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Shukla H, John D, Banerjee S, Tiwari AK. Drug repurposing for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:249-319. [PMID: 38942541 DOI: 10.1016/bs.pmbts.2024.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Neurodegenerative diseases (NDDs) are neuronal problems that include the brain and spinal cord and result in loss of sensory and motor dysfunction. Common NDDs include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Multiple Sclerosis (MS), and Amyotrophic Lateral Sclerosis (ALS) etc. The occurrence of these diseases increases with age and is one of the challenging problems among elderly people. Though, several scientific research has demonstrated the key pathologies associated with NDDs still the underlying mechanisms and molecular details are not well understood and need to be explored and this poses a lack of effective treatments for NDDs. Several lines of evidence have shown that NDDs have a high prevalence and affect more than a billion individuals globally but still, researchers need to work forward in identifying the best therapeutic target for NDDs. Thus, several researchers are working in the directions to find potential therapeutic targets to alter the disease pathology and treat the diseases. Several steps have been taken to identify the early detection of the disease and drug repurposing for effective treatment of NDDs. Moreover, it is logical that current medications are being evaluated for their efficacy in treating such disorders; therefore, drug repurposing would be an efficient, safe, and cost-effective way in finding out better medication. In the current manuscript we discussed the utilization of drugs that have been repurposed for the treatment of AD, PD, HD, MS, and ALS.
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Affiliation(s)
- Halak Shukla
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India
| | - Diana John
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India
| | - Shuvomoy Banerjee
- Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India
| | - Anand Krishna Tiwari
- Genetics and Developmental Biology Laboratory, Department of Biotechnology and Bioengineering, Institute of Advanced Research (IAR), Gandhinagar, Gujarat, India.
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2
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Pal S, Nare Z, Rao VA, Smith BO, Morrison I, Fitzgerald EA, Scott A, Bingham MJ, Pesnot T. Accelerating BRPF1b hit identification with BioPhysical and Active Learning Screening (BioPALS). ChemMedChem 2024; 19:e202300590. [PMID: 38372199 DOI: 10.1002/cmdc.202300590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/25/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
We report the development of BioPhysical and Active Learning Screening (BioPALS); a rapid and versatile hit identification protocol combining AI-powered virtual screening with a GCI-driven biophysical confirmation workflow. Its application to the BRPF1b bromodomain afforded a range of novel micromolar binders with favorable ADMET properties. In addition to the excellent in silico/in vitro confirmation rate demonstrated with BRPF1b, binding kinetics were determined, and binding topologies predicted for all hits. BioPALS is a lean, data-rich, and standardized approach to hit identification applicable to a wide range of biological targets.
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Affiliation(s)
- Sandeep Pal
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Zandile Nare
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Vincenzo A Rao
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Brian O Smith
- University of Glasgow, School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, G12 8QQ, Glasgow, UK
| | - Ian Morrison
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | | | - Andrew Scott
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Matilda J Bingham
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Thomas Pesnot
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
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3
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Chakraborty S, Luchena C, Elton JJ, Schilling MP, Reischl M, Roux M, Levkin PA, Popova AA. "Cells-to-cDNA on Chip": Phenotypic Assessment and Gene Expression Analysis from Live Cells in Nanoliter Volumes Using Droplet Microarrays. Adv Healthc Mater 2022; 11:e2102493. [PMID: 35285171 DOI: 10.1002/adhm.202102493] [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: 11/15/2021] [Revised: 02/08/2022] [Indexed: 11/11/2022]
Abstract
In vitro cell-based experiments are particularly important in fundamental biological research. Microscopy-based readouts to identify cellular changes in response to various stimuli are a popular choice, but gene expression analysis is essential to delineate the underlying molecular dynamics in cells. However, cell-based experiments often suffer from interexperimental variation, especially while using different readout methods. Therefore, establishment of platforms that allow for cell screening, along with parallel investigations of morphological features, as well as gene expression levels, is crucial. The droplet microarray (DMA) platform enables cell screening in hundreds of nanoliter droplets. In this study, a "Cells-to-cDNA on Chip" method is developed enabling on-chip mRNA isolation from live cells and conversion to cDNA in individual droplets of 200 nL. This novel method works efficiently to obtain cDNA from different cell numbers, down to single cell per droplet. This is the first established miniaturized on-chip strategy that enables the entire course of cell screening, phenotypic microscopy-based assessments along with mRNA isolation and its conversion to cDNA for gene expression analysis by real-time PCR on an open DMA platform. The principle demonstrated in this study sets a beginning for myriad of possible applications to obtain detailed information about the molecular dynamics in cultured cells.
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Affiliation(s)
- Shraddha Chakraborty
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Jonathan J. Elton
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Marcel P. Schilling
- Institute for Automation and Applied Informatics Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Margaux Roux
- Cellenion SASU Bioserra 2, 60 avenue Rockefeller Lyon 69008 France
| | - Pavel A. Levkin
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
- Institute of Organic Chemistry Karlsruhe Institute of Technology Fritz‐Haber Weg 6 Karlsruhe 76131 Germany
| | - Anna A. Popova
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
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4
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Organoids in image-based phenotypic chemical screens. Exp Mol Med 2021; 53:1495-1502. [PMID: 34663938 PMCID: PMC8569209 DOI: 10.1038/s12276-021-00641-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Image-based phenotypic screening relies on the extraction of multivariate information from cells cultured under a large variety of conditions. Technical advances in high-throughput microscopy enable screening in increasingly complex and biologically relevant model systems. To this end, organoids hold great potential for high-content screening because they recapitulate many aspects of parent tissues and can be derived from patient material. However, screening is substantially more difficult in organoids than in classical cell lines from both technical and analytical standpoints. In this review, we present an overview of studies employing organoids for screening applications. We discuss the promises and challenges of small-molecule treatments in organoids and give practical advice on designing, running, and analyzing high-content organoid-based phenotypic screens.
