51
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Saxena C. Identification of protein binding partners of small molecules using label-free methods. Expert Opin Drug Discov 2016; 11:1017-25. [DOI: 10.1080/17460441.2016.1227316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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McGown A, Shaw DPJ, Ramesh T. ZNStress: a high-throughput drug screening protocol for identification of compounds modulating neuronal stress in the transgenic mutant sod1G93R zebrafish model of amyotrophic lateral sclerosis. Mol Neurodegener 2016; 11:56. [PMID: 27460825 PMCID: PMC4962399 DOI: 10.1186/s13024-016-0122-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease with death on average within 2–3 years of symptom onset. Mutations in superoxide dismutase 1 (SOD1) have been identified to cause ALS. Riluzole, the only neuroprotective drug for ALS provides life extension of only 3 months on average. Thishighlights the need for compound screening in disease models to identify new neuroprotective therapies for this disease. Zebrafish is an emerging model system that is well suited for the study of diseasepathophysiology and also for high throughput (HT) drug screening. The mutant sod1 zebrafish model of ALS mimics the hallmark features of ALS. Using a fluorescence based readout of neuronal stress, we developed a high throughput (HT) screen to identify neuroprotective compounds. Results Here we show that the zebrafish screen is a robust system that can be used to rapidly screen thousands ofcompounds and also demonstrate that riluzole is capable of reducing neuronal stress in this model system. The screen shows optimal quality control, maintaining a high sensitivity and specificity withoutcompromising throughput. Most importantly, we demonstrate that many compounds previously failed in human clinical trials, showed no stress reducing activity in the zebrafish assay. Conclusion We conclude that HT drug screening using a mutant sod1 zebrafish is a reliable model system which supplemented with secondary assays would be useful in identifying drugs with potential for neuroprotective efficacy in ALS. Electronic supplementary material The online version of this article (doi:10.1186/s13024-016-0122-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander McGown
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385A Glossop Road, Sheffield, UK
| | - Dame Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385A Glossop Road, Sheffield, UK
| | - Tennore Ramesh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385A Glossop Road, Sheffield, UK.
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Abstract
Phenotypic drug discovery (PDD) strategies are defined by screening and selection of hit or lead compounds based on quantifiable phenotypic endpoints without prior knowledge of the drug target. We outline the challenges associated with traditional phenotypic screening strategies and propose solutions and new opportunities to be gained by adopting modern PDD technologies. We highlight both historical and recent examples of approved drugs and new drug candidates discovered by modern phenotypic screening. Finally, we offer a prospective view of a new era of PDD underpinned by a wealth of technology advances in the areas of in vitro model development, high-content imaging and image informatics, mechanism-of-action profiling and target deconvolution.
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Trindade RV, Pinto AFM, Santos DS, Bizarro CV. Pulse Proteolysis and Precipitation for Target Identification. J Proteome Res 2016; 15:2236-45. [DOI: 10.1021/acs.jproteome.6b00214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rogério V. Trindade
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Antônio F. M. Pinto
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diógenes S. Santos
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano V. Bizarro
- Centro
de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto
Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A. Av. Ipiranga-TECNOPUC-Prédio 92A 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
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Yang HT, Yang H, Chiang JH, Wang SJ. Translating genomic sequences into antibody efficacy and safety against influenza toward clinical trial outcomes: a case study. Drug Discov Today 2016; 21:1664-1671. [PMID: 27319290 DOI: 10.1016/j.drudis.2016.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/26/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022]
Abstract
Antibodies (Abs) are regarded as a newly emerging form of therapeutics that can provide passive protection against influenza. Although the application of genomics in clinics has increased dramatically, the number of therapeutics available for the treatment of many diseases remains insufficient. To translate genomics into medicines, we established a computational workflow to reconstruct 3D structures of hemagglutinin [HA, antigen (Ag)] and Ab for modeling Ab-HA interactions, based on their protein sequences. This platform was capable of testing the validity of bioinformatics predictions against viral neutralization titers for four Abs: CH65, CR8020, C05, and 5J8. By considering off-target effects, CR8020, the only successful candidate in clinical trials, was prospectively identified. Our approach could facilitate the discovery of Ab drugs against infectious diseases.
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Affiliation(s)
- Hsih-Te Yang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan; Institute of Oral Medicine, National Cheng Kung University College of Medicine, Taiwan.
| | - Hong Yang
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Jung-Hsien Chiang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan
| | - Shih-Jon Wang
- Department of Bioscience Technology, Chang Jung Christian University, Taiwan
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Caicedo JC, Singh S, Carpenter AE. Applications in image-based profiling of perturbations. Curr Opin Biotechnol 2016; 39:134-142. [PMID: 27089218 DOI: 10.1016/j.copbio.2016.04.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022]
Abstract
A dramatic shift has occurred in how biologists use microscopy images. Whether experiments are small-scale or high-throughput, automatically quantifying biological properties in images is now widespread. We see yet another revolution under way: a transition towards using automated image analysis to not only identify phenotypes a biologist specifically seeks to measure ('screening') but also as an unbiased and sensitive tool to capture a wide variety of subtle features of cell (or organism) state ('profiling'). Mapping similarities among samples using image-based (morphological) profiling has tremendous potential to transform drug discovery, functional genomics, and basic biological research. Applications include target identification, lead hopping, library enrichment, functionally annotating genes/alleles, and identifying small molecule modulators of gene activity and disease-specific phenotypes.
