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Signore MA, De Pascali C, Giampetruzzi L, Siciliano PA, Francioso L. Gut-on-Chip microphysiological systems: Latest advances in the integration of sensing strategies and adoption of mature detection mechanisms. SENSING AND BIO-SENSING RESEARCH 2021. [DOI: 10.1016/j.sbsr.2021.100443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Laufkötter O, Sturm N, Bajorath J, Chen H, Engkvist O. Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability. J Cheminform 2019; 11:54. [PMID: 31396716 PMCID: PMC6686534 DOI: 10.1186/s13321-019-0376-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/31/2019] [Indexed: 11/29/2022] Open
Abstract
This study aims at improving upon existing activity predictions methods by augmenting chemical structure fingerprints with bio-activity based fingerprints derived from high-throughput screening (HTS) data (HTSFPs) and thereby showcasing the benefits of combining different descriptor types. This type of descriptor would be applied in an iterative screening scenario for more targeted compound set selection. The HTSFPs were generated from HTS data obtained from PubChem and combined with an ECFP4 structural fingerprint. The bioactivity-structure hybrid (BaSH) fingerprint was benchmarked against the individual ECFP4 and HTSFP fingerprints. Their performance was evaluated via retrospective analysis of a subset of the PubChem HTS data. Results showed that the BaSH fingerprint has improved predictive performance as well as scaffold hopping capability. The BaSH fingerprint identified unique compounds compared to both the ECFP4 and the HTSFP fingerprint indicating synergistic effects between the two fingerprints. A feature importance analysis showed that a small subset of the HTSFP features contribute most to the overall performance of the BaSH fingerprint. This hybrid approach allows for activity prediction of compounds with only sparse HTSFPs due to the supporting effect from the structural fingerprint.![]()
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Affiliation(s)
- Oliver Laufkötter
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden. .,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany.
| | - Noé Sturm
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Hongming Chen
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
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Abstract
The nanomaterial landscape is so vast that a high-throughput combinatorial approach is required to understand structure-function relationships. To address this challenge, an approach for the synthesis and screening of megalibraries of unique nanoscale features (>10,000,000) with tailorable location, size, and composition has been developed. Polymer pen lithography, a parallel lithographic technique, is combined with an ink spray-coating method to create pen arrays, where each pen has a different but deliberately chosen quantity and composition of ink. With this technique, gradients of Au-Cu bimetallic nanoparticles have been synthesized and then screened for activity by in situ Raman spectroscopy with respect to single-walled carbon nanotube (SWNT) growth. Au3Cu, a composition not previously known to catalyze SWNT growth, has been identified as the most active composition.
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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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High-throughput organ-on-a-chip systems: Current status and remaining challenges. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018. [DOI: 10.1016/j.cobme.2018.02.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Two-dimensional (2D) barcodes ubiquitously used to label, track and authenticate objects face increasing challenges of being damaged, altered and falsified. The past effort in nanomaterials has paved the way for controlled synthesis of nanomaterials with desired size, shape and function. Due to their extremely small sizes, these nanomaterials are promising as next generation barcodes that can be added into or mixed with objects of interest without being noticed. These barcodes can be effectively read owing to their physical properties by manufacturers, law enforcement and security agencies. Meanwhile, nanomaterial-based barcodes are hard to reverse-engineer or imitate without advanced knowledge and technical expertise. This review describes how nanomaterials can be used as barcodes, discusses advantages and limitations of each type of nanomaterial-based barcode, and points out ways that could help design and prepare better nanomaterial-based barcodes.
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Affiliation(s)
- Miao Wang
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, USA.
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7
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Shen K, Lee J, Yarmush ML, Parekkadan B. Microcavity substrates casted from self-assembled microsphere monolayers for spheroid cell culture. Biomed Microdevices 2014; 16:609-15. [PMID: 24781882 PMCID: PMC4415162 DOI: 10.1007/s10544-014-9863-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Multicellular spheroids are an important 3-dimensional cell culture model that reflects many key aspects of in vivo microenvironments. This paper presents a scalable, self-assembly based approach for fabricating microcavity substrates for multicellular spheroid cell culture. Hydrophobic glass microbeads were self-assembled into a tightly packed monolayer through the combined actions of surface tension, gravity, and lateral capillary forces at the water-air interface of a polymer solution. The packed bead monolayer was subsequently embedded in the dried polymer layer. The surface was used as a template for replicating microcavity substrates with perfect spherical shapes. We demonstrated the use of the substrate in monitoring the formation process of tumor spheroids, a proof-of-concept scale-up fabrication procedure into standard microplate formats, and its application in testing cancer drug responses in the context of bone marrow stromal cells. The presented technique offers a simple and effective way of forming high-density uniformly-sized spheroids without microfabrication equipment for biological and drug screening applications.
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Affiliation(s)
- Keyue Shen
- Department of Surgery, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA 02114, USA
| | - Jungwoo Lee
- Department of Surgery, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA 02114, USA
| | - Martin L. Yarmush
- Department of Surgery, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA 02114, USA. Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Biju Parekkadan
- Department of Surgery, Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA 02114, USA. Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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8
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Riniker S, Wang Y, Jenkins JL, Landrum GA. Using information from historical high-throughput screens to predict active compounds. J Chem Inf Model 2014; 54:1880-91. [PMID: 24933016 DOI: 10.1021/ci500190p] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Modern high-throughput screening (HTS) is a well-established approach for hit finding in drug discovery that is routinely employed in the pharmaceutical industry to screen more than a million compounds within a few weeks. However, as the industry shifts to more disease-relevant but more complex phenotypic screens, the focus has moved to piloting smaller but smarter chemically/biologically diverse subsets followed by an expansion around hit compounds. One standard method for doing this is to train a machine-learning (ML) model with the chemical fingerprints of the tested subset of molecules and then select the next compounds based on the predictions of this model. An alternative approach would be to take advantage of the wealth of bioactivity information contained in older (full-deck) screens using so-called HTS fingerprints, where each element of the fingerprint corresponds to the outcome of a particular assay, as input to machine-learning algorithms. We constructed HTS fingerprints using two collections of data: 93 in-house assays and 95 publicly available assays from PubChem. For each source, an additional set of 51 and 46 assays, respectively, was collected for testing. Three different ML methods, random forest (RF), logistic regression (LR), and naïve Bayes (NB), were investigated for both the HTS fingerprint and a chemical fingerprint, Morgan2. RF was found to be best suited for learning from HTS fingerprints yielding area under the receiver operating characteristic curve (AUC) values >0.8 for 78% of the internal assays and enrichment factors at 5% (EF(5%)) >10 for 55% of the assays. The RF(HTS-fp) generally outperformed the LR trained with Morgan2, which was the best ML method for the chemical fingerprint, for the majority of assays. In addition, HTS fingerprints were found to retrieve more diverse chemotypes. Combining the two models through heterogeneous classifier fusion led to a similar or better performance than the best individual model for all assays. Further validation using a pair of in-house assays and data from a confirmatory screen--including a prospective set of around 2000 compounds selected based on our approach--confirmed the good performance. Thus, the combination of machine-learning with HTS fingerprints and chemical fingerprints utilizes information from both domains and presents a very promising approach for hit expansion, leading to more hits. The source code used with the public data is provided.
