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  4. 2016
Showing papers on "Phenotypic screening published in 2016"
Journal Article•10.1038/NBT.3460•
High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

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Channing Yu1, Aristotle M. Mannan1, Griselda Metta Yvone1, Kenneth N. Ross1, Yan Ling Zhang1, Melissa A. Marton1, Bradley Taylor1, Andrew Crenshaw1, Joshua Gould1, Pablo Tamayo1, Barbara A. Weir1, Aviad Tsherniak1, Bang Wong1, Levi A. Garraway2, Levi A. Garraway1, Alykhan F. Shamji1, Michelle Palmer1, Michael Foley1, Wendy Winckler1, Stuart L. Schreiber3, Stuart L. Schreiber2, Stuart L. Schreiber1, Andrew L. Kung2, Todd R. Golub •
Broad Institute1, Harvard University2, Howard Hughes Medical Institute3
01 Apr 2016-Nature Biotechnology
TL;DR: A method called PRISM is reported that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes and revealed the expected patterns of cell killing seen in conventional (unpooled) assays.
Abstract: Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control. Here we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM revealed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo.

322 citations

Journal Article•10.1016/J.CHEMBIOL.2016.05.021•
The Emerging Role of RNA as a Therapeutic Target for Small Molecules

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Colleen M. Connelly1, Michelle H. Moon1, John S. Schneekloth1•
National Institutes of Health1
22 Sep 2016-Chemistry & Biology
TL;DR: This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.

276 citations

Journal Article•10.1038/SREP24356•
CRISPR-Cas9 D10A nickase-based genotypic and phenotypic screening to enhance genome editing

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Ting-Wei Will Chiang1, Ting-Wei Will Chiang2, Carlos le Sage1, Delphine Larrieu1, Mukerrem Demir1, Stephen P. Jackson2, Stephen P. Jackson1, Stephen P. Jackson3 •
Wellcome Trust/Cancer Research UK Gurdon Institute1, University of Cambridge2, Wellcome Trust Sanger Institute3
15 Apr 2016-Scientific Reports
TL;DR: A versatile screening approach that combines an All-in-One Cas9D10A nickase vector with fluorescence-activated cell sorting enrichment followed by high-throughput genotypic and phenotypic clonal screening strategies to generate isogenic knockouts and knock-ins highly efficiently, with minimal off-target effects is described.
Abstract: The RNA-guided Cas9 nuclease is being widely employed to engineer the genomes of various cells and organisms. Despite the efficient mutagenesis induced by Cas9, off-target effects have raised concerns over the system's specificity. Recently a "double-nicking" strategy using catalytic mutant Cas9(D10A) nickase has been developed to minimise off-target effects. Here, we describe a Cas9(D10A)-based screening approach that combines an All-in-One Cas9(D10A) nickase vector with fluorescence-activated cell sorting enrichment followed by high-throughput genotypic and phenotypic clonal screening strategies to generate isogenic knockouts and knock-ins highly efficiently, with minimal off-target effects. We validated this approach by targeting genes for the DNA-damage response (DDR) proteins MDC1, 53BP1, RIF1 and P53, plus the nuclear architecture proteins Lamin A/C, in three different human cell lines. We also efficiently obtained biallelic knock-in clones, using single-stranded oligodeoxynucleotides as homologous templates, for insertion of an EcoRI recognition site at the RIF1 locus and introduction of a point mutation at the histone H2AFX locus to abolish assembly of DDR factors at sites of DNA double-strand breaks. This versatile screening approach should facilitate research aimed at defining gene functions, modelling of cancers and other diseases underpinned by genetic factors, and exploring new therapeutic opportunities.

175 citations

Journal Article•10.1016/J.DRUDIS.2015.08.001•
Identifying compound efficacy targets in phenotypic drug discovery

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Markus Schirle1, Jeremy L. Jenkins1•
Novartis1
01 Jan 2016-Drug Discovery Today
TL;DR: This short review discusses the most important technologies currently available for characterizing the direct and indirect target space of bioactive compounds following phenotypic screening and presents a comprehensive strategy employing complementary approaches to balance individual technology strengths and weaknesses.

156 citations

Journal Article•10.1038/NCOMMS12444•
Novel gene function revealed by mouse mutagenesis screens for models of age-related disease.

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Paul Potter, Michael R. Bowl, Prashanthini Jeyarajan, Laura Wisby, A Blease, Michelle Goldsworthy, Michelle Simon, Simon Greenaway, Vincent Michel1, Alun R. Barnard2, Carlos A. Aguilar, Thomas Agnew, Gareth Banks, Andrew Blake, Lauren Chessum, Joanne Dorning, Sara Falcone, Laurence Goosey, Shelley Harris, Andy Haynes, Ines Heise, Rosie Hillier, Tertius Hough, Angela Hoslin, Marie Hutchison, Ruairidh King, Saumya Kumar, Heena V. Lad, Gemma Law, Robert E MacLaren2, Susan Morse, T Nicol, Andrew Parker, Karen Pickford, Siddharth Sethi, Becky Starbuck, Femke Stelma, Michael Cheeseman3, Sally H. Cross4, Russell G. Foster5, Ian J. Jackson4, Ian J. Jackson3, Stuart N. Peirson5, Rajesh V. Thakker2, Tonia L. Vincent2, Cheryl L. Scudamore, Sara Wells, Aziz El-Amraoui1, Christine Petit1, Abraham Acevedo-Arozena, Patrick M. Nolan, Roger D. Cox, Anne-Marie Mallon, Steve D. M. Brown •
Collège de France1, University of Oxford2, University of Edinburgh3, Western General Hospital4, John Radcliffe Hospital5
18 Aug 2016-Nature Communications
TL;DR: A large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive, reveals a number of novel pathways involved with age- related disease.
Abstract: Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss. Random mutagenesis can uncover novel genes involved in phenotypic traits. Here the authors perform a large-scale phenotypic screen on over 100 mouse strains generated by ENU mutagenesis to identify mice with age-related diseases, which they attribute to specific mutations revealed by whole-genome sequencing.

