1
|
Li S, Li J, Shi W, Nie Z, Zhang S, Ma F, Hu J, Chen J, Li P, Xie X. Pharmaceuticals Promoting Premature Termination Codon Readthrough: Progress in Development. Biomolecules 2023; 13:988. [PMID: 37371567 DOI: 10.3390/biom13060988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Around 11% of all known gene lesions causing human genetic diseases are nonsense mutations that introduce a premature stop codon (PTC) into the protein-coding gene sequence. Drug-induced PTC readthrough is a promising therapeutic strategy for treating hereditary diseases caused by nonsense mutations. To date, it has been found that more than 50 small-molecular compounds can promote PTC readthrough, known as translational readthrough-inducing drugs (TRIDs), and can be divided into two major categories: aminoglycosides and non-aminoglycosides. This review summarizes the pharmacodynamics and clinical application potential of the main TRIDs discovered so far, especially some newly discovered TRIDs in the past decade. The discovery of these TRIDs brings hope for treating nonsense mutations in various genetic diseases. Further research is still needed to deeply understand the mechanism of eukaryotic cell termination and drug-induced PTC readthrough so that patients can achieve the greatest benefit from the various TRID treatments.
Collapse
Affiliation(s)
- Shan Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Juan Li
- Central Laboratory, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Genetic Study of Hematopathy, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wenjing Shi
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ziyan Nie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shasha Zhang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fengdie Ma
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jun Hu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jianjun Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Peiqiang Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
2
|
Spelier S, van Doorn EPM, van der Ent CK, Beekman JM, Koppens MAJ. Readthrough compounds for nonsense mutations: bridging the translational gap. Trends Mol Med 2023; 29:297-314. [PMID: 36828712 DOI: 10.1016/j.molmed.2023.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/28/2022] [Accepted: 01/19/2023] [Indexed: 02/24/2023]
Abstract
Approximately 10% of all pathological mutations are nonsense mutations that are responsible for several severe genetic diseases for which no treatment regimens are currently available. The most widespread strategy for treating nonsense mutations is by enhancing ribosomal readthrough of premature termination codons (PTCs) to restore the production of the full-length protein. In the past decade several compounds with readthrough potential have been identified. However, although preclinical results on these compounds are promising, clinical studies have not yielded positive outcomes. We review preclinical and clinical research related to readthrough compounds and characterize factors that contribute to the observed translational gap.
Collapse
Affiliation(s)
- Sacha Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Eveline P M van Doorn
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Martijn A J Koppens
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands.
| |
Collapse
|
3
|
Recoding of Nonsense Mutation as a Pharmacological Strategy. Biomedicines 2023; 11:biomedicines11030659. [PMID: 36979640 PMCID: PMC10044939 DOI: 10.3390/biomedicines11030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Approximately 11% of genetic human diseases are caused by nonsense mutations that introduce a premature termination codon (PTC) into the coding sequence. The PTC results in the production of a potentially harmful shortened polypeptide and activation of a nonsense-mediated decay (NMD) pathway. The NMD pathway reduces the burden of unproductive protein synthesis by lowering the level of PTC mRNA. There is an endogenous rescue mechanism that produces a full-length protein from a PTC mRNA. Nonsense suppression therapies aim to increase readthrough, suppress NMD, or are a combination of both strategies. Therefore, treatment with translational readthrough-inducing drugs (TRIDs) and NMD inhibitors may increase the effectiveness of PTC suppression. Here we discuss the mechanism of PTC readthrough and the development of novel approaches to PTC suppression. We also discuss the toxicity and bioavailability of therapeutics used to stimulate PTC readthrough.
Collapse
|
4
|
2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases. Proc Natl Acad Sci U S A 2022; 119:e2122004119. [PMID: 35994666 PMCID: PMC9436315 DOI: 10.1073/pnas.2122004119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Nonsense mutations account for approximately 11% of all described gene lesions causing human inherited diseases. This premature termination codon (PTC) leads to the premature arrest of translation that generates a truncated peptide and the degradation of the corresponding mRNA through the nonsense-mediated mRNA decay (NMD) pathway. The possibility of restoring the protein expression by promoting PTC readthrough using drugs appears to be an important therapeutic strategy. Unfortunately, this strategy is limited by the small number of molecules known to promote PTC readthrough without affecting normal translation termination. In this work, we identify a new molecule, TLN468, that promotes a high level of PTC readthrough without a detectable effect on normal stop codons. Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).