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Jörg M, Madden KS. The right tools for the job: the central role for next generation chemical probes and chemistry-based target deconvolution methods in phenotypic drug discovery. RSC Med Chem 2021; 12:646-665. [PMID: 34124668 PMCID: PMC8152813 DOI: 10.1039/d1md00022e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The reconnection of the scientific community with phenotypic drug discovery has created exciting new possibilities to develop therapies for diseases with highly complex biology. It promises to revolutionise fields such as neurodegenerative disease and regenerative medicine, where the development of new drugs has consistently proved elusive. Arguably, the greatest challenge in readopting the phenotypic drug discovery approach exists in establishing a crucial chain of translatability between phenotype and benefit to patients in the clinic. This remains a key stumbling block for the field which needs to be overcome in order to fully realise the potential of phenotypic drug discovery. Excellent quality chemical probes and chemistry-based target deconvolution techniques will be a crucial part of this process. In this review, we discuss the current capabilities of chemical probes and chemistry-based target deconvolution methods and evaluate the next advances necessary in order to fully support phenotypic screening approaches in drug discovery.
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Affiliation(s)
- Manuela Jörg
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
| | - Katrina S Madden
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
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Berdigaliyev N, Aljofan M. An overview of drug discovery and development. Future Med Chem 2020; 12:939-947. [PMID: 32270704 DOI: 10.4155/fmc-2019-0307] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/18/2020] [Indexed: 01/01/2023] Open
Abstract
A new medicine will take an average of 10-15 years and more than US$2 billion before it can reach the pharmacy shelf. Traditionally, drug discovery relied on natural products as the main source of new drug entities, but was later shifted toward high-throughput synthesis and combinatorial chemistry-based development. New technologies such as ultra-high-throughput drug screening and artificial intelligence are being heavily employed to reduce the cost and the time of early drug discovery, but they remain relatively unchanged. However, are there other potentially faster and cheaper means of drug discovery? Is drug repurposing a viable alternative? In this review, we discuss the different means of drug discovery including their advantages and disadvantages.
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Affiliation(s)
- Nurken Berdigaliyev
- Department of biomedical Science, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan
| | - Mohamad Aljofan
- Department of biomedical Science, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan
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A Strategy to Optimize the Generation of Stable Chromobody Cell Lines for Visualization and Quantification of Endogenous Proteins in Living Cells. Antibodies (Basel) 2019; 8:antib8010010. [PMID: 31544816 PMCID: PMC6640688 DOI: 10.3390/antib8010010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 02/07/2023] Open
Abstract
Single-domain antibodies have emerged as highly versatile nanoprobes for advanced cellular imaging. For real-time visualization of endogenous antigens, fluorescently labelled nanobodies (chromobodies, CBs) are introduced as DNA-encoded expression constructs in living cells. Commonly, CB expression is driven from strong, constitutively active promoters. However, high expression levels are sometimes accompanied by misfolding and aggregation of those intracellular nanoprobes. Moreover, stable cell lines derived from random genomic insertion of CB-encoding transgenes bear the risk of disturbed cellular processes and inhomogeneous CB signal intensities due to gene positioning effects and epigenetic silencing. In this study we propose a strategy to generate optimized CB expressing cell lines. We demonstrate that expression as ubiquitin fusion increases the fraction of intracellularly functional CBs and identified the elongation factor 1α (EF1-α) promoter as highly suited for constitutive CB expression upon long-term cell line cultivation. Finally, we applied a CRISPR/Cas9-based gene editing approach for targeted insertion of CB expression constructs into the adeno-associated virus integration site 1 (AAVS1) safe harbour locus of human cells. Our results indicate that this combinatorial approach facilitates the generation of fully functional and stable CB cell lines for quantitative live-cell imaging of endogenous antigens.
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8
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Functional annotation of chemical libraries across diverse biological processes. Nat Chem Biol 2017; 13:982-993. [PMID: 28759014 PMCID: PMC6056180 DOI: 10.1038/nchembio.2436] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 06/13/2017] [Indexed: 11/08/2022]
Abstract
Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.
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9
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Alsehli H, Gari M, Abuzinadah M, Abuzenadah A. The emerging importance of high content screening for future therapeutics. J Microsc Ultrastruct 2017. [DOI: 10.1016/j.jmau.2017.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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10
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Nierode G, Kwon PS, Dordick JS, Kwon SJ. Cell-Based Assay Design for High-Content Screening of Drug Candidates. J Microbiol Biotechnol 2016; 26:213-25. [PMID: 26428732 DOI: 10.4014/jmb.1508.08007] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To reduce attrition in drug development, it is crucial to consider the development and implementation of translational phenotypic assays as well as decipher diverse molecular mechanisms of action for new molecular entities. High-throughput fluorescence and confocal microscopes with advanced analysis software have simplified the simultaneous identification and quantification of various cellular processes through what is now referred to as highcontent screening (HCS). HCS permits automated identification of modifiers of accessible and biologically relevant targets and can thus be used to detect gene interactions or identify toxic pathways of drug candidates to improve drug discovery and development processes. In this review, we summarize several HCS-compatible, biochemical, and molecular biology-driven assays, including immunohistochemistry, RNAi, reporter gene assay, CRISPR-Cas9 system, and protein-protein interactions to assess a variety of cellular processes, including proliferation, morphological changes, protein expression, localization, post-translational modifications, and protein-protein interactions. These cell-based assay methods can be applied to not only 2D cell culture but also 3D cell culture systems in a high-throughput manner.
