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Peng B, Yu C, Du S, Liew SS, Mao X, Yuan P, Na Z, Yao SQ. MSN-on-a-Chip: Cell-Based Screenings Made Possible on a Small-Molecule Microarray of Native Natural Products. Chembiochem 2018; 19:986-996. [PMID: 29465822 DOI: 10.1002/cbic.201800101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Indexed: 12/17/2022]
Abstract
Standard small-molecule microarrays (SMMs) are not well-suited for cell-based screening assays. Of the few attempts made thus far to render SMMs cell-compatible, all encountered major limitations. Here we report the first mesoporous silica nanoparticle (MSN)-on-a-chip platform capable of allowing high-throughput cell-based screening to be conducted on SMMs. By making use of a glass surface on which hundreds of MSNs, each encapsulated with a different native natural product, were immobilized in spatially defined manner, followed by on-chip mammalian cell growth and on-demand compound release, high-content screening was successfully carried out with readily available phenotypic detection methods. By combining this new MSN-on-a-chip system with small interfering RNA technology for the first time, we discovered that (+)-usniacin possesses synergistic inhibitory properties similar to those of olaparib (an FDA-approved drug) in BRCA1-knockdown cancer cells.
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Affiliation(s)
- Bo Peng
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Changmin Yu
- Institute of Advanced Materials (IAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 21816, China
| | - Shubo Du
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Si S Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Xin Mao
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Peiyan Yuan
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
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Papp K, Szittner Z, Prechl J. Life on a microarray: assessing live cell functions in a microarray format. Cell Mol Life Sci 2012; 69:2717-25. [PMID: 22391673 PMCID: PMC11115177 DOI: 10.1007/s00018-012-0947-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 02/14/2012] [Accepted: 02/16/2012] [Indexed: 01/07/2023]
Abstract
Microarray technology outgrew the detection of simple intermolecular interactions, as incubation of slides with living cells opened new vistas. Cell-based array technology permits simultaneous detection of several different cell surface molecules, allowing the complex characterization of cells with an amount of information that is hardly assessed by any other technique. Furthermore, binding of cells to printed antibodies or ligands may induce their activation, and consequently the outcome of these interactions, such as phosphorylation, gene expression, secretion of various products; differentiation, proliferation and apoptosis of the cells are also measurable on arrays. Moreover, since cells can be transfected with printed vectors, over- or under-expression of selected genes is also achievable simultaneously, creating a nice tool for assessing the function of a given gene. The enormously high-throughput cell-based microarray technology enables testing the effect of external stimuli on a scale that was earlier unthinkable. This review summarizes the possible applications of cell-based arrays.
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Affiliation(s)
- Krisztián Papp
- Immunology Research Group, Hungarian Academy of Sciences, MTA-ELTE, Pázmány P.s. 1/C, Budapest 1117, Hungary.
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Kemp MM, Weïwer M, Koehler AN. Unbiased binding assays for discovering small-molecule probes and drugs. Bioorg Med Chem 2011; 20:1979-89. [PMID: 22230199 DOI: 10.1016/j.bmc.2011.11.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 11/28/2022]
Abstract
2011 marks the 10-year anniversary of milestone manuscripts describing drafts of the human genome sequence. Over the past decade, a number of new proteins have been linked to disease-many of which fall into classes that have been historically considered challenging from the perspective of drug discovery. Several of these newly associated proteins lack structural information or strong annotation with regard to function, making development of conventional in vitro functional assays difficult. A recent resurgence in the popularity of simple small molecule binding assays has led to new approaches that do not require knowledge of protein structure or function in advance. Here we briefly review selected methods for executing binding assays that have been used successfully to discover small-molecule probes or drug candidates.
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Affiliation(s)
- Melissa M Kemp
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Vera B, Rodríguez AD, La Clair JJ. Aplysqualenol A binds to the light chain of dynein type 1 (DYNLL1). Angew Chem Int Ed Engl 2011; 50:8134-8. [PMID: 21744448 DOI: 10.1002/anie.201102546] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 01/29/2023]
Abstract
A bidirectional affinity system has been developed for the identification of cancer-related natural products and their biological targets. Aplysqualenol A is thus selectively identified as a ligand of the dynein light chain. The use of forward and reverse affinity methods suggests that both small-molecule isolation and target identification can be conducted using conventional molecular biological methods.
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Affiliation(s)
- Brunilda Vera
- Department of Chemistry, University of Puerto Rico, UPR Station, San Juan, 00931-3346, USA
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Kingston DGI. Modern natural products drug discovery and its relevance to biodiversity conservation. JOURNAL OF NATURAL PRODUCTS 2011; 74:496-511. [PMID: 21138324 PMCID: PMC3061248 DOI: 10.1021/np100550t] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural products continue to provide a diverse and unique source of bioactive lead compounds for drug discovery, but maintaining their continued eminence as source compounds is challenging in the face of the changing face of the pharmaceutical industry and the changing nature of biodiversity prospecting brought about by the Convention on Biological Diversity. This review provides an overview of some of these challenges and suggests ways in which they can be addressed so that natural products research can remain a viable and productive route to drug discovery. Results from International Cooperative Biodiversity Groups (ICBGs) working in Madagascar, Panama, and Suriname are used as examples of what can be achieved when biodiversity conservation is linked to drug discovery.