Collapse
|
5
|
Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
Collapse
Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Baradaran-Heravi A, Bauer CC, Pickles IB, Hosseini-Farahabadi S, Balgi AD, Choi K, Linley DM, Beech DJ, Roberge M, Bon RS. Nonselective TRPC channel inhibition and suppression of aminoglycoside-induced premature termination codon readthrough by the small molecule AC1903. J Biol Chem 2022; 298:101546. [PMID: 34999117 PMCID: PMC8808171 DOI: 10.1016/j.jbc.2021.101546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022] Open
Abstract
Nonsense mutations, which occur in ∼11% of patients with genetic disorders, introduce premature termination codons (PTCs) that lead to truncated proteins and promote nonsense-mediated mRNA decay. Aminoglycosides such as G418 permit PTC readthrough and so may be used to address this problem. However, their effects are variable between patients, making clinical use of aminoglycosides challenging. In this study, we tested whether TRPC nonselective cation channels contribute to the variable PTC readthrough effect of aminoglycosides by controlling their cellular uptake. Indeed, a recently reported selective TRPC5 inhibitor, AC1903, consistently suppressed G418 uptake and G418-induced PTC readthrough in the DMS-114 cancer cell line and junctional epidermolysis bullosa (JEB) patient-derived keratinocytes. Interestingly, the effect of AC1903 in DMS-114 cells was mimicked by nonselective TRPC inhibitors, but not by well-characterized inhibitors of TRPC1/4/5 (Pico145, GFB-8438) or TRPC3/6/7 (SAR7334), suggesting that AC1903 may work through additional or undefined targets. Indeed, in our experiments, AC1903 inhibited multiple TRPC channels including TRPC3, TRPC4, TRPC5, TRPC6, TRPC4-C1, and TRPC5-C1, as well as endogenous TRPC1:C4 channels in A498 renal cancer cells, all with low micromolar IC50 values (1.8-18 μM). We also show that AC1903 inhibited TRPV4 channels, but had weak or no effects on TRPV1 and no effect on the nonselective cation channel PIEZO1. Our study reveals that AC1903 has previously unrecognized targets, which need to be considered when interpreting results from experiments with this compound. In addition, our data strengthen the hypothesis that nonselective calcium channels are involved in aminoglycoside uptake.
Collapse
Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Claudia C Bauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Isabelle B Pickles
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; School of Chemistry, University of Leeds, Leeds, UK
| | - Sara Hosseini-Farahabadi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aruna D Balgi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kunho Choi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Deborah M Linley
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - David J Beech
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robin S Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| |
Collapse
|
8
|
Perez H, Abdallah MF, Chavira JI, Norris AS, Egeland MT, Vo KL, Buechsenschuetz CL, Sanghez V, Kim JL, Pind M, Nakamura K, Hicks GG, Gatti RA, Madrenas J, Iacovino M, McKinnon PJ, Mathews PJ. A novel, ataxic mouse model of ataxia telangiectasia caused by a clinically relevant nonsense mutation. eLife 2021; 10:64695. [PMID: 34723800 PMCID: PMC8601662 DOI: 10.7554/elife.64695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
Ataxia Telangiectasia (A-T) and Ataxia with Ocular Apraxia Type 1 (AOA1) are devastating neurological disorders caused by null mutations in the genome stability genes, A-T mutated (ATM) and Aprataxin (APTX), respectively. Our mechanistic understanding and therapeutic repertoire for treating these disorders are severely lacking, in large part due to the failure of prior animal models with similar null mutations to recapitulate the characteristic loss of motor coordination (i.e., ataxia) and associated cerebellar defects. By increasing genotoxic stress through the insertion of null mutations in both the Atm (nonsense) and Aptx (knockout) genes in the same animal, we have generated a novel mouse model that for the first time develops a progressively severe ataxic phenotype associated with atrophy of the cerebellar molecular layer. We find biophysical properties of cerebellar Purkinje neurons (PNs) are significantly perturbed (e.g., reduced membrane capacitance, lower action potential [AP] thresholds, etc.), while properties of synaptic inputs remain largely unchanged. These perturbations significantly alter PN neural activity, including a progressive reduction in spontaneous AP firing frequency that correlates with both cerebellar atrophy and ataxia over the animal’s first year of life. Double mutant mice also exhibit a high predisposition to developing cancer (thymomas) and immune abnormalities (impaired early thymocyte development and T-cell maturation), symptoms characteristic of A-T. Finally, by inserting a clinically relevant nonsense-type null mutation in Atm, we demonstrate that Small Molecule Read-Through (SMRT) compounds can restore ATM production, indicating their potential as a future A-T therapeutic.
Collapse
Affiliation(s)
- Harvey Perez
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - May F Abdallah
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Jose I Chavira
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Angelina S Norris
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Martin T Egeland
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Karen L Vo
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Callan L Buechsenschuetz
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Valentina Sanghez
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Jeannie L Kim
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Molly Pind
- Department of Biochemistry and Medical Genetics,Max Rady College of Medicine, University of Manitoba, Manitoba, Canada
| | - Kotoka Nakamura
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, United States
| | - Geoffrey G Hicks
- Department of Biochemistry and Medical Genetics,Max Rady College of Medicine, University of Manitoba, Manitoba, Canada
| | - Richard A Gatti
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, United States
| | - Joaquin Madrenas
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Medicine, Harbor-UCLA Medical Center, Torrance, United States
| | - Michelina Iacovino
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, United States
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, St. Jude Children's Research Hospital, Memphis, United States
| | - Paul J Mathews
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Neurology, Harbor-UCLA Medical Center, Torrance, United States
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Ataluren and aminoglycosides stimulate read-through of nonsense codons by orthogonal mechanisms. Proc Natl Acad Sci U S A 2021; 118:2020599118. [PMID: 33414181 PMCID: PMC7812769 DOI: 10.1073/pnas.2020599118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nonsense mutations giving rise to premature stop codons (PSCs) cause many diseases, creating the need to develop safe and effective translational read-through–inducing drugs (TRIDs). The current best-characterized TRIDs are ataluren and aminoglycosides. Only ataluren has been approved for clinical use, albeit in a limited context. Here, we provide rate measurements of elementary steps in a single eukaryotic translation elongation cycle, allowing us to demonstrate that ataluren and the aminoglycoside G418 employ orthogonal mechanisms in stimulating PSC read-through: ataluren by inhibiting release factor-dependent termination of protein synthesis and G418 by increasing functional near-cognate transfer RNA mispairing, which permits continuation of synthesis. We conclude that development of new TRIDs combatting PSC diseases should prioritize those directed toward inhibiting termination. During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), and some cancers. Small molecule nonsense suppressors, known as TRIDs (translational read-through–inducing drugs), stimulate stop codon read-through. The best characterized TRIDs are ataluren, which has been approved by the European Medicines Agency for the treatment of DMD, and G418, a structurally dissimilar aminoglycoside. Previously [1], we applied a highly purified in vitro eukaryotic translation system to demonstrate that both aminoglycosides like G418 and more hydrophobic molecules like ataluren stimulate read-through by direct interaction with the cell’s protein synthesis machinery. Our results suggested that they might do so by different mechanisms. Here, we pursue this suggestion through a more-detailed investigation of ataluren and G418 effects on read-through. We find that ataluren stimulation of read-through derives exclusively from its ability to inhibit release factor activity. In contrast, G418 increases functional near-cognate tRNA mispairing with a PSC, resulting from binding to its tight site on the ribosome, with little if any effect on release factor activity. The low toxicity of ataluren suggests that development of new TRIDs exclusively directed toward inhibiting termination should be a priority in combatting PSC diseases. Our results also provide rate measurements of some of the elementary steps during the eukaryotic translation elongation cycle, allowing us to determine how these rates are modified when cognate tRNA is replaced by near-cognate tRNA ± TRIDs.
