexes which owning various types of ligands, such as, amine carrier ligands, leaving groups, reactive molecule, steric hindrance groups, non-covalently binding platinum (II) complexes, Platinum(IV) complexes and polynuclear platinum complexes. Overall, platinum-based anticancer complexes reported recently years upon modern structure are emphasized.
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Affiliation(s)
- Linkui Bai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Chuanzhu Gao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Qinghua Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Congtao Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Zhuxin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Linxiang Cai
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Bo Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yunxu Qian
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jian Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiali Liao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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33
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Jiang KM, Luesakul U, Zhao SY, An K, Muangsin N, Neamati N, Jin Y, Lin J. Tautomeric-Dependent Lactam Cycloaddition with Nitrile Oxide: Facile Synthesis of 1,2,4-Oxadiazole[4,5- a]indolone Derivatives. ACS OMEGA 2017; 2:3123-3134. [PMID: 30023685 PMCID: PMC6044867 DOI: 10.1021/acsomega.7b00490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/19/2017] [Indexed: 06/08/2023]
Abstract
A concise, metal-free, and gram-scale strategy to convert indoline-2,3-diones to 1,2,4-oxadiazole[4,5-a]indolones through an improved [3 + 2] cycloaddition of α-ketone-lactam with nitrile oxides has been developed. The lactim form of the resonance structure of isatin in protic solvents is the key active dipolarophile that shows chemo- and regioselectivity under experimental and theoretical conditions. This strategy conveniently enabled the assembly of several 1,2,4-oxadiazole[4,5-a]indolines with a broad range of functional groups. Compounds 3a and 4b exhibit cytotoxicity in the NCI/ADR-RES, SKOV3, and OVCAR8 cell lines.
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Affiliation(s)
- Kun-Ming Jiang
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Urarika Luesakul
- Department
of Medicinal Chemistry, College of Pharmacy, and Translational Oncology
Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Shu-Yue Zhao
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Kun An
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Nongnuj Muangsin
- Department
of Chemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Nouri Neamati
- Department
of Medicinal Chemistry, College of Pharmacy, and Translational Oncology
Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yi Jin
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
- Department
of Medicinal Chemistry, College of Pharmacy, and Translational Oncology
Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jun Lin
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
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Kosmidis G, Veerman CC, Casini S, Verkerk AO, van de Pas S, Bellin M, Wilde AAM, Mummery CL, Bezzina CR. Readthrough-Promoting Drugs Gentamicin and PTC124 Fail to Rescue Nav1.5 Function of Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Carrying Nonsense Mutations in the Sodium Channel Gene SCN5A. Circ Arrhythm Electrophysiol 2017; 9:CIRCEP.116.004227. [PMID: 27784737 DOI: 10.1161/circep.116.004227] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/09/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND Several compounds have been reported to induce translational readthrough of premature stop codons resulting in the production of full-length protein by interfering with ribosomal proofreading. Here we examined the effect of 2 of these compounds, gentamicin and PTC124, in human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes bearing nonsense mutations in the sodium channel gene SCN5A, which are associated with conduction disease and potential lethal arrhythmias. METHODS AND RESULTS We generated hiPSC from 2 patients carrying the mutations R1638X and W156X. hiPSC-derived cardiomyocytes from both patients recapitulated the expected electrophysiological phenotype, as evidenced by reduced Na+ currents and action potential upstroke velocities compared with hiPSC-derived cardiomyocytes from 2 unrelated control individuals. While we were able to confirm the readthrough efficacy of the 2 drugs in Human Embryonic Kidney 293 cells, we did not observe rescue of the electrophysiological phenotype in hiPSC-derived cardiomyocytes from the patients. CONCLUSIONS We conclude that these drugs are unlikely to present an effective treatment for patients carrying the loss-of-function SCN5A gene mutations examined in this study.