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Affiliation(s)
- Juan C Caicedo
- Imaging Platform of the Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, USA; Fundación Universitaria Konrad Lorenz, Bogotá, Colombia
| | - Shantanu Singh
- Imaging Platform of the Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform of the Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, USA.
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CETSA: a target engagement assay with potential to transform drug discovery. Future Med Chem 2016; 7:975-8. [PMID: 26062395 DOI: 10.4155/fmc.15.50] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Vincent F, Loria P, Pregel M, Stanton R, Kitching L, Nocka K, Doyonnas R, Steppan C, Gilbert A, Schroeter T, Peakman MC. Developing predictive assays: the phenotypic screening "rule of 3". Sci Transl Med 2016; 7:293ps15. [PMID: 26109101 DOI: 10.1126/scitranslmed.aab1201] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phenotypic drug discovery approaches can positively affect the translation of preclinical findings to patients. However, not all phenotypic assays are created equal. A critical question then follows: What are the characteristics of the optimal assays? We analyze this question and propose three specific criteria related to the disease relevance of the assay-system, stimulus, and end point-to help design the most predictive phenotypic assays.
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Affiliation(s)
- Fabien Vincent
- Hit Discovery and Lead Profiling, Pfizer, Groton, CT 06340, USA.
| | - Paula Loria
- Hit Discovery and Lead Profiling, Pfizer, Groton, CT 06340, USA
| | - Marko Pregel
- Rare Diseases Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Robert Stanton
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT 06340, USA
| | | | - Karl Nocka
- Immunology and Inflammation Research Unit, Pfizer, Cambridge, MA 02139, USA
| | - Regis Doyonnas
- Hit Discovery and Lead Profiling, Pfizer, Groton, CT 06340, USA
| | - Claire Steppan
- Hit Discovery and Lead Profiling, Pfizer, Groton, CT 06340, USA
| | - Adam Gilbert
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT 06340, USA
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Fraietta I, Gasparri F. The development of high-content screening (HCS) technology and its importance to drug discovery. Expert Opin Drug Discov 2016; 11:501-14. [PMID: 26971542 DOI: 10.1517/17460441.2016.1165203] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION High-content screening (HCS) was introduced about twenty years ago as a promising analytical approach to facilitate some critical aspects of drug discovery. Its application has spread progressively within the pharmaceutical industry and academia to the point that it today represents a fundamental tool in supporting drug discovery and development. AREAS COVERED Here, the authors review some of significant progress in the HCS field in terms of biological models and assay readouts. They highlight the importance of high-content screening in drug discovery, as testified by its numerous applications in a variety of therapeutic areas: oncology, infective diseases, cardiovascular and neurodegenerative diseases. They also dissect the role of HCS technology in different phases of the drug discovery pipeline: target identification, primary compound screening, secondary assays, mechanism of action studies and in vitro toxicology. EXPERT OPINION Recent advances in cellular assay technologies, such as the introduction of three-dimensional (3D) cultures, induced pluripotent stem cells (iPSCs) and genome editing technologies (e.g., CRISPR/Cas9), have tremendously expanded the potential of high-content assays to contribute to the drug discovery process. Increasingly predictive cellular models and readouts, together with the development of more sophisticated and affordable HCS readers, will further consolidate the role of HCS technology in drug discovery.
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Affiliation(s)
- Ivan Fraietta
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
| | - Fabio Gasparri
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
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Šileikytė J, Forte M. Shutting down the pore: The search for small molecule inhibitors of the mitochondrial permeability transition. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1197-1202. [PMID: 26924772 DOI: 10.1016/j.bbabio.2016.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 01/31/2023]
Abstract
The mitochondrial permeability transition pore (PTP) is now recognized as playing a key role in a wide variety of human diseases whose common pathology may be based in mitochondrial dysfunction. Recently, PTP assays have been adapted to high-throughput screening approaches to identify small molecules specifically inhibiting the PTP. Following extensive secondary chemistry, the most potent inhibitors of the PTP described to date have been developed. This review will provide an overview of each of these screening efforts, use of resulting compounds in animal models of PTP-based diseases, and problems that will require further study. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Justina Šileikytė
- Department of Biomedical Sciences, University of Padova, Padova I-35131, Italy
| | - Michael Forte
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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62
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Reichman M, Simpson PB. Open innovation in early drug discovery: roadmaps and roadblocks. Drug Discov Today 2015; 21:779-88. [PMID: 26743597 DOI: 10.1016/j.drudis.2015.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/26/2015] [Accepted: 12/21/2015] [Indexed: 01/16/2023]
Abstract
Open innovation in pharmaceutical R&D evolved from a triple helix of convergent paradigm shifts in academic, industrial and government research sectors. The birth of the biotechnology sector catalyzed shifts in location dynamics that led to the first wave of open innovation in pharmaceutical R&D between big pharma and startup companies. The National Institutes of Health (NIH) Roadmap was a crucial inflection point that set the stage for a new wave of open innovation models between pharmaceutical companies and universities that have the potential to transform the pharmaceutical R&D landscape. We highlight the attributes of leading protected open innovation models that foster the sharing of proprietary small molecule collections by lowering the risk of premature escape of intellectual property, particularly structure-activity data.