Collapse
|
11
|
Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
Collapse
Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| |
Collapse
|
14
|
Wang K, Romm EL, Kouznetsova VL, Tsigelny IF. Prediction of Premature Termination Codon Suppressing Compounds for Treatment of Duchenne Muscular Dystrophy Using Machine Learning. Molecules 2020; 25:molecules25173886. [PMID: 32858918 PMCID: PMC7503396 DOI: 10.3390/molecules25173886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022] Open
Abstract
A significant percentage of Duchenne muscular dystrophy (DMD) cases are caused by premature termination codon (PTC) mutations in the dystrophin gene, leading to the production of a truncated, non-functional dystrophin polypeptide. PTC-suppressing compounds (PTCSC) have been developed in order to restore protein translation by allowing the incorporation of an amino acid in place of a stop codon. However, limitations exist in terms of efficacy and toxicity. To identify new compounds that have PTC-suppressing ability, we selected and clustered existing PTCSC, allowing for the construction of a common pharmacophore model. Machine learning (ML) and deep learning (DL) models were developed for prediction of new PTCSC based on known compounds. We conducted a search of the NCI compounds database using the pharmacophore-based model and a search of the DrugBank database using pharmacophore-based, ML and DL models. Sixteen drug compounds were selected as a consensus of pharmacophore-based, ML, and DL searches. Our results suggest notable correspondence of the pharmacophore-based, ML, and DL models in prediction of new PTC-suppressing compounds.
Collapse
Affiliation(s)
- Kate Wang
- MAP program, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
| | - Eden L. Romm
- Curematch Inc., 6440 Lusk Blvd, Suite D206, San Diego, CA 92121, USA;
| | - Valentina L. Kouznetsova
- San Diego Supercomputer Center, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
| | - Igor F. Tsigelny
- Curematch Inc., 6440 Lusk Blvd, Suite D206, San Diego, CA 92121, USA;
- San Diego Supercomputer Center, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
- Dept. of Neurosciences, University of California San Diego (UCSD), La Jolla, CA 92093, USA
- Correspondence:
| |
Collapse
|
15
|
CTELS: A Cell-Free System for the Analysis of Translation Termination Rate. Biomolecules 2020; 10:biom10060911. [PMID: 32560154 PMCID: PMC7356799 DOI: 10.3390/biom10060911] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3′ UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a “leaky” stop codon context, which likely defines the basis of nonsense suppression.
Collapse
|
16
|
Way CM, Lima Cunha D, Moosajee M. Translational readthrough inducing drugs for the treatment of inherited retinal dystrophies. EXPERT REVIEW OF OPHTHALMOLOGY 2020. [DOI: 10.1080/17469899.2020.1762489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Christopher M Way
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Dulce Lima Cunha
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
2-Aminothiazole-4-carboxamides Enhance Readthrough of Premature Termination Codons by Aminoglycosides. ACS Med Chem Lett 2019; 10:726-731. [PMID: 31097990 DOI: 10.1021/acsmedchemlett.8b00610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 02/06/2023] Open
Abstract
Nonsense mutations introduce a premature termination codon (PTC) and are the underlying cause of multiple rare genetic diseases and cancers. Although certain aminoglycosides bind to eukaryotic ribosomes enabling incorporation of an amino acid at the PTC and formation of full-length protein, they are inefficient and toxic at therapeutic doses. Library screening in assays that measure readthrough at a PTC in the TP53 gene in human HDQ-P1 cells identified six novel 2-aminothiazole-4-carboxamide derivatives that potentiate the PTC readthrough (PTCR) efficiency of G418 when used in combination. The two most potent compounds incorporated a 4-indazole motif on the 2-aminothiazole nitrogen and a hydrophobic aryl substituent on the carboxamide nitrogen. These compounds are valuable tools to further investigate the therapeutic potential of aminoglycoside-induced PTCR.