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Affiliation(s)
- Sereina Riniker
- Novartis Institutes for BioMedical Research, Novartis Pharma AG , Novartis Campus, 4056 Basel, Switzerland
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Annabi N, Selimović Š, Cox JPA, Ribas J, Bakooshli MA, Heintze D, Weiss AS, Cropek D, Khademhosseini A. Hydrogel-coated microfluidic channels for cardiomyocyte culture. LAB ON A CHIP 2013; 13:3569-77. [PMID: 23728018 PMCID: PMC3744594 DOI: 10.1039/c3lc50252j] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The research areas of tissue engineering and drug development have displayed increased interest in organ-on-a-chip studies, in which physiologically or pathologically relevant tissues can be engineered to test pharmaceutical candidates. Microfluidic technologies enable the control of the cellular microenvironment for these applications through the topography, size, and elastic properties of the microscale cell culture environment, while delivering nutrients and chemical cues to the cells through continuous media perfusion. Traditional materials used in the fabrication of microfluidic devices, such as poly(dimethylsiloxane) (PDMS), offer high fidelity and high feature resolution, but do not facilitate cell attachment. To overcome this challenge, we have developed a method for coating microfluidic channels inside a closed PDMS device with a cell-compatible hydrogel layer. We have synthesized photocrosslinkable gelatin and tropoelastin-based hydrogel solutions that were used to coat the surfaces under continuous flow inside 50 μm wide, straight microfluidic channels to generate a hydrogel layer on the channel walls. Our observation of primary cardiomyocytes seeded on these hydrogel layers showed preferred attachment as well as higher spontaneous beating rates on tropoelastin coatings compared to gelatin. In addition, cellular attachment, alignment and beating were stronger on 5% (w/v) than on 10% (w/v) hydrogel-coated channels. Our results demonstrate that cardiomyocytes respond favorably to the elastic, soft tropoelastin culture substrates, indicating that tropoelastin-based hydrogels may be a suitable coating choice for some organ-on-a-chip applications. We anticipate that the proposed hydrogel coating method and tropoelastin as a cell culture substrate may be useful for the generation of elastic tissues, e.g. blood vessels, using microfluidic approaches.
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Affiliation(s)
- Nasim Annabi
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Šeila Selimović
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - João Ribas
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- PhD Programme in Experimental Biology and Biomedicine, CNC-Center for Neuroscience and Cell Biology and Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
- Biocant - Center of Innovation in Biotechnology, 3060-197 Cantanhede, Portugal
| | - Mohsen Afshar Bakooshli
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Déborah Heintze
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute of Bioengineering and School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Anthony S. Weiss
- School of Molecular Bioscience, University of Sydney, 2006, Australia
- Bosch Institute, University of Sydney, 2006, Australia
- Charles Perkins Centre, University of Sydney, 2006, Australia
| | - Donald Cropek
- US Army Corps of Engineers Construction Engineering Research Laboratory, Champaign, IL61822, USA
| | - Ali Khademhosseini
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, Massachusetts 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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10
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Highly efficient incorporation of amino-reactive dyes into silica particles by a multi-step approach. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2013.02.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Neu V, Steiner R, Müller S, Fattinger C, Zenobi R. Development and Characterization of a Capillary Gap Sampler as New Microfluidic Device for Fast and Direct Analysis of Low Sample Amounts by ESI-MS. Anal Chem 2013; 85:4628-35. [DOI: 10.1021/ac400186t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Volker Neu
- Department of Chemistry
and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Roger Steiner
- F. Hoffmann-La Roche AG, pRED, Pharma Research & Early Development, Discovery Technologies, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Stephan Müller
- F. Hoffmann-La Roche AG, pRED, Pharma Research & Early Development, Discovery Technologies, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Christof Fattinger
- F. Hoffmann-La Roche AG, pRED, Pharma Research & Early Development, Discovery Technologies, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Renato Zenobi
- Department of Chemistry
and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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12
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Sun Q, Klaseboer E, Khoo BC, Chan DYC. Stokesian dynamics of pill-shaped Janus particles with stick and slip boundary conditions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:043009. [PMID: 23679515 DOI: 10.1103/physreve.87.043009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Indexed: 06/02/2023]
Abstract
We study the forces and torques experienced by pill-shaped Janus particles of different aspect ratios where half of the surface obeys the no-slip boundary condition and the other half obeys the Navier slip condition of varying slip lengths. Using a recently developed boundary integral formulation whereby the traditional singular behavior of this approach is removed analytically, we quantify the strength of the forces and torques experienced by such particles in a uniform flow field in the Stokes regime. Depending on the aspect ratio and the slip length, the force transverse to the flow direction can change sign. This is a novel property unique to the Janus nature of the particles.
