1
|
Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
Collapse
Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| |
Collapse
|
2
|
Vlodavets DV. [Risdiplam for the treatment of spinal muscular atrophy]. Zh Nevrol Psikhiatr Im S S Korsakova 2024; 124:45-57. [PMID: 38465810 DOI: 10.17116/jnevro202412402145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Spinal muscular atrophy (SMA) is a devastating disease that is the leading genetic cause of death in infants and young children. It includes a broad spectrum of phenotypes that are classified into clinical groups based on the age of onset and maximum motor function achieved. The most common form of SMA is due to a defect in the survival motor neuron 1 gene (SMN1) localized to 5q11.2-q13.3. The development of clinical symptoms and disease progression is thought to be due to decreased levels of survival motor neuron (SMN) protein. SMA type 1 results in almost inevitable mortality within the first 2 years of life. The first two drugs approved globally for the treatment of SMA were the antisense oligonucleotide nusinersen (Spinraza), and the gene therapy onasemnogene abeparvovec-xioi (Zolgensma). Both interventions have approval and restrictions on use in different countries around the world. Despite these approved therapies, the medical unmet need in SMA (the majority of patients with SMA are not on a disease-modifying therapy) remains high with therapies in the pipeline to address some of the remaining limitations. The third and more recently approved drug for SMA is risdiplam (Evrysdi), an orally administered, centrally and peripherally distributed small molecule that modulates SMN2 pre-mRNA splicing toward the production of full-length SMN2 mRNA to increase functional SMN protein levels. In Russia the drug risdiplam was approved for use on November 26, 2020 with indications for the treatment of SMA in patients aged 2 months and older, and in 2023 the indications were expanded - use is allowed starting from the birth. Risdiplam is widely distributed into the CNS and peripheral tissues including muscles. Following risdiplam administration, SMN protein levels compared with baseline levels increase between 2- and 6-fold depending on the SMA phenotype treated. The risdiplam clinical development program currently has four ongoing clinical trials assessing its safety and efficacy. Clinical trials included more than 450 patients receiving risdiplam to date, has been well tolerated and no treatment-related safety findings leading to study withdrawal have been observed. Data from real clinical practice - more than 11.000 patients worldwide receive therapy with risdiplam, also confirm the safety and good tolerability of the drug.
Collapse
Affiliation(s)
- D V Vlodavets
- Veltischev Clinical Pediatric Research Institute of Pirogov Russian National Research Medical University, Moscow, Russia
| |
Collapse
|
3
|
Liu L, Malagu K, Haughan AF, Khetarpal V, Stott AJ, Esmieu W, Vater HD, Webster SJ, Van de Poël AJ, Clissold C, Cosgrove B, Sutton B, Spencer JA, Breccia P, Gancia E, Bonomo S, Ladduwahetty T, Lazari O, Patel H, Atton HC, Clifton S, Mota DM, Magnani D, O'Neill A, Stebbeds M, Macabuag N, Todd D, Herva ME, Mitchell P, Visser M, Compte Sancerni S, Grand Moursel L, da Silva M, Kritikou E, Heikkinen TT, Bolkvadze T, Fodale V, Spadafora D, Daldin M, Bresciani A, Mangette JE, Doherty EM, Lee MR, Herbst T, Monteagudo E, Macdonald D, Plotnikov NV, Chambers M, McAllister G, Muňoz-Sanjuan I, Dominguez C. Identification and Optimization of RNA-Splicing Modulators as Huntingtin Protein-Lowering Agents for the Treatment of Huntington's Disease. J Med Chem 2023; 66:13205-13246. [PMID: 37712656 DOI: 10.1021/acs.jmedchem.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Huntington's disease (HD) is caused by an expanded CAG trinucleotide repeat in exon 1 of the huntingtin (HTT) gene. We report the design of a series of HTT pre-mRNA splicing modulators that lower huntingtin (HTT) protein, including the toxic mutant huntingtin (mHTT), by promoting insertion of a pseudoexon containing a premature termination codon at the exon 49-50 junction. The resulting transcript undergoes nonsense-mediated decay, leading to a reduction of HTT mRNA transcripts and protein levels. The starting benzamide core was modified to pyrazine amide and further optimized to give a potent, CNS-penetrant, and orally bioavailable HTT-splicing modulator 27. This compound reduced canonical splicing of the HTT RNA exon 49-50 and demonstrated significant HTT-lowering in both human HD stem cells and mouse BACHD models. Compound 27 is a structurally diverse HTT-splicing modulator that may help understand the mechanism of adverse effects such as peripheral neuropathy associated with branaplam.
Collapse
Affiliation(s)
- Longbin Liu
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Karine Malagu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Alan F Haughan
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Vinod Khetarpal
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Andrew J Stott
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - William Esmieu
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Huw D Vater
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Stephen J Webster
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amanda J Van de Poël
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Cole Clissold
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Brett Cosgrove
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Benjamin Sutton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jonathan A Spencer
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Perla Breccia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Emanuela Gancia
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Silvia Bonomo
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Tammy Ladduwahetty
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ovadia Lazari
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Hiral Patel
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Helen C Atton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Steve Clifton
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel M Mota
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Dario Magnani
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amy O'Neill
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marta Stebbeds
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Natsuko Macabuag
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Daniel Todd
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maria E Herva
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Mitchell
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mijke Visser
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | - Marta da Silva
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | - Eva Kritikou
- Charles River, Darwinweg 24, 2333 CR Leiden, The Netherlands
| | | | | | | | | | | | | | | | - Elizabeth M Doherty
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Matthew R Lee
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Todd Herbst
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Edith Monteagudo
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Douglas Macdonald
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Nikolay V Plotnikov
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Mark Chambers
- Discovery from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Ignacio Muňoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| |
Collapse
|
4
|
Dupommier D, Boisbrun M, Monard G, Comoy C. Unexplored Vinylic-Substituted 5-Benzylidenethiazolidine-2,4-diones: Synthesis and DFT/NMR Stereochemical Assignment. J Org Chem 2023; 88:3724-3739. [PMID: 36847759 DOI: 10.1021/acs.joc.2c02996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
By exploring an efficient and versatile method for the 6-functionalization of its scaffold, we investigated the opening of a new chemical space around benzylidenethiazolidine-2,4-dione (BTZD). The 6-chloro- and 6-formyl BTZD obtained in two steps starting from 5-lithioTZD were selected as key intermediates and involved in a Pd-catalyzed cross-coupling or Wittig olefination. A variety of aryl, heteroaryl, or alkenyl substituents was successfully introduced on the vinylic position of BTZD, and particular attention was paid to elucidate the stereochemistry of the benzylidene derivatives by using a combined DFT/NMR study.