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Affiliation(s)
- Georgios Kosmidis
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Christiaan C Veerman
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Simona Casini
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Arie O Verkerk
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Simone van de Pas
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Milena Bellin
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Arthur A M Wilde
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Christine L Mummery
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands
| | - Connie R Bezzina
- From the Department of Anatomy and Embryology, Leiden University Medical Center, Leiden (G.K., S.C., S.v.d.P., M.B., C.L.M.); and Heart Center, Department of Experimental and Clinical Cardiology (C.C.V., A.A.M.W., C.R.B.) and Department of Anatomy and Embryology, Academic Medical Center (A.O.V.), Amsterdam, The Netherlands.
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Caruso Bavisotto C, Nikolic D, Marino Gammazza A, Barone R, Lo Cascio F, Mocciaro E, Zummo G, Conway de Macario E, Macario AJL, Cappello F, Giacalone V, Pace A, Barone G, Palumbo Piccionello A, Campanella C. The dissociation of the Hsp60/pro-Caspase-3 complex by bis(pyridyl)oxadiazole copper complex ( CubipyOXA ) leads to cell death in NCI-H292 cancer cells. J Inorg Biochem 2017; 170:8-16. [DOI: 10.1016/j.jinorgbio.2017.02.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 01/16/2017] [Accepted: 02/09/2017] [Indexed: 11/24/2022]
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Bolze F, Mocek S, Zimmermann A, Klingenspor M. Aminoglycosides, but not PTC124 (Ataluren), rescue nonsense mutations in the leptin receptor and in luciferase reporter genes. Sci Rep 2017; 7:1020. [PMID: 28432296 PMCID: PMC5430635 DOI: 10.1038/s41598-017-01093-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/23/2017] [Indexed: 11/09/2022] Open
Abstract
In rare cases, monogenetic obesity is caused by nonsense mutations in genes regulating energy balance. A key factor herein is the leptin receptor. Here, we focus on leptin receptor nonsense variants causing obesity, namely the human W31X, murine Y333X and rat Y763X mutations, and explored their susceptibilities to aminoglycoside and PTC124 mediated translational read-through in vitro. In a luciferase based assay, all mutations - when analysed within the mouse receptor - were prone to aminoglycoside mediated nonsense suppression with the highest susceptibility for W31X, followed by Y763X and Y333X. For the latter, the corresponding rodent models appear valuable for in vivo experiments. When W31X was studied in the human receptor, its superior read-through susceptibility – initially observed in the mouse receptor – was eliminated, likely due to the different nucleotide context surrounding the mutation in the two orthologues. The impact of the surrounding context on the read-through opens the possibility to discover novel sequence elements influencing nonsense suppression. As an alternative to toxic aminoglycosides, PTC124 was indicated as a superior nonsense suppressor but inconsistent data concerning its read-through activity are reported. PTC124 failed to rescue W31X as well as different nonsense mutated luciferase reporters, thus, challenging its ability to induce translational read-through.
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Affiliation(s)
- Florian Bolze
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Chair of Molecular Nutritional Medicine, Technical University of Munich, EKFZ - Else Kröner-Fresenius-Center for Nutritional Medicine, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Sabine Mocek
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Chair of Molecular Nutritional Medicine, Technical University of Munich, EKFZ - Else Kröner-Fresenius-Center for Nutritional Medicine, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Anika Zimmermann
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany.,Chair of Molecular Nutritional Medicine, Technical University of Munich, EKFZ - Else Kröner-Fresenius-Center for Nutritional Medicine, Gregor-Mendel-Str. 2, 85354, Freising, Germany
| | - Martin Klingenspor
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354, Freising, Germany. .,Chair of Molecular Nutritional Medicine, Technical University of Munich, EKFZ - Else Kröner-Fresenius-Center for Nutritional Medicine, Gregor-Mendel-Str. 2, 85354, Freising, Germany.