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Affiliation(s)
- Gregory Nierode
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul S Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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11
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Kapoor S, Waldmann H, Ziegler S. Novel approaches to map small molecule–target interactions. Bioorg Med Chem 2016; 24:3232-45. [DOI: 10.1016/j.bmc.2016.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 10/24/2022]
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12
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Gfeller D, Zoete V. Protein homology reveals new targets for bioactive small molecules. Bioinformatics 2015; 31:2721-7. [PMID: 25900917 DOI: 10.1093/bioinformatics/btv214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/14/2015] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species. RESULTS Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification. AVAILABILITY AND IMPLEMENTATION Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch. CONTACT david.gfeller@unil.ch or vincent.zoete@isb-sib.ch. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Gfeller
- Department of Fundamental Oncology, Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland and Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, 1015 Lausanne, Switzerland
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Koeberle A, Werz O. Multi-target approach for natural products in inflammation. Drug Discov Today 2014; 19:1871-82. [DOI: 10.1016/j.drudis.2014.08.006] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/11/2014] [Accepted: 08/20/2014] [Indexed: 12/30/2022]
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Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res 2014; 42:W32-8. [PMID: 24792161 PMCID: PMC4086140 DOI: 10.1093/nar/gku293] [Citation(s) in RCA: 817] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. For this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. Recently, large datasets of protein–small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. Here, we introduce SwissTargetPrediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2D and 3D similarity measures with known ligands. Predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. SwissTargetPrediction is accessible free of charge and without login requirement at http://www.swisstargetprediction.ch.
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Affiliation(s)
- David Gfeller
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | - Aurélien Grosdidier
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | - Matthias Wirth
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland Ludwig Institute for Cancer Research, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland Oncology Department, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
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Marsden CJ, Eckersley S, Hebditch M, Kvist AJ, Milner R, Mitchell D, Warwicker J, Marley AE. The Use of Antibodies in Small-Molecule Drug Discovery. ACTA ACUST UNITED AC 2014; 19:829-38. [PMID: 24695620 DOI: 10.1177/1087057114527770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 12/08/2013] [Indexed: 12/17/2022]
Abstract
Antibodies are powerful research tools that can be used in many areas of biology to probe, measure, and perturb various biological structures. Successful drug discovery is dependent on the correct identification of a target implicated in disease, coupled with the successful selection, optimization, and development of a candidate drug. Because of their specific binding characteristics, with regard to specificity, affinity, and avidity, coupled with their amenability to protein engineering, antibodies have become a key tool in drug discovery, enabling the quantification, localization, and modulation of proteins of interest. This review summarizes the application of antibodies and other protein affinity reagents as specific research tools within the drug discovery process.
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17
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Medina-Franco JL, Martinez-Mayorga K, Meurice N. Balancing novelty with confined chemical space in modern drug discovery. Expert Opin Drug Discov 2013; 9:151-65. [DOI: 10.1517/17460441.2014.872624] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Huart AS, Saxty B, Merritt A, Nekulova M, Lewis S, Huang Y, Vojtesek B, Kettleborough C, Hupp TR. A Casein kinase 1/Checkpoint kinase 1 pyrazolo-pyridine protein kinase inhibitor as novel activator of the p53 pathway. Bioorg Med Chem Lett 2013; 23:5578-85. [PMID: 24007918 DOI: 10.1016/j.bmcl.2013.08.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 11/28/2022]
Abstract
Reactivation of the wild-type p53 pathway is one key goal aimed at developing targeted therapeutics in the cancer research field. Although most p53 protein kinases form 'p53-activating' signals, there are few kinases whose action can contribute to the inhibition of p53, as Casein kinase 1 (CK1) and Checkpoint kinase 1 (CHK1). Here we report on a pyrazolo-pyridine analogue showing activity against both CK1 and CHK1 kinases that lead to p53 pathway stabilisation, thus having pharmacological similarities to the p53-activator Nutlin-3. These data demonstrate the emerging potential utility of multivalent kinase inhibitors.
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Affiliation(s)
- Anne-Sophie Huart
- p53 Signal Transduction Group, University of Edinburgh Cancer Research Centre in the Institute of Genetics and Molecular Medicine, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
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Saha SK, Khuda-Bukhsh AR. Molecular approaches towards development of purified natural products and their structurally known derivatives as efficient anti-cancer drugs: current trends. Eur J Pharmacol 2013; 714:239-48. [PMID: 23819913 DOI: 10.1016/j.ejphar.2013.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 06/01/2013] [Accepted: 06/08/2013] [Indexed: 12/14/2022]
Abstract
Several natural products and their derivatives, either in purified or structurally identified form, exhibit immense pharmacological and biological properties, some of them showing considerable anticancer potential. Although the molecular mechanisms of action of some of these products are yet to be elucidated, extensive research in this area continues to generate new data that are clinically exploitable. Recent advancement in molecular biology, high throughput screening, biomarker identifications, target selection and genomic approaches have enabled us to understand salient interactions of natural products and their derivatives with cancer cells vis-à-vis normal cells. In this review we highlight the recent approaches and application of innovative technologies made to improve quality as well as efficiency of structurally identified natural products and their derivatives, particularly in small molecular forms capable of being used in "targeted therapies" in oncology. These products preferentially involve multiple mechanistic pathways and overcome chemo-resistance in tumor types with cumulative action. We also mention briefly a few physico-chemical features that compare natural products with drugs in recent natural product discovery approaches. We further report here a few purified natural products as examples that provide molecular interventions in cancer therapeutics to give the reader a glimpse of the current trends of approach for discovering useful anticancer drugs.