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Affiliation(s)
- Qiang Sun
- Department of Mechanical Engineering, National University of Singapore, Singapore 119260
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13
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Karagoz B, Durmaz YY, Gacal BN, Bicak N, Yagci Y. Functionalization of Poly(divinylbenzene) Microspheres by Combination of Hydrobromination and Click Chemistry Processes: A Model Study. Des Monomers Polym 2012. [DOI: 10.1163/138577209x12478288343198] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Bunyamin Karagoz
- a Department of Chemistry, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
| | - Yasemin Yuksel Durmaz
- b Department of Chemistry, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
| | - Bahadir N. Gacal
- c Department of Chemistry, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
| | - Niyazi Bicak
- d Department of Chemistry, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
| | - Yusuf Yagci
- e Department of Chemistry, Istanbul Technical University, Maslak, Istanbul, 34469, Turkey
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14
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A Digitally Controllable Polymer-Based Microfluidic Mixing Module Array. MICROMACHINES 2012. [DOI: 10.3390/mi3020279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Baker BA, Milam VT. Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments. Nucleic Acids Res 2011; 39:e99. [PMID: 21613238 PMCID: PMC3159461 DOI: 10.1093/nar/gkr293] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 04/05/2011] [Accepted: 04/14/2011] [Indexed: 12/27/2022] Open
Abstract
We have investigated the time-dependent strand displacement activity of several targets with double-stranded DNA probes (dsProbes) of varying affinity. Here, the relative affinity of various dsProbes is altered through choices in hybridization length (11-15 bases) and the selective inclusion of center mismatches in the duplexes. While the dsProbes are immobilized on microspheres, the soluble, 15 base-long complementary sequence is presented either alone as a short target strand or as a recognition segment embedded within a longer target strand. Compared to the short target, strand displacement activity of the longer targets is slower, but still successful. Additionally, the longer targets exhibit modest differences in the observed displacement rates, depending on the location of recognition segment within the long target. Overall, our study demonstrates that the kinetics of strand displacement activity can be tuned through dsProbe sequence design parameters and is only modestly affected by the location of the complementary segment within a longer target strand.
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Affiliation(s)
- Bryan A. Baker
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA
| | - Valeria T. Milam
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA
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16
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Przybylo M, Borowik T, Langner M. Fluorescence Techniques for Determination of the Membrane Potentials in High Throughput Screening. J Fluoresc 2010; 20:1139-57. [DOI: 10.1007/s10895-010-0665-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 04/05/2010] [Indexed: 01/14/2023]
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Abstract
This review presents an application of micromixer technologies, which have driven a number of critical research trends over the past few decades, particularly for chemical and biological fields. Micromixer technologies in this review are categorized according to their applications: (1) chemical applications, including chemical synthesis, polymerization, and extraction; (2) biological applications, including DNA analysis, biological screening enzyme assays, protein folding; and (3) detection/analysis of chemical or biochemical content combined with NMR, FTIR, or Raman spectroscopies. In the chemical application, crystallization, extraction, polymerization, and organic synthesis have been reported, not only for laboratory studies, but also for industrial applications. Microscale techniques are used in chemical synthesis to develop microreactors. In clinical medicine and biological studies, microfluidic systems have been widely applied to the identification of biochemical products, diagnosis, drug discovery, and investigation of disease symptoms. The biological and biochemical applications also include enzyme assays, biological screening assays, cell lysis, protein folding, and biological analytical assays. Nondestructive analytical/detection methods have yielded a number of benefits to chemical and biochemical processes. In this chapter, we introduce analytical methods those are frequently integrated into micromixing technologies, such as NMR, FT-IR, and Raman spectroscopies. From the study of micromixers, we discovered that the Re number and mixing time depends on the specific application, and we clustered micromixers in various applications according to the Re number and mixing performance (mixing time). We expect that this clustering will be helpful in designing of micromixers for specific applications.
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Affiliation(s)
- Gi Seok Jeong
- Department of Biomedical Engineering, College of Health Science, Korea University, 1-boneji San, Jeongneung-dong, Seongbuk-gu, 136-100, Seoul, Korea
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Marcon L, Battersby BJ, Rühmann A, Ford K, Daley M, Lawrie GA, Trau M. 'On-the-fly' optical encoding of combinatorial peptide libraries for profiling of protease specificity. MOLECULAR BIOSYSTEMS 2009; 6:225-33. [PMID: 20024084 DOI: 10.1039/b909087h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large solid-phase combinatorial libraries currently play an important role in areas such as infectious disease biomarker discovery, profiling of protease specificity and anticancer drug discovery. Because compounds on solid support beads are not positionally-encoded as they are in microarrays, innovative methods of encoding are required. There are many advantages associated with optical encoding and several strategies have been described in the literature to combine fluorescence encoding methods with solid-phase library synthesis. We have previously introduced an alternative fluorescence-based encoding method ("colloidal barcoding"), which involves encoding 10-20 mum support beads during a split-and-mix synthesis with smaller 0.6-0.8 mum silica colloids that contain specific and identifiable combinations of fluorescent dye. The power of this 'on-the-fly' encoding approach lies in the efficient use of a small number of fluorescent dyes to encode millions of compounds. Described herein, for the first time, is the use of a colloid-barcoded library in a biological assay (i.e., protease profiling) combined with the use of confocal microscopy to decode the colloidal barcode. In this proof-of-concept demonstration, a small focussed peptide library was optically-encoded during a combinatorial synthesis, incubated with a protease (trypsin), analysed by flow cytometry and decoded via confocal microscopy. During assay development, a range of parameters were investigated and optimised, including substrate (or probe) loading, barcode stability, characteristics of the peptide-tagging fluorophore, and spacer group configuration. Through successful decoding of the colloidal barcodes, it was confirmed that specific peptide sequences presenting one or two cleavage sites were recognised by trypsin while peptide sequences not cleavable by trypsin remained intact.