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Li S, Wan P, Ai J, Sheng R, Hu Y, Hu Y. Palladium-Catalyzed, Silver-Assisted Direct C-5-H Arylation of 3-Substituted 1,2,4-Oxadiazoles under Microwave Irradiation. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201600913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shan Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou 310058 People's Republic of China
| | - Penghui Wan
- State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 ZuChongZhi Road Shanghai 201203 People's Republic of China
| | - Jing Ai
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 ZuChongZhi Road Shanghai 201203 People's Republic of China
| | - Rong Sheng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou 310058 People's Republic of China
| | - Yongzhou Hu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research; College of Pharmaceutical Sciences; Zhejiang University; Hangzhou 310058 People's Republic of China
| | - Youhong Hu
- State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 ZuChongZhi Road Shanghai 201203 People's Republic of China
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Richardson R, Smart M, Tracey-White D, Webster AR, Moosajee M. Mechanism and evidence of nonsense suppression therapy for genetic eye disorders. Exp Eye Res 2017; 155:24-37. [PMID: 28065590 DOI: 10.1016/j.exer.2017.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
Between 5 and 70% of genetic disease is caused by in-frame nonsense mutations, which introduce a premature termination codon (PTC) within the disease-causing gene. Consequently, during translation, non-functional or gain-of-function truncated proteins of pathological significance, are formed. Approximately 50% of all inherited retinal disorders have been associated with PTCs, highlighting the importance of novel pharmacological or gene correction therapies in ocular disease. Pharmacological nonsense suppression of PTCs could delineate a therapeutic strategy that treats the mutation in a gene- and disease-independent manner. This approach aims to suppress the fidelity of the ribosome during protein synthesis so that a near-cognate aminoacyl-tRNA, which shares two of the three nucleotides of the PTC, can be inserted into the peptide chain, allowing translation to continue, and a full-length functional protein to be produced. Here we discuss the mechanisms and evidence of nonsense suppression agents, including the small molecule drug ataluren (or PTC124) and next generation 'designer' aminoglycosides, for the treatment of genetic eye disease.
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Affiliation(s)
- Rose Richardson
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Matthew Smart
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Dhani Tracey-White
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK
| | - Andrew R Webster
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Department of Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK.
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Targeting Nonsense Mutations in Diseases with Translational Read-Through-Inducing Drugs (TRIDs). BioDrugs 2016; 30:49-74. [PMID: 26886021 DOI: 10.1007/s40259-016-0157-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, remarkable advances in the ability to diagnose genetic disorders have been made. The identification of disease-causing genes allows the development of gene-specific therapies with the ultimate goal to develop personalized medicines for each patient according to their own specific genetic defect. In-depth genotyping of many different genes has revealed that ~12% of inherited genetic disorders are caused by in-frame nonsense mutations. Nonsense (non-coding) mutations are caused by point mutations, which generate premature termination codons (PTCs) that cause premature translational termination of the mRNA, and subsequently inhibit normal full-length protein expression. Recently, a gene-based therapeutic approach for genetic diseases caused by nonsense mutations has emerged, namely the so-called translational read-through (TR) therapy. Read-through therapy is based on the discovery that small molecules, known as TR-inducing drugs (TRIDs), allow the translation machinery to suppress a nonsense codon, elongate the nascent peptide chain, and consequently result in the synthesis of full-length protein. Several TRIDs are currently under investigation and research has been performed on several genetic disorders caused by nonsense mutations over the years. These findings have raised hope for the usage of TR therapy as a gene-based pharmacogenetic therapy for nonsense mutations in various genes responsible for a variety of genetic diseases.
