1
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Lopes RR, Tomé CS, Russo R, Paterna R, Leandro J, Candeias NR, Gonçalves LMD, Teixeira M, Sousa PMF, Guedes RC, Vicente JB, Gois PMP, Leandro P. Modulation of Human Phenylalanine Hydroxylase by 3-Hydroxyquinolin-2(1H)-One Derivatives. Biomolecules 2021; 11:biom11030462. [PMID: 33808760 PMCID: PMC8003416 DOI: 10.3390/biom11030462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/08/2021] [Accepted: 03/13/2021] [Indexed: 01/14/2023] Open
Abstract
Phenylketonuria (PKU) is a genetic disease caused by deficient activity of human phenylalanine hydroxylase (hPAH) that, when untreated, can lead to severe psychomotor impairment. Protein misfolding is recognized as the main underlying pathogenic mechanism of PKU. Therefore, the use of stabilizers of protein structure and/or activity is an attractive therapeutic strategy for this condition. Here, we report that 3-hydroxyquinolin-2(1H)-one derivatives can act as protectors of hPAH enzyme activity. Electron paramagnetic resonance spectroscopy demonstrated that the 3-hydroxyquinolin-2(1H)-one compounds affect the coordination of the non-heme ferric center at the enzyme active-site. Moreover, surface plasmon resonance studies showed that these stabilizing compounds can be outcompeted by the natural substrate l-phenylalanine. Two of the designed compounds functionally stabilized hPAH by maintaining protein activity. This effect was observed on the recombinant purified protein and in a cellular model. Besides interacting with the catalytic iron, one of the compounds also binds to the N-terminal regulatory domain, although to a different location from the allosteric l-Phe binding site, as supported by the solution structures obtained by small-angle X-ray scattering.
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Affiliation(s)
- Raquel R. Lopes
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Catarina S. Tomé
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
- Instituto de Biologia Experimental e Tecnológica, Quinta do Marquês, 2780-155 Oeiras, Portugal;
| | - Roberto Russo
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Roberta Paterna
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - João Leandro
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Nuno R. Candeias
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33101 Tampere, Finland;
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Lídia M. D. Gonçalves
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
| | - Pedro M. F. Sousa
- Instituto de Biologia Experimental e Tecnológica, Quinta do Marquês, 2780-155 Oeiras, Portugal;
| | - Rita C. Guedes
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal;
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
| | - Pedro M. P. Gois
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
| | - Paula Leandro
- Research Institute for Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (R.R.L.); (C.S.T.); (R.R.); (R.P.); (J.L.); (L.M.D.G.); (R.C.G.)
- Correspondence: (J.B.V.); (P.M.P.G.); (P.L.); Tel.: +351-217946400 (P.L.)
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2
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Au PYB, Eaton A, Dyment DA. Genetic mechanisms of neurodevelopmental disorders. HANDBOOK OF CLINICAL NEUROLOGY 2020; 173:307-326. [PMID: 32958182 DOI: 10.1016/b978-0-444-64150-2.00024-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Neurodevelopmental disorders encompass a broad range of conditions, which include autism, epilepsy, and intellectual disability. These disorders are relatively common and have associated clinical and genetic heterogeneity. Technology has driven much of our understanding of these diseases and their genetic underlying mechanisms, particularly highlighted by the study of large cohorts with comparative genomic hybridization and the more recent implementation of next-generation sequencing (NGS). The mapping of copy number variants throughout the genome has highlighted the recurrent, highly penetrant, de novo variation in syndromic forms of neurodevelopmental disease. NGS of affected individuals and their parents led to a dramatic shift in our understanding as these studies showed that a significant proportion of affected individuals carry rare, de novo variants within single genes that explain their disease presentation. Deep sequencing studies further implicate mosaicism as another mechanism of disease. However, it has also become clear that while rare variants explain a significant proportion of sporadic neurodevelopmental disease, rare variation still does not fully account for the familial clustering and high heritability observed. Common variants, including those within these known disease genes, are also shown to contribute significantly to overall risk. There is also increasing awareness of the important contribution of epigenetic factors and gene-environment interactions.