98 citations

Journal Article•10.1371/JOURNAL.PNTD.0004356•
Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni.

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Thavy Long1, R. Jeffrey Neitz1, Rachel Beasley2, Chakrapani Kalyanaraman1, Brian M. Suzuki1, Matthew P. Jacobson1, Colette Dissous3, James H. McKerrow1, David H. Drewry4, William J. Zuercher4, Rahul Singh2, Rahul Singh1, Conor R. Caffrey1 •
University of California, San Francisco1, San Francisco State University2, Pasteur Institute3, Research Triangle Park4
11 Jan 2016-PLOS Neglected Tropical Diseases
TL;DR: The reverse genetic and chemical SAR data support a continued investigation of SmPLK1 as a possible drug target and/or the prosecution of the benzimidazole thiophene chemotype as a source of novel anti-schistosomals.
Abstract: Author(s): Long, Thavy; Neitz, R Jeffrey; Beasley, Rachel; Kalyanaraman, Chakrapani; Suzuki, Brian M; Jacobson, Matthew P; Dissous, Colette; McKerrow, James H; Drewry, David H; Zuercher, William J; Singh, Rahul; Caffrey, Conor R | Abstract: BackgroundSchistosoma flatworm parasites cause schistosomiasis, a chronic and debilitating disease of poverty in developing countries. Praziquantel is employed for treatment and disease control. However, its efficacy spectrum is incomplete (less active or inactive against immature stages of the parasite) and there is a concern of drug resistance. Thus, there is a need to identify new drugs and drug targets.Methodology/principal findingsWe show that RNA interference (RNAi) of the Schistosoma mansoni ortholog of human polo-like kinase (huPLK)1 elicits a deleterious phenotypic alteration in post-infective larvae (schistosomula or somules). Phenotypic screening and analysis of schistosomula and adult S. mansoni with small molecule inhibitors of huPLK1 identified a number of potent anti-schistosomals. Among these was a GlaxoSmithKline (GSK) benzimidazole thiophene inhibitor that has completed Phase I clinical trials for treatment of solid tumor malignancies. We then obtained GSKs Published Kinase Inhibitor Sets (PKIS) 1 and 2, and phenotypically screened an expanded series of 38 benzimidazole thiophene PLK1 inhibitors. Computational analysis of controls and PLK1 inhibitor-treated populations of somules demonstrated a distinctive phenotype distribution. Using principal component analysis (PCA), the phenotypes exhibited by these populations were mapped, visualized and analyzed through projection to a low-dimensional space. The phenotype distribution was found to have a distinct shape and topology, which could be elicited using cluster analysis. A structure-activity relationship (SAR) was identified for the benzimidazole thiophenes that held for both somules and adult parasites. The most potent inhibitors produced marked phenotypic alterations at 1-2 μM within 1 h. Among these were compounds previously characterized as potent inhibitors of huPLK1 in cell assays.Conclusions/significanceThe reverse genetic and chemical SAR data support a continued investigation of SmPLK1 as a possible drug target and/or the prosecution of the benzimidazole thiophene chemotype as a source of novel anti-schistosomals.

64 citations

Journal Article•10.1021/ACS.JMEDCHEM.6B00065•
Rapid Discovery and Structure–Activity Relationships of Pyrazolopyrimidines That Potently Suppress Breast Cancer Cell Growth via SRC Kinase Inhibition with Exceptional Selectivity over ABL Kinase

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Craig Fraser, John C. Dawson1, Reece Dowling, Douglas R. Houston2, Jason T. Weiss, Alison F. Munro, Morwenna Muir, Lea Harrington3, Scott P. Webster2, Margaret C. Frame1, Valerie G. Brunton1, E. Elizabeth Patton, Neil O. Carragher1, Asier Unciti-Broceta1 •
Edinburgh Cancer Research Centre1, University of Edinburgh2, Université de Montréal3
26 May 2016-Journal of Medicinal Chemistry
TL;DR: ECF506 is the first small molecule with subnanomolar IC50 for SRC that requires 3 orders of magnitude greater concentration to inhibit ABL, and exhibits excellent water solubility, an optimal DMPK profile and oral bioavailability, and inhibits SRC phosphorylation in tumor xenografts in mice.
Abstract: Novel pyrazolopyrimidines displaying high potency and selectivity toward SRC family kinases have been developed by combining ligand-based design and phenotypic screening in an iterative manner. Compounds were derived from the promiscuous kinase inhibitor PP1 to search for analogs that could potentially target a broad spectrum of kinases involved in cancer. Phenotypic screening against MCF7 mammary adenocarcinoma cells generated target-agnostic structure–activity relationships that biased subsequent designs toward breast cancer treatment rather than to a particular target. This strategy led to the discovery of two potent antiproliferative leads with phenotypically distinct anticancer mode of actions. Kinase profiling and further optimization resulted in eCF506, the first small molecule with subnanomolar IC50 for SRC that requires 3 orders of magnitude greater concentration to inhibit ABL. eCF506 exhibits excellent water solubility, an optimal DMPK profile and oral bioavailability, halts SRC-associated neur...

60 citations

Journal Article•10.1016/J.STEMCR.2016.10.001•
High-Throughput Toxicity and Phenotypic Screening of 3D Human Neural Progenitor Cell Cultures on a Microarray Chip Platform.