Collapse
Affiliation(s)
| | | | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, Nancy F-54000, France
| | - Corinne Comoy
- Université de Lorraine, CNRS, L2CM, Nancy F-54000, France
| |
Collapse
|
5
|
Morini E, Chekuri A, Logan EM, Bolduc JM, Kirchner EG, Salani M, Krauson AJ, Narasimhan J, Gabbeta V, Grover S, Dakka A, Mollin A, Jung SP, Zhao X, Zhang N, Zhang S, Arnold M, Woll MG, Naryshkin NA, Weetall M, Slaugenhaupt SA. Development of an oral treatment that rescues gait ataxia and retinal degeneration in a phenotypic mouse model of familial dysautonomia. Am J Hum Genet 2023; 110:531-547. [PMID: 36809767 PMCID: PMC10027479 DOI: 10.1016/j.ajhg.2023.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Familial dysautonomia (FD) is a rare neurodegenerative disease caused by a splicing mutation in elongator acetyltransferase complex subunit 1 (ELP1). This mutation leads to the skipping of exon 20 and a tissue-specific reduction of ELP1, mainly in the central and peripheral nervous systems. FD is a complex neurological disorder accompanied by severe gait ataxia and retinal degeneration. There is currently no effective treatment to restore ELP1 production in individuals with FD, and the disease is ultimately fatal. After identifying kinetin as a small molecule able to correct the ELP1 splicing defect, we worked on its optimization to generate novel splicing modulator compounds (SMCs) that can be used in individuals with FD. Here, we optimize the potency, efficacy, and bio-distribution of second-generation kinetin derivatives to develop an oral treatment for FD that can efficiently pass the blood-brain barrier and correct the ELP1 splicing defect in the nervous system. We demonstrate that the novel compound PTC258 efficiently restores correct ELP1 splicing in mouse tissues, including brain, and most importantly, prevents the progressive neuronal degeneration that is characteristic of FD. Postnatal oral administration of PTC258 to the phenotypic mouse model TgFD9;Elp1Δ20/flox increases full-length ELP1 transcript in a dose-dependent manner and leads to a 2-fold increase in functional ELP1 in the brain. Remarkably, PTC258 treatment improves survival, gait ataxia, and retinal degeneration in the phenotypic FD mice. Our findings highlight the great therapeutic potential of this novel class of small molecules as an oral treatment for FD.
Collapse
Affiliation(s)
- Elisabetta Morini
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA.
| | - Anil Chekuri
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA; Grousbeck Gene Therapy Center, Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Emily M Logan
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Jessica M Bolduc
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Emily G Kirchner
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Aram J Krauson
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | | | | | | | - Amal Dakka
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Anna Mollin
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | | | - Xin Zhao
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Nanjing Zhang
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Sophie Zhang
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | | | | | | | - Marla Weetall
- PTC Therapeutics, Inc., South Plainfield, NJ 07080, USA
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Ma J, Tan Y, Tang Y, Cui X, Xu J, Li Y, Wang X. Base‐Promoted Cascade C–N and C–C Formation: An Approach to Pyrido[1,2‐a]pyrimidinones from Ynones and 2‐Methylpyrimidin‐4‐ols. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianting Ma
- Hainan Medical University School of Pharmacy CHINA
| | - Yinfeng Tan
- Hainan Medical University School of Pharmacy CHINA
| | - Yao Tang
- Hainan Medical University School of Pharmacy CHINA
| | - Xue Cui
- Hainan Medical University School of Pharmacy CHINA
| | - Junyu Xu
- Hainan Medical University School of Pharmacy CHINA
| | - Youbin Li
- Hainan Medical University School of Pharmacy CHINA
| | - Xuesong Wang
- Hainan Medical University school of pharmacy Xueyuan Road 571199 Haikou CHINA
| |
Collapse
|
7
|
Kanda S, Moulton E, Butchbach MER. Effects of inhibitors of SLC9A-type sodium-protein exchangers on Survival Motor Neuron 2 ( SMN2) mRNA splicing and expression. Mol Pharmacol 2022; 102:92-105. [PMID: 35667685 PMCID: PMC9341265 DOI: 10.1124/molpharm.122.000529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive, pediatric-onset disorder caused by the loss of spinal motor neurons thereby leading to muscle atrophy. SMA is caused by the loss of or mutations in the survival motor neuron 1 (SMN1) gene. SMN1 is duplicated in humans to give rise to the paralogous SMN2 gene. This paralog is nearly identical except for a cytosine to thymine (C-to-T) transition within an exonic splicing enhancer (ESE) element within exon 7. As a result, the majority of SMN2 transcripts lack exon 7 (SMNΔ7) which produces a truncated and unstable SMN protein. Since SMN2 copy number is inversely related to disease severity, it is a well-established target for SMA therapeutics development. 5-(N-ethyl-N-isopropyl)amiloride (EIPA), an inhibitor of sodium/proton exchangers (NHEs), has previously been shown to increase exon 7 inclusion and SMN protein levels in SMA cells. In this study, NHE inhibitors were evaluated for their ability to modulate SMN2 expression. EIPA as well as 5-(N,N-hexamethylene)amiloride (HMA) increase exon 7 inclusion in SMN2 splicing reporter lines as well as in SMA fibroblasts. The EIPA-induced exon 7 inclusion occurs via a unique mechanism that does not involve previously identified splicing factors. Transcriptome analysis identified novel targets, including TIA1 and FABP3, for further characterization. EIPA and HMA are more selective at inhibiting the NHE5 isoform, which is expressed in fibroblasts as well as in neuronal cells. These results show that NHE5 inhibition increases SMN2 expression and may be a novel target for therapeutics development. Significance Statement This study demonstrates a molecular mechanism by which inhibitors of the sodium-protein exchanger increase the alternative splicing of SMN2 in spinal muscular atrophy cells. NHE5 selective inhibitors increase the inclusion of full-length SMN2 mRNAs by targeting TIA1 and FABP3 expression, which is distinct from other small molecule regulators of SMN2 alternative splicing. This study provides a novel means to increase full-length SMN2 expression and a novel target for therapeutics development.