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Affiliation(s)
- P Y Billie Au
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Alison Eaton
- Department of Medical Genetics, The Stollery Children's Hospital, Edmonton, AB, Canada
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.
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3
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Hadwen J, Schock S, Mears A, Yang R, Charron P, Zhang L, Xi HS, MacKenzie A. Transcriptomic RNAseq drug screen in cerebrocortical cultures: toward novel neurogenetic disease therapies. Hum Mol Genet 2019; 27:3206-3217. [PMID: 29901742 DOI: 10.1093/hmg/ddy221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 06/04/2018] [Indexed: 01/19/2023] Open
Abstract
Rare monogenic diseases affect millions worldwide; although over 4500 rare disease genotypes are known, disease-modifying drugs are available for only 5% of them. The sheer number of these conditions combined with their rarity precludes traditional costly drug discovery programs. An economically viable alternative is to repurpose established drugs for rare diseases. Many genetic diseases result from increased or decreased protein activity and identification of clinically approved drugs which moderate this pathogenic dosage holds therapeutic potential. To identify such agents for neurogenetic diseases, we have generated genome-wide transcriptome profiles of mouse primary cerebrocortical cultures grown in the presence of 218 blood-brain barrier (BBB) penetrant clinic-tested drugs. RNAseq and differential expression analyses were used to generate transcriptomic profiles; therapeutically relevant drug-gene interactions related to rare neurogenetic diseases identified in this fashion were further analyzed by quantitative reverse transcriptase-polymerase chain reaction, western blot and immunofluorescence. We have created a transcriptome-wide searchable database for easy access to the gene expression data resulting from the cerebrocortical drug screen (Neuron Screen) and have mined this data to identify a novel link between thyroid hormone and expression of the peripheral neuropathy associated gene Pmp22. Our results demonstrate the utility of cerebrocortical cultures for transcriptomic drug screening, and the database we have created will foster further discovery of novel links between over 200 clinic-tested BBB penetrant drugs and genes related to diverse neurologic conditions.
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Affiliation(s)
- Jeremiah Hadwen
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Sarah Schock
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Alan Mears
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Robert Yang
- Computational Sciences Centre of Emphasis, Pfizer, Boston, MA, USA
| | - Philippe Charron
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Liying Zhang
- Computational Sciences Centre of Emphasis, Pfizer, Boston, MA, USA
| | - Hualin S Xi
- Computational Sciences Centre of Emphasis, Pfizer, Boston, MA, USA
| | - Alex MacKenzie
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
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4
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Substrate reduction therapy for inborn errors of metabolism. Emerg Top Life Sci 2019; 3:63-73. [PMID: 33523197 PMCID: PMC7289018 DOI: 10.1042/etls20180058] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/02/2019] [Accepted: 01/09/2019] [Indexed: 12/13/2022]
Abstract
Inborn errors of metabolism (IEM) represent a growing group of monogenic disorders each associated with inherited defects in a metabolic enzyme or regulatory protein, leading to biochemical abnormalities arising from a metabolic block. Despite the well-established genetic linkage, pathophysiology and clinical manifestations for many IEMs, there remains a lack of transformative therapy. The available treatment and management options for a few IEMs are often ineffective or expensive, incurring a significant burden to individual, family, and society. The lack of IEM therapies, in large part, relates to the conceptual challenge that IEMs are loss-of-function defects arising from the defective enzyme, rendering pharmacologic rescue difficult. An emerging approach that holds promise and is the subject of a flurry of pre-/clinical applications, is substrate reduction therapy (SRT). SRT addresses a common IEM phenotype associated with toxic accumulation of substrate from the defective enzyme, by inhibiting the formation of the substrate instead of directly repairing the defective enzyme. This minireview will summarize recent highlights towards the development of emerging SRT, with focussed attention towards repurposing of currently approved drugs, approaches to validate novel targets and screen for hit molecules, as well as emerging advances in gene silencing as a therapeutic modality.