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Gregory J. Nierode1, Brian C. Perea2, Sean McFarland2, Jorge F. Pascoal3, Douglas S. Clark2, David V. Schaffer2, Jonathan S. Dordick1 •
Rensselaer Polytechnic Institute1, University of California, Berkeley2, Instituto Superior Técnico3
08 Nov 2016-Stem cell reports
TL;DR: A 3D cell culture chip was used for high-throughput screening of a human neural progenitor cell line and has potential use in phenotypic screening to elucidate molecular toxicology on human stem cells.
Abstract: A 3D cell culture chip was used for high-throughput screening of a human neural progenitor cell line The differential toxicity of 24 compounds was determined on undifferentiated and differentiating NPCs Five compounds led to significant differences in IC50 values between undifferentiated and differentiating cultures This platform has potential use in phenotypic screening to elucidate molecular toxicology on human stem cells

59 citations

Journal Article•10.1016/J.EURURO.2015.09.019•
Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue

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Anna Aakula1, Anna Aakula2, Anna Aakula3, Pekka Kohonen1, Suvi-Katri Leivonen1, Rami Mäkelä1, Petteri Hintsanen2, John-Patrick Mpindi1, Elena S. Martens-Uzunova4, Tero Aittokallio2, Guido Jenster4, Merja Perälä1, Olli Kallioniemi1, Olli Kallioniemi2, Päivi Östling1, Päivi Östling2 •
VTT Technical Research Centre of Finland1, University of Helsinki2, University of Turku3, Erasmus University Rotterdam4
01 Jun 2016-European Urology
TL;DR: Novel regulatory molecules are identified, which impact on PCa proliferation and are aberrantly expressed in clinical tumors, which reveals regulatory nodes with potential for therapy.

59 citations

Journal Article•10.1039/C5NP00120J•
Natural products-prompted chemical biology: phenotypic screening and a new platform for target identification.

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Hideaki Kakeya1•
Kyoto University1
04 May 2016-Natural Product Reports
TL;DR: The research team has discovered several novel bioactive small molecules using in vivo cell-based phenotypic screening, and has investigated their modes of action using chemical genetics and chemical genomics.

59 citations

Journal Article•10.18632/ONCOTARGET.11943•
Phenotypic screening reveals TNFR2 as a promising target for cancer immunotherapy.

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Geoffrey S. Williams1, Bina Mistry1, Sandrine Guillard1, Jane Coates Ulrichsen1, Alan Sandercock1, Jun Wang2, Andrea L. Gonzalez-Munoz1, Julie Parmentier3, Chelsea Black1, Jo Soden, Jim Freeth, Jelena Jovanovic1, Rebecca Leyland1, Rafia S. Al-Lamki2, Andrew J. Leishman1, Steven Rust1, Ross Stewart1, Lutz Jermutus1, John Bradley2, Vahe Bedian3, Viia Valge-Archer1, Ralph Minter1, Robert W. Wilkinson1 •
MedImmune1, University of Cambridge2, AstraZeneca3
10 Sep 2016-Oncotarget
TL;DR: Data indicate a novel mechanism for TNF-α-independent TNFR2 agonism in cancer immunotherapy, and demonstrate the utility of target-agnostic screening in highlighting important targets during drug discovery.
Abstract: // Geoffrey S. Williams 1 , Bina Mistry 1 , Sandrine Guillard 1 , Jane Coates Ulrichsen 1 , Alan M. Sandercock 1 , Jun Wang 2 , Andrea Gonzalez-Munoz 1 , Julie Parmentier 3 , Chelsea Black 4 , Jo Soden 5 , Jim Freeth 5 , Jelena Jovanovic 1 , Rebecca Leyland 1 , Rafia S. Al-Lamki 2 , Andrew J. Leishman 1 , Steven J. Rust 1 , Ross Stewart 1 , Lutz Jermutus 1 , John R. Bradley 2 , Vahe Bedian 3 , Viia Valge-Archer 1 , Ralph Minter 1 , Robert W. Wilkinson 1 1 MedImmune Ltd., Granta Park, Cambridge, CB21 6GH, UK 2 Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK 3 Oncology iMED, AstraZeneca-R&D Boston, Waltham, MA 02451, USA 4 MedImmune LLC, Gaithersburg, MD 20878, USA 5 Retrogenix Ltd, Whaley Bridge, High Peak, SK23 7LY, UK Correspondence to: Geoffrey S. Williams, email: williamsge@medimmune.com Keywords: TNFR2, regulatory T cell, cancer immunotherapy, drug discovery, phenotypic screening Received: May 27, 2016 Accepted: August 13, 2016 Published: September 10, 2016 ABSTRACT Antibodies that target cell-surface molecules on T cells can enhance anti-tumor immune responses, resulting in sustained immune-mediated control of cancer. We set out to find new cancer immunotherapy targets by phenotypic screening on human regulatory T (Treg) cells and report the discovery of novel activators of tumor necrosis factor receptor 2 (TNFR2) and a potential role for this target in immunotherapy. A diverse phage display library was screened to find antibody mimetics with preferential binding to Treg cells, the most Treg-selective of which were all, without exception, found to bind specifically to TNFR2. A subset of these TNFR2 binders were found to agonise the receptor, inducing iκ-B degradation and NF-κB pathway signalling in vitro . TNFR2 was found to be expressed by tumor-infiltrating Treg cells, and to a lesser extent Teff cells, from three lung cancer patients, and a similar pattern was also observed in mice implanted with CT26 syngeneic tumors. In such animals, TNFR2-specific agonists inhibited tumor growth, enhanced tumor infiltration by CD8 + T cells and increased CD8 + T cell IFN-γ synthesis. Together, these data indicate a novel mechanism for TNF-α-independent TNFR2 agonism in cancer immunotherapy, and demonstrate the utility of target-agnostic screening in highlighting important targets during drug discovery.
Journal Article•10.1128/MSPHERE.00217-16•
A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence.