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Affiliation(s)
- Lionel Marcon
- Centre for Biomarker Research and Development, Level 5 East, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
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19
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Marcon L, Spriet C, Meehan TD, Battersby BJ, Lawrie GA, Héliot L, Trau M. Synthesis and application of FRET nanoparticles in the profiling of a protease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2053-2056. [PMID: 19517488 DOI: 10.1002/smll.200801887] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Lionel Marcon
- Centre for Nanotechnology and Biomaterials, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD, Australia
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20
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Sukuru SCK, Jenkins JL, Beckwith RE, Scheiber J, Bender A, Mikhailov D, Davies JW, Glick M. Plate-Based Diversity Selection Based on Empirical HTS Data to Enhance the Number of Hits and Their Chemical Diversity. ACTA ACUST UNITED AC 2009; 14:690-9. [DOI: 10.1177/1087057109335678] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Typically, screening collections of pharmaceutical companies contain more than a million compounds today. However, for certain high-throughput screening (HTS) campaigns, constraints posed by the assay throughput and/or the reagent costs make it impractical to screen the entire deck. Therefore, it is desirable to effectively screen subsets of the collection based on a hypothesis or a diversity selection. How to select compound subsets is a subject of ongoing debate. The authors present an approach based on extended connectivity fingerprints to carry out diversity selection on a per plate basis (instead of a per compound basis). HTS data from 35 Novartis screens spanning 5 target classes were investigated to assess the performance of this approach. The analysis shows that selecting a fingerprint-diverse subset of 250K compounds, representing 20% of the screening deck, would have achieved significantly higher hit rates for 86% of the screens. This measure also outperforms the Murcko scaffold-based plate selection described previously, where only 49% of the screens showed similar improvements. Strikingly, the 2-fold improvement in average hit rates observed for 3 of 5 target classes in the data set indicates a target bias of the plate (and thus compound) selection method. Even though the diverse subset selection lacks any target hypothesis, its application shows significantly better results for some targets—namely, G-protein-coupled receptors, proteases, and protein-protein interactions—but not for kinase and pathway screens. The synthetic origin of the compounds in the diverse subset appears to influence the screening hit rates. Natural products were the most diverse compound class, with significantly higher hit rates compared to the compounds from the traditional synthetic and combinatorial libraries. These results offer empirical guidelines for plate-based diversity selection to enhance hit rates, based on target class and the library type being screened. ( Journal of Biomolecular Screening 2009:690-699)
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Affiliation(s)
- Sai Chetan K. Sukuru
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeremy L. Jenkins
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Rohan E.J. Beckwith
- Hit to Lead Optimization, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Josef Scheiber
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Andreas Bender
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Leiden, The Netherlands
| | - Dmitri Mikhailov
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John W. Davies
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Meir Glick
- Lead Discovery Informatics, Center for Proteomic Chemistry Novartis Institutes for BioMedical Research, Cambridge, Massachusetts,
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Abstract
High-throughput screening (HTS) covers a range of measurements, from primary screens of either large libraries (>250 K) or small, focused collections (100-1,000 s) of test compounds, to secondary screens used to characterize the mechanism of action of a relatively small number of compounds. Data analysis of assay results from HTS relies upon assay performance and the control wells used to define the assay system. This chapter discusses parameters that must be considered when defining controls and plate maps for primary and secondary assays in HTS. Control wells and plate maps are suggested, which can gene-rally be applied toward a variety of biochemical and cellular assays. The controls and plate-map options can be matched to the scale of the screening campaign; examples are primary screens with % inhibition or % activation as endpoints or secondary screens with IC(50) or EC(50) values as endpoints.
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Deshpande K, Ahamed T, van der Wielen LAM, Horst JHT, Jansens PJ, Ottens M. Protein self-interaction chromatography on a microchip. LAB ON A CHIP 2009; 9:600-605. [PMID: 19190796 DOI: 10.1039/b810741f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This paper presents the development of a novel miniaturized experimental procedure for the measurement of protein-protein interactions through Self-Interaction Chromatography (SIC) on a microchip, without the use of chromatographic resins. SIC was recently demonstrated to be a relatively easy method to obtain quantitative thermodynamic information about protein-protein interactions, like the osmotic second virial coefficient B(22), which relates to protein phase behavior including protein crystallization. This successful miniaturization to microchip level of a measurement device for protein self-interaction data is a first key step to a complete microfluidic screening platform for the rational design of protein crystallizations, using substantially less expensive protein and experimentation time.
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Affiliation(s)
- Kedar Deshpande
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628BC, Delft, The Netherlands
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23
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Zhou J, Wang YH, Chu J, Gou BQ, Zhuang YP, Zhang SL, Yuan ZY. Penicillin G acylase purification with the aid of high-throughput screening approach. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.jcice.2007.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Surawski PPT, Battersby BJ, Lawrie GA, Ford K, Rühmann A, Marcon L, Kozak D, Trau M. Flow cytometric detection of proteolysis in peptide libraries synthesised on optically encoded supports. MOLECULAR BIOSYSTEMS 2008; 4:774-8. [PMID: 18563252 DOI: 10.1039/b718513h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concept of optically encoding particles for solid phase organic synthesis has existed in the literature for several years. However, there remains a significant challenge to producing particles that are capable of withstanding harsh solvents and reagents whilst maintaining the integrity and range of the optical encoding. In this study, a new generation of fluorescently encoded support particles was used for both solid phase peptide synthesis and on-particle analysis of proteolysis in a multiplexed, flow cytometric assay. The success of the assay was demonstrated through the use of a model protease, trypsin. Our results show that the use of solid supports with high peptide yield, high swellability in water and high penetration of the enzyme into the interior of the particle is not absolutely necessary for proteolysis assays.
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Affiliation(s)
- Peter P T Surawski
- Centre for Nanotechnology and Biomaterials, Level 5 East, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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25
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Jennings TL, Rahman KS, Fournier-Bidoz S, Chan WCW. Effects of Microbead Surface Chemistry on DNA Loading and Hybridization Efficiency. Anal Chem 2008; 80:2849-56. [DOI: 10.1021/ac7026035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- T. L. Jennings
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Center for Cellular and Biomoecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3G9, Canada
| | - K. S. Rahman
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Center for Cellular and Biomoecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3G9, Canada
| | - S. Fournier-Bidoz
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Center for Cellular and Biomoecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3G9, Canada
| | - W. C. W. Chan
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Center for Cellular and Biomoecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3G9, Canada
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26
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Tamarit-López J, Morais S, Puchades R, Maquieira Á. Use of polystyrene spin-coated compact discs for microimmunoassaying. Anal Chim Acta 2008; 609:120-30. [DOI: 10.1016/j.aca.2007.12.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 12/17/2007] [Accepted: 12/19/2007] [Indexed: 11/24/2022]
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27
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Abstract
This article reviews the origin and evolution of high throughput screening (HTS) through the experience of an individual pharmaceutical company, revealing some of the mysteries of the early stages of drug discovery to the wider pharmacology audience. HTS in this company (Pfizer, Groton, USA) had its origin in natural products screening in 1986, by substituting fermentation broths with dimethyl sulphoxide solutions of synthetic compounds, using 96-well plates and reduced assay volumes of 50-100 microl. A nominal 30 mM source compound concentration provided high microM assay concentrations. Starting at 800 compounds each week, the process reached a steady state of 7200 compounds per week by 1989. Screening in the Applied Biotechnology and Screening Group was centralized with screens operating in lock-step to maximize efficiency. Initial screens were full files run in triplicate. Autoradiography and image analysis were introduced for (125)I receptor ligand screens. Reverse transcriptase (RT) coupled with quantitative PCR and multiplexing addressed several targets in a single assay. By 1992 HTS produced 'hits' as starting matter for approximately 40% of the Discovery portfolio. In 1995, the HTS methodology was expanded to include ADMET targets. ADME targets required each compound to be physically detected leading to the development of automated high throughput LC-MS. In 1996, 90 compounds/week were screened in microsomal, protein binding and serum stability assays. Subsequently, the mutagenic Ames assay was adapted to a 96-well plate liquid assay and novel algorithms permitted automated image analysis of the micronucleus assay. By 1999 ADME HTS was fully integrated into the discovery cycle.