Collapse
|
19
|
Mass Spectrometry-Based Tissue Imaging of Small Molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:99-109. [PMID: 31347043 DOI: 10.1007/978-3-030-15950-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
20
|
Ng M, Zhang H, Weil A, Singh V, Jamiolkowski R, Baradaran-Heravi A, Roberge M, Jacobson A, Friesen W, Welch E, Goldman YE, Cooperman BS. New in Vitro Assay Measuring Direct Interaction of Nonsense Suppressors with the Eukaryotic Protein Synthesis Machinery. ACS Med Chem Lett 2018; 9:1285-1291. [PMID: 30613341 PMCID: PMC6295867 DOI: 10.1021/acsmedchemlett.8b00472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/21/2018] [Indexed: 02/06/2023] Open
Abstract
Nonsense suppressors (NonSups) induce "readthrough", i.e., the selection of near cognate tRNAs at premature termination codons and insertion of the corresponding amino acid into nascent polypeptide. Prior readthrough measurements utilized contexts in which NonSups can promote readthrough directly, by binding to one or more of the components of the protein synthesis machinery, or indirectly, by several other mechanisms. Here we utilize a new, highly purified in vitro assay to measure exclusively direct nonsense suppressor-induced readthrough. Of 16 NonSups tested, 12 display direct readthrough, with results suggesting that such NonSups act by at least two different mechanisms. In preliminary work we demonstrate the potential of single molecule fluorescence energy transfer measurements to elucidate mechanisms of NonSup-induced direct readthrough, which will aid efforts to identify NonSups having improved clinical efficacy.
Collapse
Affiliation(s)
- Martin
Y. Ng
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Haibo Zhang
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amy Weil
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vijay Singh
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ryan Jamiolkowski
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alireza Baradaran-Heravi
- Department
of Biochemistry and Molecular Biology, University
of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michel Roberge
- Department
of Biochemistry and Molecular Biology, University
of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Allan Jacobson
- Department
of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Westley Friesen
- PTC
Therapeutics, 100 Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Ellen Welch
- PTC
Therapeutics, 100 Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Yale E. Goldman
- Department
of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Barry S. Cooperman
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
21
|
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: 99] [Impact Index Per Article: 16.5] [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.
Collapse
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.
| |
Collapse
|
22
|
Markossian S, Ang KK, Wilson CG, Arkin MR. Small-Molecule Screening for Genetic Diseases. Annu Rev Genomics Hum Genet 2018; 19:263-288. [PMID: 29799800 DOI: 10.1146/annurev-genom-083117-021452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic determinants of many diseases, including monogenic diseases and cancers, have been identified; nevertheless, targeted therapy remains elusive for most. High-throughput screening (HTS) of small molecules, including high-content analysis (HCA), has been an important technology for the discovery of molecular tools and new therapeutics. HTS can be based on modulation of a known disease target (called reverse chemical genetics) or modulation of a disease-associated mechanism or phenotype (forward chemical genetics). Prominent target-based successes include modulators of transthyretin, used to treat transthyretin amyloidoses, and the BCR-ABL kinase inhibitor Gleevec, used to treat chronic myelogenous leukemia. Phenotypic screening successes include modulators of cystic fibrosis transmembrane conductance regulator, splicing correctors for spinal muscular atrophy, and histone deacetylase inhibitors for cancer. Synthetic lethal screening, in which chemotherapeutics are screened for efficacy against specific genetic backgrounds, is a promising approach that merges phenotype and target. In this article, we introduce HTS technology and highlight its contributions to the discovery of drugs and probes for monogenic diseases and cancer.
Collapse
Affiliation(s)
- Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Kenny K Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Christopher G Wilson
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| |
Collapse
|
23
|
Gu Y, Chang X, Dai S, Song Q, Zhao H, Lei P. Identification of four novel XPC mutations in two xeroderma pigmentosum complementation group C patients and functional study of XPC Q320X mutant. Gene 2017; 628:162-169. [PMID: 28669926 DOI: 10.1016/j.gene.2017.06.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/24/2017] [Accepted: 06/28/2017] [Indexed: 11/12/2022]
Abstract
Xeroderma pigmentosum (XP) is a rare, recessive hereditary disease characterized by sunlight hypersensitivity and high incidence of skin cancer with clinical and genetic heterogeneity. We collected two unrelated Chinese patients showing typical symptoms of XPC without neurologic symptoms. Direct sequencing of XPC gene revealed that patient 1 carried IVS1+1G>A and c.958 C>T mutations, and patient 2 carried c.545_546delTA and c.2257_2258insC mutations. All these four mutations introduced premature terminal codons (PTCs) in XPC gene. The nonsense mutation c.958 C>T yielded truncated mutant Q320X, and we studied its function for global genome repair kinetics. Overexpressed Q320X mutant can localize to site of DNA damage, but it is defective in CPD and 6-4PP repair. Readthrough of PTCs is a new approach to treatment of genetic diseases. We found that aminoglycosides could significantly increase the full length protein expression of Q320X mutant, but NER defects were not rescued in vitro.