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Daniel R. Kirienko1, Alexey V. Revtovich1, Natalia V. Kirienko1•
Rice University1
31 Aug 2016
TL;DR: A high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence and shows that 5-fluorouridine, in contrast to 5- fluorouracil, is a genuine antivirulence compound, with no bacteriostatic or bactericidal activity.
Abstract: Pseudomonas aeruginosa is an opportunistic pathogen that causes severe health problems. Despite intensive investigation, many aspects of microbial virulence remain poorly understood. We used a high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence in Caenorhabditis elegans. Approximately half of the hits were known antimicrobials. A large number of hits were nonantimicrobial bioactive compounds, including the cancer chemotherapeutic 5-fluorouracil. We determined that 5-fluorouracil both transiently inhibits bacterial growth and reduces pyoverdine biosynthesis. Pyoverdine is a siderophore that regulates the expression of several virulence determinants and is critical for pathogenesis in mammals. We show that 5-fluorouridine, a downstream metabolite of 5-fluorouracil, is responsible for inhibiting pyoverdine biosynthesis. We also show that 5-fluorouridine, in contrast to 5-fluorouracil, is a genuine antivirulence compound, with no bacteriostatic or bactericidal activity. To our knowledge, this is the first report utilizing a whole-organism screen to identify novel compounds with antivirulent properties effective against P. aeruginosa. IMPORTANCE Despite intense research effort from scientists and the advent of the molecular age of biomedical research, many of the mechanisms that underlie pathogenesis are still understood poorly, if at all. The opportunistic human pathogen Pseudomonas aeruginosa causes a variety of soft tissue infections and is responsible for over 50,000 hospital-acquired infections per year. In addition, P. aeruginosa exhibits a striking degree of innate and acquired antimicrobial resistance, complicating treatment. It is increasingly important to understand P. aeruginosa virulence. In an effort to gain this information in an unbiased fashion, we used a high-throughput phenotypic screen to identify small molecules that disrupted bacterial pathogenesis and increased host survival using the model nematode Caenorhabditis elegans. This method led to the unexpected discovery that addition of a modified nucleotide, 5-fluorouridine, disrupted bacterial RNA metabolism and inhibited synthesis of pyoverdine, a critical toxin. Our results demonstrate that this compound specifically functions as an antivirulent.
Journal Article•10.1002/ANIE.201605707•
Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide.

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Gisbert Schneider1, Daniel Reker1, Tao Chen1, Kurt Hauenstein1, Petra Schneider1, Karl-Heinz Altmann1 •
ETH Zurich1
01 Sep 2016-Angewandte Chemie
TL;DR: This proof-of-concept study demonstrates the in silico deorphanization of phenotypic screening hits as a viable concept for future natural-product-inspired chemical biology and drug discovery efforts.
Abstract: The cyclodepsipeptide doliculide is a marine natural product with strong actin-polymerizing and anticancer activities. Evidence for doliculide acting as a potent and subtype-selective antagonist of prostanoid E receptor 3 (EP3) is presented. Computational target prediction suggested that this membrane receptor is a likely macromolecular target and enabled immediate in vitro validation. This proof-of-concept study demonstrates the in silico deorphanization of phenotypic screening hits as a viable concept for future natural-product-inspired chemical biology and drug discovery efforts.
Journal Article•10.1016/J.YJMCC.2016.04.015•
Discovery of Novel Small Molecule Inhibitors of Cardiac Hypertrophy Using High Throughput, High Content Imaging

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Brian Reid1, Matthew S. Stratton2, Samantha Bowers1, Maria A. Cavasin2, Kimberley M. Demos-Davies2, Isidro Susano1, Timothy A. McKinsey2 •
University of Montana1, Anschutz Medical Campus2
01 Aug 2016-Journal of Molecular and Cellular Cardiology
TL;DR: P phenotypic screening with primary cardiomyocytes can be used to discover anti-hypertrophic lead compounds for heart failure drug discovery and facilitates chemical biological dissection of signaling networks that control pathological growth of the heart.
Journal Article•10.1038/SREP38986•
Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high-throughput phenotypic screen

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Jonathan A. G. Cox1, Grace Mugumbate2, Laura Vela-Glez Del Peral3, Monika Jankute4, Katherine A. Abrahams4, Peter J. Jervis4, Stefan Jackenkroll4, Arancha Pérez3, Carlos Alemparte3, Jorge Esquivias3, Joël Lelièvre3, Fernando Ramón3, David Barros3, Lluis Ballell3, Gurdyal S. Besra4 •
Aston University1, European Bioinformatics Institute2, GlaxoSmithKline3, University of Birmingham4
16 Dec 2016-Scientific Reports
TL;DR: This work demonstrates the versatility and potential of GuaB2 as an anti-tubercular drug target and identified 7 new chemical series from a high-throughput resistance-based phenotypic screen using Mycobacterium bovis BCG over-expressing Gua B2.
Abstract: High-throughput phenotypic screens have re-emerged as screening tools in antibiotic discovery. The advent of such technologies has rapidly accelerated the identification of ‘hit’ compounds. A pre-requisite to medicinal chemistry optimisation programmes required to improve the drug-like properties of a ‘hit’ molecule is identification of its mode of action. Herein, we have combined phenotypic screening with a biased target-specific screen. The inosine monophosphate dehydrogenase (IMPDH) protein GuaB2 has been identified as a drugable target in Mycobacterium tuberculosis, however previously identified compounds lack the desired characteristics necessary for further development into lead-like molecules. This study has identified 7 new chemical series from a high-throughput resistance-based phenotypic screen using Mycobacterium bovis BCG over-expressing GuaB2. Hit compounds were identified in a single shot high-throughput screen, validated by dose response and subjected to further biochemical analysis. The compounds were also assessed using molecular docking experiments, providing a platform for their further optimisation using medicinal chemistry. This work demonstrates the versatility and potential of GuaB2 as an anti-tubercular drug target.
Journal Article•10.1021/ACSCHEMNEURO.6B00125•
Microglia-Based Phenotypic Screening Identifies a Novel Inhibitor of Neuroinflammation Effective in Alzheimer’s Disease Models

