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Matsuo B, Granados A, Levitre G, Molander GA. Photochemical Methods Applied to DNA Encoded Library (DEL) Synthesis. Acc Chem Res 2023; 56:385-401. [PMID: 36656960 PMCID: PMC10415088 DOI: 10.1021/acs.accounts.2c00778] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA-encoded library technology (DELT) is a new screening modality that allows efficient, cost-effective, and rapid identification of small molecules with potential biological activity. This emerging technique represents an enormous advancement that, in combination with other technologies such as high-throughput screening (HTS), fragment-based lead generation, and structure-based drug design, has the potential to transform how drug discovery is carried out. DELT is a hybrid technique in which chemically synthesized compounds are linked to unique genetic tags (or "barcodes") that contain readable information. In this way, millions to billions of building blocks (BBs) attached on-DNA via split-and-pool synthesis can be evaluated against a biological target in a single experiment. Polymerase chain reaction (PCR) amplification and next-generation sequencing (NGS) analysis of the unique sequence of oligonucleotides in the DNA tag are used to identify those ligands with high affinity for the target. This innovative fusion of genetic and chemical technologies was conceived in 1992 by Brenner and Lerner (Proc. Natl. Acad. Sci. 1992, 89, 5381-5383) and is under accelerated development with the implementation of new synthetic techniques and protocols that are compatible with DNA. In fact, reaction compatibility is a key parameter to increasing the chances of identification of a drug target ligand, and a central focus has been the development of new transformations and the transition to robust protocols for on-DNA synthesis. Because the sole use of the DNA tag is as an amplifiable identification barcode, its structural integrity during a new chemical process is mandatory. As such, the use of these sensitive, polyfunctional biological molecules as substrates typically requires aqueous solutions within defined pH and temperature ranges, which is considered a notable challenge in DEL synthesis.Using low-energy visible light as the driving force to promote chemical transformations represents an attractive alternative to classical synthetic methods, and it is an important and well-established synthetic tool for forging chemical bonds in a unique way via radical intermediates. Recent advances in the field of photocatalysis are extraordinary, and this powerful research arena is still under continuous development. Several applications taking advantage of the mild reaction conditions of photoinduced transformations have been directed toward DEL synthesis, allowing the expansion of chemical space available for the evaluation of new building blocks on-DNA. There are no doubts that visible-light-driven reactions have become one of the most powerful approaches for DELT, given the easy way they provide to construct new bonds and the challenges to achieve equal success via classical protocols.Key characteristics of photocatalytic synthesis include the short reaction times and efficiency, which translate into retention of DNA integrity. In this Account, we describe recent advances in the photoinduced diversification of building blocks prepared on-DNA, highlighting the amenability of the techniques employed for preserving the genetic structure of the molecules. We demonstrate with recent research from our group the applicability of photocatalysis to the field and include in the summary a table containing all the photoinduced methods reported to date for DELT, demonstrating their key aspects such as scope, applications, and DNA compatibilities. With this information, practitioners are provided with compelling reasons for developing/choosing photocatalytic methods for DELT applications.
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Affiliation(s)
- Bianca Matsuo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Albert Granados
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Guillaume Levitre
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
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2
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Zhang YL, Moran SP, Allen A, Baez-Nieto D, Xu Q, Wang LA, Martenis WE, Sacher JR, Gale JP, Weïwer M, Wagner FF, Pan JQ. Novel Fluorescence-Based High-Throughput FLIPR Assay Utilizing Membrane-Tethered Genetic Calcium Sensors to Identify T-Type Calcium Channel Modulators. ACS Pharmacol Transl Sci 2022; 5:156-168. [PMID: 35311021 PMCID: PMC8923061 DOI: 10.1021/acsptsci.1c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Indexed: 11/28/2022]
Abstract
T-type voltage-gated Ca2+ channels have been implicated in many human disorders, and there has been increasing interest in developing highly selective and potent T-type Ca2+ channel modulators for potential clinical use. However, the unique biophysical properties of T-type Ca2+ channels are not conducive for developing high-throughput screening (HTS) assays to identify modulators, particularly potentiators. To illustrate, T-type Ca2+ channels are largely inactivated and unable to open to allow Ca2+ influx at -25 mV, the typical resting membrane potential of the cell lines commonly used in cellular screening assays. To address this issue, we developed cell lines that express Kir2.3 channels to hyperpolarize the membrane potential to -70 mV, thus allowing T-type channels to return to their resting state where they can be subsequently activated by membrane depolarization in the presence of extracellular KCl. Furthermore, to simplify the HTS assay and to reduce reagent cost, we stably expressed a membrane-tethered genetic calcium sensor, GCaMP6s-CAAX, that displays superior signal to the background compared to the untethered GCaMP6s or the synthetic Ca2+ sensor Fluo-4AM. Here, we describe a novel GCaMP6s-CAAX-based calcium assay utilizing a high-throughput fluorometric imaging plate reader (Molecular Devices, Sunnyvale, CA) format that can identify both activators and inhibitors of T-type Ca2+ channels. Lastly, we demonstrate the utility of this novel fluorescence-based assay to evaluate the activities of two distinct G-protein-coupled receptors, thus expanding the use of GCaMP6s-CAAX to a wide range of applications relevant for developing cellular assays in drug discovery.