Collapse
Affiliation(s)
- Sambee Kanda
- Biological Sciences, University of Delaware, United States
| | - Emily Moulton
- Biomedical Research, Nemours Children's Hospital Delaware, United States
| | | |
Collapse
|
8
|
Zhang L, Abendroth F, Vázquez O. A Chemical Biology Perspective to Therapeutic Regulation of RNA Splicing in Spinal Muscular Atrophy (SMA). ACS Chem Biol 2022; 17:1293-1307. [PMID: 35639849 DOI: 10.1021/acschembio.2c00161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulation of RNA splicing machinery has emerged as a drug modality. Here, we illustrate the potential of this novel paradigm to correct aberrant splicing events focused on the recent therapeutic advances in spinal muscular atrophy (SMA). SMA is an incurable neuromuscular disorder and at present the primary genetic cause of early infant death. This Review summarizes the exciting journey from the first reported SMA cases to the currently approved splicing-switching treatments, i.e., antisense oligonucleotides and small-molecule modifiers. We emphasize both chemical structures and molecular bases for recognition. We briefly discuss the advantages and disadvantages of these treatments and include the remaining challenges and future directions. Finally, we also predict that these success stories will contribute to further therapies for human diseases by RNA-splicing control.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
| |
Collapse
|
9
|
Tang Z, Hegde S, Zhao J, Zhu S, Johnson KA, Lorson CL, Wang J. CRISPR-mediated Enzyme Fragment Complementation Assay for Quantification of the Stability of Splice Isoforms. Chembiochem 2022; 23:e202200012. [PMID: 35235240 DOI: 10.1002/cbic.202200012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Indexed: 11/06/2022]
Abstract
Small-molecule splicing modulators exemplified by an FDA-approved drug, risdiplam, are a new pharmacological modality for regulating the expression and stability of splice isoforms. We report a CRISPR-mediated enzyme fragment complementation (EFC) assay to quantify the splice isoform stability. The EFC assay harnessed a 42 amino acid split of a β-galactosidase (designate α-tag), which could be fused at the termini of the target genes using CRISPR/cas9. The α-tagged splice isoform would be quantified by measuring the enzymatic activity upon complementation with the rest of β-galactosidase. This EFC assay retained all the sequences of introns and exons of the target gene in the native genomic environment that recapitulates the cell biology of the diseases of interest. For a proof-of-concept, we developed a CRISPR-mediated EFC assay targeting the exon 7 of the survival of motor neuron 2 (SMN2) gene. The EFC assay compatible with 384-well plates robustly quantified the splicing modulation activity of small molecules. In this study, we also discovered that a coumarin derivative, compound 4, potently modulate SMN2 splicing at as low as 1.1 nM.
Collapse
Affiliation(s)
- Zhichao Tang
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Shalakha Hegde
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Junxing Zhao
- University of Kansas School of Pharmacy, Medicinal Chemistry, UNITED STATES
| | - Shoutian Zhu
- PhenoTarget BioSciences, Inc., Biology, UNITED STATES
| | | | | | - Jingxin Wang
- University of Kansas, Medicinal Chemistry, 2034 Becker Dr, 1050, 66047, Lawrence, UNITED STATES
| |
Collapse
|
10
|
Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
Collapse
Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| |
Collapse
|
11
|
Alternative Splicing Role in New Therapies of Spinal Muscular Atrophy. Genes (Basel) 2021; 12:genes12091346. [PMID: 34573328 PMCID: PMC8468182 DOI: 10.3390/genes12091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is observed in many disorders, including neuromuscular diseases and carcinomas. Spinal Muscular Atrophy (SMA) is an autosomal recessive neurodegenerative disease. Homozygous deletion in 5q13 (the region coding for the motor neuron survival gene (SMN1)) is responsible for 95% of SMA cases. The nearly identical SMN2 gene does not compensate for SMN loss caused by SMN1 gene mutation due to different splicing of exon 7. A pathologically low level of survival motor neuron protein (SMN) causes degeneration of the anterior horn cells in the spinal cord with associated destruction of α-motor cells and manifested by muscle weakness and loss. Understanding the regulation of the SMN2 pre-mRNA splicing process has allowed for innovative treatment and the introduction of new medicines for SMA. After describing the concept of splicing modulation, this review will cover the progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of SMA using the mechanism of alternative splicing.
Collapse
|
12
|
A deep learning approach to identify gene targets of a therapeutic for human splicing disorders. Nat Commun 2021; 12:3332. [PMID: 34099697 PMCID: PMC8185002 DOI: 10.1038/s41467-021-23663-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/07/2021] [Indexed: 01/16/2023] Open
Abstract
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a target for therapy. We describe herein the identification of BPN-15477, a SMC that restores correct splicing of ELP1 exon 20. Using transcriptome sequencing from treated fibroblast cells and a machine learning approach, we identify BPN-15477 responsive sequence signatures. We then leverage this model to discover 155 human disease genes harboring ClinVar mutations predicted to alter pre-mRNA splicing as targets for BPN-15477. Splicing assays confirm successful correction of splicing defects caused by mutations in CFTR, LIPA, MLH1 and MAPT. Subsequent validations in two disease-relevant cellular models demonstrate that BPN-15477 increases functional protein, confirming the clinical potential of our predictions.
Collapse
|
13
|
Axford J, Sung MJ, Manchester J, Chin D, Jain M, Shin Y, Dix I, Hamann LG, Cheung AK, Sivasankaran R, Briner K, Dales NA, Hurley B. Use of Intramolecular 1,5-Sulfur-Oxygen and 1,5-Sulfur-Halogen Interactions in the Design of N-Methyl-5-aryl- N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3,4-thiadiazol-2-amine SMN2 Splicing Modulators. J Med Chem 2021; 64:4744-4761. [PMID: 33822618 DOI: 10.1021/acs.jmedchem.0c02173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA) is a debilitating neuromuscular disease caused by low levels of functional survival motor neuron protein (SMN) resulting from a deletion or loss of function mutation of the survival motor neuron 1 (SMN1) gene. Branaplam (1) elevates levels of full-length SMN protein in vivo by modulating the splicing of the related gene SMN2 to enhance the exon-7 inclusion and increase levels of the SMN. The intramolecular hydrogen bond present in the 2-hydroxyphenyl pyridazine core of 1 enforces a planar conformation of the biaryl system and is critical for the compound activity. Scaffold morphing revealed that the pyridazine could be replaced by a 1,3,4-thiadiazole, which provided additional opportunities for a conformational constraint of the biaryl through intramolecular 1,5-sulfur-oxygen (S···O) or 1,5-sulfur-halogen (S···X) noncovalent interactions. Compound 26, which incorporates a 2-fluorophenyl thiadiazole motif, demonstrated a greater than 50% increase in production of full-length SMN protein in a mouse model of SMA.