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Affiliation(s)
- Melvin Reichman
- Lankenau Institute for Medical Research, Chemical Genomics Center, 100 Lancaster Ave, Wynnewood, PA, USA.
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63
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Stadler M, Walter S, Walzl A, Kramer N, Unger C, Scherzer M, Unterleuthner D, Hengstschläger M, Krupitza G, Dolznig H. Increased complexity in carcinomas: Analyzing and modeling the interaction of human cancer cells with their microenvironment. Semin Cancer Biol 2015; 35:107-24. [DOI: 10.1016/j.semcancer.2015.08.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 02/08/2023]
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Schirle M, Jenkins JL. Identifying compound efficacy targets in phenotypic drug discovery. Drug Discov Today 2015; 21:82-89. [PMID: 26272035 DOI: 10.1016/j.drudis.2015.08.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/10/2015] [Accepted: 08/03/2015] [Indexed: 12/30/2022]
Abstract
The identification of the efficacy target(s) for hits from phenotypic compound screens remains a key step to progress compounds into drug development. In addition to efficacy targets, the characterization of epistatic proteins influencing compound activity often facilitates the elucidation of the underlying mechanism of action; and, further, early determination of off-targets that cause potentially unwanted secondary phenotypes helps in assessing potential liabilities. This short review discusses the most important technologies currently available for characterizing the direct and indirect target space of bioactive compounds following phenotypic screening. We present a comprehensive strategy employing complementary approaches to balance individual technology strengths and weaknesses.
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Affiliation(s)
- Markus Schirle
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Jeremy L Jenkins
- Developmental & Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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65
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Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:689-707. [PMID: 25805180 PMCID: PMC4606936 DOI: 10.1177/1087057115578273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022]
Abstract
Modern flow cytometers can make optical measurements of 10 or more parameters per cell at tens of thousands of cells per second and more than five orders of magnitude dynamic range. Although flow cytometry is used in most drug discovery stages, "sip-and-spit" sampling technology has restricted it to low-sample-throughput applications. The advent of HyperCyt sampling technology has recently made possible primary screening applications in which tens of thousands of compounds are analyzed per day. Target-multiplexing methodologies in combination with extended multiparameter analyses enable profiling of lead candidates early in the discovery process, when the greatest numbers of candidates are available for evaluation. The ability to sample small volumes with negligible waste reduces reagent costs, compound usage, and consumption of cells. Improved compound library formatting strategies can further extend primary screening opportunities when samples are scarce. Dozens of targets have been screened in 384- and 1536-well assay formats, predominantly in academic screening lab settings. In concert with commercial platform evolution and trending drug discovery strategies, HyperCyt-based systems are now finding their way into mainstream screening labs. Recent advances in flow-based imaging, mass spectrometry, and parallel sample processing promise dramatically expanded single-cell profiling capabilities to bolster systems-level approaches to drug discovery.
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Affiliation(s)
- Bruce S Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
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66
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Target selection for FDA-approved medicines. Drug Discov Today 2015; 20:784-9. [DOI: 10.1016/j.drudis.2014.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/22/2014] [Accepted: 11/04/2014] [Indexed: 11/19/2022]
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Silveira-Dorta G, Sousa IJ, Fernandes MX, Martín VS, Padrón JM. Synthesis and identification of unprecedented selective inhibitors of CK1ε. Eur J Med Chem 2015; 96:308-17. [PMID: 25899335 DOI: 10.1016/j.ejmech.2015.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 12/26/2022]
Abstract
A small and structure-biased library of enantiopure anti-β-amino alcohols was prepared in a straightforward manner by a simplified version of the Reetz protocol. Antiproliferative activity testing against a panel of five human solid tumor cell lines gave GI50 values in the range 1-20 μM. The reverse screening by computational methods against 58 proteins involved in cancer pointed to kinases as possible therapeutic target candidates. The experimental determination of the interaction with 456 kinases indicated that the compounds behave as selective CK1ε inhibitors. Our results demonstrate that the lead compound represents the first selective CK1ε inhibitor with proven antiproliferative activity in cancer cell lines.