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3
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Melander RJ, Mattingly AE, Melander C. Phenotypic screening of compound libraries as a platform for the identification of antibiotic adjuvants: Identification of colistin adjuvants from a natural product library. Methods Enzymol 2021; 665:153-176. [PMID: 35379433 PMCID: PMC10942738 DOI: 10.1016/bs.mie.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The identification of antibiotic adjuvants, small molecules that potentiate the activity of conventional antibiotics, provides an orthogonal approach to the development of new antibiotics in the fight against drug resistant bacterial infections. Methods to identify novel adjuvants could potentially aid efforts to overcome the increasing prevalence of resistance and stave off the onset of a "post-antibiotic era." Phenotypic whole cell screens allow for the identification of hits with the necessary properties to access their biomolecular target, and may also facilitate the discovery of novel adjuvant targets. A phenotypic screening platform is outlined, in which a natural product library was explored for activity with antibiotics from several mechanistically distinct classes against clinically important bacterial species. General approaches to delineating the mechanism of action of hit compounds identified from phenotypic screens are described, followed by specific approaches to uncovering the mechanism of action of the colistin adjuvants identified from the natural product screen.
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Affiliation(s)
- Roberta J Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Anne E Mattingly
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Christian Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.
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4
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Mathai N, Stork C, Kirchmair J. BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space. Int J Mol Sci 2021; 22:ijms22157773. [PMID: 34360558 PMCID: PMC8346018 DOI: 10.3390/ijms22157773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022] Open
Abstract
Experimental screening of large sets of compounds against macromolecular targets is a key strategy to identify novel bioactivities. However, large-scale screening requires substantial experimental resources and is time-consuming and challenging. Therefore, small to medium-sized compound libraries with a high chance of producing genuine hits on an arbitrary protein of interest would be of great value to fields related to early drug discovery, in particular biochemical and cell research. Here, we present a computational approach that incorporates drug-likeness, predicted bioactivities, biological space coverage, and target novelty, to generate optimized compound libraries with maximized chances of producing genuine hits for a wide range of proteins. The computational approach evaluates drug-likeness with a set of established rules, predicts bioactivities with a validated, similarity-based approach, and optimizes the composition of small sets of compounds towards maximum target coverage and novelty. We found that, in comparison to the random selection of compounds for a library, our approach generates substantially improved compound sets. Quantified as the "fitness" of compound libraries, the calculated improvements ranged from +60% (for a library of 15,000 compounds) to +184% (for a library of 1000 compounds). The best of the optimized compound libraries prepared in this work are available for download as a dataset bundle ("BonMOLière").
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Affiliation(s)
- Neann Mathai
- Computational Biology Unit (CBU) and Department of Chemistry, University of Bergen, N-5020 Bergen, Norway;
| | - Conrad Stork
- Center for Bioinformatics (ZBH), Department of Informatics, Universität Hamburg, 20146 Hamburg, Germany;
| | - Johannes Kirchmair
- Computational Biology Unit (CBU) and Department of Chemistry, University of Bergen, N-5020 Bergen, Norway;
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
- Correspondence:
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5
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Clemons PA, Bittker JA, Wagner FF, Hands A, Dančík V, Schreiber SL, Choudhary A, Wagner BK. The Use of Informer Sets in Screening: Perspectives on an Efficient Strategy to Identify New Probes. SLAS DISCOVERY 2021; 26:855-861. [PMID: 34130532 DOI: 10.1177/24725552211019410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Small-molecule discovery typically involves large-scale screening campaigns, spanning multiple compound collections. However, such activities can be cost- or time-prohibitive, especially when using complex assay systems, limiting the number of compounds tested. Further, low hit rates can make the process inefficient. Sparse coverage of chemical structure or biological activity space can lead to limited success in a primary screen and represents a missed opportunity by virtue of selecting the "wrong" compounds to test. Thus, the choice of screening collections becomes of paramount importance. In this perspective, we discuss the utility of generating "informer sets" for small-molecule discovery, and how this strategy can be leveraged to prioritize probe candidates. While many researchers may assume that informer sets are focused on particular targets (e.g., kinases) or processes (e.g., autophagy), efforts to assemble informer sets based on historical bioactivity or successful human exposure (e.g., repurposing collections) have shown promise as well. Another method for generating informer sets is based on chemical structure, particularly when the compounds have unknown activities and targets. We describe our efforts to screen an informer set representing a collection of 100,000 small molecules synthesized through diversity-oriented synthesis (DOS). This process enables researchers to identify activity early and more extensively screen only a few chemical scaffolds, rather than the entire collection. This elegant and economic outcome is a goal of the informer set approach. Here, we aim not only to shed light on this process, but also to promote the use of informer sets more widely in small-molecule discovery projects.