Collapse
Affiliation(s)
- Jake Axford
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Moo Je Sung
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John Manchester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Donovan Chin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Monish Jain
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Youngah Shin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ina Dix
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lawrence G Hamann
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Atwood K Cheung
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Natalie A Dales
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brian Hurley
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
14
|
He H, Nie J, Duan Y, Lin J, Yan S. An environmentally benign cascade reaction of 1,2,3-indantriones with ethyl 2-(pyridine-2-yl)acetates for site-selective synthesis of 5H-isochromeno[4,3-b]indolizin-5-ones. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
15
|
Yang LS, Wang Y, Wang EH, Yang J, Pan X, Liao X, Yang XS. Polyphosphoric acid-promoted synthesis of coumarins lacking substituents at positions 3 and 4. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1792498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Li-Shou Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Yu Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - En-Hua Wang
- Department of Medicine and Food, Guizhou Vocational College of Agriculture, Guiyang, PR China
| | - Jan Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiong Pan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiu Liao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| | - Xiao-Sheng Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, P. R. China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, P. R. China
| |
Collapse
|
16
|
Wadman RI, van der Pol WL, Bosboom WMJ, Asselman F, van den Berg LH, Iannaccone ST, Vrancken AFJE. Drug treatment for spinal muscular atrophy types II and III. Cochrane Database Syst Rev 2020; 1:CD006282. [PMID: 32006461 PMCID: PMC6995983 DOI: 10.1002/14651858.cd006282.pub5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is caused by a homozygous deletion of the survival motor neuron 1 (SMN1) gene on chromosome 5, or a heterozygous deletion in combination with a (point) mutation in the second SMN1 allele. This results in degeneration of anterior horn cells, which leads to progressive muscle weakness. Children with SMA type II do not develop the ability to walk without support and have a shortened life expectancy, whereas children with SMA type III develop the ability to walk and have a normal life expectancy. This is an update of a review first published in 2009 and previously updated in 2011. OBJECTIVES To evaluate if drug treatment is able to slow or arrest the disease progression of SMA types II and III, and to assess if such therapy can be given safely. SEARCH METHODS We searched the Cochrane Neuromuscular Specialised Register, CENTRAL, MEDLINE, Embase, and ISI Web of Science conference proceedings in October 2018. In October 2018, we also searched two trials registries to identify unpublished trials. SELECTION CRITERIA We sought all randomised or quasi-randomised trials that examined the efficacy of drug treatment for SMA types II and III. Participants had to fulfil the clinical criteria and have a homozygous deletion or hemizygous deletion in combination with a point mutation in the second allele of the SMN1 gene (5q11.2-13.2) confirmed by genetic analysis. The primary outcome measure was change in disability score within one year after the onset of treatment. Secondary outcome measures within one year after the onset of treatment were change in muscle strength, ability to stand or walk, change in quality of life, time from the start of treatment until death or full-time ventilation and adverse events attributable to treatment during the trial period. Treatment strategies involving SMN1-replacement with viral vectors are out of the scope of this review, but a summary is given in Appendix 1. Drug treatment for SMA type I is the topic of a separate Cochrane Review. DATA COLLECTION AND ANALYSIS We followed standard Cochrane methodology. MAIN RESULTS The review authors found 10 randomised, placebo-controlled trials of treatments for SMA types II and III for inclusion in this review, with 717 participants. We added four of the trials at this update. The trials investigated creatine (55 participants), gabapentin (84 participants), hydroxyurea (57 participants), nusinersen (126 participants), olesoxime (165 participants), phenylbutyrate (107 participants), somatotropin (20 participants), thyrotropin-releasing hormone (TRH) (nine participants), valproic acid (33 participants), and combination therapy with valproic acid and acetyl-L-carnitine (ALC) (61 participants). Treatment duration was from three to 24 months. None of the studies investigated the same treatment and none was completely free of bias. All studies had adequate blinding, sequence generation and reporting of primary outcomes. Based on moderate-certainty evidence, intrathecal nusinersen improved motor function (disability) in children with SMA type II, with a 3.7-point improvement in the nusinersen group on the Hammersmith Functional Motor Scale Expanded (HFMSE; range of possible scores 0 to 66), compared to a 1.9-point decline on the HFMSE in the sham procedure group (P < 0.01; n = 126). On all motor function scales used, higher scores indicate better function. Based on moderate-certainty evidence from two studies, the following interventions had no clinically important effect on motor function scores in SMA types II or III (or both) in comparison to placebo: creatine (median change 1 higher, 95% confidence interval (CI) -1 to 2; on the Gross Motor Function Measure (GMFM), scale 0 to 264; n = 40); and combination therapy with valproic acid and carnitine (mean difference (MD) 0.64, 95% CI -1.1 to 2.38; on the Modified Hammersmith Functional Motor Scale (MHFMS), scale 0 to 40; n = 61). Based on low-certainty evidence from other single studies, the following interventions had no clinically important effect on motor function scores in SMA types II or III (or both) in comparison to placebo: gabapentin (median change 0 in the gabapentin group and -2 in the placebo group on the SMA Functional Rating Scale (SMAFRS), scale 0 to 50; n = 66); hydroxyurea (MD -1.88, 95% CI -3.89 to 0.13 on the GMFM, scale 0 to 264; n = 57), phenylbutyrate (MD -0.13, 95% CI -0.84 to 0.58 on the Hammersmith Functional Motor Scale (HFMS) scale 0 to 40; n = 90) and monotherapy of valproic acid (MD 0.06, 95% CI -1.32 to 1.44 on SMAFRS, scale 0 to 50; n = 31). Very low-certainty evidence suggested that the following interventions had little or no effect on motor function: olesoxime (MD 2, 95% -0.25 to 4.25 on the Motor Function Measure (MFM) D1 + D2, scale 0 to 75; n = 160) and somatotropin (median change at 3 months 0.25 higher, 95% CI -1 to 2.5 on the HFMSE, scale 0 to 66; n = 19). One small TRH trial did not report effects on motor function and the certainty of evidence for other outcomes from this trial were low or very low. Results of nine completed trials investigating 4-aminopyridine, acetyl-L-carnitine, CK-2127107, hydroxyurea, pyridostigmine, riluzole, RO6885247/RG7800, salbutamol and valproic acid were awaited and not available for analysis at the time of writing. Various trials and studies investigating treatment strategies other than nusinersen (e.g. SMN2-augmentation by small molecules), are currently ongoing. AUTHORS' CONCLUSIONS Nusinersen improves motor function in SMA type II, based on moderate-certainty evidence. Creatine, gabapentin, hydroxyurea, phenylbutyrate, valproic acid and the combination of valproic acid and ALC probably have no clinically important effect on motor function in SMA types II or III (or both) based on low-certainty evidence, and olesoxime and somatropin may also have little to no clinically important effect but evidence was of very low-certainty. One trial of TRH did not measure motor function.