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Affiliation(s)
- Gastón Silveira-Dorta
- Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, C/ Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain
| | - Inês J Sousa
- Centro de Química da Madeira, Centro de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Miguel X Fernandes
- Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, C/ Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain; Centro de Química da Madeira, Centro de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Victor S Martín
- Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, C/ Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain
| | - José M Padrón
- Instituto Universitario de Bio-Orgánica "Antonio González" (IUBO-AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna, C/ Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain.
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Lee HW, Khan SQ, Faridi MH, Wei C, Tardi NJ, Altintas MM, Elshabrawy HA, Mangos S, Quick KL, Sever S, Reiser J, Gupta V. A Podocyte-Based Automated Screening Assay Identifies Protective Small Molecules. J Am Soc Nephrol 2015; 26:2741-52. [PMID: 25858967 DOI: 10.1681/asn.2014090859] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/08/2015] [Indexed: 12/30/2022] Open
Abstract
Podocyte injury and loss mark an early step in the pathogenesis of various glomerular diseases, making these cells excellent targets for therapeutics. However, cell-based high-throughput screening assays for the rational development of podocyte-directed therapeutics are currently lacking. Here, we describe a novel high-content screening-based phenotypic assay that analyzes thousands of podocytes per assay condition in 96-well plates to quantitatively measure dose-dependent changes in multiple cellular features. Our assay consistently produced a Z' value >0.44, making it suitable for compound screening. On screening with >2100 pharmacologically active agents, we identified 24 small molecules that protected podocytes against injury in vitro (1% hit rate). Among the identified hits, we confirmed an β1-integrin agonist, pyrintegrin, as a podocyte-protective agent. Treatment with pyrintegrin prevented damage-induced decreases in F-actin stress fibers, focal adhesions, and active β1-integrin levels in cultured cells. In vivo, administration of pyrintegrin protected mice from LPS-induced podocyte foot process effacement and proteinuria. Analysis of the murine glomeruli showed that LPS administration reduced the levels of active β1 integrin in the podocytes, which was prevented by cotreatment with pyrintegrin. In rats, pyrintegrin reduced peak proteinuria caused by puromycin aminonucleoside-induced nephropathy. Our findings identify pyrintegrin as a potential therapeutic candidate and show the use of podocyte-based screening assays for identifying novel therapeutics for proteinuric kidney diseases.
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Affiliation(s)
- Ha Won Lee
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Samia Q Khan
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Mohd Hafeez Faridi
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Changli Wei
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Nicholas J Tardi
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Mehmet M Altintas
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Hatem A Elshabrawy
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Steve Mangos
- Department of Medicine, Rush University Medical Center, Chicago, Illinois
| | - Kevin L Quick
- Cellular Imaging and Analysis, PerkinElmer Life Sciences, Waltham, Massachusetts; and
| | - Sanja Sever
- Department of Medicine, Harvard Medical School, Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts
| | - Jochen Reiser
- Department of Medicine, Rush University Medical Center, Chicago, Illinois;
| | - Vineet Gupta
- Department of Medicine, Rush University Medical Center, Chicago, Illinois;
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Dahlin JL, Inglese J, Walters MA. Mitigating risk in academic preclinical drug discovery. Nat Rev Drug Discov 2015; 14:279-94. [PMID: 25829283 PMCID: PMC6002840 DOI: 10.1038/nrd4578] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of academic drug discovery centres has grown considerably in recent years, providing new opportunities to couple the curiosity-driven research culture in academia with rigorous preclinical drug discovery practices used in industry. To fully realize the potential of these opportunities, it is important that academic researchers understand the risks inherent in preclinical drug discovery, and that translational research programmes are effectively organized and supported at an institutional level. In this article, we discuss strategies to mitigate risks in several key aspects of preclinical drug discovery at academic drug discovery centres, including organization, target selection, assay design, medicinal chemistry and preclinical pharmacology.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | - James Inglese
- 1] National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, USA. [2] National Human Genome Research Institute, Bethesda, Maryland, 20892, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota Twin Cities, 717 Delaware St SE, Room 609, Minneapolis, Minnesota 55414, USA
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Nybond S, Ghemtio L, Nawrot DA, Karp M, Xhaard H, Tammela P. Integrated In Vitro–In Silico Screening Strategy for the Discovery of Antibacterial Compounds. Assay Drug Dev Technol 2015; 13:25-33. [DOI: 10.1089/adt.2014.625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Susanna Nybond
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Leo Ghemtio
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dorota A. Nawrot
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Matti Karp
- Department of Chemistry and Bioengineering, Tampere University of Technology, Tampere, Finland
| | - Henri Xhaard
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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Practical strategies for small-molecule probe development in chemical biology. Methods Mol Biol 2015. [PMID: 25618348 DOI: 10.1007/978-1-4939-2269-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The effective identification, selection, and implementation of small molecules for the interrogation of biological systems require an intricate understanding of the chemical principles underlying their cellular activities. While much has been published regarding the use of screening techniques in forward chemical genetics platforms and on small-molecule target identification, less emphasis has been placed on detailed strategies for evaluating, selecting, and optimizing screening hits. This chapter provides practical tools for identifying and developing promising screening hit compounds into effective tools for biological discovery.