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Affiliation(s)
- D A Pereira
- Exploratory Medicinal Sciences, Pfizer Global R&D Groton, CT, USA
| | - J A Williams
- Exploratory Medicinal Sciences, Pfizer Global R&D Groton, CT, USA
- Author for correspondence:
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28
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Warrick J, Meyvantsson I, Ju J, Beebe DJ. High-throughput microfluidics: improved sample treatment and washing over standard wells. LAB ON A CHIP 2007; 7:316-21. [PMID: 17330162 DOI: 10.1039/b613350a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Fluid flow in microchannels is used to treat or wash samples and can be incorporated into high-throughput applications such as drug screening, which currently use standard microtiter wells for performing assays. This paper provides theoretical and experimental data comparing microchannels and standard wells on the metrics of sample washing and experimental error in treatment concentrations. It is shown numerically and experimentally that microchannel concentration can be approximated with an inverse linear relationship to input volume. The experimentally supported mathematical approximation and error propagation methods are used to compare the accuracy and precision of treatments in microchannels vs. standard wells. Mathematical results suggest microchannels can provide 10 or more times the treatment precision of standard wells for volume ratios typical of high-throughput screening. Passive-pumping and diffusion are utilized to improve microchannel accuracy and precision even further in a treat-wait-treat method. The advantages of microchannels outlined here can have large-scale effects on cost and accuracy in screening applications.
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Affiliation(s)
- Jay Warrick
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, W 53706, USA
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29
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Battersby BJ, Trau M. Optically Encoded Particles and Their Applications in Multiplexed Biomedical Assays. Aust J Chem 2007. [DOI: 10.1071/ch07006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the future, the rapid discovery of new cures, vaccines, and diagnostics for common diseases will depend on the ability of biomedical researchers to investigate complex mixtures of proteins or DNA. The need to measure the abundance of these entities, together with their level of interaction, has driven the development of new research tools that enable simultaneous analysis of multiple analytes (multiplexing). Optically encoded particles are emerging as the multiplexing tools of choice, especially for clinical research. In this Review, an overview of various new optical encoding methods will be presented, together with important biomedical applications in which particle-based assays are currently being used.
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30
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Wang HQ, Liu TC, Cao YC, Huang ZL, Wang JH, Li XQ, Zhao YD. A flow cytometric assay technology based on quantum dots-encoded beads. Anal Chim Acta 2006; 580:18-23. [PMID: 17723751 DOI: 10.1016/j.aca.2006.07.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/16/2006] [Accepted: 07/21/2006] [Indexed: 11/22/2022]
Abstract
A flow cytometric detecting technology based on quantum dots (QDs)-encoded beads has been described. Using this technology, several QDs-encoded beads with different code were identified effectively, and the target molecule (DNA sequence) in solution was also detected accurately by coupling to its complementary sequence probed on QDs-encoded beads through DNA hybridization assay. The resolution of this technology for encoded beads is resulted from two longer wavelength fluorescence identification signals (yellow and red fluorescent signals of QDs), and the third shorter wavelength fluorescence signal (green reporting signal of fluorescein isothiocyanate (FITC)) for the determination of reaction between probe and target. In experiment, because of QDs' unique optical character, only one excitation light source was needed to excite the QDs and probe dye FITC synchronously comparing with other flow cytometric assay technology. The results show that this technology has present excellent repeatability and good accuracy. It will become a promising multiple assay platform in various application fields after further improvement.
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Affiliation(s)
- Hai-Qiao Wang
- Key Laboratory of Biomedical Photonics of Ministry of Education-Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
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31
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Porschewski P, Grättinger MAM, Klenzke K, Erpenbach A, Blind MR, Schäfer F. Using aptamers as capture reagents in bead-based assay systems for diagnostics and hit identification. ACTA ACUST UNITED AC 2006; 11:773-81. [PMID: 16943392 DOI: 10.1177/1087057106292138] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most applications of xMAP (Luminex) bead-based assay technology in diagnostics and drug discovery use immobilized antigens or antibodies. Here the authors describe the development of novel assay systems in which synthetic oligonucleotides that specifically bind and inhibit other biomolecules--so-called aptamers--are directly immobilized on beads. The robustness, specificity, and sensitivity of aptamer-based assays were demonstrated in a test system that detected human alpha-thrombin in serum samples. xMAP technology was also adapted to competitive screening formats where an aptamer/protein complex was disrupted by a functionally analogous competitor. The results indicate that such assays are excellently suited for diagnostic applications or drug screening, where aptamers serve as competitive binding probes for the identification of small-molecule hits. These methods should be transferable to a large number of applications because specific aptamers can be rapidly generated for almost any protein target.
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32
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Salimullah M, Mori M, Nishigaki K. High-throughput three-dimensional gel electrophoresis for versatile utilities: a stacked slice-gel system for separation and reactions (4SR). GENOMICS PROTEOMICS & BIOINFORMATICS 2006; 4:26-33. [PMID: 16689699 PMCID: PMC5054028 DOI: 10.1016/s1672-0229(06)60013-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A novel high-throughput system, called the stacked slice-gel system for separation and reactions (4SR), was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional (m × n) sample loading system. For this purpose, high-throughput multi-micro vessels (MMVs) containing variable numbers of wells (100 wells in this paper) have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.
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Affiliation(s)
- Md. Salimullah
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
| | - Masaki Mori
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan
- Rational Evolutionary Design of Advanced Biomolecules (REDS) Group, Saitama Small Enterprise Promotion Corporation, SKIP City, Kawaguchi 333-0844, Japan
- Corresponding author.