Collapse
Affiliation(s)
- Renske I Wadman
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - W Ludo van der Pol
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Wendy MJ Bosboom
- Onze Lieve Vrouwe Gasthuis locatie WestDepartment of NeurologyAmsterdamNetherlands
| | - Fay‐Lynn Asselman
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Leonard H van den Berg
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Susan T Iannaccone
- University of Texas Southwestern Medical CenterDepartment of Pediatrics5323 Harry Hines BoulevardDallasTexasUSA75390
| | - Alexander FJE Vrancken
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | | |
Collapse
|
17
|
Wu X, Jia M, Huang M, Kim JK, Zhao Z, Liu J, Xi J, Li Y, Wu Y. A visible-light-induced “on–off” one-pot synthesis of 3-arylacetylene coumarins with AIE properties. Org Biomol Chem 2020; 18:3346-3353. [DOI: 10.1039/d0ob00479k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A mild one-pot approach to 3-arylacetylene coumarins with potential AIE activities was developed via photosensitizer-free photocatalysis and thermocatalysis.
Collapse
Affiliation(s)
- Xinjie Wu
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| | - Ming Jia
- School of Materials Science and Engineering
- Zhengzhou University
- Zhengzhou 450052
- P.R. China
| | - Mengmeng Huang
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| | - Jung Keun Kim
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| | - Zheng Zhao
- Department of Chemistry
- The Hong Kong University of Science and Technology
- P.R. China
| | - Junkai Liu
- Department of Chemistry
- The Hong Kong University of Science and Technology
- P.R. China
| | - Jinhu Xi
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| | - Yabo Li
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| | - Yangjie Wu
- College of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou
| |
Collapse
|
18
|
Wadman RI, van der Pol WL, Bosboom WMJ, Asselman F, van den Berg LH, Iannaccone ST, Vrancken AFJE. Drug treatment for spinal muscular atrophy type I. Cochrane Database Syst Rev 2019; 12:CD006281. [PMID: 31825542 PMCID: PMC6905354 DOI: 10.1002/14651858.cd006281.pub5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is caused by a homozygous deletion of the survival motor neuron 1 (SMN1) gene on chromosome 5, or a heterozygous deletion in combination with a point mutation in the second SMN1 allele. This results in degeneration of anterior horn cells, which leads to progressive muscle weakness. By definition, children with SMA type I are never able to sit without support and usually die or become ventilator dependent before the age of two years. There have until very recently been no drug treatments to influence the course of SMA. We undertook this updated review to evaluate new evidence on emerging treatments for SMA type I. The review was first published in 2009 and previously updated in 2011. OBJECTIVES To assess the efficacy and safety of any drug therapy designed to slow or arrest progression of spinal muscular atrophy (SMA) type I. SEARCH METHODS We searched the Cochrane Neuromuscular Specialised Register, CENTRAL, MEDLINE, Embase, and ISI Web of Science conference proceedings in October 2018. We also searched two trials registries to identify unpublished trials (October 2018). SELECTION CRITERIA We sought all randomised controlled trials (RCTs) or quasi-RCTs that examined the efficacy of drug treatment for SMA type I. Included participants had to fulfil clinical criteria and have a genetically confirmed deletion or mutation of the SMN1 gene (5q11.2-13.2). The primary outcome measure was age at death or full-time ventilation. Secondary outcome measures were acquisition of motor milestones, i.e. head control, rolling, sitting or standing, motor milestone response on disability scores within one year after the onset of treatment, and adverse events and serious adverse events attributable to treatment during the trial period. Treatment strategies involving SMN1 gene replacement with viral vectors are out of the scope of this review. DATA COLLECTION AND ANALYSIS We followed standard Cochrane methodology. MAIN RESULTS We identified two RCTs: one trial of intrathecal nusinersen in comparison to a sham (control) procedure in 121 randomised infants with SMA type I, which was newly included at this update, and one small trial comparing riluzole treatment to placebo in 10 children with SMA type I. The RCT of intrathecally-injected nusinersen was stopped early for efficacy (based on a predefined Hammersmith Infant Neurological Examination-Section 2 (HINE-2) response). At the interim analyses after 183 days of treatment, 41% (21/51) of nusinersen-treated infants showed a predefined improvement on HINE-2, compared to 0% (0/27) of participants in the control group. This trial was largely at low risk of bias. Final analyses (ranging from 6 months to 13 months of treatment), showed that fewer participants died or required full-time ventilation (defined as more than 16 hours daily for 21 days or more) in the nusinersen-treated group than the control group (hazard ratio (HR) 0.53, 95% confidence interval (CI) 0.32 to 0.89; N = 121; a 47% lower risk; moderate-certainty evidence). A proportion of infants in the nusinersen group and none of 37 infants in the control group achieved motor milestones: 37/73 nusinersen-treated infants (51%) achieved a motor milestone response on HINE-2 (risk ratio (RR) 38.51, 95% CI 2.43 to 610.14; N = 110; moderate-certainty evidence); 16/73 achieved head control (RR 16.95, 95% CI 1.04 to 274.84; moderate-certainty evidence); 6/73 achieved independent sitting (RR 6.68, 95% CI 0.39 to 115.38; moderate-certainty evidence); 7/73 achieved rolling over (RR 7.70, 95% CI 0.45 to 131.29); and 1/73 achieved standing (RR 1.54, 95% CI 0.06 to 36.92; moderate-certainty evidence). Seventy-one per cent of nusinersen-treated infants versus 3% of infants in the control group were responders on the Children's Hospital of Philadelphia Infant Test of Neuromuscular Disorders (CHOP INTEND) measure of motor disability (RR 26.36, 95% CI 3.79 to 183.18; N = 110; moderate-certainty evidence). Adverse events and serious adverse events occurred in the majority of infants but were no more frequent in the nusinersen-treated group than the control group (RR 0.99, 95% CI 0.92 to 1.05 and RR 0.70, 95% CI 0.55 to 0.89, respectively; N = 121; moderate-certainty evidence). In the riluzole trial, three of seven children treated with riluzole were still alive at the ages of 30, 48, and 64 months, whereas all three children in the placebo group died. None of the children in the riluzole or placebo group developed the ability to sit, which was the only milestone reported. There were no adverse effects. The certainty of the evidence for all measured outcomes from this study was very low, because the study was too small to detect or rule out an effect, and had serious limitations, including baseline