Collapse
Affiliation(s)
- Yajuan Gu
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xiaodan Chang
- Department of Dermatology, Peking University Third Hospital, Beijing, China
| | - Shan Dai
- Department of Dermatology, Peking University Third Hospital, Beijing, China
| | - Qinghua Song
- Department of Dermatology, Peking University Third Hospital, Beijing, China.
| | - Hongshan Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China; Human Disease Genomics Center, Peking University, Beijing, China.
| | - Pengcheng Lei
- Department of Dermatology, Peking University Third Hospital, Beijing, China
| |
Collapse
|
24
|
Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics. Biochem Pharmacol 2017; 134:56-73. [DOI: 10.1016/j.bcp.2016.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
|
25
|
Wang X, Gregory-Evans K, Wasan KM, Sivak O, Shan X, Gregory-Evans CY. Efficacy of Postnatal In Vivo Nonsense Suppression Therapy in a Pax6 Mouse Model of Aniridia. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624217 PMCID: PMC5440746 DOI: 10.1016/j.omtn.2017.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nonsense mutations leading to premature stop codons are common occurring in approximately 12% of all human genetic diseases. Thus, pharmacological nonsense mutation suppression strategies would be beneficial to a large number of patients if the drugs could be targeted to the affected tissues at the appropriate time. Here, we used nonsense suppression to manipulate Pax6 dosage at different developmental times in the eye of the small eye (Pax6Sey/+; G194X) mouse model of aniridia. Efficacy was assessed by functional assays for visual capacity, including electroretinography and optokinetic tracking (OKT), in addition to histological and biochemical studies. Malformation defects in the Pax6Sey/+ postnatal eye responded to topically delivered nonsense suppression in a dose- and time-dependent manner. Elevated levels of Mmp9, a direct downstream target of Pax6 in the cornea, were observed with the different treatment regimens. The lens capsule was particularly sensitive to Pax6 dosage, revealing a potential new role for Pax6 in lens capsule maintenance and development. The remarkable capacity of malformed ocular tissue to respond postnatally to Pax6 dosage in vivo demonstrates that the use of nonsense suppression could be a valuable therapeutic approach for blinding diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Xia Wang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Kevin Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Kishor M Wasan
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
| | - Olena Sivak
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Xianghong Shan
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
| | - Cheryl Y Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada.
| |
Collapse
|
26
|
Bidou L, Bugaud O, Belakhov V, Baasov T, Namy O. Characterization of new-generation aminoglycoside promoting premature termination codon readthrough in cancer cells. RNA Biol 2017; 14:378-388. [PMID: 28145797 DOI: 10.1080/15476286.2017.1285480] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nonsense mutations, generating premature termination codons (PTCs), account for 10% to 30% of the mutations in tumor suppressor genes. Nonsense translational suppression, induced by small molecules including gentamicin and G418, has been suggested as a potential therapy to counteract the deleterious effects of nonsense mutations in several genetic diseases and cancers. We describe here that NB124, a synthetic aminoglycoside derivative recently developed especially for PTC suppression, strongly induces apoptosis in human tumor cells by promoting high level of PTC readthrough. Using a reporter system, we showed that NB124 suppressed several of the PTCs encountered in tumor suppressor genes, such as the p53 and APC genes. We also showed that NB124 counteracted p53 mRNA degradation by nonsense-mediated decay (NMD). Both PTC suppression and mRNA stabilization contributed to the production of a full-length p53 protein capable of activating p53-dependent genes, thereby specifically promoting high levels of apoptosis. This new-generation aminoglycoside thus outperforms the only clinically available readthrough inducer (gentamicin). These results have important implications for the development of personalised treatments of PTC-dependent diseases and for the development of new drugs modifying translation fidelity.
Collapse
Affiliation(s)
- Laure Bidou
- a Université Pierre et Marie Curie , Paris , France.,b Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex , France
| | - Olivier Bugaud
- b Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex , France
| | - Valery Belakhov
- c Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry Technion IIT , Haifa , Israel
| | - Timor Baasov
- c Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry Technion IIT , Haifa , Israel
| | - Olivier Namy
- b Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex , France
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Mol Cell 2017; 65:191-201. [PMID: 28017590 PMCID: PMC5301997 DOI: 10.1016/j.molcel.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/05/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs containing a premature termination codon (PTC). PTCs are a frequent cause of human genetic diseases, and the NMD pathway is known to modulate disease severity. Since partial NMD attenuation can potentially enhance nonsense suppression therapies, better definition of human-specific NMD is required. However, the majority of NMD factors were first discovered in model organisms and then subsequently identified by homology in human. Sensitivity and throughput limitations of existing approaches have hindered systematic forward genetic screening for NMD factors in human cells. We developed a method of in vivo amplification of NMD reporter fluorescence (Fireworks) that enables CRISPR-based forward genetic screening for NMD pathway defects in human cells. The Fireworks genetic screen identifies multiple known NMD factors and numerous human candidate genes, providing a platform for discovery of additional key factors in human mRNA degradation.
Collapse
Affiliation(s)
- Andrei Alexandrov
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| |
Collapse
|
29
|
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: 73] [Impact Index Per Article: 9.1] [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.