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72
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Zhou C, Zhou Y, Wang J, Zhu Y, Deng J, Wang MW. Emergence of Chinese drug discovery research: impact of hit and lead identification. ACTA ACUST UNITED AC 2014; 20:318-29. [PMID: 25520370 DOI: 10.1177/1087057114561950] [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] [Indexed: 01/16/2023]
Abstract
The identification of hits and the generation of viable leads is an early and yet crucial step in drug discovery. In the West, the main players of drug discovery are pharmaceutical and biotechnology companies, while in China, academic institutions remain central in the field of drug discovery. There has been a tremendous amount of investment from the public as well as private sectors to support infrastructure buildup and expertise consolidation relative to drug discovery and development in the past two decades. A large-scale compound library has been established in China, and a series of high-impact discoveries of lead compounds have been made by integrating information obtained from different technology-based strategies. Natural products are a major source in China's drug discovery efforts. Knowledge has been enhanced via disruptive breakthroughs such as the discovery of Boc5 as a nonpeptidic agonist of glucagon-like peptide 1 receptor (GLP-1R), one of the class B G protein-coupled receptors (GPCRs). Most of the original hit identification and lead generation were carried out by academic institutions, including universities and specialized research institutes. The Chinese pharmaceutical industry is gradually transforming itself from manufacturing low-end generics and active pharmaceutical ingredients to inventing new drugs.
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Affiliation(s)
- Caihong Zhou
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan Zhou
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jia Wang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yue Zhu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiejie Deng
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ming-Wei Wang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
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73
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Unger C, Kramer N, Walzl A, Scherzer M, Hengstschläger M, Dolznig H. Modeling human carcinomas: physiologically relevant 3D models to improve anti-cancer drug development. Adv Drug Deliv Rev 2014; 79-80:50-67. [PMID: 25453261 DOI: 10.1016/j.addr.2014.10.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/02/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Anti-cancer drug development is inefficient, mostly due to lack of efficacy in human patients. The high fail rate is partly due to the lack of predictive models or the inadequate use of existing preclinical test systems. However, progress has been made and preclinical models were improved or newly developed, which all account for basic features of solid cancers, three-dimensionality and heterotypic cell interaction. Here we give an overview of available in vivo and in vitro models of cancer, which meet the criteria of being 3D and mirroring human tumor-stroma interactions. We only focus on drug response models without touching models for pharmacokinetic and dynamic, toxicity or delivery aspects.
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74
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Aijian AP, Garrell RL. Digital microfluidics for automated hanging drop cell spheroid culture. ACTA ACUST UNITED AC 2014; 20:283-95. [PMID: 25510471 DOI: 10.1177/2211068214562002] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 11/15/2022]
Abstract
Cell spheroids are multicellular aggregates, grown in vitro, that mimic the three-dimensional morphology of physiological tissues. Although there are numerous benefits to using spheroids in cell-based assays, the adoption of spheroids in routine biomedical research has been limited, in part, by the tedious workflow associated with spheroid formation and analysis. Here we describe a digital microfluidic platform that has been developed to automate liquid-handling protocols for the formation, maintenance, and analysis of multicellular spheroids in hanging drop culture. We show that droplets of liquid can be added to and extracted from through-holes, or "wells," and fabricated in the bottom plate of a digital microfluidic device, enabling the formation and assaying of hanging drops. Using this digital microfluidic platform, spheroids of mouse mesenchymal stem cells were formed and maintained in situ for 72 h, exhibiting good viability (>90%) and size uniformity (% coefficient of variation <10% intraexperiment, <20% interexperiment). A proof-of-principle drug screen was performed on human colorectal adenocarcinoma spheroids to demonstrate the ability to recapitulate physiologically relevant phenomena such as insulin-induced drug resistance. With automatable and flexible liquid handling, and a wide range of in situ sample preparation and analysis capabilities, the digital microfluidic platform provides a viable tool for automating cell spheroid culture and analysis.