differences. This trial was stopped prematurely because the pharmaceutical company withdrew funding. Various trials and studies investigating treatment strategies other than nusinersen, such as SMN2 augmentation by small molecules, are ongoing. AUTHORS' CONCLUSIONS Based on the very limited evidence currently available regarding drug treatments for SMA type 1, intrathecal nusinersen probably prolongs ventilation-free and overall survival in infants with SMA type I. It is also probable that a greater proportion of infants treated with nusinersen than with a sham procedure achieve motor milestones and can be classed as responders to treatment on clinical assessments (HINE-2 and CHOP INTEND). The proportion of children experiencing adverse events and serious adverse events on nusinersen is no higher with nusinersen treatment than with a sham procedure, based on evidence of moderate certainty. It is uncertain whether riluzole has any effect in patients with SMA type I, based on the limited available evidence. Future trials could provide more high-certainty, longer-term evidence to confirm this result, or focus on comparing new treatments to nusinersen or evaluate them as an add-on therapy to nusinersen.
Collapse
Affiliation(s)
- Renske I Wadman
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - W Ludo van der Pol
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Wendy MJ Bosboom
- Onze Lieve Vrouwe Gasthuis locatie WestDepartment of NeurologyAmsterdamNetherlands
| | - Fay‐Lynn Asselman
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Leonard H van den Berg
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | - Susan T Iannaccone
- University of Texas Southwestern Medical CenterDepartment of Pediatrics5323 Harry Hines BoulevardDallasTexasUSA75390
| | - Alexander FJE Vrancken
- University Medical Center Utrecht, Brain Center Rudolf MagnusDepartment of NeurologyHeidelberglaan 100UtrechtNetherlands3584 CX
| | | |
Collapse
|
19
|
Hrynyshyn YV, Musiychuk AR, Tsizorik NM, Bol’but AV, Vovk MV. Synthesis of 4-aryl(hetaryl)pyrazolo[1,5-a]pyrazines by palladium-catalyzed Suzuki–Miyaura cross coupling. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02579-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
20
|
Brown DG, Wobst HJ. Opportunities and Challenges in Phenotypic Screening for Neurodegenerative Disease Research. J Med Chem 2019; 63:1823-1840. [PMID: 31268707 DOI: 10.1021/acs.jmedchem.9b00797] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Toxic misfolded proteins potentially underly many neurodegenerative diseases, but individual targets which regulate these proteins and their downstream detrimental effects are often unknown. Phenotypic screening is an unbiased method to screen for novel targets and therapeutic molecules and span the range from primitive model organisms such as Sacchaomyces cerevisiae, which allow for high-throughput screening to patient-derived cell-lines that have a close connection to the disease biology but are limited in screening capacity. This perspective will review current phenotypic models, as well as the chemical screening strategies most often employed. Advances in in 3D cell cultures, high-content screens, robotic microscopy, CRISPR screening, and use of machine learning methods to process the enormous amount of data generated by these screens are certain to change the paradigm for phenotypic screening and will be discussed.
Collapse
Affiliation(s)
- Dean G Brown
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Heike J Wobst
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| |
Collapse
|
21
|
More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
Collapse
|
22
|
Taladriz-Sender A, Campbell E, Burley GA. Splice-switching small molecules: A new therapeutic approach to modulate gene expression. Methods 2019; 167:134-142. [PMID: 31203161 DOI: 10.1016/j.ymeth.2019.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Manipulating alternative RNA splicing events with small molecules is emerging as a viable mechanism for the development of therapeutics. A salient challenge in the field is understanding the molecular determinants defining the selectivity of splice-switching events and their mechanisms of action. In this review, the current state-of-the-art in splice-switching small molecules is described. Three examples of splice-switching small molecules are presented, and the differences in their modes of action compared.
Collapse
Affiliation(s)
- Andrea Taladriz-Sender
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Emma Campbell
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
| |
Collapse
|
23
|
Ratni H, Mueller L, Ebeling M. Rewriting the (tran)script: Application to spinal muscular atrophy. PROGRESS IN MEDICINAL CHEMISTRY 2019; 58:119-156. [PMID: 30879473 DOI: 10.1016/bs.pmch.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Targeting RNA drastically expands our target space to therapeutically modulate numerous cellular processes implicated in human diseases. Of particular interest, drugging pre-mRNA splicing appears a very viable strategy; to control levels of splicing product by promoting the inclusion or exclusion of exons. After describing the concept of "splicing modulation", this chapter will cover the outstanding progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of spinal muscular atrophy using two therapeutic modalities: splice switching oligonucleotides and small molecules. This review discusses the vital but feasible requirement for such drugs to deliver selectivity, and critical safety aspects are highlighted. Transformational medicines such as those developed to treat SMA are likely just the beginning of this story.
Collapse
Affiliation(s)
- Hasane Ratni
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Lutz Mueller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Martin Ebeling
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| |
Collapse
|
24
|
Montes M, Sanford BL, Comiskey DF, Chandler DS. RNA Splicing and Disease: Animal Models to Therapies. Trends Genet 2019; 35:68-87. [PMID: 30466729 PMCID: PMC6339821 DOI: 10.1016/j.tig.2018.10.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023]
Abstract
Alternative splicing of pre-mRNA increases genetic diversity, and recent studies estimate that most human multiexon genes are alternatively spliced. If this process is not highly regulated and accurate, it leads to mis-splicing events, which may result in proteins with altered function. A growing body of work has implicated mis-splicing events in a range of diseases, including cancer, neurodegenerative diseases, and muscular dystrophies. Understanding the mechanisms that cause aberrant splicing events and how this leads to disease is vital for designing effective therapeutic strategies. In this review, we focus on advances in therapies targeting splicing, and highlight the animal models developed to recapitulate disease phenotypes as a model for testing these therapies.