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33
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Corrie SR, Lawrie GA, Trau M. Quantitative analysis and characterization of biofunctionalized fluorescent silica particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:2731-7. [PMID: 16519476 DOI: 10.1021/la052433r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A strategy for the production and subsequent characterization of biofunctionalized silica particles is presented. The particles were engineered to produce a bifunctional material capable of both (a) the attachment of fluorescent dyes for particle encoding and (b) the sequential modification of the surface of the particles to couple oligonucleotide probes. A combination of microscopic and analytical methods is implemented to demonstrate that modification of the particles with 3-aminopropyl trimethoxysilane results in an even distribution of amine groups across the particle surface. Evidence is provided to indicate that there are negligible interactions between the bound fluorescent dyes and the attached biomolecules. A unique approach was adopted to provide direct quantification of the oligonucleotide probe loading on the particle surface through X-ray photoelectron spectroscopy, a technique which may have a major impact for current researchers and users of bead-based technologies. A simple hybridization assay showing high sequence specificity is included to demonstrate the applicability of these particles to DNA screening.
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Affiliation(s)
- Simon R Corrie
- Centre for Nanotechnology and Biomaterials, The University of Queensland, QLD 4072, Australia
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34
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de Boer AR, Bruyneel B, Krabbe JG, Lingeman H, Niessen WMA, Irth H. A microfluidic-based enzymatic assay for bioactivity screening combined with capillary liquid chromatography and mass spectrometry. LAB ON A CHIP 2005; 5:1286-92. [PMID: 16234953 DOI: 10.1039/b506559c] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The design and implementation of a continuous-flow microfluidic assay for the screening of (complex) mixtures for bioactive compounds is described. The microfluidic chip featured two microreactors (1.6 and 2.4 microL) in which an enzyme inhibition and a substrate conversion reaction were performed, respectively. Enzyme inhibition was detected by continuously monitoring the products formed in the enzyme-substrate reaction by electrospray ionization mass spectrometry (ESI-MS). In order to enable the screening of mixtures of compounds, the chip-based assay was coupled on-line to capillary reversed-phase high-performance liquid chromatography (HPLC) with the HPLC column being operated either in isocratic or gradient elution mode. In order to improve the detection limits of the current method, sample preconcentration based on a micro on-line solid-phase extraction column was employed. The use of electrospray MS allowed the simultaneous detection of chemical (MS spectra) and biological parameters (enzyme inhibition) of ligands eluting from the HPLC column. The present system was optimized and validated using the protease cathepsin B as enzyme of choice. Inhibition of cathepsin B is detected by monitoring three product traces, obtained by cleavage of the substrate. The two microreactors provided 32 and 36 s reaction time, respectively, which resulted in sufficient assay dynamics to enable the screening of bioactive compounds. The total flow rate was 4 microL min-1, which a 25-fold decrease was compared with a macro-scale system described earlier. Detection limits of 0.17-2.6 micromol L-1 were obtained for the screening of inhibitors, which is comparable to either microtiter plate assays or continuous-flow assays described in the literature.
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Affiliation(s)
- Arjen R de Boer
- Vrije Universiteit Amsterdam, Faculty of Sciences, Department of Chemistry and Pharmaceutical Sciences, Section Analytical Chemistry & Applied Spectroscopy, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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35
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Woodward PW, Williams C, Sewing A, Benson N. Improving the Design and Analysis of High-Throughput Screening Technology Comparison Experiments Using Statistical Modeling. ACTA ACUST UNITED AC 2005; 11:5-12. [PMID: 16234338 DOI: 10.1177/1087057105280779] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Contemporary small-molecule drug discovery frequently involves the screening of large compound files as a core activity. Subsequently cost, speed, and safety become critical issues. In order to meet this need, numerous technologies have been developed to allowmix andmeasure approaches, facilitate miniaturization, and to increase speed and tominimize the use of potentially hazardous reagents such as radioactive materials. However, despite the on-paper advantages of these new technologies, risks can remain undefined. For example, the question of whether the novel method will facilitate identification of active chemical series in a way that is comparable with conventional methods arises. In order to address this question, we have taken the approach of carrying out experiments to directly compare the output of high-throughput screens using a given novel approach and a traditionalmethod. The concordance between the screening methods can then be determined via comparison of the numbers and structures of the active molecules identified. This article describes the approach taken in our laboratory to minimize variability in such experiments and shows data that exemplifies the general result of lower than expected concordance. Statistical modeling was subsequently used to facilitate this interpretation. The model used distribution function to generate a real-activity frequency relationship with added normal random error and occasional outliers to represent assay variability. Hence, the effect of assay parameters such as the threshold, the number of real actives, and the number of outliers and the standard deviation could readily be explored. The model was found to describe the data reasonably and moreoverwas found to be of great utility when it came to planning further optimal experiments. A key conclusion from the model was that concordance between screening methods could appear poor even when one approach is compared with itself. This occurs simply because the result is a function of assay threshold, standard deviation and the true compound activity. In response to this finding we have adopted alternative experimental designs that more reliably measure the concordance between screening methods.
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Affiliation(s)
- Philip W Woodward
- Non-Clinical Statistics Group, Pfizer Development Operations, Sandwich, UK
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36
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del Campo A, Bruce IJ. Substrate Patterning and Activation Strategies for DNA Chip Fabrication. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b137073] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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37
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Miller CR, Vogel R, Surawski PPT, Corrie SR, Rühmann A, Trau M. Biomolecular screening with novel organosilica microspheres. Chem Commun (Camb) 2005:4783-5. [PMID: 16193113 DOI: 10.1039/b509503d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organosilica microspheres synthesised via a novel surfactant-free emulsion-based method show applicability towards optical encoding, solid-phase synthesis and high-throughput screening of bound oligonucleotide and peptide sequences.