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Wei Zhou1, Wei Zhou2, Guifa Zhong2, Sihai Fu, Hui Xie3, Tianyan Chi4, Lu-Yi Li4, Xiurong Rao2, Shaogao Zeng2, Dengfeng Xu2, Hao Wang2, Guoqing Sheng2, Xing Ji, Xiaorong Liu2, Xuefei Ji4, Donghai Wu2, Libo Zou4, Micky D. Tortorella2, Kejian Zhang, Wenhui Hu2 •
Guangdong University of Technology1, Guangzhou Institutes of Biomedicine and Health2, Guangzhou Medical University3, Shenyang Pharmaceutical University4
02 Sep 2016-ACS Chemical Neuroscience
TL;DR: GIBH-130 constitutes a unique chemical probe for pathogenesis research and drug development of AD, and it suggests microglia-based phenotypic screenings that target neuroinflammation as an effective and feasible strategy to identify novel anti-AD agents.
Abstract: Currently, anti-AD drug discovery using target-based approaches is extremely challenging due to unclear etiology of AD and absence of validated therapeutic protein targets. Neuronal death, regardless of causes, plays a key role in AD progression, and it is directly linked to neuroinflammation. Meanwhile, phenotypic screening is making a resurgence in drug discovery process as an alternative to target-focused approaches. Herein, we employed microglia-based phenotypic screenings to search for small molecules that modulate the release of detrimental proinflammatory cytokines. The identified novel pharmacological inhibitor of neuroinflammation (named GIBH-130) was validated to alter phenotypes of neuroinflammation in AD brains. Notably, this molecule exhibited comparable in vivo efficacy of cognitive impairment relief to donepezil and memantine respectively in both β amyloid-induced and APP/PS1 double transgenic Alzheimer’s murine models at a substantially lower dose (0.25 mg/kg). Therefore, GIBH-130 constitu...
Journal Article•10.1016/J.CSBJ.2016.09.001•
Zebrafish small molecule screens: Taking the phenotypic plunge.

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Charles H. Williams1, Charles C. Hong1•
Vanderbilt University1
18 Sep 2016-Computational and structural biotechnology journal
TL;DR: The various model organisms used in phenotypic screens are discussed, with particular focus on zebrafish, which has emerged as a leading model of in vivo phenotypesic screens.
Abstract: Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early drug discovery. We discuss the various model organisms used in phenotypic screens, with particular focus on zebrafish, which has emerged as a leading model of in vivo phenotypic screens. Additionally, we anticipate therapeutic opportunities, particularly in orphan disease space, in the context of rapid advances in human Mendelian genetics, electronic health record (EHR)-enabled genome-phenome associations, and genome editing.
Journal Article•10.1007/S10295-015-1681-Y•
Discovery of novel drug targets and their functions using phenotypic screening of natural products

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Junghwa Chang1, Ho Jeong Kwon1•
Yonsei University1
01 Mar 2016-Journal of Industrial Microbiology & Biotechnology
TL;DR: A systematic approach to understanding the mode of action of natural products isolated using phenotypic screening involving chemical proteomics-based target identification is introduced.
Abstract: Natural products are valuable resources that provide a variety of bioactive compounds and natural pharmacophores in modern drug discovery. Discovery of biologically active natural products and unraveling their target proteins to understand their mode of action have always been critical hurdles for their development into clinical drugs. For effective discovery and development of bioactive natural products into novel therapeutic drugs, comprehensive screening and identification of target proteins are indispensable. In this review, a systematic approach to understanding the mode of action of natural products isolated using phenotypic screening involving chemical proteomics-based target identification is introduced. This review highlights three natural products recently discovered via phenotypic screening, namely glucopiericidin A, ecumicin, and terpestacin, as representative case studies to revisit the pivotal role of natural products as powerful tools in discovering the novel functions and druggability of targets in biological systems and pathological diseases of interest.
Journal Article•10.1080/17460441.2016.1227316•
Identification of protein binding partners of small molecules using label-free methods

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Chaitanya Saxena
31 Aug 2016-Expert Opinion on Drug Discovery
TL;DR: These methods are significantly shortening the time required for the identification and the downstream validation of targets and hence are gaining popularity as the method of choice for target identification.
Abstract: Introduction: Drug discovery efforts across the globe are chasing new drug targets and novel mechanisms of action. To support the identification of novel mechanisms of action, phenotype-based drug screening has significantly increased over the last decade. Along with the rise in phenotypic screening, methods and technologies that can help to identify drug targets of phenotypically screened ‘hits’ have also evolved significantly.Areas covered: This article provides an overview of successful examples, limitations and advances in small-molecule target identification methodologies. Primarily, the methods are described, where small-molecules without derivatization are used as test-molecules for identifying their direct binding protein partners, the targets, in detail. A brief discussion of other affinity chromatography coupled mass-spectrometry based target identification methods are also presented for comparative appreciation of label-free methods.Expert opinion: Label-free methods do not require (a) ...
Journal Article•10.1021/ACSCHEMBIO.6B00358•
Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation.