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Affiliation(s)
- Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Joshua A Bittker
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA.,Vertex Pharmaceuticals, Boston, MA, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Allison Hands
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
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6
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Quancard J, Bach A, Cox B, Craft R, Finsinger D, Guéret SM, Hartung IV, Laufer S, Messinger J, Sbardella G, Koolman HF. The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Phenotypic Drug Discovery. ChemMedChem 2021; 16:1736-1739. [PMID: 33825353 DOI: 10.1002/cmdc.202100041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 12/16/2022]
Abstract
Phenotypic drug discovery has a long track record of delivering innovative drugs and has received renewed attention in the last few years. The promise of this approach, however, comes with several challenges that should be addressed to avoid wasting time and resources on drugs with undesired modes of action or, worse, false-positive hits. In this set of best practices, we go over the essential steps of phenotypic drug discovery and provide guidance on how to increase the chance of success in identifying validated and relevant chemical starting points for optimization: selecting the right assay, selecting the right compound screening library and developing appropriate hit validation assays. Then, we highlight the importance of initiating studies to determine the mode of action of the identified hits early and present the current state of the art.
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Affiliation(s)
- Jean Quancard
- Global Discovery Chemistry, Novartis Institute For Biomedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Brian Cox
- Pharmaceutical Chemistry, School of Life Sciences, University of Sussex, Falmer, East Sussex, BN1 9RH, UK
| | - Russell Craft
- Medicinal Chemistry, Symeres, Kadijk 3, 9747AT, Groningen (The, Netherlands
| | - Dirk Finsinger
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Stéphanie M Guéret
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Stefan Laufer
- Pharmaceutical&Medicinal Chemistry, Institute of Pharmacy & Biochemistry, Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72070 Tuebingen, Germany
| | - Josef Messinger
- Medicine Design, Orionpharma, Orionintie 1, 02101, Espoo, Finland
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab., University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano-SA, Italy
| | - Hannes F Koolman
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
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7
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Demeritte A, Wuest WM. A look around the West Indies: The spices of life are secondary metabolites. Bioorg Med Chem 2020; 28:115792. [PMID: 33038665 PMCID: PMC7528826 DOI: 10.1016/j.bmc.2020.115792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/22/2022]
Abstract
Natural products possess a wide range of bioactivities with potential for therapeutic usage. While the distribution of these molecules can vary greatly there is some correlation that exists between the biodiversity of an environment and the uniqueness and concentration of natural products found in that region or area. The Caribbean and pan-Caribbean area is home to thousands of species of endemic fauna and flora providing huge potential for natural product discovery and by way, potential leads for drug development. This can especially be said for marine natural products as many of are rapidly diluted through diffusion once released and therefore are highly potent to achieve long reaching effects. This review seeks to highlight a small selection of marine natural products from the Caribbean region which possess antiproliferative, anti-inflammatory and antipathogenic properties while highlighting any synthetic efforts towards bioactive analogs.
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Affiliation(s)
- Adrian Demeritte
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - William M Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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8
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Busby SA, Carbonneau S, Concannon J, Dumelin CE, Lee Y, Numao S, Renaud N, Smith TM, Auld DS. Advancements in Assay Technologies and Strategies to Enable Drug Discovery. ACS Chem Biol 2020; 15:2636-2648. [PMID: 32880443 DOI: 10.1021/acschembio.0c00495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Assays drive drug discovery from the exploratory phases to the clinical testing of drug candidates. As such, numerous assay technologies and methodologies have arisen to support drug discovery efforts. Robust identification and characterization of tractable chemical matter requires biochemical, biophysical, and cellular approaches and often benefits from high-throughput methods. To increase throughput, efforts have been made to provide assays in miniaturized volumes which can be arrayed in microtiter plates to support the testing of as many as 100,000 samples/day. Alongside these efforts has been the growth of microtiter plate-free formats with encoded libraries that can support the screening of billions of compounds, a hunt for new drug modalities, as well as emphasis on more disease relevant formats using complex cell models of disease states. This review will focus on recent developments in high-throughput assay technologies applied to identify starting points for drug discovery. We also provide recommendations on strategies for implementing various assay types to select high quality leads for drug development.