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Affiliation(s)
- Santu Kumar Saha
- Cytogenetics and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani-741235, India
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20
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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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21
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Medina-Franco JL, Giulianotti MA, Welmaker GS, Houghten RA. Shifting from the single to the multitarget paradigm in drug discovery. Drug Discov Today 2013; 18:495-501. [PMID: 23340113 PMCID: PMC3642214 DOI: 10.1016/j.drudis.2013.01.008] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/03/2012] [Accepted: 01/14/2013] [Indexed: 01/30/2023]
Abstract
Increasing evidence that several drug compounds exert their effects through interactions with multiple targets is boosting the development of research fields that challenge the data reductionism approach. In this article, we review and discuss the concepts of drug repurposing, polypharmacology, chemogenomics, phenotypic screening and high-throughput in vivo testing of mixture-based libraries in an integrated manner. These research fields offer alternatives to the current paradigm of drug discovery, from a one target-one drug model to a multiple-target approach. Furthermore, the goals of lead identification are being expanded accordingly to identify not only 'key' compounds that fit with a single-target 'lock', but also 'master key' compounds that favorably interact with multiple targets (i.e. operate a set of desired locks to gain access to the expected clinical effects).
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Affiliation(s)
- José L Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, D.F. 04510, Mexico.
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22
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Kell DB. Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 2013; 280:5957-80. [PMID: 23552054 DOI: 10.1111/febs.12268] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/16/2022]
Abstract
Despite the sequencing of the human genome, the rate of innovative and successful drug discovery in the pharmaceutical industry has continued to decrease. Leaving aside regulatory matters, the fundamental and interlinked intellectual issues proposed to be largely responsible for this are: (a) the move from 'function-first' to 'target-first' methods of screening and drug discovery; (b) the belief that successful drugs should and do interact solely with single, individual targets, despite natural evolution's selection for biochemical networks that are robust to individual parameter changes; (c) an over-reliance on the rule-of-5 to constrain biophysical and chemical properties of drug libraries; (d) the general abandoning of natural products that do not obey the rule-of-5; (e) an incorrect belief that drugs diffuse passively into (and presumably out of) cells across the bilayers portions of membranes, according to their lipophilicity; (f) a widespread failure to recognize the overwhelmingly important role of proteinaceous transporters, as well as their expression profiles, in determining drug distribution in and between different tissues and individual patients; and (g) the general failure to use engineering principles to model biology in parallel with performing 'wet' experiments, such that 'what if?' experiments can be performed in silico to assess the likely success of any strategy. These facts/ideas are illustrated with a reasonably extensive literature review. Success in turning round drug discovery consequently requires: (a) decent systems biology models of human biochemical networks; (b) the use of these (iteratively with experiments) to model how drugs need to interact with multiple targets to have substantive effects on the phenotype; (c) the adoption of polypharmacology and/or cocktails of drugs as a desirable goal in itself; (d) the incorporation of drug transporters into systems biology models, en route to full and multiscale systems biology models that incorporate drug absorption, distribution, metabolism and excretion; (e) a return to 'function-first' or phenotypic screening; and (f) novel methods for inferring modes of action by measuring the properties on system variables at all levels of the 'omes. Such a strategy offers the opportunity of achieving a state where we can hope to predict biological processes and the effect of pharmaceutical agents upon them. Consequently, this should both lower attrition rates and raise the rates of discovery of effective drugs substantially.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester, UK; Manchester Institute of Biotechnology, The University of Manchester, UK
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23
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Schenone M, Dančík V, Wagner BK, Clemons PA. Target identification and mechanism of action in chemical biology and drug discovery. Nat Chem Biol 2013; 9:232-40. [PMID: 23508189 PMCID: PMC5543995 DOI: 10.1038/nchembio.1199] [Citation(s) in RCA: 634] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/28/2013] [Indexed: 12/12/2022]
Abstract
Target-identification and mechanism-of-action studies have important roles in small-molecule probe and drug discovery. Biological and technological advances have resulted in the increasing use of cell-based assays to discover new biologically active small molecules. Such studies allow small-molecule action to be tested in a more disease-relevant setting at the outset, but they require follow-up studies to determine the precise protein target or targets responsible for the observed phenotype. Target identification can be approached by direct biochemical methods, genetic interactions or computational inference. In many cases, however, combinations of approaches may be required to fully characterize on-target and off-target effects and to understand mechanisms of small-molecule action.
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Affiliation(s)
- Monica Schenone
- Proteomics Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Vlado Dančík
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Bridget K Wagner
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Paul A Clemons
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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24
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Abstract
Contemporary drug target discovery relies on a continuum of genetic and chemical-based screening technologies. These approaches conflate pharmaceutical and genetic principles, providing a conceptual platform that links dominant genetics with drug action. Thus, phenotypic genetic screens using vector-expressed dominant genetic effectors - trans-acting molecules that modulate gene function, such as peptides or RNA interference triggers - can reveal genes whose inhibition engenders a therapeutic effect. The correlation of this genetic inhibition with a specific protein activity defines a drug target candidate. Retroviruses provide a unique opportunity to stably deliver a variety of dominant genetic effectors to mammalian cells in a flexible predetermined fashion and are a favoured system for phenotypic screening. Here, the authors review recent innovations and approaches to therapeutic target discovery using retroviral vectors.
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Affiliation(s)
- Magnus Blø
- University of Bergen, Bergen, Department of Biomedicine, Jonas Lies vei 91, N-5009, Bergen, Norway +47 55 58 67 76 ; +47 55 58 63 60 ;
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25
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Xia X, Wong ST. Concise review: a high-content screening approach to stem cell research and drug discovery. Stem Cells 2013; 30:1800-7. [PMID: 22821636 DOI: 10.1002/stem.1168] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
High-throughput screening (HTS) is a technology widely used for early stages of drug discovery in pharmaceutical and biotechnology industries. Recent hardware and software improvements have enabled HTS to be used in combination with subcellular resolution microscopy, resulting in cell image-based HTS, called high-content screening (HCS). HCS allows the acquisition of deeper knowledge at a single-cell level such that more complex biological systems can be studied in a high-throughput manner. The technique is particularly well-suited for stem cell research and drug discovery, which almost inevitably require single-cell resolutions for the detection of rare phenotypes in heterogeneous cultures. With growing availability of facilities, instruments, and reagent libraries, small-to-moderate scale HCS can now be carried out in regular academic labs. We envision that the HCS technique will play an increasing role in both basic mechanism study and early-stage drug discovery on stem cells. Here, we review the development of HCS technique and its past application on stem cells and discuss possible future developments.