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Alvaro Cortes Cabrera1, Daniel Lucena-Agell2, Mariano Redondo-Horcajo2, Isabel Barasoain2, José Fernando Díaz2, Bernhard Fasching1, Paula M. Petrone1 •
Hoffmann-La Roche1, Spanish National Research Council2
14 Sep 2016-ACS Chemical Biology
TL;DR: For target identification, it is shown that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects.
Abstract: Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns.
Journal Article•10.1186/S12885-016-2816-X•
Hepatocellular carcinoma-targeted drug discovery through image-based phenotypic screening in co-cultures of HCC cells with hepatocytes.

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Jae Woo Jang1, Jae Woo Jang2, Yeonhwa Song1, Yeonhwa Song2, Kang Mo Kim3, Jin Sun Kim3, Eun Kyung Choi3, Joon Kim1, Haengran Seo2 •
Korea University1, Institut Pasteur Korea2, Asan Medical Center3
18 Oct 2016-BMC Cancer
TL;DR: This in vitro image-based phenotypic screening platform has the potential to be widely adopted in drug discovery research, since it promptly estimated anticancer activity and hepatotoxicity and elucidated functional roles of pyrimethamine during the apoptosis process in HCC.
Abstract: Hepatocellular carcinoma (HCC) is one of the most common malignant cancers worldwide and is associated with substantial mortality. Because HCCs have strong resistance to conventional chemotherapeutic agents, novel therapeutic strategies are needed to improve survival in HCC patients. Here, we developed a fluorescence image-based phenotypic screening system in vitro to identify HCC-specific drugs in co-cultures of HCC cells with hepatocytes. To this end, we identified two distinctive markers of HCC, CHALV1 and AFP, which are highly expressed in HCC cell lines and liver cancer patient-derived materials. We applied these markers to an HCC-specific drug screening system. Through pilot screening, we identified three anti-folate compounds that had HCC-specific cytotoxicity. Among them, pyrimethamine exhibited the greatest HCC-specific cytotoxicity. Interestingly, pyrimethamine significantly increased the size and number of lysosomes and subsequently induced the release of cathepsin B from the lysosome to the cytosol, which triggered caspase-3-dependent apoptosis in Huh7 (HCC) but not Fa2N-4 cells (immortalized hepatocytes). Importantly, Fa2N-4 cells had strong resistance to pyrimethamine relative to Huh7 cells in 2D and 3D culture systems. These results demonstrate that this in vitro image-based phenotypic screening platform has the potential to be widely adopted in drug discovery research, since we promptly estimated anticancer activity and hepatotoxicity and elucidated functional roles of pyrimethamine during the apoptosis process in HCC.
Journal Article•10.1158/1535-7163.MCT-15-0444•
Target identification in small cell lung cancer via integrated phenotypic screening and activity-based protein profiling

[...]

Jiannong Li, Bin Fang, Fumi Kinose, Yun Bai, Jae-Young Kim, Yian Ann Chen, Uwe Rix, John M. Koomen, Eric B. Haura 
15 Jan 2016-Molecular Cancer Therapeutics
TL;DR: Results demonstrate that phenotypic screening combined with ABPP can identify key disease drivers, suggesting that this approach, which combines new chemical probes and disease cell screens, has the potential to identify other important targets in other cancer types.
Abstract: To overcome hurdles in identifying key kinases in small cell lung cancer (SCLC), we integrated a target-agnostic phenotypic screen of kinase inhibitors with target identification using activity-based protein profiling (ABPP) in which a desthiobiotin-ATP probe was used. We screened 21 SCLC cell lines with known c-MYC amplification status for alterations in viability using a chemical library of 235 small-molecule kinase inhibitors. One screen hit compound was interrogated with ABPP, and, through this approach, we reidentified Aurora kinase B as a critical kinase in MYC-amplified SCLC cells. We next extended the platform to a second compound that had activity in SCLC cell lines lacking c-MYC amplification and identified TANK-binding kinase 1, a kinase that affects cell viability, polo-like kinase-1 signaling, G2-M arrest, and apoptosis in SCLC cells lacking MYC amplification. These results demonstrate that phenotypic screening combined with ABPP can identify key disease drivers, suggesting that this approach, which combines new chemical probes and disease cell screens, has the potential to identify other important targets in other cancer types. Mol Cancer Ther; 15(2); 334-42. ©2016 AACR.
Journal Article•10.1039/C5MD00493D•
eCF309 : a potent, selective and cell-permeable mTOR inhibitor

[...]

Craig Fraser1, Neil O. Carragher1, Asier Unciti-Broceta1•
University of Edinburgh1
16 Mar 2016-MedChemComm
TL;DR: A cell cycle inhibitor with micromolar potency that inhibits mTOR kinase activity is identified and following a rapid lead optimization campaign, the development of eCF309, an mTOR inhibitor displaying low nanomolar potency both in vitro and in cells and an excellent selectivity profile is reported.
Abstract: Kinase inhibitors capable of blocking the phosphorylation of protein substrates with high selectivity are essential to probe and elucidate the etiological role of such molecules and their signalling pathways. By addressing these biochemical questions in disease relevant cell-based and in vivo models, strong pharmacological evidence can be generated towards validating or disproving a target hypothesis. Pharmacological studies can also provide fundamental information to identify appropriate biomarkers and rational drug combination strategies and thereby facilitate clinical translation. However, due to the high number of kinases encoded by the human genome (>500) and their highly conserved catalytic domains, the development of such an elite class of inhibitors—a.k.a. high-quality chemical probes—represents a major challenge. Through a ligand-based inhibitor design, focused library synthesis and phenotypic screening to prioritize compounds with potent cell activity, we recently identified a cell cycle inhibitor with micromolar potency that inhibits mTOR kinase activity. Following a rapid lead optimization campaign, we report the development of eCF309, an mTOR inhibitor displaying low nanomolar potency both in vitro and in cells and an excellent selectivity profile (S-score (35%) = 0.01 at 10 μM).
Journal Article•10.1039/C6MT00003G•
Combinatorial phenotypic screen uncovers unrecognized family of extended thiourea inhibitors with copper-dependent anti-staphylococcal activity

[...]