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Affiliation(s)
- Chris R Miller
- Nanotechnology and Biomaterials Centre, University of Queensland, St. Lucia, Australia
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38
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Potyrailo RA, Morris WG, Wroczynski RJ, McCloskey PJ. Resonant Multisensor System for High-Throughput Determinations of Solvent/Polymer Interactions. ACTA ACUST UNITED AC 2004; 6:869-73. [PMID: 15530112 DOI: 10.1021/cc049925r] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Solvent-resistant polymers are important in numerous research, engineering, and consumer applications. To address the limitations of existing methods of evaluation of polymer solubility and solvent resistance, we developed and built a 6 x 4 array of resonant acoustic-wave sensors operating in the thickness shear mode (TSM). The application of this system makes possible analysis of nanogram quantities of polymers in small amounts of solvent and permits the simultaneous analysis of multiple samples, such as those produced in combinatorial polymerization reactions. These parallel determinations of polymer/solvent interactions eliminate errors associated with serial determinations. During the periodic exposure of the TSM crystals to polymer/solvent combinations, the mass increase of the crystal is determined, which is proportional to the amount of polymer dissolved and deposited onto the sensor from a polymer solution. We demonstrate our sensor system for reliable quantification of solubility of several types of polymers in various solvents. The high mass sensitivity of our resonant TSM sensors (10 ng), use of only a minute volume of a solvent (< 2 mL), and parallel operation (matching a layout of available 24 well plates) make this system a good fit with available polymer combinatorial synthesis equipment.
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Affiliation(s)
- Radislav A Potyrailo
- Biosciences, Combichemistry, and Characterization Technologies, Global Research Center, General Electric Company, Niskayuna, New York 12309, USA.
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39
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Affiliation(s)
- Todd A Thorsen
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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40
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Abstract
PURPOSE OF REVIEW Small-molecule inhibitors and activators of gene products or cell functions can be valuable research tools for analyzing gene function ('chemical genetics'), and as leads for the development of new therapies ('drug discovery'). The recent National Institutes of Health roadmap highlights small-molecule discovery and applications in cellular and in-vivo systems as an important new research direction. The purpose of this review is to explain the small-molecule discovery process for investigators doing research in an academic setting, with emphasis on advances and directions in epithelial transport physiology. RECENT FINDINGS The small-molecule discovery process involves the identification and validation of gene or phenotype targets, the screening of collections of small compounds for activity against the target, and the evaluation and optimization of compounds of interest. Many potential targets in renal epithelial physiology are suitable for small-molecule identification. Although small-molecule discovery in epithelial biology is in its infancy, recent advances have been reported in modulating the function of epithelial chloride channels, including the cystic fibrosis transmembrane conductance regulator and ClC-type chloride channels. SUMMARY Small-molecule discovery by the screening of chemical libraries is feasible in the academic setting, and holds great potential for the elucidation of gene function and complex regulatory pathways, and the identification of lead drug candidates for rare diseases and diseases of limited commercial interest. The rapid chemical turn-off of gene function addresses the concerns of compensatory/developmental changes in cell and animal models of gene deletion.
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Affiliation(s)
- Alan S Verkman
- Departments of Medicine and Physiology, Cardiovascular Research Institute, University of California, San Francisco, CA 94143-0521, USA.
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Pris AD, Porter MD. Nanoparticle coding: size-based assays using atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:6969-6973. [PMID: 15301472 DOI: 10.1021/la049918k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Described herein is a novel strategy for the construction and interrogation of an assay platform based on (1) the size encoding of labeled nanoparticles; (2) the high imaging resolution of atomic force microscopy; and (3) evaporatively driven self-assembly of dense nanoparticle layers. This strategy employs two different sized nanoparticles that couple in the presence of a target analyte. In this example, one set of particles is a few hundred nanometers in size and acts as a capture substrate, while a second set of smaller particles serve as the analyte label. Thus, by forming an evaporatively assembled layer from a mixture of the two particle dispersions, the imaged size of the smaller particles when bound to the larger capture particles identifies the presence of the analyte. This letter demonstrates the feasibility of our bar-code strategy by concept tests using the binding specificity of biotin-modified silica nanoparticles (300-nm diameter) with streptavidin-labeled gold nanoparticles (10-nm diameter). The potential to extensively multiplex this assay strategy is briefly discussed.
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Affiliation(s)
- Andrew D Pris
- Ames Laboratory-USDOE, Institute for Combinatorial Discovery, and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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42
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Rapid screening for affinity-improved scFvs by means of single-molecule-PCR-linked in vitro expression. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2004.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Abstract
High-throughput screening (HTS), systematically testing thousands of small molecules to find candidates for lead optimization, primarily involves exposure of purified proteins to arrayed collections of small molecules. More complex phenotypic assays, such as cell-based or whole-organism assays, traditionally have flanked HTS, preceding it to validate new therapeutic targets, and following it to characterize new lead compounds in cellular contexts. Recently, however, cell- and organism-based phenotypic assays have increasingly been adopted as a primary screening platform for annotating small molecules.
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Affiliation(s)
- Paul A Clemons
- Initiative for Chemical Genetics, ICCB-Broad Institute, Harvard University, 320 Charles Street, Room 184, Cambridge, Massachusetts 02141, USA.
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Abstract
Drug discovery and development is generally done in the commercial rather than the academic realm. Drug discovery involves target discovery and validation, lead identification by high-throughput screening, and lead optimization by medicinal chemistry. Follow-up preclinical evaluation includes analysis in animal models of compound efficacy and pharmacology (ADME: administration, distribution, metabolism, elimination) and studies of toxicology, specificity, and drug interactions. Notwithstanding the high-cost, labor-intensive, and non-hypothesis-driven aspects of drug discovery, the academic setting has a unique and expanding niche in this important area of investigation. For example, academic drug discovery can focus on targets of limited commercial value, such as third-world and rare diseases, and on the development of research reagents such as high-affinity inhibitors for pharmacological “gene knockout” in animal models (“chemical genetics”). This review describes the practical aspects of the preclinical drug discovery process for academic investigators. The discovery of small molecule inhibitors and activators of the cystic fibrosis transmembrane conductance regulator is presented as an example of an academic drug discovery program that has yielded new compounds for physiology research and clinical development.
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Affiliation(s)
- A S Verkman
- Departments of Medicine and Physiology, Cardiovascular Research Institute, University of California, San Francisco, California 94143-0521, USA.