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Affiliation(s)
- Scott A. Busby
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - John Concannon
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | | | - YounKyoung Lee
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Shin Numao
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Thomas M. Smith
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Douglas S. Auld
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
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9
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Lee OW, Austin S, Gamma M, Cheff DM, Lee TD, Wilson KM, Johnson J, Travers J, Braisted JC, Guha R, Klumpp-Thomas C, Shen M, Hall MD. Cytotoxic Profiling of Annotated and Diverse Chemical Libraries Using Quantitative High-Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:9-20. [PMID: 31498718 PMCID: PMC10791069 DOI: 10.1177/2472555219873068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cell-based phenotypic screening is a commonly used approach to discover biological pathways, novel drug targets, chemical probes, and high-quality hit-to-lead molecules. Many hits identified from high-throughput screening campaigns are ruled out through a series of follow-up potency, selectivity/specificity, and cytotoxicity assays. Prioritization of molecules with little or no cytotoxicity for downstream evaluation can influence the future direction of projects, so cytotoxicity profiling of screening libraries at an early stage is essential for increasing the likelihood of candidate success. In this study, we assessed the cell-based cytotoxicity of nearly 10,000 compounds in the National Institutes of Health, National Center for Advancing Translational Sciences annotated libraries and more than 100,000 compounds in a diversity library against four normal cell lines (HEK 293, NIH 3T3, CRL-7250, and HaCat) and one cancer cell line (KB 3-1, a HeLa subline). This large-scale library profiling was analyzed for overall screening outcomes, hit rates, pan-activity, and selectivity. For the annotated library, we also examined the primary targets and mechanistic pathways regularly associated with cell death. To our knowledge, this is the first study to use high-throughput screening to profile a large screening collection (>100,000 compounds) for cytotoxicity in both normal and cancer cell lines. The results generated here constitute a valuable resource for the scientific community and provide insight into the extent of cytotoxic compounds in screening libraries, allowing for the identification and avoidance of compounds with cytotoxicity during high-throughput screening campaigns.
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Affiliation(s)
- Olivia W. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Shelley Austin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Madison Gamma
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Dorian M. Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Tobie D. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Joseph Johnson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - John C. Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Rajarshi Guha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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10
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Geerts H, Wikswo J, van der Graaf PH, Bai JPF, Gaiteri C, Bennett D, Swalley SE, Schuck E, Kaddurah-Daouk R, Tsaioun K, Pelleymounter M. Quantitative Systems Pharmacology for Neuroscience Drug Discovery and Development: Current Status, Opportunities, and Challenges. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2019; 9:5-20. [PMID: 31674729 PMCID: PMC6966183 DOI: 10.1002/psp4.12478] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022]
Abstract
The substantial progress made in the basic sciences of the brain has yet to be adequately translated to successful clinical therapeutics to treat central nervous system (CNS) diseases. Possible explanations include the lack of quantitative and validated biomarkers, the subjective nature of many clinical endpoints, and complex pharmacokinetic/pharmacodynamic relationships, but also the possibility that highly selective drugs in the CNS do not reflect the complex interactions of different brain circuits. Although computational systems pharmacology modeling designed to capture essential components of complex biological systems has been increasingly accepted in pharmaceutical research and development for oncology, inflammation, and metabolic disorders, the uptake in the CNS field has been very modest. In this article, a cross-disciplinary group with representatives from academia, pharma, regulatory, and funding agencies make the case that the identification and exploitation of CNS therapeutic targets for drug discovery and development can benefit greatly from a system and network approach that can span the gap between molecular pathways and the neuronal circuits that ultimately regulate brain activity and behavior. The National Institute of Neurological Disorders and Stroke (NINDS), in collaboration with the National Institute on Aging (NIA), National Institute of Mental Health (NIMH), National Institute on Drug Abuse (NIDA), and National Center for Advancing Translational Sciences (NCATS), convened a workshop to explore and evaluate the potential of a quantitative systems pharmacology (QSP) approach to CNS drug discovery and development. The objective of the workshop was to identify the challenges and opportunities of QSP as an approach to accelerate drug discovery and development in the field of CNS disorders. In particular, the workshop examined the potential for computational neuroscience to perform QSP-based interrogation of the mechanism of action for CNS diseases, along with a more accurate and comprehensive method for evaluating drug effects and optimizing the design of clinical trials. Following up on an earlier white paper on the use of QSP in general disease mechanism of action and drug discovery, this report focuses on new applications, opportunities, and the accompanying limitations of QSP as an approach to drug development in the CNS therapeutic area based on the discussions in the workshop with various stakeholders.