Alex G. Dalecki1, Aruni P. Malalasekera2, Kaitlyn Schaaf1, Olaf Kutsch1, Stefan H. Bossmann2, Frank Wolschendorf1 •
University of Alabama at Birmingham1, Kansas State University2
20 Apr 2016-Metallomics
TL;DR: The first concerted screening effort to identify copper-dependent inhibitors of Staphylococcus aureus was described, and it was demonstrated that copper binding by the NNSN motif is highly unusual and likely responsible for the promising biological qualities of these compounds.
Abstract: The continuous rise of multi-drug resistant pathogenic bacteria has become a significant challenge for the health care system. In particular, novel drugs to treat infections of methicillin-resistant Staphylococcus aureus strains (MRSA) are needed, but traditional drug discovery campaigns have largely failed to deliver clinically suitable antibiotics. More than simply new drugs, new drug discovery approaches are needed to combat bacterial resistance. The recently described phenomenon of copper-dependent inhibitors has galvanized research exploring the use of metal-coordinating molecules to harness copper's natural antibacterial properties for therapeutic purposes. Here, we describe the results of the first concerted screening effort to identify copper-dependent inhibitors of Staphylococcus aureus. A standard library of 10 000 compounds was assayed for anti-staphylococcal activity, with hits defined as those compounds with a strict copper-dependent inhibitory activity. A total of 53 copper-dependent hit molecules were uncovered, similar to the copper independent hit rate of a traditionally executed campaign conducted in parallel on the same library. Most prominent was a hit family with an extended thiourea core structure, termed the NNSN motif. This motif resulted in copper-dependent and copper-specific S. aureus inhibition, while simultaneously being well tolerated by eukaryotic cells. Importantly, we could demonstrate that copper binding by the NNSN motif is highly unusual and likely responsible for the promising biological qualities of these compounds. A subsequent chemoinformatic meta-analysis of the ChEMBL chemical database confirmed the NNSNs as an unrecognized staphylococcal inhibitor, despite the family's presence in many chemical screening libraries. Thus, our copper-biased screen has proven able to discover inhibitors within previously screened libraries, offering a mechanism to reinvigorate exhausted molecular collections.
Journal Article•10.1016/J.BMCL.2016.09.043•
Identification and optimization of a new series of anti-tubercular quinazolinones.

[...]

Cédric Couturier, Christine Lair, Alain Pellet, Anna M. Upton, Takushi Kaneko, Corinne Perron, Eric Cogo, Jerome Menegotto, Armin Bauer, Bodo Scheiper, Sophie Lagrange, Eric Bacqué 
01 Nov 2016-Bioorganic & Medicinal Chemistry Letters
TL;DR: A high throughput phenotypic screening against Mycobacterium smegmatis led to the discovery of a new class of bacteriostatic, highly hydrophobic antitubercular quinazolinones that potently inhibited the in vitro growth of either extracellular or intramacrophagic M. tuberculosis (Mtb), via modulation of an unidentified but yet novel target.
Journal Article•10.1039/C6MD00159A•
Discovery of 4,6-disubstituted pyrimidines as potent inhibitors of the heat shock factor 1 (HSF1) stress pathway and CDK9.

[...]

Carl S. Rye1, Nicola E. A. Chessum1, Scott G. Lamont2, Kurt Gordon Pike2, Paul Faulder2, Julie Demeritt2, Paul D. Kemmitt2, Julie A. Tucker2, Lorenzo Zani1, Matthew D. Cheeseman1, Rosie Isaac2, Louise Goodwin2, Joanna Boros2, Florence I. Raynaud1, Angela Hayes1, Alan T. Henley1, Emmanuel de Billy1, Christopher J. Lynch1, Swee Y. Sharp1, Robert te Poele1, Lisa O’ Fee1, Kevin Michael Foote2, Stephen Green2, Paul Workman1, Keith Jones1 •
Institute of Cancer Research1, AstraZeneca2
11 Aug 2016-MedChemComm
TL;DR: In this paper, an unbiased phenotypic screen was employed to discover inhibitors of the heat shock factor 1 (HSF1) stress pathway, and an initial hit (1) based on a 4,6 pyrimidine scaffold (2.00 μM) was identified.
Abstract: Heat shock factor 1 (HSF1) is a transcription factor that plays key roles in cancer, including providing a mechanism for cell survival under proteotoxic stress. Therefore, inhibition of the HSF1-stress pathway represents an exciting new opportunity in cancer treatment. We employed an unbiased phenotypic screen to discover inhibitors of the HSF1-stress pathway. Using this approach we identified an initial hit (1) based on a 4,6-pyrimidine scaffold (2.00 μM). Optimisation of cellular SAR led to an inhibitor with improved potency (25, 15 nM) in the HSF1 phenotypic assay. The 4,6-pyrimidine 25 was also shown to have high potency against the CDK9 enzyme (3 nM).
Journal Article•10.1016/J.BBRC.2016.08.108•
Selective killing of cancer cells by small molecules targeting heat shock stress response

[...]