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5
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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6
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Kwon YJ, Falk MJ, Bennett MJ. Flunarizine rescues reduced lifespan in CLN3 triple knock-out Caenorhabditis elegans model of batten disease. J Inherit Metab Dis 2017; 40:291-296. [PMID: 27766444 PMCID: PMC5309197 DOI: 10.1007/s10545-016-9986-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 01/22/2023]
Abstract
CLN3 disease (Spielmeyer-Vogt-Sjogren-Batten disease, previously known as classic juvenile neuronal ceroid lipofuscinosis, NCL) is a pediatric-onset progressive neurodegenerative disease characterized by progressive vision loss, seizures, loss of cognitive and motor function, and early death. While no precise biochemical mechanism or therapies are known, the pathogenesis of CLN3 disease involves intracellular calcium accumulation that may trigger apoptosis. Our prior work in in vitro cell models of CLN3 deficiency suggested that FDA-approved calcium channel antagonists may have therapeutic value. To further evaluate the potential efficacy of this approach in an otherwise untreatable disorder, we sought to compare the therapeutic effects and underlying mechanisms in an animal model of CLN3 disease. Here, we used the well-characterized XT7 complete cln-3 knockout strain of C. elegans to evaluate the therapeutic efficacy of calcium channel antagonist therapy in a living animal model of Batten disease. Therapeutic effects of five calcium channel antagonists were evaluated on XT7 animal lifespan and in vivo mitochondrial physiology. Remarkably, maximal therapeutic efficacy in this model animal was observed with 1 μM flunarizine, the identical concentration previously identified in cell-based neuronal models of CLN3 disease. Specifically, flunarizine rescued the short lifespan of XT7 worms and prevented their pathophysiologic mitochondrial accumulation. These results confirm the treatment efficacy and dosing of flunarizine in cln-3 disease in a translational model organism. Clinical treatment trials in CLN3 human patients are now needed to test the dosing regimen and efficacy of flunarizine in individuals suffering with this otherwise untreatable and ultimately lethal neurologic disease.
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Affiliation(s)
- Young Joon Kwon
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, ARC 1002C, 3615 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, ARC 1002C, 3615 Civic Center Boulevard, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Michael J Bennett
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, 34th and Civic Center Blvd, 5NW58, Philadelphia, PA, 19104, USA.
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7
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Yue WW. From structural biology to designing therapy for inborn errors of metabolism. J Inherit Metab Dis 2016; 39:489-98. [PMID: 27240455 PMCID: PMC4920855 DOI: 10.1007/s10545-016-9923-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 12/11/2022]
Abstract
At the SSIEM Symposium in Istanbul 2010, I presented an overview of protein structural approaches in the study of inborn errors of metabolism (Yue and Oppermann 2011). Five years on, the field is going strong with new protein structures, uncovered catalytic functions and novel chemical matters for metabolic enzymes, setting the stage for the next generation of drug discovery. This article aims to update on recent advances and lessons learnt on inborn errors of metabolism via the protein-centric approach, citing examples of work from my group, collaborators and co-workers that cover diverse pathways of transsulfuration, cobalamin and glycogen metabolism. Taking into consideration that many inborn errors of metabolism result in the loss of enzyme function, this presentation aims to outline three key principles that guide the design of small molecule therapy in this technically challenging field: (1) integrating structural, biochemical and cell-based data to evaluate the wide spectrum of mutation-driven enzyme defects in stability, catalysis and protein-protein interaction; (2) studying multi-domain proteins and multi-protein complexes as examples from nature, to learn how enzymes are activated by small molecules; (3) surveying different regions of the enzyme, away from its active site, that can be targeted for the design of allosteric activators and inhibitors.