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Affiliation(s)
- Andrew P Aijian
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Robin L Garrell
- Department of Bioengineering, University of California, Los Angeles, CA, USA Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA California NanoSystems Institute, University of California, Los Angeles, CA, USA
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75
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Tosh DK, Finley A, Paoletta S, Moss S, Gao ZG, Gizewski ET, Auchampach JA, Salvemini D, Jacobson KA. In vivo phenotypic screening for treating chronic neuropathic pain: modification of C2-arylethynyl group of conformationally constrained A3 adenosine receptor agonists. J Med Chem 2014; 57:9901-14. [PMID: 25422861 PMCID: PMC4266358 DOI: 10.1021/jm501021n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 12/30/2022]
Abstract
(N)-Methanocarba adenosine 5'-methyluronamides containing 2-arylethynyl groups were synthesized as A3 adenosine receptor (AR) agonists and screened in vivo (po) for reduction of neuropathic pain. A small N(6)-methyl group maintained binding affinity, with human > mouse A3AR and MW < 500 and other favorable physicochemical properties. Emax (maximal efficacy in a mouse chronic constriction injury pain model) of previously characterized A3AR agonist, 2-(3,4-difluorophenylethynyl)-N(6)-(3-chlorobenzyl) derivative 6a, MRS5698, was surpassed. More efficacious analogues (in vivo) contained the following C2-arylethynyl groups: pyrazin-2-yl 23 (binding Ki, hA3AR, nM 1.8), fur-2-yl 27 (0.6), thien-2-yl 32 (0.6) and its 5-chloro 33, MRS5980 (0.7) and 5-bromo 34 (0.4) equivalents, and physiologically unstable ferrocene 36, MRS5979 (2.7). 33 and 36 displayed particularly long in vivo duration (>3 h). Selected analogues were docked to an A3AR homology model to explore the environment of receptor-bound C2 and N(6) groups. Various analogues bound with μM affinity at off-target biogenic amine (M2, 5HT2A, β3, 5HT2B, 5HT2C, and α2C) or other receptors. Thus, we have expanded the structural range of orally active A3AR agonists for chronic pain treatment.
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Affiliation(s)
- Dilip K. Tosh
- Molecular Recognition Section, Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Building 8A,
Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Amanda Finley
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Silvia Paoletta
- Molecular Recognition Section, Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Building 8A,
Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Steven
M. Moss
- Molecular Recognition Section, Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Building 8A,
Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Building 8A,
Room B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Elizabeth T. Gizewski
- Department of Pharmacology, Medical College
of Wisconsin, 8701 Watertown
Plank Road, Milwaukee, Wisconsin 53226, United States
| | - John A. Auchampach
- Department of Pharmacology, Medical College
of Wisconsin, 8701 Watertown
Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Daniela Salvemini
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes
of Health, Building 8A,
Room B1A-19, Bethesda, Maryland 20892-0810, United States
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76
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Blaazer AR, Orrling KM, Shanmugham A, Jansen C, Maes L, Edink E, Sterk GJ, Siderius M, England P, Bailey D, de Esch IJP, Leurs R. Fragment-Based Screening in Tandem with Phenotypic Screening Provides Novel Antiparasitic Hits. ACTA ACUST UNITED AC 2014; 20:131-40. [DOI: 10.1177/1087057114549735] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Methods to discover biologically active small molecules include target-based and phenotypic screening approaches. One of the main difficulties in drug discovery is elucidating and exploiting the relationship between drug activity at the protein target and disease modification, a phenotypic endpoint. Fragment-based drug discovery is a target-based approach that typically involves the screening of a relatively small number of fragment-like (molecular weight <300) molecules that efficiently cover chemical space. Here, we report a fragment screening on TbrPDEB1, an essential cyclic nucleotide phosphodiesterase (PDE) from Trypanosoma brucei, and human PDE4D, an off-target, in a workflow in which fragment hits and a series of close analogs are subsequently screened for antiparasitic activity in a phenotypic panel. The phenotypic panel contained T. brucei, Trypanosoma cruzi, Leishmania infantum, and Plasmodium falciparum, the causative agents of human African trypanosomiasis (sleeping sickness), Chagas disease, leishmaniasis, and malaria, respectively, as well as MRC-5 human lung cells. This hybrid screening workflow has resulted in the discovery of various benzhydryl ethers with antiprotozoal activity and low toxicity, representing interesting starting points for further antiparasitic optimization.