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Affiliation(s)
- Hugo Geerts
- In Silico Biosciences, Berwyn, Pennsylvania, USA
| | - John Wikswo
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Jane P F Bai
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University, Chicago, Illinois, USA
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University, Chicago, Illinois, USA
| | | | | | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, USA
| | - Katya Tsaioun
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mary Pelleymounter
- Division of Translational Research, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
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11
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Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. Cell Chem Biol 2019; 26:765-777.e3. [PMID: 30956147 DOI: 10.1016/j.chembiol.2019.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/28/2018] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Abstract
Libraries of well-annotated small molecules have many uses in chemical genetics, drug discovery, and therapeutic repurposing. Multiple libraries are available, but few data-driven approaches exist to compare them and design new libraries. We describe an approach to scoring and creating libraries based on binding selectivity, target coverage, and induced cellular phenotypes as well as chemical structure, stage of clinical development, and user preference. The approach, available via the online tool http://www.smallmoleculesuite.org, assembles sets of compounds with the lowest possible off-target overlap. Analysis of six kinase inhibitor libraries using our approach reveals dramatic differences among them and led us to design a new LSP-OptimalKinase library that outperforms existing collections in target coverage and compact size. We also describe a mechanism of action library that optimally covers 1,852 targets in the liganded genome. Our tools facilitate creation, analysis, and updates of both private and public compound collections.
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Affiliation(s)
- Nienke Moret
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Marc Hafner
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuan Wang
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Eugen Lounkine
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 360 Longwood Avenue, Longwood Center 2209, Boston, MA 02115, USA
| | - Nathanael Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 360 Longwood Avenue, Longwood Center 2209, Boston, MA 02115, USA
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Peter K Sorger
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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12
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Uliassi E, Peña-Altamira LE, Morales AV, Massenzio F, Petralla S, Rossi M, Roberti M, Martinez Gonzalez L, Martinez A, Monti B, Bolognesi ML. A Focused Library of Psychotropic Analogues with Neuroprotective and Neuroregenerative Potential. ACS Chem Neurosci 2019; 10:279-294. [PMID: 30253086 DOI: 10.1021/acschemneuro.8b00242] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Overcoming the lack of effective treatments and the continuous clinical trial failures in neurodegenerative drug discovery might require a shift from the prevailing paradigm targeting pathogenesis to the one targeting simultaneously neuroprotection and neuroregeneration. In the studies reported herein, we sought to identify small molecules that might exert neuroprotective and neuroregenerative potential as tools against neurodegenerative diseases. In doing so, we started from the reported neuroprotective/neuroregenerative mechanisms of psychotropic drugs featuring a tricyclic alkylamine scaffold. Thus, we designed a focused-chemical library of 36 entries aimed at exploring the structural requirements for efficient neuroprotective/neuroregenerative cellular activity, without the manifestation of toxicity. To this aim, we developed a synthetic protocol, which overcame the limited applicability of previously reported procedures. Next, we evaluated the synthesized compounds through a phenotypic screening pipeline, based on primary neuronal systems. Phenothiazine 2Bc showed improved neuroregenerative and neuroprotective properties with respect to reference drug desipramine (2Aa). Importantly, we have also shown that 2Bc outperformed currently available drugs in cell models of Alzheimer's and Parkinson's diseases and attenuates microglial activation by reducing iNOS expression.
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Affiliation(s)
- Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Luis Emiliano Peña-Altamira
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Aixa V. Morales
- Department of Cellular, Molecular and Developmental Neurobiology, Cajal Institute, Consejo Superior de Investigaciones Científicas (CSIC), Av. Doctor Arce, 37, Madrid 28002, Spain
| | - Francesca Massenzio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Sabrina Petralla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Michele Rossi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Loreto Martinez Gonzalez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - Ana Martinez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - Barbara Monti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
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13
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Brown DG, Boström J. Where Do Recent Small Molecule Clinical Development Candidates Come From? J Med Chem 2018; 61:9442-9468. [DOI: 10.1021/acs.jmedchem.8b00675] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Dean G. Brown
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jonas Boström
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Gothenburg SE-431 83, Sweden
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14
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Orellana A, García-González V, López R, Pascual-Guiral S, Lozoya E, Díaz J, Casals D, Barrena A, Paris S, Andrés M, Segarra V, Vilella D, Malhotra R, Eastwood P, Planagumà A, Miralpeix M, Nueda A. Application of a phenotypic drug discovery strategy to identify biological and chemical starting points for inhibition of TSLP production in lung epithelial cells. PLoS One 2018; 13:e0189247. [PMID: 29320511 PMCID: PMC5761851 DOI: 10.1371/journal.pone.0189247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
Thymic stromal lymphopoietin (TSLP) is a cytokine released by human lung epithelium in response to external insult. Considered as a master switch in T helper 2 lymphocyte (Th2) mediated responses, TSLP is believed to play a key role in allergic diseases including asthma. The aim of this study was to use a phenotypic approach to identify new biological and chemical starting points for inhibition of TSLP production in human bronchial epithelial cells (NHBE), with the objective of reducing Th2-mediated airway inflammation. To this end, a phenotypic screen was performed using poly I:C / IL-4 stimulated NHBE cells interrogated with a 44,974 compound library. As a result, 85 hits which downregulated TSLP protein and mRNA levels were identified and a representative subset of 7 hits was selected for further characterization. These molecules inhibited the activity of several members of the MAPK, PI3K and tyrosine kinase families and some of them have been reported as modulators of cellular phenotypic endpoints like cell-cell contacts, microtubule polymerization and caspase activation. Characterization of the biological profile of the hits suggested that mTOR could be a key activity involved in the regulation of TSLP production in NHBE cells. Among other targeted kinases, inhibition of p38 MAPK and JAK kinases showed different degrees of correlation with TSLP downregulation, while Syk kinase did not seem to be related. Overall, inhibition of TSLP production by the selected hits, rather than resulting from inhibition of single isolated targets, appeared to be due to a combination of activities with different levels of relevance. Finally, a hit expansion exercise yielded additional active compounds that could be amenable to further optimization, providing an opportunity to dissociate TSLP inhibition from other non-desired activities. This study illustrates the potential of phenotypic drug discovery to complement target based approaches by providing new chemistry and biology leads.