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Affiliation(s)
- Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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8
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Ekins S, Wood J. Incentives for Starting Small Companies Focused on Rare and Neglected Diseases. Pharm Res 2015; 33:809-15. [PMID: 26666772 DOI: 10.1007/s11095-015-1841-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/07/2015] [Indexed: 12/30/2022]
Abstract
Starting biotech or pharmaceutical companies is traditionally thought to be based around a scientist, their technology platform or a clinical candidate spun out from another company. Between us we have taken a different approach and formed two small early stage companies after initially leveraging the perspective of a parent with a child with a life-threatening rare disease. Phoenix Nest ( http://www.phoenixnestbiotech.com/ ) was co-founded to work on treatments for Sanfilippo syndrome a devastating neurodegenerative lysosomal storage disorder. In the space of just over 3 years we have built up collaborations with leading scientists in academia and industry and been awarded multiple NIH small business grants. The second company, Collaborations Pharmaceuticals Inc. ( http://www.collaborationspharma.com/ ) was founded to address some of the other 7000 or so rare diseases as well as neglected infectious diseases. The Rare Pediatric Disease Priority Review Voucher is likely the most important incentive for companies working on rare diseases with very small populations. This may also be partially responsible for the recent acquisitions of rare disease companies with late stage candidates. Lessons learned in the process of starting our companies are that rare disease parents or patients can readily partner with a scientist and fund research through NIH grants rather than venture capital or angel investors initially. This process may be slow so patience and perseverance is key. We would encourage other pharmaceutical scientists to meet rare disease parents, patients or advocates and work with them to further the science on their diseases and create a source of future drugs.
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Affiliation(s)
- Sean Ekins
- Phoenix Nest, Inc., P.O. BOX 150057, Brooklyn, New York, 11215, USA. .,Collaborations Pharmaceuticals Inc., 5616 Hilltop Needmore Road, Fuquay Varina, North Carolina, 27526, USA.
| | - Jill Wood
- Phoenix Nest, Inc., P.O. BOX 150057, Brooklyn, New York, 11215, USA.,Jonah's Just Begun, P.O. Box 150057, Brooklyn, New York, 11215, USA
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9
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Lim JS, Lee JH. Molecular genetic decoding of malformations of cortical development. ACTA ACUST UNITED AC 2015. [DOI: 10.5734/jgm.2015.12.1.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jae Seok Lim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
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10
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Ekins S, Litterman NK, Arnold RJG, Burgess RW, Freundlich JS, Gray SJ, Higgins JJ, Langley B, Willis DE, Notterpek L, Pleasure D, Sereda MW, Moore A. A brief review of recent Charcot-Marie-Tooth research and priorities. F1000Res 2015; 4:53. [PMID: 25901280 PMCID: PMC4392824 DOI: 10.12688/f1000research.6160.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/14/2022] Open
Abstract
This brief review of current research progress on Charcot-Marie-Tooth (CMT) disease is a summary of discussions initiated at the Hereditary Neuropathy Foundation (HNF) scientific advisory board meeting on November 7, 2014. It covers recent published and unpublished
in vitro and
in vivo research. We discuss recent promising preclinical work for CMT1A, the development of new biomarkers, the characterization of different animal models, and the analysis of the frequency of gene mutations in patients with CMT. We also describe how progress in related fields may benefit CMT therapeutic development, including the potential of gene therapy and stem cell research. We also discuss the potential to assess and improve the quality of life of CMT patients. This summary of CMT research identifies some of the gaps which may have an impact on upcoming clinical trials. We provide some priorities for CMT research and areas which HNF can support. The goal of this review is to inform the scientific community about ongoing research and to avoid unnecessary overlap, while also highlighting areas ripe for further investigation. The general collaborative approach we have taken may be useful for other rare neurological diseases.