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Affiliation(s)
- Antoni R. Blaazer
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Kristina M. Orrling
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
- TI Pharma, Leiden, The Netherlands
| | | | - Chimed Jansen
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
- University of Dundee, Dundee, UK
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Belgium
| | - Ewald Edink
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Geert Jan Sterk
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Marco Siderius
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | | | | | - Iwan J. P. de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
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77
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Falcon BL, Swearingen M, Gough WH, Lee L, Foreman R, Uhlik M, Hanson JC, Lee JA, McClure DB, Chintharlapalli S. An in vitro cord formation assay identifies unique vascular phenotypes associated with angiogenic growth factors. PLoS One 2014; 9:e106901. [PMID: 25210890 PMCID: PMC4161374 DOI: 10.1371/journal.pone.0106901] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/11/2014] [Indexed: 01/08/2023] Open
Abstract
Vascular endothelial growth factor (VEGF) plays a dominant role in angiogenesis. While inhibitors of the VEGF pathway are approved for the treatment of a number of tumor types, the effectiveness is limited and evasive resistance is common. One mechanism of evasive resistance to inhibition of the VEGF pathway is upregulation of other pro-angiogenic factors such as fibroblast growth factor (FGF) and epidermal growth factor (EGF). Numerous in vitro assays examine angiogenesis, but many of these assays are performed in media or matrix with multiple growth factors or are driven by VEGF. In order to study angiogenesis driven by other growth factors, we developed a basal medium to use on a co-culture cord formation system of adipose derived stem cells (ADSCs) and endothelial colony forming cells (ECFCs). We found that cord formation driven by different angiogenic factors led to unique phenotypes that could be differentiated and combination studies indicate dominant phenotypes elicited by some growth factors. VEGF-driven cords were highly covered by smooth muscle actin, and bFGF-driven cords had thicker nodes, while EGF-driven cords were highly branched. Multiparametric analysis indicated that when combined EGF has a dominant phenotype. In addition, because this assay system is run in minimal medium, potential proangiogenic molecules can be screened. Using this assay we identified an inhibitor that promoted cord formation, which was translated into in vivo tumor models. Together this study illustrates the unique roles of multiple anti-angiogenic agents, which may lead to improvements in therapeutic angiogenesis efforts and better rational for anti-angiogenic therapy.
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Affiliation(s)
- Beverly L. Falcon
- Department of Cancer Angiogenesis, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Michelle Swearingen
- Department of Cancer Angiogenesis, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Wendy H. Gough
- Department of Quantitative Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Linda Lee
- Department of Cancer Angiogenesis, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Robert Foreman
- Department of In Vivo Pharmacology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Mark Uhlik
- Department of Cancer Angiogenesis, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Jeff C. Hanson
- Department of Informatics Capabilities, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Jonathan A. Lee
- Department of Quantitative Biology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Don B. McClure
- Department of BioTDR, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
| | - Sudhakar Chintharlapalli
- Department of Cancer Angiogenesis, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, United States of America
- * E-mail:
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78
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Abstract
Analysis of the origins of new drugs approved by the US Food and Drug Administration (FDA) from 1999 to 2008 suggested that phenotypic screening strategies had been more productive than target-based approaches in the discovery of first-in-class small-molecule drugs. However, given the relatively recent introduction of target-based approaches in the context of the long time frames of drug development, their full impact might not yet have become apparent. Here, we present an analysis of the origins of all 113 first-in-class drugs approved by the FDA from 1999 to 2013, which shows that the majority (78) were discovered through target-based approaches (45 small-molecule drugs and 33 biologics). In addition, of 33 drugs identified in the absence of a target hypothesis, 25 were found through a chemocentric approach in which compounds with known pharmacology served as the starting point, with only eight coming from what we define here as phenotypic screening: testing a large number of compounds in a target-agnostic assay that monitors phenotypic changes. We also discuss the implications for drug discovery strategies, including viewing phenotypic screening as a novel discipline rather than as a neoclassical approach.
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79
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Swinney DC. The value of translational biomarkers to phenotypic assays. Front Pharmacol 2014; 5:171. [PMID: 25076910 PMCID: PMC4097030 DOI: 10.3389/fphar.2014.00171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/02/2014] [Indexed: 11/13/2022] Open
Abstract
Phenotypic assays are tools essential for drug discovery. Phenotypic assays have different types of endpoints depending on the goals; (1) empirical endpoints for basic research to understand the underlying biology that will lead to identification of translation biomarkers, (2) empirical endpoints to identify undesired effects related to toxicity of drug candidates, and (3) knowledge-based endpoints (biomarkers) for drug discovery which ideally are translational biomarkers that will be used to identify new drug candidates and their corresponding molecular mechanisms of action. The value of phenotypic assays is increased through effective alignment of phenotypic assay endpoints with the objectives of the relevant stage in the drug discovery and development cycle.
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Affiliation(s)
- David C. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain ViewCA, USA
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80
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Dawson JC, Carragher NO. Quantitative phenotypic and pathway profiling guides rational drug combination strategies. Front Pharmacol 2014; 5:118. [PMID: 24904421 PMCID: PMC4035564 DOI: 10.3389/fphar.2014.00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/01/2014] [Indexed: 12/18/2022] Open
Abstract
Advances in target-based drug discovery strategies have enabled drug discovery groups in academia and industry to become very effective at generating molecules that are potent and selective against single targets. However, it has become apparent from disappointing results in recent clinical trials that a major challenge to the development of successful targeted therapies for treating complex multifactorial diseases is overcoming heterogeneity in target mechanism among patients and inherent or acquired drug resistance. Consequently, reductionist target directed drug-discovery approaches are not appropriately tailored toward identifying and optimizing multi-targeted therapeutics or rational drug combinations for complex disease. In this article, we describe the application of emerging high-content phenotypic profiling and analysis tools to support robust evaluation of drug combination performance following dose-ratio matrix screening. We further describe how the incorporation of high-throughput reverse phase protein microarrays with phenotypic screening can provide rational drug combination hypotheses but also confirm the mechanism-of-action of novel drug combinations, to facilitate future preclinical and clinical development strategies.