Collapse
Affiliation(s)
- Matías Montes
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Brianne L Sanford
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel F Comiskey
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Dawn S Chandler
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
| |
Collapse
|
25
|
Cheung AK, Hurley B, Kerrigan R, Shu L, Chin DN, Shen Y, O'Brien G, Sung MJ, Hou Y, Axford J, Cody E, Sun R, Fazal A, Fridrich C, Sanchez CC, Tomlinson RC, Jain M, Deng L, Hoffmaster K, Song C, Van Hoosear M, Shin Y, Servais R, Towler C, Hild M, Curtis D, Dietrich WF, Hamann LG, Briner K, Chen KS, Kobayashi D, Sivasankaran R, Dales NA. Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA). J Med Chem 2018; 61:11021-11036. [PMID: 30407821 DOI: 10.1021/acs.jmedchem.8b01291] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinal muscular atrophy (SMA), a rare neuromuscular disorder, is the leading genetic cause of death in infants and toddlers. SMA is caused by the deletion or a loss of function mutation of the survival motor neuron 1 (SMN1) gene. In humans, a second closely related gene SMN2 exists; however it codes for a less stable SMN protein. In recent years, significant progress has been made toward disease modifying treatments for SMA by modulating SMN2 pre-mRNA splicing. Herein, we describe the discovery of LMI070/branaplam, a small molecule that stabilizes the interaction between the spliceosome and SMN2 pre-mRNA. Branaplam (1) originated from a high-throughput phenotypic screening hit, pyridazine 2, and evolved via multiparameter lead optimization. In a severe mouse SMA model, branaplam treatment increased full-length SMN RNA and protein levels, and extended survival. Currently, branaplam is in clinical studies for SMA.
Collapse
Affiliation(s)
- Atwood K Cheung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Brian Hurley
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ryan Kerrigan
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lei Shu
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Donovan N Chin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Yiping Shen
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Gary O'Brien
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Moo Je Sung
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ying Hou
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jake Axford
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Emma Cody
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Robert Sun
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Aleem Fazal
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cary Fridrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Carina C Sanchez
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Ronald C Tomlinson
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Monish Jain
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lin Deng
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Keith Hoffmaster
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Cheng Song
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Mailin Van Hoosear
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Youngah Shin
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Rebecca Servais
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Christopher Towler
- Novartis Pharmaceuticals , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Marc Hild
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Daniel Curtis
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - William F Dietrich
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Lawrence G Hamann
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Karen S Chen
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Dione Kobayashi
- SMA Foundation , 888 Seventh Avenue, Suite 400 , New York , New York 10019 , United States
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Natalie A Dales
- Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| |
Collapse
|
26
|
Abd ul-Malik MA, Zaki RM, Kamal El-Dean AM, Radwan SM. A Concise Review on the Synthesis and Reactions of Pyrazolopyrazine Heterocycles. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mokhtar A. Abd ul-Malik
- Chemistry Department, Faculty of Science; Assiut University; Assiut 71516 Egypt
- Chemistry Department, Faculty of Applied Science; Taiz University; Taiz Yemen
| | - Remon M. Zaki
- Chemistry Department, Faculty of Science; Assiut University; Assiut 71516 Egypt
| | | | - Shaban M. Radwan
- Chemistry Department, Faculty of Science; Assiut University; Assiut 71516 Egypt
| |
Collapse
|
27
|
Scoto M, Finkel R, Mercuri E, Muntoni F. Genetic therapies for inherited neuromuscular disorders. THE LANCET CHILD & ADOLESCENT HEALTH 2018; 2:600-609. [PMID: 30119719 DOI: 10.1016/s2352-4642(18)30140-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/15/2023]
Abstract
Inherited neuromuscular disorders encompass a broad group of genetic conditions, and the discovery of these underlying genes has expanded greatly in the past three decades. The discovery of such genes has enabled more precise diagnosis of these disorders and the development of specific therapeutic approaches that target the genetic basis and pathophysiological pathways. Such translational research has led to the approval of two genetic therapies by the US Food and Drug Administration: eteplirsen for Duchenne muscular dystrophy and nusinersen for spinal muscular atrophy, which are both antisense oligonucleotides that modify pre-mRNA splicing. In this Review we aim to discuss new genetic therapies and ongoing clinical trials for Duchenne muscular dystrophy, spinal muscular atrophy, and other less common childhood neuromuscular disorders.
Collapse
Affiliation(s)
- Mariacristina Scoto
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Richard Finkel
- Division of Pediatric Neurology, Nemours Children's Hospital, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Eugenio Mercuri
- Pediatric Neurology and Centro Nemo, IRCSS Fondazione Policlinico Gemelli, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, UK; National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre, London, UK.
| |
Collapse
|
28
|
Brown DG, Boström J. Where Do Recent Small Molecule Clinical Development Candidates Come From? J Med Chem 2018; 61:9442-9468. [DOI: 10.1021/acs.jmedchem.8b00675] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Dean G. Brown
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jonas Boström
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Gothenburg SE-431 83, Sweden
| |
Collapse
|
29
|
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes. Nat Commun 2018; 9:2032. [PMID: 29795225 PMCID: PMC5966403 DOI: 10.1038/s41467-018-04110-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/04/2018] [Indexed: 01/04/2023] Open
Abstract
Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5' splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted.