Collapse
|
30
|
Lavin MF, Yeo AJ, Kijas AW, Wolvetang E, Sly PD, Wainwright C, Sinclair K. Therapeutic targets and investigated treatments for Ataxia-Telangiectasia. Expert Opin Orphan Drugs 2016. [DOI: 10.1080/21678707.2016.1254618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
31
|
Baradaran-Heravi A, Balgi AD, Zimmerman C, Choi K, Shidmoossavee FS, Tan JS, Bergeaud C, Krause A, Flibotte S, Shimizu Y, Anderson HJ, Mouly V, Jan E, Pfeifer T, Jaquith JB, Roberge M. Novel small molecules potentiate premature termination codon readthrough by aminoglycosides. Nucleic Acids Res 2016; 44:6583-98. [PMID: 27407112 PMCID: PMC5001621 DOI: 10.1093/nar/gkw638] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 01/28/2023] Open
Abstract
Nonsense mutations introduce premature termination codons and underlie 11% of genetic disease cases. High concentrations of aminoglycosides can restore gene function by eliciting premature termination codon readthrough but with low efficiency. Using a high-throughput screen, we identified compounds that potentiate readthrough by aminoglycosides at multiple nonsense alleles in yeast. Chemical optimization generated phthalimide derivative CDX5-1 with activity in human cells. Alone, CDX5-1 did not induce readthrough or increase TP53 mRNA levels in HDQ-P1 cancer cells with a homozygous TP53 nonsense mutation. However, in combination with aminoglycoside G418, it enhanced readthrough up to 180-fold over G418 alone. The combination also increased readthrough at all three nonsense codons in cancer cells with other TP53 nonsense mutations, as well as in cells from rare genetic disease patients with nonsense mutations in the CLN2, SMARCAL1 and DMD genes. These findings open up the possibility of treating patients across a spectrum of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Aruna D Balgi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Carla Zimmerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kunho Choi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Fahimeh S Shidmoossavee
- The Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason S Tan
- The Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Célia Bergeaud
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Alexandra Krause
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Stéphane Flibotte
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yoko Shimizu
- The Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hilary J Anderson
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Vincent Mouly
- Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, 47 Boulevard de l'hôpital, 75013 Paris, France
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Tom Pfeifer
- The Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - James B Jaquith
- The Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
32
|
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.
Collapse
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)
| |
Collapse
|
33
|
Evaluation of Aminoglycoside and Non-Aminoglycoside Compounds for Stop-Codon Readthrough Therapy in Four Lysosomal Storage Diseases. PLoS One 2015; 10:e0135873. [PMID: 26287674 PMCID: PMC4545610 DOI: 10.1371/journal.pone.0135873] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/27/2015] [Indexed: 11/21/2022] Open
Abstract
Nonsense mutations are quite prevalent in inherited diseases. Readthrough drugs could provide a therapeutic option for any disease caused by this type of mutation. Geneticin (G418) and gentamicin were among the first to be described. Novel compounds have been generated, but only a few have shown improved results. PTC124 is the only compound to have reached clinical trials. Here we first investigated the readthrough effects of gentamicin on fibroblasts from one patient with Sanfilippo B, one with Sanfilippo C, and one with Maroteaux-Lamy. We found that ARSB activity (Maroteaux-Lamy case) resulted in an increase of 2–3 folds and that the amount of this enzyme within the lysosomes was also increased, after treatment. Since the other two cases (Sanfilippo B and Sanfilippo C) did not respond to gentamicin, the treatments were extended with the use of geneticin and five non-aminoglycoside (PTC124, RTC13, RTC14, BZ6 and BZ16) readthrough compounds (RTCs). No recovery was observed at the enzyme activity level. However, mRNA recovery was observed in both cases, nearly a two-fold increase for Sanfilippo B fibroblasts with G418 and around 1.5 fold increase for Sanfilippo C cells with RTC14 and PTC124. Afterwards, some of the products were assessed through in vitro analyses for seven mutations in genes responsible for those diseases and, also, for Niemann-Pick A/B. Using the coupled transcription/translation system (TNT), the best results were obtained for SMPD1 mutations with G418, reaching a 35% recovery at 0.25 μg/ml, for the p.W168X mutation. The use of COS cells transfected with mutant cDNAs gave positive results for most of the mutations with some of the drugs, although to a different extent. The higher enzyme activity recovery, of around two-fold increase, was found for gentamicin on the ARSB p.W146X mutation. Our results are promising and consistent with those of other groups. Further studies of novel compounds are necessary to find those with more consistent efficacy and fewer toxic effects.
Collapse
|
34
|
Subramony S, Moscovich M, Ashizawa T. Genetics and Clinical Features of Inherited Ataxias. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00062-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
35
|
|
36
|
Gintjee TJJ, Magh ASH, Bertoni C. High throughput screening in duchenne muscular dystrophy: from drug discovery to functional genomics. BIOLOGY 2014; 3:752-80. [PMID: 25405319 PMCID: PMC4280510 DOI: 10.3390/biology3040752] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 01/16/2023]
Abstract
Centers for the screening of biologically active compounds and genomic libraries are becoming common in the academic setting and have enabled researchers devoted to developing strategies for the treatment of diseases or interested in studying a biological phenomenon to have unprecedented access to libraries that, until few years ago, were accessible only by pharmaceutical companies. As a result, new drugs and genetic targets have now been identified for the treatment of Duchenne muscular dystrophy (DMD), the most prominent of the neuromuscular disorders affecting children. Although the work is still at an early stage, the results obtained to date are encouraging and demonstrate the importance that these centers may have in advancing therapeutic strategies for DMD as well as other diseases. This review will provide a summary of the status and progress made toward the development of a cure for this disorder and implementing high-throughput screening (HTS) technologies as the main source of discovery. As more academic institutions are gaining access to HTS as a valuable discovery tool, the identification of new biologically active molecules is likely to grow larger. In addition, the presence in the academic setting of experts in different aspects of the disease will offer the opportunity to develop novel assays capable of identifying new targets to be pursued as potential therapeutic options. These assays will represent an excellent source to be used by pharmaceutical companies for the screening of larger libraries providing the opportunity to establish strong collaborations between the private and academic sectors and maximizing the chances of bringing into the clinic new drugs for the treatment of DMD.