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Affiliation(s)
- John C Dawson
- Edinburgh Cancer Discovery Unit, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
| | - Neil O Carragher
- Edinburgh Cancer Discovery Unit, Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK
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81
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Conway JRW, Carragher NO, Timpson P. Developments in preclinical cancer imaging: innovating the discovery of therapeutics. Nat Rev Cancer 2014; 14:314-28. [PMID: 24739578 DOI: 10.1038/nrc3724] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Integrating biological imaging into early stages of the drug discovery process can provide invaluable readouts of drug activity within complex disease settings, such as cancer. Iterating this approach from initial lead compound identification in vitro to proof-of-principle in vivo analysis represents a key challenge in the drug discovery field. By embracing more complex and informative models in drug discovery, imaging can improve the fidelity and statistical robustness of preclinical cancer studies. In this Review, we highlight how combining advanced imaging with three-dimensional systems and intravital mouse models can provide more informative and disease-relevant platforms for cancer drug discovery.
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Affiliation(s)
- James R W Conway
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre Sydney, St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales 2010, Sydney, Australia
| | - Neil O Carragher
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Paul Timpson
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre Sydney, St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales 2010, Sydney, Australia
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82
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L. Berg E, Hsu YC, Lee JA. Consideration of the cellular microenvironment: physiologically relevant co-culture systems in drug discovery. Adv Drug Deliv Rev 2014; 69-70:190-204. [PMID: 24524933 DOI: 10.1016/j.addr.2014.01.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/16/2014] [Accepted: 01/28/2014] [Indexed: 01/15/2023]
Abstract
There is renewed interest in phenotypic approaches to drug discovery, using cell-based assays to select new drugs, with the goal of improving pharmaceutical success. Assays that are more predictive of human biology can help researchers achieve this goal. Primary cells are more physiologically relevant to human biology and advances are being made in methods to expand the available cell types and improve the potential clinical translation of these assays through the use of co-cultures or three-dimensional (3D) technologies. Of particular interest are assays that may be suitable for industrial scale drug discovery. Here we review the use of primary human cells and co-cultures in drug discovery and describe the characteristics of co-culture models for inflammation biology (BioMAP systems), neo-vascularization and tumor microenvironments. Finally we briefly describe technical trends that may enable and impact the development of physiologically relevant co-culture assays in the near future.
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83
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Onwuha-Ekpete L, Tack L, Knapinska A, Smith L, Kaushik G, Lavoi T, Giulianotti M, Houghten RA, Fields GB, Minond D. Novel pyrrolidine diketopiperazines selectively inhibit melanoma cells via induction of late-onset apoptosis. J Med Chem 2014; 57:1599-608. [PMID: 24471466 PMCID: PMC3983399 DOI: 10.1021/jm4019542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A common liability of cancer drugs is toxicity to noncancerous cells. Thus, molecules are needed that are potent toward cancer cells while sparing healthy cells. The cost of traditional cell-based HTS is dictated by the library size, which is typically in the hundreds of thousands of individual compounds. Mixture-based combinatorial libraries offer a cost-effective alternative to single-compound libraries while eliminating the need for molecular target validation. Presently, lung cancer and melanoma cells were screened in parallel with healthy cells using a mixture-based library. A novel class of compounds was discovered that selectively inhibited melanoma cell growth via apoptosis with submicromolar potency while sparing healthy cells. Additionally, the cost of screening and biological follow-up experiments was significantly lower than in typical HTS. Our findings suggest that mixture-based phenotypic HTS can significantly reduce cost and hit-to-lead time while yielding novel compounds with promising pharmacology.
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Affiliation(s)
- Lillian Onwuha-Ekpete
- Torrey Pines Institute for Molecular Studies , 11350 South West Village Parkway, Port St. Lucie, Florida 34987, United States
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84
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Berg EL. Systems biology in drug discovery and development. Drug Discov Today 2013; 19:113-25. [PMID: 24120892 DOI: 10.1016/j.drudis.2013.10.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 09/14/2013] [Accepted: 10/03/2013] [Indexed: 11/25/2022]
Abstract
The complexity of human biology makes it challenging to develop safe and effective new medicines. Systems biology omics-based efforts have led to an explosion of high-throughput data and focus is now shifting to the integration of diverse data types to connect molecular and pathway information to predict disease outcomes. Better models of human disease biology, including more integrated network-based models that can accommodate multiple omics data types, as well as more relevant experimental systems, will help predict drug effects in patients, enabling personalized medicine, improvement of the success rate of new drugs in the clinic, and the finding of new uses for existing drugs.
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Affiliation(s)
- Ellen L Berg
- BioSeek, A Division of DiscoveRx, 310 Utah Avenue, Suite 100, South San Francisco, CA 94080, USA.
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