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Affiliation(s)
- Xiaofeng Xia
- Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Houston, TX 77030, USA.
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Cortes-Ciriano I, Koutsoukas A, Abian O, Glen RC, Velazquez-Campoy A, Bender A. Experimental validation of in silico target predictions on synergistic protein targets. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20286g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Two relatively recent trends have become apparent in current early stage drug discovery settings: firstly, a revival of phenotypic screening strategies and secondly, the increasing acceptance that some drugs work by modulating multiple targets in parallel (‘multi-target drugs’).
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Affiliation(s)
- Isidro Cortes-Ciriano
- Institute of Biocomputation and Physics of Complex Systems (BIFI)
- Unidad Asociada IQFR-CSIC-BIFI, and Department of Biochemistry and Molecular and Cellular Biology
- Universidad de Zaragoza
- Zaragoza
- Spain
| | - Alexios Koutsoukas
- Unilever Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI)
- Unidad Asociada IQFR-CSIC-BIFI, and Department of Biochemistry and Molecular and Cellular Biology
- Universidad de Zaragoza
- Zaragoza
- Spain
| | - Robert C. Glen
- Unilever Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI)
- Unidad Asociada IQFR-CSIC-BIFI, and Department of Biochemistry and Molecular and Cellular Biology
- Universidad de Zaragoza
- Zaragoza
- Spain
| | - Andreas Bender
- Unilever Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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27
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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28
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Adams WJ, García-Cardeña G. Novel stem cell-based drug discovery platforms for cardiovascular disease. ACTA ACUST UNITED AC 2012; 17:1117-27. [PMID: 22853930 DOI: 10.1177/1087057112454741] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The complexity and diversity of many human diseases pose significant hurdles to the development of novel therapeutics. New scientific and technological advances, such as pharmacogenetics, provide valuable frameworks for understanding genetic predisposition to disease and tools for diagnosis and drug development. However, another framework is emerging based on recent scientific advances, one we suggest to call pharmacoempirics. Pharmacoempirics takes advantage of merging two nascent fields: first, the generation of induced pluripotent stem cells, which are differentiated into mature cell types and represent patient-specific genetic backgrounds, and, second, bioengineering advances allowing sophisticated re-creation of human pathophysiology in laboratory settings. The combination of these two innovative technologies should allow new experimentation on disease biology and drug discovery, efficacy, and toxicology unencumbered by hypothesis generation and testing. In this review, we discuss the challenges and promises of this exciting new type of discovery platform and outline its implementation for cardiovascular drug discovery.
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Affiliation(s)
- William J Adams
- Program in Developmental and Regenerative Biology, Harvard Medical School, Boston, MA, USA.
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29
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Lu Q, Quinn AM, Patel MP, Semus SF, Graves AP, Bandyopadhyay D, Pope AJ, Thrall SH. Perspectives on the discovery of small-molecule modulators for epigenetic processes. ACTA ACUST UNITED AC 2012; 17:555-71. [PMID: 22392809 DOI: 10.1177/1087057112437763] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Epigenetic gene regulation is a critical process controlling differentiation and development, the malfunction of which may underpin a variety of diseases. In this article, we review the current landscape of small-molecule epigenetic modulators including drugs on the market, key compounds in clinical trials, and chemical probes being used in epigenetic mechanistic studies. Hit identification strategies for the discovery of small-molecule epigenetic modulators are summarized with respect to writers, erasers, and readers of histone marks. Perspectives are provided on opportunities for new hit discovery approaches, some of which may define the next generation of therapeutic intervention strategies for epigenetic processes.
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Affiliation(s)
- Quinn Lu
- GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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30
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Walker SL, Ariga J, Mathias JR, Coothankandaswamy V, Xie X, Distel M, Köster RW, Parsons MJ, Bhalla KN, Saxena MT, Mumm JS. Automated reporter quantification in vivo: high-throughput screening method for reporter-based assays in zebrafish. PLoS One 2012; 7:e29916. [PMID: 22238673 PMCID: PMC3251595 DOI: 10.1371/journal.pone.0029916] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 12/06/2011] [Indexed: 11/18/2022] Open
Abstract
Reporter-based assays underlie many high-throughput screening (HTS) platforms, but most are limited to in vitro applications. Here, we report a simple whole-organism HTS method for quantifying changes in reporter intensity in individual zebrafish over time termed, Automated Reporter Quantification in vivo (ARQiv). ARQiv differs from current “high-content” (e.g., confocal imaging-based) whole-organism screening technologies by providing a purely quantitative data acquisition approach that affords marked improvements in throughput. ARQiv uses a fluorescence microplate reader with specific detection functionalities necessary for robust quantification of reporter signals in vivo. This approach is: 1) Rapid; achieving true HTS capacities (i.e., >50,000 units per day), 2) Reproducible; attaining HTS-compatible assay quality (i.e., Z'-factors of ≥0.5), and 3) Flexible; amenable to nearly any reporter-based assay in zebrafish embryos, larvae, or juveniles. ARQiv is used here to quantify changes in: 1) Cell number; loss and regeneration of two different fluorescently tagged cell types (pancreatic beta cells and rod photoreceptors), 2) Cell signaling; relative activity of a transgenic Notch-signaling reporter, and 3) Cell metabolism; accumulation of reactive oxygen species. In summary, ARQiv is a versatile and readily accessible approach facilitating evaluation of genetic and/or chemical manipulations in living zebrafish that complements current “high-content” whole-organism screening methods by providing a first-tier in vivo HTS drug discovery platform.