Collapse
Affiliation(s)
- Thomas J J Gintjee
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, 710 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Alvin S H Magh
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, 710 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Carmen Bertoni
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, 710 Westwood Plaza, Los Angeles, CA 90095, USA.
| |
Collapse
|
37
|
Bushby K, Finkel R, Wong B, Barohn R, Campbell C, Comi GP, Connolly AM, Day JW, Flanigan KM, Goemans N, Jones KJ, Mercuri E, Quinlivan R, Renfroe JB, Russman B, Ryan MM, Tulinius M, Voit T, Moore SA, Lee Sweeney H, Abresch RT, Coleman KL, Eagle M, Florence J, Gappmaier E, Glanzman AM, Henricson E, Barth J, Elfring GL, Reha A, Spiegel RJ, O'donnell MW, Peltz SW, Mcdonald CM, FOR THE PTC124-GD-007-DMD STUDY GROUP. Ataluren treatment of patients with nonsense mutation dystrophinopathy. Muscle Nerve 2014; 50:477-87. [PMID: 25042182 PMCID: PMC4241581 DOI: 10.1002/mus.24332] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/10/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Dystrophinopathy is a rare, severe muscle disorder, and nonsense mutations are found in 13% of cases. Ataluren was developed to enable ribosomal readthrough of premature stop codons in nonsense mutation (nm) genetic disorders. METHODS Randomized, double-blind, placebo-controlled study; males ≥ 5 years with nm-dystrophinopathy received study drug orally 3 times daily, ataluren 10, 10, 20 mg/kg (N=57); ataluren 20, 20, 40 mg/kg (N=60); or placebo (N=57) for 48 weeks. The primary endpoint was change in 6-Minute Walk Distance (6MWD) at Week 48. RESULTS Ataluren was generally well tolerated. The primary endpoint favored ataluren 10, 10, 20 mg/kg versus placebo; the week 48 6MWD Δ=31.3 meters, post hoc P=0.056. Secondary endpoints (timed function tests) showed meaningful differences between ataluren 10, 10, 20 mg/kg, and placebo. CONCLUSIONS As the first investigational new drug targeting the underlying cause of nm-dystrophinopathy, ataluren offers promise as a treatment for this orphan genetic disorder with high unmet medical need.
Collapse
Affiliation(s)
- Katharine Bushby
- Institute of Genetic Medicine, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Richard Finkel
- The Children's Hospital of PhiladelphiaPennsylvania, USA
| | - Brenda Wong
- Cincinnati Children's Hospital Medical CenterOhio, USA
| | | | | | - Giacomo P Comi
- Dino Ferrari Centre, Department of Neurological Sciences, University of MilanI.R.C.C.S. Foundation Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Anne M Connolly
- Washington University School of Medicine at St. LouisMissouri, USA
| | - John W Day
- University of MinnesotaMinneapolis, Minnesota, USA
| | - Kevin M Flanigan
- Nationwide Children's Hospital and the Ohio State UniversityColumbus, Ohio, USA
| | | | - Kristi J Jones
- Department of Clinical Genetics, Sydney Children's Hospital Network, and Disciplines of Genetics and Paediatrics and Child Health, Faculty of Medicine University of SydneyAustralia
| | - Eugenio Mercuri
- Pediatric Neurology Unit, Polilcinico Gemelli, Università Cattolica Sacro CuoreRome, Italy
| | | | | | - Barry Russman
- Oregon Health & Science University and Shriners Hospital for ChildrenOregon, USA
| | - Monique M Ryan
- Royal Children's Hospital, Murdoch Childrens Research Institute and University of MelbourneParkville, Victoria, Australia
| | - Mar Tulinius
- Department of Pediatrics, The University of GothenburgGothenburg, Sweden
| | - Thomas Voit
- Institut de Myologie, University Pierre et Marie Curie Paris 6UM 76, INSERM U 974, CNRS UMR 7215, Paris, France
| | | | | | - Richard T Abresch
- UC Davis Children's Hospital, Lawrence J. Ellison Ambulatory Care Center, Physical Medicine & Rehabilitation4860 Y St., Suite 1700, Sacramento, California, 95817, USA
| | - Kim L Coleman
- OrthoCare InnovationsMountlake Terrace, Washington, USA
| | - Michelle Eagle
- Institute of Genetic Medicine, Newcastle UniversityNewcastle upon Tyne, United Kingdom
| | - Julaine Florence
- Washington University School of Medicine at St. LouisMissouri, USA
| | | | | | - Erik Henricson
- UC Davis Children's Hospital, Lawrence J. Ellison Ambulatory Care Center, Physical Medicine & Rehabilitation4860 Y St., Suite 1700, Sacramento, California, 95817, USA
| | - Jay Barth
- PTC TherapeuticsSouth Plainfield, New Jersey, USA
| | | | - Allen Reha
- PTC TherapeuticsSouth Plainfield, New Jersey, USA
| | | | | | | | - Craig M Mcdonald
- UC Davis Children's Hospital, Lawrence J. Ellison Ambulatory Care Center, Physical Medicine & Rehabilitation4860 Y St., Suite 1700, Sacramento, California, 95817, USA
| | | |
Collapse
|
38
|
|
39
|
Abstract
Nonsense suppression therapy encompasses approaches aimed at suppressing translation termination at in-frame premature termination codons (PTCs, also known as nonsense mutations) to restore deficient protein function. In this review, we examine the current status of PTC suppression as a therapy for genetic diseases caused by nonsense mutations. We discuss what is currently known about the mechanism of PTC suppression as well as therapeutic approaches under development to suppress PTCs. The approaches considered include readthrough drugs, suppressor tRNAs, PTC pseudouridylation, and inhibition of nonsense-mediated mRNA decay. We also discuss the barriers that currently limit the clinical application of nonsense suppression therapy and suggest how some of these difficulties may be overcome. Finally, we consider how PTC suppression may play a role in the clinical treatment of genetic diseases caused by nonsense mutations.
