1
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Automated defect detection for coatings via height profiles obtained by laser-scanning microscopy. MACHINE LEARNING WITH APPLICATIONS 2022. [DOI: 10.1016/j.mlwa.2022.100413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2
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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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3
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Spatiotemporal identification of druggable binding sites using deep learning. Commun Biol 2020; 3:618. [PMID: 33110179 PMCID: PMC7591901 DOI: 10.1038/s42003-020-01350-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Identification of novel protein binding sites expands druggable genome and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble the object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, that considers protein conformations as 3D-images, binding sites as objects on these images to detect, and conformational ensembles of proteins as 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding site in G protein-coupled receptor. BiteNet outperforms state-of-the-art methods both in terms of accuracy and speed, taking about 1.5 minutes to analyze 1000 conformations of a protein with ~2000 atoms. Kozlovskii and Popov present BiteNet, a new computational method utilizing deep learning principles for rapid detection of binding sites. BiteNet considers proteins as 3D images, enabling rapid detection of allosteric sites from either static protein structures or its dynamic ensembles.
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4
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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5
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Tsafou K, Tiwari PB, Forman-Kay JD, Metallo SJ, Toretsky JA. Targeting Intrinsically Disordered Transcription Factors: Changing the Paradigm. J Mol Biol 2018; 430:2321-2341. [PMID: 29655986 DOI: 10.1016/j.jmb.2018.04.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022]
Abstract
Increased understanding of intrinsically disordered proteins (IDPs) and protein regions has revolutionized our view of the relationship between protein structure and function. Data now support that IDPs can be functional in the absence of a single, fixed, three-dimensional structure. Due to their dynamic morphology, IDPs have the ability to display a range of kinetics and affinity depending on what the system requires, as well as the potential for large-scale association. Although several studies have shed light on the functional properties of IDPs, the class of intrinsically disordered transcription factors (TFs) is still poorly characterized biophysically due to their combination of ordered and disordered sequences. In addition, TF modulation by small molecules has long been considered a difficult or even impossible task, limiting functional probe development. However, with evolving technology, it is becoming possible to characterize TF structure-function relationships in unprecedented detail and explore avenues not available or not considered in the past. Here we provide an introduction to the biophysical properties of intrinsically disordered TFs and we discuss recent computational and experimental efforts toward understanding the role of intrinsically disordered TFs in biology and disease. We describe a series of successful TF targeting strategies that have overcome the perception of the "undruggability" of TFs, providing new leads on drug development methodologies. Lastly, we discuss future challenges and opportunities to enhance our understanding of the structure-function relationship of intrinsically disordered TFs.
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Affiliation(s)
- K Tsafou
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - P B Tiwari
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA
| | - J D Forman-Kay
- Molecular Medicine, The Hospital for Sick Children, Toronto M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto M5G 1X8, Canada
| | - S J Metallo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - J A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, 3970 Reservoir Road Northwest, Washington, DC 20057, USA.
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6
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Troshin K, Hartwig JF. Snap deconvolution: An informatics approach to high-throughput discovery of catalytic reactions. Science 2017; 357:175-181. [DOI: 10.1126/science.aan1568] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/30/2017] [Indexed: 12/27/2022]
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7
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Wang Y, Patil P, Kurpiewska K, Kalinowska-Tluscik J, Dömling A. Two Cycles with One Catch: Hydrazine in Ugi 4-CR and Its Postcyclizations. ACS COMBINATORIAL SCIENCE 2017; 19:193-198. [PMID: 28181791 PMCID: PMC5350607 DOI: 10.1021/acscombsci.7b00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Isocyanide-based
multicomponent reactions (IMCR) are by far the
most versatile reactions that can construct relatively complex molecules
by one-pot synthesis. More importantly, the development of post IMCR
modifications significantly improves the scaffold’s diversity.
Here, we describe the use of N-Boc protected hydrazine
together with α-amino acid derived isocyanides in the Ugi tetrazole
reaction and its post cyclization under both acidic and basic conditions.
The cyclization in acidic conditions was conducted in a one pot fashion,
which give 7-aminotetrazolopyrazinone (6) and tetrazolotriazepinone
(7) cyclic products. The post cyclization under basic
condition could selectively afford Boc-protected 7-aminotetrazolopyrazinone
(8) products in yield of 38–87%.