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Affiliation(s)
- Steven L. Walker
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Junko Ariga
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | | | - Veena Coothankandaswamy
- Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Xiayang Xie
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Martin Distel
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Reinhard W. Köster
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael J. Parsons
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kapil N. Bhalla
- Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Meera T. Saxena
- Luminomics, Inc., Augusta, Georgia, United States of America
| | - Jeff S. Mumm
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
- * E-mail:
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31
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Jacques RM, Fieller NR, Ainscow EK. A classification updating procedure motivated by high-content screening data. J Appl Stat 2012. [DOI: 10.1080/02664763.2011.580335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Chen PC, Huang YY, Juang JL. MEMS microwell and microcolumn arrays: novel methods for high-throughput cell-based assays. LAB ON A CHIP 2011; 11:3619-25. [PMID: 21904742 DOI: 10.1039/c0lc00696c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Although the cell-based assay is becoming more popular for high throughput drug screening and the functional characterization of disease-associated genes, most researchers in these areas do not use it because it is a complex and expensive process. We wanted to create a simple method of performing an on-chip cell-based assay. To do this, we used micro-electro-mechanical systems (MEMS) to fabricate a microwell array chip comprised of a glass substrate covered with a photoresist film patterned to form multiple microwells and tested it in two reverse transfection experiments, an exogenous gene expression study and an endogenous gene knockdown study. It was used effectively in both. Then, using the same MEMS technology, we fabricated a complementary microcolumn array to be used as a drug carrier device to topically apply drugs to cells cultured in the microwell array. We tested the effectiveness of microwell-microcolumn on-chip cell-based assay by using it in experiments to identify epidermal growth factor receptor (EGFR) activity inhibitors, for which it was found to provide effective high throughput and high content functional screening. In conclusion, this new method of cell-based screening proved to be a simple and efficient method of characterizing gene function and discovering drug leads.
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Affiliation(s)
- Po-Cheng Chen
- Institute of Biomedical Engineering, College of Engineering, College of Medicine, National Taiwan University, No.1, Sec.1, Jen-Ai Road, Taipei, 100, Taiwan
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33
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Eglen R, Reisine T. Primary cells and stem cells in drug discovery: emerging tools for high-throughput screening. Assay Drug Dev Technol 2010; 9:108-24. [PMID: 21186936 DOI: 10.1089/adt.2010.0305] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many drug discovery screening programs employ immortalized cells, recombinantly engineered to express a defined molecular target. Several technologies are now emerging that render it feasible to employ more physiologically, and clinically relevant, cell phenotypes. Consequently, numerous approaches use primary cells, which retain many functions seen in vivo, as well as endogenously expressing the target of interest. Furthermore, stem cells, of either embryonic or adult origin, as well as those derived from differentiated cells, are now finding a place in drug discovery. Collectively, these cells are expanding the utility of authentic human cells, either as screening tools or as therapeutics, as well as providing cells derived directly from patients. Nonetheless, the growing use of phenotypically relevant cells (including primary cells or stem cells) is not without technical difficulties, particularly when their envisioned use lies in high-throughput screening (HTS) protocols. In particular, the limited availability of homogeneous primary or stem cell populations for HTS mandates that novel technologies be developed to accelerate their adoption. These technologies include detection of responses with very few cells as well as protocols to generate cell lines in abundant, homogeneous populations. In parallel, the growing use of changes in cell phenotype as the assay readout is driving greater use of high-throughput imaging techniques in screening. Taken together, the greater availability of novel primary and stem cell phenotypes as well as new detection technologies is heralding a new era of cellular screening. This convergence offers unique opportunities to identify drug candidates for disorders at which few therapeutics are presently available.
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Affiliation(s)
- Richard Eglen
- Bio-discovery, PerkinElmer, Waltham, Massachusetts 02451-1457, USA.
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34
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Jain S, Heutink P. From single genes to gene networks: high-throughput-high-content screening for neurological disease. Neuron 2010; 68:207-17. [PMID: 20955929 DOI: 10.1016/j.neuron.2010.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2010] [Indexed: 11/30/2022]
Abstract
Neuronal development, function, and the subsequent degeneration of the brain are still an enigma in both the normal and pathologic states, and there is an urgent need to find better targets for developing therapeutic intervention. Current techniques to deconstruct the architecture of brain and disease-related pathways are best suited for following up on single genes but would take an impractical amount of time for the leads from the current wave of genetic and genomic data. New technical developments have made combined high-throughput-high-content (HT-HC) cellular screens possible, which have the potential to contextualize the information, gathered from a combination of genetic and genomic approaches, into networks and functional biology and can be utilized for the identification of therapeutic targets. Herein we discuss the potential impact of HT-HC cellular screens on medical neuroscience.
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Affiliation(s)
- Shushant Jain
- Department of Clinical Genetics, VU University Medical Center Amsterdam, The Netherlands
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35
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Soleilhac E, Nadon R, Lafanechere L. High-content screening for the discovery of pharmacological compounds: advantages, challenges and potential benefits of recent technological developments. Expert Opin Drug Discov 2010; 5:135-44. [DOI: 10.1517/17460440903544456] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Adding more content to screening: reactivation of FOXO as a therapeutic strategy. Clin Transl Oncol 2009; 11:651-8. [DOI: 10.1007/s12094-009-0420-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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37
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Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling. Curr Opin Chem Biol 2009; 13:539-48. [PMID: 19825513 DOI: 10.1016/j.cbpa.2009.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 09/13/2009] [Accepted: 09/16/2009] [Indexed: 12/11/2022]
Abstract
Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe-discovery and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of 'virtual' profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe-discovery and drug-discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections.