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Affiliation(s)
- Sean Ekins
- Hereditary Neuropathy Foundation, New York, NY, 10016, USA ; Collaborations in Chemistry, Fuquay Varina, NC, 27526, USA ; Collaborative Drug Discovery, Burlingame, CA, 94010, USA
| | | | - Renée J G Arnold
- Arnold Consultancy & Technology LLC, New York, NY, 10023, USA ; Master of Public Health Program, Mount Sinai School of Medicine, New York, NY, 10029, USA ; Quorum Consulting, Inc, San Francisco, CA, 94104, USA
| | - Robert W Burgess
- The Jackson Laboratory in Bar Harbor, Bar Harbour, ME, 04609, USA
| | - Joel S Freundlich
- Department of Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University - New Jersey Medical School, Newark, NJ, 07103, USA
| | - Steven J Gray
- Gene Therapy Center and Dept. of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7352, USA
| | | | - Brett Langley
- Burke-Cornell Medical Research Institute, White Plains, NY, 10605, USA ; Department of Neurology and Neuroscience, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Dianna E Willis
- Burke-Cornell Medical Research Institute, White Plains, NY, 10605, USA
| | - Lucia Notterpek
- Department of Neuroscience, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - David Pleasure
- Institute for Pediatric Regenerative Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA ; Department of Neurology, University of California, Davis, School of Medicine, c/o Shriners Hospital, Sacramento, CA, 95817, USA
| | - Michael W Sereda
- Department of Neurogenetics, Max Planck Institute (MPI) of Experimental Medicine, Göttingen, 37075, Germany ; Department of Clinical Neurophysiology, University Medical Center (UMG), Göttingen, D-37075, Germany
| | - Allison Moore
- Hereditary Neuropathy Foundation, New York, NY, 10016, USA
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Abstract
Drug repositioning or repurposing has received much coverage in the scientific literature in recent years and has been responsible for the generation of both new intellectual property and investigational new drug submissions. The literature indicates a significant trend toward the use of computational- or informatics-based methods for generating initial repositioning hypotheses, followed by focused assessment of biological activity in phenotypic assays. Another viable method for drug repositioning is in vitro screening of known drugs or drug-like molecules, initially in disease-relevant phenotypic assays, to identify and validate candidates for repositioning. This approach can use large compound libraries or can focus on subsets of known drugs or drug-like molecules. In this short review, we focus on ways to generate and validate repositioning candidates in disease-related in vitro and phenotypic assays, and we discuss specific examples of this approach as applied to a variety of disease areas. We propose that in vitro screens offer several advantages over biochemical or in vivo methods as a starting point for drug repositioning.
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Affiliation(s)
- Graeme F. Wilkinson
- Emerging Innovations, Innovative Medicines, AstraZeneca, Macclesfield, Cheshire, UK
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12
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Bellgard MI, Sleeman MW, Guerrero FD, Fletcher S, Baynam G, Goldblatt J, Rubinstein Y, Bell C, Groft S, Barrero R, Bittles AH, Wilton SD, Mason CE, Weeramanthri T. Rare Disease Research Roadmap: Navigating the bioinformatics and translational challenges for improved patient health outcomes. HEALTH POLICY AND TECHNOLOGY 2014. [DOI: 10.1016/j.hlpt.2014.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Abstract
Rare disease research has reached a tipping point, with the confluence of scientific and technologic developments that if appropriately harnessed, could lead to key breakthroughs and treatments for this set of devastating disorders. Industry-wide trends have revealed that the traditional drug discovery research and development (R&D) model is no longer viable, and drug companies are evolving their approach. Rather than only pursue blockbuster therapeutics for heterogeneous, common diseases, drug companies have increasingly begun to shift their focus to rare diseases. In academia, advances in genetics analyses and disease mechanisms have allowed scientific understanding to mature, but the lack of funding and translational capability severely limits the rare disease research that leads to clinical trials. Simultaneously, there is a movement towards increased research collaboration, more data sharing, and heightened engagement and active involvement by patients, advocates, and foundations. The growth in networks and social networking tools presents an opportunity to help reach other patients but also find researchers and build collaborations. The growth of collaborative software that can enable researchers to share their data could also enable rare disease patients and foundations to manage their portfolio of funded projects for developing new therapeutics and suggest drug repurposing opportunities. Still there are many thousands of diseases without treatments and with only fragmented research efforts. We will describe some recent progress in several rare diseases used as examples and propose how collaborations could be facilitated. We propose that the development of a center of excellence that integrates and shares informatics resources for rare diseases sponsored by all of the stakeholders would help foster these initiatives.