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40
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Veit G, Avramescu RG, Chiang AN, Houck SA, Cai Z, Peters KW, Hong JS, Pollard HB, Guggino WB, Balch WE, Skach WR, Cutting GR, Frizzell RA, Sheppard DN, Cyr DM, Sorscher EJ, Brodsky JL, Lukacs GL. From CFTR biology toward combinatorial pharmacotherapy: expanded classification of cystic fibrosis mutations. Mol Biol Cell 2016; 27:424-33. [PMID: 26823392 PMCID: PMC4751594 DOI: 10.1091/mbc.e14-04-0935] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 2000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) have been described that confer a range of molecular cell biological and functional phenotypes. Most of these mutations lead to compromised anion conductance at the apical plasma membrane of secretory epithelia and cause cystic fibrosis (CF) with variable disease severity. Based on the molecular phenotypic complexity of CFTR mutants and their susceptibility to pharmacotherapy, it has been recognized that mutations may impose combinatorial defects in CFTR channel biology. This notion led to the conclusion that the combination of pharmacotherapies addressing single defects (e.g., transcription, translation, folding, and/or gating) may show improved clinical benefit over available low-efficacy monotherapies. Indeed, recent phase 3 clinical trials combining ivacaftor (a gating potentiator) and lumacaftor (a folding corrector) have proven efficacious in CF patients harboring the most common mutation (deletion of residue F508, ΔF508, or Phe508del). This drug combination was recently approved by the U.S. Food and Drug Administration for patients homozygous for ΔF508. Emerging studies of the structural, cell biological, and functional defects caused by rare mutations provide a new framework that reveals a mixture of deficiencies in different CFTR alleles. Establishment of a set of combinatorial categories of the previously defined basic defects in CF alleles will aid the design of even more efficacious therapeutic interventions for CF patients.
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Affiliation(s)
- Gudio Veit
- Department of Physiology, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Radu G Avramescu
- Department of Physiology, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Annette N Chiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Scott A Houck
- Marsico Lung Institute, School of Medicine, University of North Carolina, Chapel Hill, NC 27514
| | - Zhiwei Cai
- School of Physiology & Pharmacology, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Kathryn W Peters
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Jeong S Hong
- Department of Cellular, Developmental, and Integrative Biology, University of Alabama, Birmingham, AL 35294
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics and Center for Medical Proteomics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - William B Guggino
- Department of Physiology, Johns Hopkins University, Baltimore, MD 21205
| | - William E Balch
- Department of Chemical Physiology, Skaggs Institute of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - William R Skach
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Raymond A Frizzell
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - David N Sheppard
- School of Physiology & Pharmacology, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Douglas M Cyr
- Marsico Lung Institute, School of Medicine, University of North Carolina, Chapel Hill, NC 27514
| | - Eric J Sorscher
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montréal, QC H3G 1Y6, Canada Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada GRASP, McGill University, Montréal, QC H3G 1Y6, Canada
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Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression. Proc Natl Acad Sci U S A 2016; 113:12508-12513. [PMID: 27702906 DOI: 10.1073/pnas.1605336113] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in control, ataluren-treated, and aminoglycoside-treated cells. We find that ataluren's likely target is the ribosome and that it produces full-length protein by promoting insertion of near-cognate tRNAs at the site of the nonsense codon without apparent effects on transcription, mRNA processing, mRNA stability, or protein stability. The resulting readthrough proteins retain function and contain amino acid replacements similar to those derived from endogenous readthrough, namely Gln, Lys, or Tyr at UAA or UAG PTCs and Trp, Arg, or Cys at UGA PTCs. These insertion biases arise primarily from mRNA:tRNA mispairing at codon positions 1 and 3 and reflect, in part, the preferred use of certain nonstandard base pairs, e.g., U-G. Ataluren's retention of similar specificity of near-cognate tRNA insertion as occurs endogenously has important implications for its general use in therapeutic nonsense suppression.