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Clark SM, Konermann L. Screening for Noncovalent Ligand−Receptor Interactions by Electrospray Ionization Mass Spectrometry-Based Diffusion Measurements. Anal Chem 2004; 76:1257-63. [PMID: 14987079 DOI: 10.1021/ac035230l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of a novel method for the identification of low-molecular-weight noncovalent ligands to a macromolecular target is reported. This technique is based on the measurement of analyte diffusion coefficients by electrospray mass spectrometry (ESI-MS) (Clark et al., Rapid Commun. Mass Spectrom. 2002, 16, 1454-1462). Potential ligands have large diffusion coefficients as long as they are free in solution. Binding to a macromolecular target, however, drastically reduces the diffusional mobility of any ligand species. Mixtures containing six different saccharides [ribose, rhamnose, glucose, maltose, maltotriose, and N,N',N''-triacetylchitotriose (NAG(3))] were screened for noncovalent binding to lysozyme. Of these six compounds, only NAG(3) is known to bind to the protein. In "direct" binding tests, NAG(3) shows a significantly reduced diffusion coefficient in the presence of the protein. No changes were observed for any of the other saccharides. In a second set of experiments, the use of a "competition" screening method was explored in which mixtures of candidate saccharides were tested for their ability to displace a reference ligand from the target. The addition of NAG(3)-containing mixtures significantly increased the diffusion coefficient of the reference ligand NAG(4) (N,N',N'',N'''-tetraacetylchitotetrose), whereas mixtures that did not contain NAG(3) had no effect. These data clearly indicate the potential of ESI-MS-based diffusion measurements as a novel tool to screen compound libraries for binding to proteins and other macromolecular targets. In contrast to conventional ESI-MS-based ligand-receptor binding studies, this method does not rely on the preservation of noncovalent interactions in the gas phase.
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Affiliation(s)
- Sonya M Clark
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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Buss AD, Butler MS. A new model for utilising chemical diversity from natural sources. Drug Dev Res 2004. [DOI: 10.1002/ddr.10389] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
High-throughput screening (HTS) is the process of testing a large number of diverse chemical structures against disease targets to identify 'hits'. Compared to traditional drug screening methods, HTS is characterized by its simplicity, rapidness, low cost, and high efficiency, taking the ligand-target interactions as the principle, as well as leading to a higher information harvest. As a multidisciplinary field, HTS involves an automated operation-platform, highly sensitive testing system, specific screening model (in vitro), an abundant components library, and a data acquisition and processing system. Various technologies, especially the novel technologies such as fluorescence, nuclear-magnetic resonance, affinity chromatography, surface plasmon resonance, and DNA microarray, are now available, and the screening of more than 100,000 samples per day is already possible. Fluorescence-based assays include the scintillation proximity assay, time-resolved energy transfer, fluorescence anisotropy, fluorescence correlation spectroscopy, and fluorescence fluctuation spectroscopy. Fluorescence-based techniques are likely to be among the most important detection approaches used for HTS due to their high sensitivity and amenability to automation, giving the industry-wide drive to simplify, miniaturize, and speed up assays. The application of NMR technology to HTS is another recent trend in drug research. One advantage afforded by NMR technology is that it can provide direct information on the affinity of the screening compounds and the binding location of protein. The structure-activity relationship acquired from NMR analysis can sharpen the library design, which will be very important in furnishing HTS with well-defined drug candidates. Affinity chromatography used for library screening will provide the information on the fundamental processes of drug action, such as absorption, distribution, excretion, and receptor activation; also the eluting curve can give directly the possibility of candidate drug. SPR can measure the quantity of a complex formed between two molecules in real-time without the need for fluorescent or radioisotopic labels. SPR is capable of characterizing unmodified biopharmaceuticals, studying the interaction of drug candidates with macromolecular targets, and identifying binding partners during ligand fishing experiments. DNA microarrays can be used in HTS be used to further investigate the expression of biological targets associated with human disease, which then opens new and exciting opportunities for drug discovery. Without doubt, the addition of new technologies will further increase the application of HTS in drug screening and its related fields.
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Affiliation(s)
- Bailing Liu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, Peoples Republic of China.
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Abstract
The split-pool diversity orientated synthesis method, which requires some form of encoding to track the synthesis of discrete compounds, has been the lynchpin of most combinatorial synthesis efforts. The use of encoding methods in combinatorial chemistry has matured, and depending on their level of resources, chemists now have a diverse choice of encoding methods available. New methods of encoding have been developed that are inexpensive, simple to incorporate into any laboratory, and utilize analytical equipment such as MS, FTIR and NMR that are readily available to most organic chemists.
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Affiliation(s)
- Nicholas J Ede
- Mimotopes Pty. Ltd, 11 Duerdin Street, Clayton, Victoria 3168, Australia.
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Rungpragayphan S, Nakano H, Yamane T. PCR-linked in vitro expression: a novel system for high-throughput construction and screening of protein libraries. FEBS Lett 2003; 540:147-50. [PMID: 12681498 DOI: 10.1016/s0014-5793(03)00251-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A novel entirely in vitro strategy for generation and screening of a combinatorial protein library in an array format has been developed and is experimentally demonstrated. The strategy exploits virtues of PCR and in vitro coupled transcription/translation. Our new approach provides high-throughput construction and screening of the in vitro protein library, and compatibility with various selection methods.
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Affiliation(s)
- Suang Rungpragayphan
- Laboratory of Molecular Biotechnology, Graduate School of Biological and Agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Kreusch S, Schwedler S, Tautkus B, Cumme GA, Horn A. UV measurements in microplates suitable for high-throughput protein determination. Anal Biochem 2003; 313:208-15. [PMID: 12605857 DOI: 10.1016/s0003-2697(02)00460-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An UV spectrophotometric method for protein determination using microplates is described. Using the SPECTRAmax PLUS reader, the UVStar 96- and 384-well microplates and a 96 or 384 parallel channel liquid handling technique, large-scale determinations can be performed with intraassay precision better than 3% CV (coefficient of variation) in the range from 1 to 8000 microg of protein/ml, measuring at 205, 215, and 280 nm and using different volume-dependent light-path lengths. Since the absorbance coefficient at 205 nm is found to be 30 ml/(mgxcm) for eight different proteins with a CV of 5.6% only with the Path Check option of the reader, protein concentration can be determined without any individual calibration. Samples in the volume range of 60-250 microl can be analyzed without time-consuming and expensive treatment and without sample loss. Using a special 96 or 384 parallel dialyzing device, low molecular weight substances which interfere with the analysis by their UV absorbance, such as buffers and detergents, can effectively be removed. Application examples for serum protein separation are also shown in the presence of the strongly UV absorbing detergent Triton X-100.
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Affiliation(s)
- Stefan Kreusch
- Institute of Biochemistry I, Medical Faculty, Friedrich-Schiller University, Nonnenplan 2, D-07743 Jena, Germany
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