Daniel Zhang, Bin Zhang
30 Sep 2016-Biochemical and Biophysical Research Communications
TL;DR: Several novel functional inhibitors of HSF1 pathway were identified with different chemotypes and demonstrate nanomolar potency toward multiple cancer cell lines with relatively low cytotoxicity to normal cells, validatingHSF1 dependent mechanism of action.
Journal Article•10.1177/1087057115622431•
Target Identification of Compounds from a Cell Viability Phenotypic Screen Using a Bead/Lysate-Based Affinity Capture Platform.

[...]

Hua Tang, Shannon Duggan, Paul L. Richardson, Violeta L. Marin, Scott E. Warder, Shaun M. McLoughlin 
01 Feb 2016-Journal of Biomolecular Screening
TL;DR: A three-pronged approach to target deconvolution by affinity capture is described, including the implementation of a uniqueness index that helps discriminate between bona fide targets and background.
Abstract: The pharmaceutical industry has been continually challenged by dwindling target diversity. To obviate this trend, phenotypic screens have been adopted, complementing target-centric screening approaches. Phenotypic screens identify drug leads using clinically relevant and translatable mechanisms, remaining agnostic to targets. While target anonymity is advantageous early in the drug discovery process, it poses challenges to hit progression, including the development of backup series, retaining desired pharmacology during optimization, discovery of markers, and understanding mechanism-driven toxicity. Consequently, significant effort has been expended to elaborate the targets and mechanisms at work for promising screening hits. Affinity capture is commonly leveraged, where the compounds are linked to beads and targets are abstracted from cell homogenates. This technique has proven effective for identifying targets of kinase, PARP, and HDAC inhibitors, and examples of new targets have been reported. Herein, a three-pronged approach to target deconvolution by affinity capture is described, including the implementation of a uniqueness index that helps discriminate between bona fide targets and background. The effectiveness of this approach is demonstrated using characterized compounds that act on known and noncanonical target classes. The platform is subsequently applied to phenotypic screening hits, identifying candidate targets. The success rate of bead-based affinity capture is discussed.
Journal Article•10.1021/ACS.JPROTEOME.6B00214•
Pulse Proteolysis and Precipitation for Target Identification

[...]

Rogério Valim Trindade1, Antonio Pinto1, Diógenes Santiago Santos1, Cristiano Valim Bizarro1•
Pontifícia Universidade Católica do Rio Grande do Sul1
20 Jun 2016-Journal of Proteome Research
TL;DR: In this method, proteins incubated with or without a ligand and submitted to a brief proteolytic pulse are directly analyzed and compared using a label-free semiquantitative mass spectrometry strategy, dispensing the SDS-PAGE readout and greatly improving the throughput.
Abstract: In recent years, phenotypic screening has assumed a leading role in drug discovery efforts. However, development of new drugs from bioactive compounds obtained in screening campaigns requires identification of the cellular targets responsible for their biological activities. A new energetics-based method for target identification is presented: pulse proteolysis and precipitation for target identification (PePTID). In this method, proteins incubated with or without a ligand and submitted to a brief proteolytic pulse are directly analyzed and compared using a label-free semiquantitative mass spectrometry strategy, dispensing the SDS-PAGE readout and greatly improving the throughput. As a proof-of-concept, we applied the PePTID method to identify ATP-binding proteins in Mycobacterium smegmatis, a model system for Mycobacterium tuberculosis, the etiological agent of tuberculosis.
Journal Article•10.1021/ACSCHEMBIO.5B00772•
Discovery of Novel Small Molecules that Activate Satellite Cell Proliferation and Enhance Repair of Damaged Muscle

[...]

Andrew N. Billin1, Marcus Bantscheff, Gerard Drewes, Sonja Ghidelli-Disse, Jason A. Holt1, Henning F. Kramer1, Alan J. McDougal1, Terrence L. Smalley1, Carrow I. Wells1, William J. Zuercher1, Brad R. Henke1 •
Research Triangle Park1
07 Jan 2016-ACS Chemical Biology
TL;DR: Cell-based proteomics experiments were conducted in an attempt to identify the molecular target(s) responsible for the potentiation of the satellite cell proliferation, providing the foundation for future efforts to design improved small molecules as potential therapeutics for muscle repair and regeneration.
Abstract: Skeletal muscle progenitor stem cells (referred to as satellite cells) represent the primary pool of stem cells in adult skeletal muscle responsible for the generation of new skeletal muscle in response to injury. Satellite cells derived from aged muscle display a significant reduction in regenerative capacity to form functional muscle. This decrease in functional recovery has been attributed to a decrease in proliferative capacity of satellite cells. Hence, agents that enhance the proliferative abilities of satellite cells may hold promise as therapies for a variety of pathological settings, including repair of injured muscle and age- or disease-associated muscle wasting. Through phenotypic screening of isolated murine satellite cells, we identified a series of 2,4-diaminopyrimidines (e.g., 2) that increased satellite cell proliferation. Importantly, compound 2 was effective in accelerating repair of damaged skeletal muscle in an in vivo mouse model of skeletal muscle injury. While these compounds were originally prepared as c-Jun N-terminal kinase 1 (JNK-1) inhibitors, structure-activity analyses indicated JNK-1 inhibition does not correlate with satellite cell activity. Screening against a broad panel of kinases did not result in identification of an obvious molecular target, so we conducted cell-based proteomics experiments in an attempt to identify the molecular target(s) responsible for the potentiation of the satellite cell proliferation. These data provide the foundation for future efforts to design improved small molecules as potential therapeutics for muscle repair and regeneration.

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