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Affiliation(s)
| | - Michele Rhee
- National Brain Tumor Society, Newton, MA, 02458, USA
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery (iRND3), Mountain View, CA, 94043, USA
| | - Sean Ekins
- Collaborative Drug Discovery, Inc., Burlingame, CA, 94010, USA ; Collaborations in Chemistry, Fuquay Varina, NC, 27526, USA ; Phoenix Nest Inc., Brooklyn, NY, 11215, USA ; Hereditary Neuropathy Foundation, New York, NY, 10016, USA ; Hannah's Hope Fund, Rexford, NY, NY 12148, USA
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Ekins S. Collecting rare diseases. F1000Res 2014; 3:260. [PMID: 25580231 PMCID: PMC4288410 DOI: 10.12688/f1000research.5577.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/27/2014] [Indexed: 11/23/2022] Open
Abstract
This editorial introduces the
F1000Research rare disease collection. It is common knowledge that for new treatments to be successful there has to be a partnership between the many interested parties such as the patient, advocate, disease foundations, the academic scientists, venture funding organizations, biotech companies, pharmaceutical companies, NIH, and the FDA. Our intention is to provide a forum for discussion and dissemination of any rare disease related topics that will advance scientific understanding and progress to treatments.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay Varina, NC, 27526, USA
- Collaborative Drug Discovery, Burlingame, CA, 94010, USA
- Phoenix Nest, Brooklyn, NY, 11215, USA
- Hereditary Neuropathy Foundation, New York, NY, 10016, USA
- Hannah's Hope Fund, Rexford, NY, 12148, USA
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Ekins S, Clark AM, Swamidass SJ, Litterman N, Williams AJ. Bigger data, collaborative tools and the future of predictive drug discovery. J Comput Aided Mol Des 2014; 28:997-1008. [PMID: 24943138 PMCID: PMC4198464 DOI: 10.1007/s10822-014-9762-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/09/2014] [Indexed: 12/31/2022]
Abstract
Over the past decade we have seen a growth in the provision of chemistry data and cheminformatics tools as either free websites or software as a service commercial offerings. These have transformed how we find molecule-related data and use such tools in our research. There have also been efforts to improve collaboration between researchers either openly or through secure transactions using commercial tools. A major challenge in the future will be how such databases and software approaches handle larger amounts of data as it accumulates from high throughput screening and enables the user to draw insights, enable predictions and move projects forward. We now discuss how information from some drug discovery datasets can be made more accessible and how privacy of data should not overwhelm the desire to share it at an appropriate time with collaborators. We also discuss additional software tools that could be made available and provide our thoughts on the future of predictive drug discovery in this age of big data. We use some examples from our own research on neglected diseases, collaborations, mobile apps and algorithm development to illustrate these ideas.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC, 27526, USA,
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Ekins S, Williams AJ. Curing TB with open science. Tuberculosis (Edinb) 2013; 94:183-5. [PMID: 24388836 DOI: 10.1016/j.tube.2013.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/16/2013] [Indexed: 12/27/2022]
Abstract
There are many funded efforts going on focused on tuberculosis research and drug or vaccine development. There is little if any global coordination or collaboration and subsequently there are likely to be huge data silos and duplication of efforts. We now propose steps to remedy this by fostering more open science in TB research.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC 27526, USA; Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA.
| | - Antony J Williams
- Royal Society of Chemistry, 904 Tamaras Circle, Wake Forest, NC 27587, USA
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Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 2013; 14:681-91. [PMID: 23999272 DOI: 10.1038/nrg3555] [Citation(s) in RCA: 502] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Work over the past 25 years has resulted in the identification of genes responsible for ~50% of the estimated 7,000 rare monogenic diseases, and it is predicted that most of the remaining disease-causing genes will be identified by the year 2020, and probably sooner. This marked acceleration is the result of dramatic improvements in DNA-sequencing technologies and the associated analyses. We examine the rapid maturation of rare-disease genetic analysis and successful strategies for gene identification. We highlight the impact of discovering rare-disease-causing genes, from clinical diagnostics to insights gained into biological mechanisms and common diseases. Last, we explore the increasing therapeutic opportunities and challenges that the resulting expansion of the 'atlas' of human genetic pathology will bring.