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38
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Paslay JW, Morin JE, Harrison RK. High Throughput Screening in the Twenty-First Century. TOPICS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1007/7355_2009_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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39
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Abstract
Traditionally, the objective of high-throughput screening (HTS) has been to identify compounds that interact with a defined target protein as the starting point for a chemistry lead optimisation programme. To enable this it has become commonplace to express the drug target in a recombinant expression system and use this reagent as the source of the biological material to support the HTS campaign. In this chapter we describe an alternative HTS methodology with the objective of identifying compounds that mediate a change in a defined physiological end point as a consequence of compound activity in human primary cells. Rather than screening at a defined molecular target, such "phenotypic" screens permit the identification of compounds that act at any target protein within the cell to regulate the end point under study. As an example of such a screen we will describe an HTS campaign to identify compounds that promote the production of the cytokine interferon-alpha from human blood peripheral mononuclear cells (PBMCs) isolated from whole blood. We describe the procedures required to obtain and purify human PBMCs and the electrochemiluminescence-based assay technology used to detect interferon-alpha and highlight the challenges associated with this screening paradigm.
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Affiliation(s)
- Angela Dunne
- Screening and Compound Profiling Department, GlaxoSmithKline, Harlow, Essex, UK
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40
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Abstract
Cell-based assays represent approximately half of all high-throughput screens (HTS) currently performed. Here we review the history and status of HTS, and summarize some of the challenges and benefits associated with the use of cell-based assays in HTS, drawing upon themes that will reemerge in subsequent chapters in this book. Approaches for successful experimental design and execution of cell-based HTS are introduced, including strategies for assay development, implementation of primary and secondary screens, and target identification. In doing so, we hope to provide a comprehensive review of the cell-based HTS process and an introduction to the methodologies and techniques described in this book.
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Affiliation(s)
- W Frank An
- Chemical Biology Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
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41
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Shan L, Zhang R, Zhang W, Lee E, Sridhar R, Snyderwine EG, Wang PC. Image-based evaluation of the molecular events underlying HC11 mammary epithelial cell differentiation. Anal Biochem 2008; 382:122-8. [PMID: 18722992 DOI: 10.1016/j.ab.2008.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 08/01/2008] [Indexed: 01/27/2023]
Abstract
We have developed an image-based technique for signal pathway analysis, target validation, and compound screening related to mammary epithelial cell differentiation. This technique used the advantages of optical imaging and the HC11-Lux model system. The HC11-Lux cell line is a subclone of HC11 mammary epithelial cells transfected stably with a luciferase construct of the beta-casein gene promoter (p-344/-1betac-Lux). The promoter activity was imaged optically in real time following lactogenic induction. The imaging signal intensity was closely correlated with that measured using a luminometer following protein extraction (R=0.99, P<0.0001) and consistent with the messenger RNA (mRNA) level of the endogenous beta -casein gene. Using this technique, we examined the roles of JAK2/Stat5A, Raf-1/MEK/MAKP, and PI3K/Akt signal pathways with respect to differentiation. The imaging studies showed that treatment of the cells with epidermal growth factor (EGF), AG490 (JAK2-specific inhibitor), and LY294002 (PI3K-specific inhibitor) blocked lactogenic differentiation in a dose-dependent manner. PD98059 (MEK-specific inhibitor) could reverse EGF-mediated differentiation arrest. These results indicate that these pathways are essential in cell differentiation. This simple, sensitive, and reproducible technique permits visualization and real-time evaluation of the molecular events related to milk protein production. It can be adopted for high-throughput screening of small molecules for their effects on mammary epithelial cell growth, differentiation, and carcinogenesis.
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Affiliation(s)
- Liang Shan
- Department of Radiology, Howard University, Washington, DC 20060, USA
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42
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Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nat Chem Biol 2007; 4:59-68. [PMID: 18066055 DOI: 10.1038/nchembio.2007.53] [Citation(s) in RCA: 277] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 10/15/2007] [Indexed: 12/16/2022]
Abstract
High-content screening is transforming drug discovery by enabling simultaneous measurement of multiple features of cellular phenotype that are relevant to therapeutic and toxic activities of compounds. High-content screening studies typically generate immense datasets of image-based phenotypic information, and how best to mine relevant phenotypic data is an unsolved challenge. Here, we introduce factor analysis as a data-driven tool for defining cell phenotypes and profiling compound activities. This method allows a large data reduction while retaining relevant information, and the data-derived factors used to quantify phenotype have discernable biological meaning. We used factor analysis of cells stained with fluorescent markers of cell cycle state to profile a compound library and cluster the hits into seven phenotypic categories. We then compared phenotypic profiles, chemical similarity and predicted protein binding activities of active compounds. By integrating these different descriptors of measured and potential biological activity, we can effectively draw mechanism-of-action inferences.
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43
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Abstract
Recognition of some of the limitations of target-based drug discovery has recently led to the renaissance of a more holistic approach in which complex biological systems are investigated for phenotypic changes upon exposure to small molecules. The subsequent identification of the molecular targets that underlie an observed phenotypic response--termed target deconvolution--is an important aspect of current drug discovery, as knowledge of the molecular targets will greatly aid drug development. Here, the broad panel of experimental strategies that can be applied to target deconvolution is critically reviewed.