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Affiliation(s)
- Adelina Orellana
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Rosa López
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Estrella Lozoya
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Julia Díaz
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Daniel Casals
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Antolín Barrena
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Stephane Paris
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Miriam Andrés
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Victor Segarra
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Dolors Vilella
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Rajneesh Malhotra
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Paul Eastwood
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Anna Planagumà
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Arsenio Nueda
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
- * E-mail:
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15
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Ekins S, Clark AM, Dole K, Gregory K, Mcnutt AM, Spektor AC, Weatherall C, Litterman NK, Bunin BA. Data Mining and Computational Modeling of High-Throughput Screening Datasets. Methods Mol Biol 2018; 1755:197-221. [PMID: 29671272 DOI: 10.1007/978-1-4939-7724-6_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We are now seeing the benefit of investments made over the last decade in high-throughput screening (HTS) that is resulting in large structure activity datasets entering public and open databases such as ChEMBL and PubChem. The growth of academic HTS screening centers and the increasing move to academia for early stage drug discovery suggests a great need for the informatics tools and methods to mine such data and learn from it. Collaborative Drug Discovery, Inc. (CDD) has developed a number of tools for storing, mining, securely and selectively sharing, as well as learning from such HTS data. We present a new web based data mining and visualization module directly within the CDD Vault platform for high-throughput drug discovery data that makes use of a novel technology stack following modern reactive design principles. We also describe CDD Models within the CDD Vault platform that enables researchers to share models, share predictions from models, and create models from distributed, heterogeneous data. Our system is built on top of the Collaborative Drug Discovery Vault Activity and Registration data repository ecosystem which allows users to manipulate and visualize thousands of molecules in real time. This can be performed in any browser on any platform. In this chapter we present examples of its use with public datasets in CDD Vault. Such approaches can complement other cheminformatics tools, whether open source or commercial, in providing approaches for data mining and modeling of HTS data.
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Affiliation(s)
- Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA.
| | - Alex M Clark
- Collaborative Drug Discovery, Inc., Burlingame, CA, USA
- Molecular Materials Informatics, Inc., Montreal, QC, Canada
| | - Krishna Dole
- Collaborative Drug Discovery, Inc., Burlingame, CA, USA
| | | | | | | | | | | | - Barry A Bunin
- Collaborative Drug Discovery, Inc., Burlingame, CA, USA
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16
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CHEMGENIE: integration of chemogenomics data for applications in chemical biology. Drug Discov Today 2017; 23:151-160. [PMID: 28917822 DOI: 10.1016/j.drudis.2017.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/25/2017] [Accepted: 09/08/2017] [Indexed: 12/16/2022]
Abstract
Increasing amounts of biological data are accumulating in the pharmaceutical industry and academic institutions. However, data does not equal actionable information, and guidelines for appropriate data capture, harmonization, integration, mining, and visualization need to be established to fully harness its potential. Here, we describe ongoing efforts at Merck & Co. to structure data in the area of chemogenomics. We are integrating complementary data from both internal and external data sources into one chemogenomics database (Chemical Genetic Interaction Enterprise; CHEMGENIE). Here, we demonstrate how this well-curated database facilitates compound set design, tool compound selection, target deconvolution in phenotypic screening, and predictive model building.