Collapse
Affiliation(s)
- Kim M Keeling
- Department of Microbiology and Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama 35294; , , ,
| | | | | | | |
Collapse
|
40
|
Shalev M, Baasov T. When Proteins Start to Make Sense: Fine-tuning Aminoglycosides for PTC Suppression Therapy. MEDCHEMCOMM 2014; 5:1092-1105. [PMID: 25147726 DOI: 10.1039/c4md00081a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aminoglycosides (AGs) are highly potent antibacterial agents, which are known to exert their deleterious effects on bacterial cells by interfering with the translation process, leading to aberrant protein synthesis that usually results in cell death. Nearly 45 years ago, AGs were shown to induce read-through activity in prokaryotic systems by selectively encoding tRNA molecules at premature termination codon (PTC) positions; resulting in the generation of full length functional proteins. However, only in the last 20 years this ability has been demonstrated in eukaryotic systems, highlighting their potential as therapeutic agents to treat PTC induced genetic disorders. Despite the great potential, AGs use in these manners is quite restricted due to relatively high toxicity values observed upon their administration. Over the last few years several synthetic derivatives were developed to overcome some of the enhanced toxicity issues, while in parallel showed significantly improved PTC suppression activity in various in-vitro, ex-vivo and in-vivo models of a variety of different diseases models underling by PTC mutations. Although these derivatives hold great promise to serve as therapeutic candidates they also demonstrate the necessity to further understand the molecular mechanisms of which AGs confer their biological activity in eukaryotic cells for further rational drug design. Recent achievements in structural research shed light on AGs mechanism of action and opened a new avenue in the development of new and improved therapeutic derivatives. The following manuscript highlights these accomplishments and summarizes their contributions to the state of art rational drug design.
Collapse
Affiliation(s)
- Moran Shalev
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
41
|
Ferguson CN, Fowler JWM, Waxer JF, Gatti RA, Loo JA. Mass spectrometry-based tissue imaging of small molecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:283-99. [PMID: 24952187 DOI: 10.1007/978-3-319-06068-2_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry imaging (MSI) of tissue samples is a promising analytical tool that has quickly become associated with biomedical and pharmacokinetic studies. It eliminates several labor-intensive protocols associated with more classical imaging techniques and provides accurate histological data at a rapid pace. Because mass spectrometry is used as the readout, MSI can be applied to almost any molecule, especially those that are biologically relevant. Many examples of its utility in the study of peptides and proteins have been reported; here we discuss its value in the mass range of small molecules. We explore its success and potential in the analysis of lipids, medicinals, and metal-based compounds by featuring representative studies from MSI laboratories around the globe.
Collapse
Affiliation(s)
- Carly N Ferguson
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | | | | | | | | |
Collapse
|
42
|
Repair of UV photolesions in xeroderma pigmentosum group C cells induced by translational readthrough of premature termination codons. Proc Natl Acad Sci U S A 2013; 110:19483-8. [PMID: 24218596 DOI: 10.1073/pnas.1312088110] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
About 12% of human genetic disorders involve premature termination codons (PTCs). Aminoglycoside antibiotics have been proposed for restoring full-length proteins by readthrough of PTC. To assess the efficiency of readthrough, we selected homozygous and compound heterozygous skin fibroblasts from xeroderma pigmentosum (XP) patients with different PTCs in the XPC DNA repair gene. XP patients have a nucleotide excision repair defect and a 10,000-fold increased risk of UV-induced skin cancer. In six of eight PTC-containing XP-C cells, treatment with Geneticin and gentamicin resulted in (i) stabilized XPC-mRNA, which would have been degraded by nonsense-mediated decay; (ii) increased expression of XPC protein that localized to UV-damaged sites; (iii) recruitment of XPB and XPD proteins to UV DNA damage sites; and (iv) increased repair of 6-4 photoproducts and cyclobutane pyrimidine dimers. Expression of PTC in a transfected vector revealed that readthrough depends on the PTC sequence and its location within the gene. This sensitive DNA repair assay system demonstrates the complexity of response to PTC readthrough inducers. The efficiency of aminoglycoside-mediated readthrough depends on the type and copy number of PTC, the downstream 4+ nucleotide, and the location within the exon. Treatment with small-molecule nonaminoglycoside compounds (PTC124, BZ16, or RTC14) resulted in similarly increased XPC mRNA expression and photoproduct removal with less toxicity than with the aminoglycosides. Characterizing PTC structure and parameters governing effective PTC readthrough may provide a unique prophylactic therapy for skin cancer prevention in XP-C patients.
Collapse
|
43
|
Lavin MF. Generating SM(a)RTer compounds for translation termination suppression in A-T and other genetic disorders. Mol Ther 2013; 21:1650-2. [PMID: 24008619 PMCID: PMC3776641 DOI: 10.1038/mt.2013.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Martin F Lavin
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, Australia.
| |
Collapse
|