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Affiliation(s)
- Michael J Evans
- The Skaggs Institute for Chemical Biology and Departments of Cell Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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45
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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46
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Pollard S, Conti L, Smith A. Exploitation of adherent neural stem cells in basic and applied neurobiology. Regen Med 2007; 1:111-8. [PMID: 17465825 DOI: 10.2217/17460751.1.1.111] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evidence for neurogenesis within the adult brain has challenged traditional views that this tissue is devoid of stem cell activity. This raises the possibility of introducing new cells through cell transplantation or stimulating endogenous neurogenesis as routes to treat disease and injury. Fetal and adult neural stem/progenitor cells can be isolated and expanded in vitro and might provide a cell source for such transplantations. Embryonic stem (ES) cells, which can generate any adult tissues, offer an alternative unlimited supply of neural tissue. We recently showed that both mouse and human ES cells can be converted to adherent neural stem (NS) cell lines [1] . Here we discuss the benefits of working with NS cell lines and how they might be exploited for studies of fundamental cellular processes, such as neuronal specification and differentiation. NS cells also serve as versatile models of disease processes, either through genetic manipulations or direct isolation from disease carriers and can be exploited in pharmaceutical drug screening. Longer term, NS cells offer an opportunity to rigorously test the efficacy of cell-based therapies and develop strategies for tissue engineering.
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Affiliation(s)
- Steven Pollard
- University of Edinburgh, Centre Development in Stem Cell Biology, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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47
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Abstract
Driven by past successes and the detailed knowledge of signalling cascades and physiological processes, G-protein-coupled receptors are taking a prominent place in the portfolios of many pharmaceutical companies. To successfully address this target class, scientists need not only a good understanding of the specific receptor under investigation, but also the right tools from assay technology, reagent production to a hit-to-lead process that acknowledges the importance of parameters beyond potency and embraces the gain in knowledge of the last decade. This manuscripts attempts to summarise some of the changes and progress made across the pharmaceutical industry to design an efficient and effective strategy for finding and optimising small molecules modulating the activity of GPCRs.
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Affiliation(s)
- A Sewing
- Primary Pharmacology Group, Pfizer PDGRD, IPC 580, Ramsgate Road, CT13 9NJ Sandwich, UK.
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48
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Evans MJ, Morris GM, Wu J, Olson AJ, Sorensen EJ, Cravatt BF. Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides. MOLECULAR BIOSYSTEMS 2007; 3:495-506. [PMID: 17579775 DOI: 10.1039/b705113a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We recently reported the pharmacological screening of a natural products-inspired library of spiroepoxide probes, resulting in the discovery of an agent MJE3 that displayed anti-proliferative effects in human breast cancer cells. MJE3 was found to covalently inactivate phosphoglycerate mutase-1 (PGAM1), a glycolytic enzyme with postulated roles in cancer cell metabolism and proliferation. Considering that MJE3 is one of the first examples of a cell-permeable, small-molecule inhibitor for PGAM1, we pursued a detailed examination of its mechanism and structural requirements for covalent inactivation. MJE3 was found to label PGAM1 on lysine-100, a conserved active site residue implicated in substrate recognition. Structural features of MJE3 important for PGAM1 labeling included two key recognition elements (an indole ring and carboxylic acid), the stereochemical orientation of the spiroepoxide, and presentation of these various binding/reactive groups on a rigid cyclohexane scaffold. Modeling studies of the docked MJE3-PGAM1 complex provide a structural rationale for these stringent requirements. Overall, these studies indicate that a special combination of binding and reactive elements are united in the MJE3 structure to inactivate PGAM1. More generally, our findings provide further evidence that useful pharmacological tools can emerge from screening structurally diverse libraries of protein-reactive probes.
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Affiliation(s)
- Michael J Evans
- The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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49
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Emre N, Coleman R, Ding S. A chemical approach to stem cell biology. Curr Opin Chem Biol 2007; 11:252-8. [PMID: 17493865 DOI: 10.1016/j.cbpa.2007.04.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Accepted: 04/30/2007] [Indexed: 11/25/2022]
Abstract
Small molecule libraries have been used successfully to probe several biological systems. Recent work has translated these successes across to the field of stem cell biology. Stem cells hold promise for both modeling of early development as well as having therapeutic potential. Enhanced understanding of the molecular mechanisms that control stem cell fates as well as an improved ability to manipulate cell populations are required. Known mechanistic chemical compounds have been used with stem cells to accomplish these two goals. More recently, through the utilization of high fitness libraries in phenotype-based screens, several small molecules that control self-renewal and differentiation in stem cells have been identified. These small molecules provide useful chemical tools for both basic research and practical applications.
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Affiliation(s)
- Nil Emre
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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50
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Paran Y, Ilan M, Kashman Y, Goldstein S, Liron Y, Geiger B, Kam Z. High-throughput screening of cellular features using high-resolution light-microscopy; Application for profiling drug effects on cell adhesion. J Struct Biol 2007; 158:233-43. [PMID: 17321150 DOI: 10.1016/j.jsb.2006.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 08/29/2006] [Accepted: 12/18/2006] [Indexed: 11/17/2022]
Abstract
High-resolution light-microscopy and high-throughput screening are two essential methodologies for characterizing cellular phenotypes. Optimally combining these methodologies in cell-based screening to test detailed molecular and cellular responses to multiple perturbations constitutes a major challenge. Here we describe the development and application of a screening microscope platform that automatically acquires and interprets sub-micron resolution images at fast rates. The analysis pipeline is based on the quantification of multiple subcellular features and statistical comparisons of their distributions in treated vs. control cells. Using this platform, we screened 2200 natural extracts for their effects on the fine structure and organization of focal adhesions. This screen identified 15 effective extracts whose fractionation and characterization were further analyzed using the same microscope system. The significance of combining resolution, throughput and multi-parametric analyses for biomedical research and drug discovery is discussed.
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Affiliation(s)
- Yael Paran
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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