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Yoshimura A, Nguyen KC, Klasen SC, Postnikov PS, Yusubov MS, Saito A, Nemykin VN, Zhdankin VV. Hypervalent Iodine‐Catalyzed Synthesis of 1,2,4‐Oxadiazoles from Aldoximes and Nitriles. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600247] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Akira Yoshimura
- Department of Chemistry and Biochemistry University of Minnesota Duluth Duluth Minnesota 55812 USA
| | - Khiem C. Nguyen
- Department of Chemistry and Biochemistry University of Minnesota Duluth Duluth Minnesota 55812 USA
| | - Scott C. Klasen
- Department of Chemistry and Biochemistry University of Minnesota Duluth Duluth Minnesota 55812 USA
| | | | | | - Akio Saito
- Division of Applied Chemistry Institute of Engineering Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
| | - Victor N. Nemykin
- Department of Chemistry and Biochemistry University of Minnesota Duluth Duluth Minnesota 55812 USA
| | - Viktor V. Zhdankin
- Department of Chemistry and Biochemistry University of Minnesota Duluth Duluth Minnesota 55812 USA
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43
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The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II): A molecular dynamics study. J Inorg Biochem 2016; 160:78-84. [DOI: 10.1016/j.jinorgbio.2015.11.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/05/2015] [Accepted: 11/30/2015] [Indexed: 11/22/2022]
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Pibiri I, Lentini L, Tutone M, Melfi R, Pace A, Di Leonardo A. Exploring the readthrough of nonsense mutations by non-acidic Ataluren analogues selected by ligand-based virtual screening. Eur J Med Chem 2016; 122:429-435. [PMID: 27404557 DOI: 10.1016/j.ejmech.2016.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/09/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
Abstract
Ataluren, also known as PTC124, is a 5-(fluorophenyl)-1,2,4-oxadiazolyl-benzoic acid suggested to suppress nonsense mutations by readthrough of premature stop codons in the mRNA. Potential interaction of PTC124 with mRNA has been recently studied by molecular dynamics simulations highlighting the importance of H-bonding and stacking π-π interactions. A series of non-acidic analogues of PTC124 were selected from a large database via a ligand-based virtual screening approach. Eight of them were synthesized and tested for their readthrough activity using the Fluc reporter harboring the UGA premature stop codon. The most active compound was further tested for suppression of the UGA nonsense mutation in the bronchial epithelial IB3.1 cell line carrying the W1282X mutation in the CFTR gene.
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Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy.
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; Istituto EuroMediterraneo di Scienza e Tecnologia (IEMEST), Via Emerico Amari 123, 90139 Palermo, Italy.
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145 Palermo, Italy
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45
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A peptide from human β thymosin as a platform for the development of new anti-biofilm agents for Staphylococcus spp. and Pseudomonas aeruginosa. World J Microbiol Biotechnol 2016; 32:124. [DOI: 10.1007/s11274-016-2096-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/11/2016] [Indexed: 12/01/2022]
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46
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Synthetic approaches to the 2014 new drugs. Bioorg Med Chem 2016; 24:1937-80. [DOI: 10.1016/j.bmc.2016.03.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 12/31/2022]
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47
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Altamura E, Borgatti M, Finotti A, Gasparello J, Gambari R, Spinelli M, Castaldo R, Altamura N. Chemical-Induced Read-Through at Premature Termination Codons Determined by a Rapid Dual-Fluorescence System Based on S. cerevisiae. PLoS One 2016; 11:e0154260. [PMID: 27119736 PMCID: PMC4847774 DOI: 10.1371/journal.pone.0154260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/11/2016] [Indexed: 01/09/2023] Open
Abstract