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Affiliation(s)
- Kym M Boycott
- Department of Pediatrics, University of Ottawa and Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, Ontario K1H 8L1, Canada
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Wood J, Sames L, Moore A, Ekins S. Multifaceted roles of ultra-rare and rare disease patients/parents in drug discovery. Drug Discov Today 2013; 18:1043-51. [PMID: 23968993 DOI: 10.1016/j.drudis.2013.08.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/29/2013] [Accepted: 08/07/2013] [Indexed: 01/10/2023]
Abstract
Individual parents and patients are increasingly doing more to fund, discover and develop treatments for rare and ultra-rare diseases that afflict their children, themselves or their friends. They are performing roles in business development that would be classed as entrepreneurial; and their organizational roles in driving the science in some cases are equivalent to those of principal investigators. These roles are in addition to their usual positioning as advocates. Through their efforts and those of the collaborative networks that they have developed, they could be positioned to disrupt the usual course of drug discovery. This can be illustrated using three different ultra-rare disease parent/patient advocate groups and the diseases for which they are developing treatments. This represents an alternative model for pharmaceutical research.
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Affiliation(s)
- Jill Wood
- Jonah's Just Begun, P.O. Box 150057, Brooklyn, NY 11215, USA; Phoenix Nest, P.O. Box 150057, Brooklyn, NY 11215, USA
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Norman P. Repurposing as a strategy for orphan drug development, evidence from European approvals. Expert Opin Orphan Drugs 2013. [DOI: 10.1517/21678707.2013.796883] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Clark AM, Williams AJ, Ekins S. Cheminformatics workflows using mobile apps. CHEM-BIO INFORMATICS JOURNAL 2013. [DOI: 10.1273/cbij.13.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | - Sean Ekins
- Collaborative Drug Discovery, Inc
- Collaborations in Chemistry
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Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates. Drug Discov Today 2013; 18:58-70. [DOI: 10.1016/j.drudis.2012.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/17/2012] [Accepted: 11/08/2012] [Indexed: 02/07/2023]
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Kobayashi DT, Decker D, Zaworski P, Klott K, McGonigal J, Ghazal N, Sly L, Chung B, Vanderlugt J, Chen KS. Evaluation of peripheral blood mononuclear cell processing and analysis for Survival Motor Neuron protein. PLoS One 2012; 7:e50763. [PMID: 23226377 PMCID: PMC3511312 DOI: 10.1371/journal.pone.0050763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/24/2012] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Survival Motor Neuron (SMN) protein levels may become key pharmacodynamic (PD) markers in spinal muscular atrophy (SMA) clinical trials. SMN protein in peripheral blood mononuclear cells (PBMCs) can be quantified for trials using an enzyme-linked immunosorbent assay (ELISA). We developed protocols to collect, process, store and analyze these samples in a standardized manner for SMA clinical studies, and to understand the impact of age and intraindividual variability over time on PBMC SMN signal. METHODS Several variables affecting SMN protein signal were evaluated using an ELISA. Samples were from healthy adults, adult with respiratory infections, SMA patients, and adult SMA carriers. RESULTS Delaying PBMCs processing by 45 min, 2 hr or 24 hr after collection or isolation allows sensitive detection of SMN levels and high cell viability (>90%). SMN levels from PBMCs isolated by EDTA tubes/Lymphoprep gradient are stable with processing delays and have greater signal compared to CPT-collected samples. SMN signal in healthy individuals varies up to 8x when collected at intervals up to 1 month. SMN signals from individuals with respiratory infections show 3-5x changes, driven largely by the CD14 fraction. SMN signal in PBMC frozen lysates are relatively stable for up to 6 months. Cross-sectional analysis of PBMCs from SMA patients and carriers suggest SMN protein levels decline with age. CONCLUSIONS The sources of SMN signal variability in PBMCs need to be considered in the design and of SMA clinical trials, and interpreted in light of recent medical history. Improved normalization to DNA or PBMC subcellular fractions may mitigate signal variability and should be explored in SMA patients.
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Affiliation(s)
- Dione T Kobayashi
- Spinal Muscular Atrophy Foundation, New York, New York, United States of America.
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