Collapse
|
30
|
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
|
31
|
|
32
|
Lindsay-Scott PJ, Charlesworth NG, Grozavu A. A Flexible Strategy for the Regiocontrolled Synthesis of Pyrazolo[1,5-a]pyrazines. J Org Chem 2017; 82:11295-11303. [DOI: 10.1021/acs.joc.7b02128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter J. Lindsay-Scott
- Eli Lilly and Company Limited, Erl Wood
Manor, Windlesham, Surrey GU20 6PH, United Kingdom
| | | | - Alexandru Grozavu
- Eli Lilly and Company Limited, Erl Wood
Manor, Windlesham, Surrey GU20 6PH, United Kingdom
| |
Collapse
|
33
|
Alternative Splicing in Genetic Diseases: Improved Diagnosis and Novel Treatment Options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 335:85-141. [PMID: 29305015 DOI: 10.1016/bs.ircmb.2017.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alternative splicing is an important mechanism to regulate gene expression and to expand the repertoire of gene products in order to accommodate an increase in complexity of multicellular organisms. It needs to be precisely regulated, which is achieved via RNA structure, splicing factors, transcriptional regulation, and chromatin. Changes in any of these factors can lead to disease. These may include the core spliceosome, splicing enhancer/repressor sequences and their interacting proteins, the speed of transcription by RNA polymerase II, and histone modifications. While the basic principle of splicing is well understood, it is still very difficult to predict splicing outcome, due to the multiple levels of regulation. Current molecular diagnostics mainly uses Sanger sequencing of exons, or next-generation sequencing of gene panels or the whole exome. Functional analysis of potential splicing variants is scarce, and intronic variants are often not considered. This likely results in underestimation of the percentage of splicing variants. Understanding how sequence variants may affect splicing is not only crucial for confirmation of diagnosis and for genetic counseling, but also for the development of novel treatment options. These include small molecules, transsplicing, antisense oligonucleotides, and gene therapy. Here we review the current state of molecular mechanisms of splicing regulation and how deregulation can lead to human disease, diagnostics to detect splicing variants, and novel treatment options based on splicing correction.
Collapse
|
34
|
Pawellek A, Ryder U, Tammsalu T, King LJ, Kreinin H, Ly T, Hay RT, Hartley RC, Lamond AI. Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP. eLife 2017; 6:27402. [PMID: 28884683 PMCID: PMC5619949 DOI: 10.7554/elife.27402] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022] Open
Abstract
We have identified the plant biflavonoid hinokiflavone as an inhibitor of splicing in vitro and modulator of alternative splicing in cells. Chemical synthesis confirms hinokiflavone is the active molecule. Hinokiflavone inhibits splicing in vitro by blocking spliceosome assembly, preventing formation of the B complex. Cells treated with hinokiflavone show altered subnuclear organization specifically of splicing factors required for A complex formation, which relocalize together with SUMO1 and SUMO2 into enlarged nuclear speckles containing polyadenylated RNA. Hinokiflavone increases protein SUMOylation levels, both in in vitro splicing reactions and in cells. Hinokiflavone also inhibited a purified, E. coli expressed SUMO protease, SENP1, in vitro, indicating the increase in SUMOylated proteins results primarily from inhibition of de-SUMOylation. Using a quantitative proteomics assay we identified many SUMO2 sites whose levels increased in cells following hinokiflavone treatment, with the major targets including six proteins that are components of the U2 snRNP and required for A complex formation.
Collapse
Affiliation(s)
- Andrea Pawellek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ursula Ryder
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Triin Tammsalu
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Lewis J King
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Helmi Kreinin
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Tony Ly
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Richard C Hartley
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| |
Collapse
|
35
|
The effects of C5-substituted 2,4-diaminoquinazolines on selected transcript expression in spinal muscular atrophy cells. PLoS One 2017; 12:e0180657. [PMID: 28662219 PMCID: PMC5491266 DOI: 10.1371/journal.pone.0180657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
C5-substituted 2,4-diaminoquinazolines (2,4-DAQs) ameliorate disease severity in SMA mice. It is uncertain, however, that these compounds increase SMN protein levels in vivo even though they were identified as activators of the SMN2 promoter. These compounds also regulate the expression of other transcripts in neuroblastoma cells. In this study, we investigate the mechanism by which the 2,4-DAQs regulate the expression of SMN2 as well as other targets. D156844, D158872, D157161 and D157495 (RG3039) increased SMN2 promoter-driven reporter gene activity by at least 3-fold in NSC-34 cells. These compounds, however, did not significantly increase SMN2 mRNA levels in type II SMA fibroblasts nor in NSC-34 cells, although there was a trend for these compounds increasing SMN protein in SMA fibroblasts. The number of SMN-containing gems was increased in SMA fibroblasts in response to 2,4-DAQ treatment in a dose-dependent manner. ATOH7 mRNA levels were significantly lower in type II SMA fibroblasts. 2,4-DAQs significantly increased ATOH7, DRNT1 and DRTN2 transcript levels in type II SMA fibroblasts and restored ATOH7 levels to those observed in healthy fibroblasts. These compounds also increase Atoh7 mRNA expression in NSC-34 cells. In conclusion, 2,4-DAQs regulate SMN2 by increasing protein levels and gem localization. They also increase ATOH7, DRNT1 and DRNT2 transcript levels. This study reveals that the protective effects of 2,4-DAQs in SMA may be independent of SMN2 gene regulation. These compounds could be used in concert with a proven SMN2 inducer to develop a multi-faceted approach to treating SMA.
Collapse
|
36
|
Pinard E, Green L, Reutlinger M, Weetall M, Naryshkin NA, Baird J, Chen KS, Paushkin SV, Metzger F, Ratni H. Discovery of a Novel Class of Survival Motor Neuron 2 Splicing Modifiers for the Treatment of Spinal Muscular Atrophy. J Med Chem 2017; 60:4444-4457. [DOI: 10.1021/acs.jmedchem.7b00406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emmanuel Pinard
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Luke Green
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael Reutlinger
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marla Weetall
- PTC Therapeutics, Inc., 100
Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Nikolai A. Naryshkin
- PTC Therapeutics, Inc., 100
Corporate Court, South Plainfield, New Jersey 07080, United States
| | - John Baird
- PTC Therapeutics, Inc., 100
Corporate Court, South Plainfield, New Jersey 07080, United States
| | - Karen S. Chen
- SMA Foundation, 888 Seventh
Avenue, Suite 400, New York, New York 10019, United States
| | - Sergey V. Paushkin
- SMA Foundation, 888 Seventh
Avenue, Suite 400, New York, New York 10019, United States
| | - Friedrich Metzger
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Hasane Ratni
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
| |
Collapse
|
37
|
Govdi AI, Kulyashova AE, Vasilevsky SF, Balova IA. Functionalized buta-1,3-diynyl- N -methylpyrazoles by sequential “diacetylene zipper” and Sonogashira coupling reactions. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
38
|
Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
Collapse
Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| |
Collapse
|