Nonsense mutations generate in-frame stop codons in mRNA leading to a premature arrest of translation. Functional consequences of premature termination codons (PTCs) include the synthesis of truncated proteins with loss of protein function causing severe inherited or acquired diseases. A therapeutic approach has been recently developed that is based on the use of chemical agents with the ability to suppress PTCs (read-through) restoring the synthesis of a functional full-length protein. Research interest for compounds able to induce read-through requires an efficient high throughput large scale screening system. We present a rapid, sensitive and quantitative method based on a dual-fluorescence reporter expressed in the yeast Saccharomyces cerevisiae to monitor and quantitate read-through at PTCs. We have shown that our novel system works equally well in detecting read-through at all three PTCs UGA, UAG and UAA.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University of Bari, Bari, Italy
- * E-mail: (EA); (NA)
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Mariangela Spinelli
- Institute of Biomembranes and Bioenergetics, National Researches Council, Bari, Italy
| | - Rosa Castaldo
- Institute of Biomembranes and Bioenergetics, National Researches Council, Bari, Italy
| | - Nicola Altamura
- Institute of Biomembranes and Bioenergetics, National Researches Council, Bari, Italy
- * E-mail: (EA); (NA)
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48
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Spinello A, Barone G, Cappello F, Pace A, Buscemi S, Palumbo Piccionello A. The Binding Mechanism of Epolactaene to Hsp60 Unveiled by in Silico Modelling. ChemistrySelect 2016. [DOI: 10.1002/slct.201600125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Angelo Spinello
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche-STEBICEF; University of Palermo; V.le delle Scienze Ed.17 90128 Palermo Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia-IEMEST; Via Michele Miraglia 20 90139 Palermo Italy
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche-STEBICEF; University of Palermo; V.le delle Scienze Ed.17 90128 Palermo Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia-IEMEST; Via Michele Miraglia 20 90139 Palermo Italy
| | - Francesco Cappello
- Istituto Euro-Mediterraneo di Scienza e Tecnologia-IEMEST; Via Michele Miraglia 20 90139 Palermo Italy
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche -BIONEC; University of Palermo; Via del Vespro 129 90127 Palermo Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche-STEBICEF; University of Palermo; V.le delle Scienze Ed.17 90128 Palermo Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia-IEMEST; Via Michele Miraglia 20 90139 Palermo Italy
| | - Silvestre Buscemi
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche-STEBICEF; University of Palermo; V.le delle Scienze Ed.17 90128 Palermo Italy
| | - Antonio Palumbo Piccionello
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche-STEBICEF; University of Palermo; V.le delle Scienze Ed.17 90128 Palermo Italy
- Istituto Euro-Mediterraneo di Scienza e Tecnologia-IEMEST; Via Michele Miraglia 20 90139 Palermo Italy
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Shoseyov D, Cohen-Cymberknoh M, Wilschanski M. Ataluren for the treatment of cystic fibrosis. Expert Rev Respir Med 2016; 10:387-391. [PMID: 26840186 DOI: 10.1586/17476348.2016.1150181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Alleles causing diseases that carry premature termination codons (PTCs) will cause premature cessation of translation, leading to loss of function and consequent disease. Recently, a novel agent, Ataluren, was developed through a high throughput screening program. Ataluren is orally bioavailable and was shown to be effective in Cystic Fibrosis (CF). Phase I and II studies established the safety and dosing regimens for Ataluren. The results of a short study showed modest improvements in pulmonary function and a reduction in quantitative cough assessment. There was improvement in nasal potential difference and nasal epithelial CFTR protein. In a phase III trial this effect was not observed in patients that were concomitantly treated with tobramycin inhalation. Following these positive findings, a multinational Phase III placebo-controlled efficacy trial is currently underway.
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Affiliation(s)
- David Shoseyov
- a CF Center , Hadassah Hebrew University Medical Center , Jerusalem , Israel
| | | | - Michael Wilschanski
- a CF Center , Hadassah Hebrew University Medical Center , Jerusalem , Israel
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50
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Rubino S, Pibiri I, Costantino C, Buscemi S, Girasolo MA, Attanzio A, Tesoriere L. Synthesis of platinum complexes with 2-(5-perfluoroalkyl-1,2,4-oxadiazol-3yl)-pyridine and 2-(3-perfluoroalkyl-1-methyl-1,2,4-triazole-5yl)-pyridine ligands and their in vitro antitumor activity. J Inorg Biochem 2016; 155:92-100. [DOI: 10.1016/j.jinorgbio.2015.11.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 12/28/2022]
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