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17
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Turkez H, Arslan ME, Ozdemir O. Genotoxicity testing: progress and prospects for the next decade. Expert Opin Drug Metab Toxicol 2017; 13:1089-1098. [DOI: 10.1080/17425255.2017.1375097] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Hasan Turkez
- Faculty of Science, Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey
- Department of Pharmacy, University ‘G. d’Annunzio’, Chieti, Italy
| | - Mehmet E. Arslan
- Faculty of Science, Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey
| | - Ozlem Ozdemir
- Faculty of Science, Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey
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18
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Ono A, Sano O, Kazetani KI, Muraki T, Imamura K, Sumi H, Matsui J, Iwata H. Feedback activation of AMPK-mediated autophagy acceleration is a key resistance mechanism against SCD1 inhibitor-induced cell growth inhibition. PLoS One 2017; 12:e0181243. [PMID: 28704514 PMCID: PMC5509324 DOI: 10.1371/journal.pone.0181243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023] Open
Abstract
Elucidating the bioactive compound modes of action is crucial for increasing success rates in drug development. For anticancer drugs, defining effective drug combinations that overcome resistance improves therapeutic efficacy. Herein, by using a biologically annotated compound library, we performed a large-scale combination screening with Stearoyl-CoA desaturase-1 (SCD1) inhibitor, T-3764518, which partially inhibits colorectal cancer cell proliferation. T-3764518 induced phosphorylation and activation of AMPK in HCT-116 cells, which led to blockade of downstream fatty acid synthesis and acceleration of autophagy. Attenuation of fatty acid synthesis by small molecules suppressed the growth inhibitory effect of T-3764518. In contrast, combination of T-3764518 with autophagy flux inhibitors synergistically inhibited cellular proliferation. Experiments using SCD1 knock-out cells validated the results obtained with T-3764518. The results of our study indicated that activation of autophagy serves as a survival signal when SCD1 is inhibited in HCT-116 cells. Furthermore, these findings suggest that combining SCD1 inhibitor with autophagy inhibitors is a promising anticancer therapy.
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Affiliation(s)
- Akito Ono
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Osamu Sano
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Ken-ichi Kazetani
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Takamichi Muraki
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Keisuke Imamura
- Oncology Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Hiroyuki Sumi
- Oncology Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Junji Matsui
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
| | - Hidehisa Iwata
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, Japan
- * E-mail:
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19
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Golubev P, Krasavin M. Sterically Constrained and Encumbered: An Approach to the Naturally Occurring Peptidomimetic Tetrahydropyrazino[1,2-a]indole-1,4-dione Core. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Pavel Golubev
- Institute of Chemistry; Saint Petersburg State University; 26 Universitetsky prospekt 198504 Peterhof Russia
| | - Mikhail Krasavin
- Institute of Chemistry; Saint Petersburg State University; 26 Universitetsky prospekt 198504 Peterhof Russia
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20
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Sano O, Kazetani KI, Adachi R, Kurasawa O, Kawamoto T, Iwata H. Using a biologically annotated library to analyze the anticancer mechanism of serine palmitoyl transferase (SPT) inhibitors. FEBS Open Bio 2017; 7:495-503. [PMID: 28396835 PMCID: PMC5377399 DOI: 10.1002/2211-5463.12196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/09/2016] [Accepted: 01/11/2017] [Indexed: 01/08/2023] Open
Abstract
Mechanistic understanding is crucial to anticancer drug discovery. Here, we reveal that inhibition of serine palmitoyl transferase (SPT), the rate-limiting enzyme in sphingolipid synthesis, induced death in a lung cancer cell line via a necrosis-dependent pathway. To elucidate the mechanism of cell death induced by SPT inhibition, a biologically annotated library of diverse compounds was screened with an SPT inhibitor. This analysis identified suppressors of SPT inhibitor-mediated cell death. Further analysis using hit compounds from this screening revealed that SPT inhibitors induce COX-2 expression, leading to necrosis-dependent cell death. SPT inhibitors might therefore represent novel candidates for cancer therapy via necrosis pathway regulation. Our data illustrate that compound combination screening of biologically annotated libraries could be used for mechanistic elucidation.
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Affiliation(s)
- Osamu Sano
- BioMolecular Research Laboratories, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
| | - Ken-Ichi Kazetani
- BioMolecular Research Laboratories, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
| | - Ryutaro Adachi
- BioMolecular Research Laboratories, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
| | - Osamu Kurasawa
- Oncology Drug Discovery Unit, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
| | - Tomohiro Kawamoto
- BioMolecular Research Laboratories, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
| | - Hidehisa Iwata
- BioMolecular Research Laboratories, Research Takeda Pharmaceutical Company Ltd. Fujisawa Japan
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21
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Thakkar BS, Albrigtsen M, Svendsen JS, Andersen JH, Engh RA. Biofocussed chemoprospecting: An efficient approach for drug discovery. Chem Biol Drug Des 2017; 90:128-140. [DOI: 10.1111/cbdd.12934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022]
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22
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Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
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23
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Herrmann J, Fayad AA, Müller R. Natural products from myxobacteria: novel metabolites and bioactivities. Nat Prod Rep 2016; 34:135-160. [PMID: 27907217 DOI: 10.1039/c6np00106h] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: 2011-July 2016Myxobacteria are a rich source for structurally diverse secondary metabolites with intriguing biological activities. Here we report on new natural products that were isolated from myxobacteria in the period of 2011 to July 2016. Some examples of recent advances on modes-of-action are also summarised along with a more detailed overview on five compound classes currently assessed in preclinical studies.