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Affiliation(s)
- Yuanze Wang
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pravin Patil
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tluscik
- Jagiellonian University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Ahijado-Guzmán R, Menten J, Prasad J, Lambertz C, Rivas G, Sönnichsen C. Plasmonic Nanosensors for the Determination of Drug Effectiveness on Membrane Receptors. ACS APPLIED MATERIALS & INTERFACES 2017; 9:218-223. [PMID: 27976859 DOI: 10.1021/acsami.6b14013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We demonstrate the potential of the NanoSPR (nanoscale surface plasmon resonance sensors) method as a simple and cheap tool for the quantitative study of membrane protein-protein interactions. We use NanoSPR to determine the effectiveness of two potential drug candidates that inhibit the protein complex formation between FtsA and ZipA at initial stages of bacterial division. As the NanoSPR method relies on individual gold nanorods as sensing elements, there is no need for fluorescent labels or organic cosolvents, and it provides intrinsically high statistics. NanoSPR could become a powerful tool in drug development, drug delivery, and membrane studies.
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Affiliation(s)
- Rubén Ahijado-Guzmán
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Julia Menten
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Janak Prasad
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
- Graduate School Materials Science in Mainz , Staudingerweg 9, D-55128 Mainz, Germany
| | - Christina Lambertz
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientı́ficas , c/Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carsten Sönnichsen
- Institute of Physical Chemistry, University of Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
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9
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Pei H, Li Y, Liu M, Chen Y. Targeting Twist expression with small molecules. MEDCHEMCOMM 2016; 8:268-275. [PMID: 30108743 DOI: 10.1039/c6md00561f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/01/2016] [Indexed: 12/14/2022]
Abstract
Twist, as one of the important embryonic transcription factors, regulates epithelial-mesenchymal transition (EMT) and migration in embryo formation and cancer development. Both Twist-1 and Twist-2 are rarely detectable in healthy adult tissues, but are frequently overexpressed in multiple kinds of human cancer tissues, such as breast, prostate, uterus, liver, melanoma, etc. Twist is considered as a crucial EMT inductor and correlated with carcinoma aggression, invasion and metastasis. In the past decades, in-depth investigation has been reported in terms of the role of Twist in cancers; in addition, several kinds of small molecules have played important roles in studying the effect of Twist on cancer development, suggesting that Twist can be regarded as one of the important potential targets for cancer treatment. Hence we provide a brief overview of Twist and several small molecules targeting its expression, highlighting the biological features that make it a charming target for cancer therapy.
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Affiliation(s)
- Haixiang Pei
- Shanghai Key Laboratory of Regulatory Biology , The Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai , 200241 , China . ; ; Tel: +86 21 2420 6647
| | - Yunqi Li
- Shanghai Key Laboratory of Regulatory Biology , The Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai , 200241 , China . ; ; Tel: +86 21 2420 6647
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology , The Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai , 200241 , China . ; ; Tel: +86 21 2420 6647
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology , The Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai , 200241 , China . ; ; Tel: +86 21 2420 6647
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10
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Rossato M, Miralles G, M'Kadmi C, Maingot M, Amblard M, Mouillac B, Gagne D, Martinez J, Subra G, Enjalbal C, Cantel S. Quantitative MALDI-MS Binding Assays: An Alternative to Radiolabeling. ChemMedChem 2016; 11:2582-2587. [PMID: 27922213 DOI: 10.1002/cmdc.201600447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/27/2016] [Indexed: 12/20/2022]
Abstract
Radiolabeling of ligands is still the gold standard in the study of high-affinity receptor-ligand interactions. In an effort toward safer and simpler alternatives to the use of radioisotopes, we developed a quantitative and highly sensitive matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) method that relies on the use of chemically tagged ligands designed to be specifically detectable when present as traces in complex biological mixtures such as cellular lysates. This innovative technology allows easy, sensitive detection and accurate quantification of analytes at the sub-nanomolar level. After statistical validation, we were able to perform pharmacological evaluations of G protein-coupled receptor (V1A-R)-ligand interactions. Both saturation and competitive binding assays were successfully processed.
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Affiliation(s)
- Maxime Rossato
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Guillaume Miralles
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Céline M'Kadmi
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Mathieu Maingot
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle (IGF), 141 Rue de la Cardonille, 34090, Montpellier, France
| | - Didier Gagne
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Gilles Subra
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Christine Enjalbal
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
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