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Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States.
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Wu H, Ge J, Uttamchandani M, Yao SQ. Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 2011; 47:5664-5670. [DOI: 10.1039/c1cc11464f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular Bits and Chips: Profiling and discovering the next generation of small molecule ligands.
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Affiliation(s)
- Hao Wu
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Jingyan Ge
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Mahesh Uttamchandani
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
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Fluorous-based small-molecule microarrays for protein, antibody and enzyme screening. Future Med Chem 2009; 1:889-96. [DOI: 10.4155/fmc.09.76] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microarray techniques based on covalent and noncovalent compound immobilization have been developed for screening proteins, antibodies and enzymes to probe the possible biological roles of these interactions as well as their therapeutic and diagnostic potential. Small-molecule microarrays are particularly valuable for creating and probing multivalent displays of molecules, such as saccharides that mimic the multivalent displays of cell surface-bound compounds. After development of the method for the screening of carbohydrates in a multivalent display format, microarrays based on noncovalent fluorous interactions have seen use in probing protein-binding partners with a range of arrayed compounds. In this article, existing strategies and future perspectives for fluorous-based small-molecule microarrays for protein, antibody and enzyme screening will be presented. To date, qualitative and quantitative fluorous-based microarrays have offered important information regarding biomolecular interactions. Larger compound arrays created with automated fluorous-based synthesis and diagnostic tools based on fluorous-based microarrays are likely ahead.
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Adam GC, Parish CA, Wisniewski D, Meng J, Liu M, Calati K, Stein BD, Athanasopoulos J, Liberator P, Roemer T, Harris G, Chapman KT. Application of Affinity Selection/Mass Spectrometry to Determine the Structural Isomer of Parnafungins Responsible for Binding Polyadenosine Polymerase. J Am Chem Soc 2008; 130:16704-10. [DOI: 10.1021/ja805531w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gregory C. Adam
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Craig A. Parish
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Douglas Wisniewski
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Juncai Meng
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Min Liu
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Kathleen Calati
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Benjamin D. Stein
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - John Athanasopoulos
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Paul Liberator
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Terry Roemer
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Guy Harris
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
| | - Kevin T. Chapman
- Target Validation Chemistry, Natural Products Chemistry, and Infectious Diseases, Merck Research Laboratories, Merck and Company, P.O. Box 2000, Rahway, New Jersey 07065
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Kanoh N, Nakamura T, Honda K, Yamakoshi H, Iwabuchi Y, Osada H. Distribution of photo-cross-linked products from 3-aryl-3-trifluoromethyldiazirines and alcohols. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Vegas AJ, Fuller JH, Koehler AN. Small-molecule microarrays as tools in ligand discovery. Chem Soc Rev 2008; 37:1385-94. [PMID: 18568164 DOI: 10.1039/b703568n] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Small molecules that bind and modulate specific protein targets are increasingly used as tools to decipher protein function in a cellular context. Identifying specific small-molecule probes for each protein in the proteome will require miniaturized assays that permit screening of large collections of compounds against large numbers of proteins in a highly parallel fashion. Simple and general binding assays involving small-molecule microarrays can be used to identify probes for nearly any protein in the proteome. The assay may be used to identify ligands for proteins in the absence of knowledge about structure or function. In this tutorial review, we introduce small-molecule microarrays (SMMs) as tools for ligand discovery; discuss methods for manufacturing SMMs, including both non-covalent and covalent attachment strategies; and provide examples of ligand discovery involving SMMs.
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Affiliation(s)
- Arturo J Vegas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Charbonnier S, Gallego O, Gavin AC. The social network of a cell: recent advances in interactome mapping. BIOTECHNOLOGY ANNUAL REVIEW 2008; 14:1-28. [PMID: 18606358 DOI: 10.1016/s1387-2656(08)00001-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins very rarely act in isolation. Biomolecular interactions are central to all biological functions. In human, for example, interference with biomolecular networks often lead to disease. Protein-protein and protein-metabolite interactions have traditionally been studied one by one. Recently, significant progresses have been made in adapting suitable tools for the global analysis of biomolecular interactions. Here we review this suite of powerful technologies that enable an exponentially growing number of large-scale interaction datasets. These new technologies have already contributed to a more comprehensive cartography of several pathways relevant to human pathologies, offering a broader choice for therapeutic targets. Genome-wide scale analyses in model organisms reveal general organizational principles of eukaryotic proteomes. We also review the biochemical approaches that have been used in the past on a smaller scale for the quantification of the binding constant and the thermodynamics parameters governing biomolecular interaction. The adaptation of these technologies to the large-scale measurement of biomolecular interactions in (semi-)quantitative terms represents an important challenge.
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Affiliation(s)
- Sebastian Charbonnier
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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