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Affiliation(s)
- J Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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24
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Powell DJ, Hertzberg RP, Macarrόn R. Design and Implementation of High-Throughput Screening Assays. Methods Mol Biol 2016; 1439:1-32. [PMID: 27316985 DOI: 10.1007/978-1-4939-3673-1_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
HTS remains at the core of the drug discovery process, and so it is critical to design and implement HTS assays in a comprehensive fashion involving scientists from the disciplines of biology, chemistry, engineering, and informatics. This requires careful consideration of many options and variables, starting with the choice of screening strategy and ending with the discovery of lead compounds. At every step in this process, there are decisions to be made that can greatly impact the outcome of the HTS effort, to the point of making it a success or a failure. Although specific guidelines should be established to ensure that the screening assay reaches an acceptable level of quality, many choices require pragmatism and the ability to compromise opposing forces.
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Affiliation(s)
- David J Powell
- Alternative Drug Discovery, GSK Pharmaceuticals, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK.
| | | | - Ricardo Macarrόn
- Alternative Drug Discovery, GSK Pharmaceuticals, 1250 South Collegeville Road, Upper Providence, PA, 19426, USA
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25
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Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. Future Med Chem 2015; 7:2143-71. [DOI: 10.4155/fmc.15.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Photoaffinity labeling is a well-known biochemical technique that has grown significantly since the turn of the century, principally due to its combination with bioorthogonal/click chemistry reactions. This review highlights new developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. In particular, recent examples of clickable photoprobes for target identification, activity- or affinity-based protein profiling (ABPP or AfBPP), characterization of sterol– or lipid–protein interactions and characterization of ligand-binding sites are presented.
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26
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Vangamudi B, Paul TA, Shah PK, Kost-Alimova M, Nottebaum L, Shi X, Zhan Y, Leo E, Mahadeshwar HS, Protopopov A, Futreal A, Tieu TN, Peoples M, Heffernan TP, Marszalek JR, Toniatti C, Petrocchi A, Verhelle D, Owen DR, Draetta G, Jones P, Palmer WS, Sharma S, Andersen JN. The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies. Cancer Res 2015; 75:3865-3878. [PMID: 26139243 DOI: 10.1158/0008-5472.can-14-3798] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022]
Abstract
The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy.
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Affiliation(s)
- Bhavatarini Vangamudi
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | | | - Parantu K Shah
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Maria Kost-Alimova
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | | | - Xi Shi
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Yanai Zhan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Elisabetta Leo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Harshad S Mahadeshwar
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Alexei Protopopov
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, TX
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Mike Peoples
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Carlo Toniatti
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Alessia Petrocchi
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | | | | | - Giulio Draetta
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | - Wylie S Palmer
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
| | | | - Jannik N Andersen
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, TX
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27
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Challenges and opportunities toward enabling phenotypic screening of complex and 3D cell models. Future Med Chem 2015; 7:513-25. [DOI: 10.4155/fmc.14.163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increasingly, organotypic cellular platforms are being recognized as useful tools in drug discovery. This review offers an industry-centric perspective on the benefits of emerging complex cell models over conventional 2D systems, as well as the challenges and opportunities for incorporating these multidimensional platforms into high-density formats. We particularly highlight the need for novel chemical sensors to noninvasively quantitate 3D structures in real time, and we contend that the use of more focused chemical and genomics libraries will enable screening of complex cell models derived from primary and induced pluripotent stem cells. Finally, we offer outlooks on several emerging technologies that show great potential for future integration of complex cell systems into contemporary drug screening.
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Wassermann AM, Lounkine E, Davies JW, Glick M, Camargo LM. The opportunities of mining historical and collective data in drug discovery. Drug Discov Today 2014; 20:422-34. [PMID: 25463034 DOI: 10.1016/j.drudis.2014.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/21/2014] [Accepted: 11/10/2014] [Indexed: 12/26/2022]
Abstract
Vast amounts of bioactivity data have been generated for small molecules across public and corporate domains. Biological signatures, either derived from systematic profiling efforts or from existing historical assay data, have been successfully employed for small molecule mechanism-of-action elucidation, drug repositioning, hit expansion and screening subset design. This article reviews different types of biological descriptors and applications, and we demonstrate how biological data can outlive the original purpose or project for which it was generated. By comparing 150 HTS campaigns run at Novartis over the past decade on the basis of their active and inactive chemical matter, we highlight the opportunities and challenges associated with cross-project learning in drug discovery.
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Affiliation(s)
- Anne Mai Wassermann
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Eugen Lounkine
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - John W Davies
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Meir Glick
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - L Miguel Camargo
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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