1
|
Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
Collapse
Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| |
Collapse
|
2
|
Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
| |
Collapse
|
3
|
Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
4
|
Affiliation(s)
- Lindsey C. Szymczak
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hsin-Yu Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
5
|
Shi B, Deng Y, Zhao P, Li X. Selecting a DNA-Encoded Chemical Library against Non-immobilized Proteins Using a “Ligate–Cross-Link–Purify” Strategy. Bioconjug Chem 2017; 28:2293-2301. [PMID: 28742329 DOI: 10.1021/acs.bioconjchem.7b00343] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bingbing Shi
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yuqing Deng
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Peng Zhao
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute
of Nuclear Physics and Chemistry, China Academy of Engineering Physics, 64 Mianshan Road, Mianyang, Sichuan 621900, China
| | - Xiaoyu Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
6
|
Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| |
Collapse
|
7
|
Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
Collapse
|
8
|
Krusemark CJ, Tilmans NP, Brown PO, Harbury PB. Directed Chemical Evolution with an Outsized Genetic Code. PLoS One 2016; 11:e0154765. [PMID: 27508294 PMCID: PMC4980042 DOI: 10.1371/journal.pone.0154765] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/15/2016] [Indexed: 12/02/2022] Open
Abstract
The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution.
Collapse
Affiliation(s)
- Casey J. Krusemark
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Nicolas P. Tilmans
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Pehr B. Harbury
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
9
|
Abstract
DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
Collapse
Affiliation(s)
- Marie L. Malone
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| |
Collapse
|
10
|
Novoa A, Winssinger N. DNA display of glycoconjugates to emulate oligomeric interactions of glycans. Beilstein J Org Chem 2015; 11:707-19. [PMID: 26113879 PMCID: PMC4462854 DOI: 10.3762/bjoc.11.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Glycans (carbohydrate portion of glycoproteins and glycolipids) frequently exert their function through oligomeric interactions involving multiple carbohydrate units. In efforts to recapitulate the diverse spatial arrangements of the carbohydrate units, assemblies based on hybridization of nucleic acid conjugates have been used to display simplified ligands with tailored interligand distances and valences. The programmability of the assemblies lends itself to a combinatorial display of multiple ligands. Recent efforts in the synthesis and applications of such conjugates are discussed.
Collapse
Affiliation(s)
- Alexandre Novoa
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
| |
Collapse
|
11
|
Li G, Zheng W, Liu Y, Li X. Novel encoding methods for DNA-templated chemical libraries. Curr Opin Chem Biol 2015; 26:25-33. [PMID: 25635927 DOI: 10.1016/j.cbpa.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 12/12/2022]
Abstract
Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.
Collapse
Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| |
Collapse
|
12
|
Huang YC, Cao C, Tan XL, Li X, Liu L. Facile solid-phase synthesis of PNA–peptide conjugates using pNZ-protected PNA monomers. Org Chem Front 2014. [DOI: 10.1039/c4qo00217b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014; 53:10056-9. [DOI: 10.1002/anie.201404830] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/07/2022]
|
14
|
Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404830] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
15
|
Bahal R, McNeer NA, Ly DH, Saltzman WM, Glazer PM. Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5. ARTIFICIAL DNA, PNA & XNA 2014; 4:49-57. [PMID: 23954968 DOI: 10.4161/adna.25628] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of a new class of peptide nucleic acids (PNAs), i.e., gamma PNAs (γPNAs), creates the need for a general and effective method for its delivery into cells for regulating gene expression in mammalian cells. Here we report the antisense activity of a recently developed hydrophilic and biocompatible diethylene glycol (miniPEG)-based gamma peptide nucleic acid called MPγPNAs via its delivery by poly(lactide-co-glycolide) (PLGA)-based nanoparticle system. We show that MPγPNA oligomers designed to bind to the selective region of chemokine receptor 5 (CC R5) transcript, induce potent and sequence-specific antisense effects as compared with regular PNA oligomers. In addition, PLGA nanoparticle delivery of MPγPNAs is not toxic to the cells. The findings reported in this study provide a combination of γPNA technology and PLGA-based nanoparticle delivery method for regulating gene expression in live cells via the antisense mechanism.
Collapse
|
16
|
Sun YS, Fei Y, Luo J, Dixon S, Landry JP, Lam KS, Zhu X. Generating Encoded Compound Libraries for Fabricating Microarrays as a High-Throughput Protein Ligand Discovery Platform. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.840728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yung-Shin Sun
- a Department of Physics , Fu-Jen Catholic University , New Taipei City , Taiwan
| | - Yiyan Fei
- b Department of Optical Science and Engineering , Fudan University , Shanghai , China
- c Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Ultra-Precision Optical Manufacturing Engineering Center , Fudan University , Shanghai , China
| | - Juntao Luo
- d Department of Pharmacology , Upstate Cancer Research Institute, State University of New York Upstate Medical University , Syracuse , New York , USA
| | - Seth Dixon
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - James P. Landry
- f Department of Physics , University of California at Davis , Davis , California , USA
| | - Kit S. Lam
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
- g Department of Biochemistry and Molecular Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - Xiangdong Zhu
- f Department of Physics , University of California at Davis , Davis , California , USA
| |
Collapse
|
17
|
Doran TM, Kodadek T. A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions. ACS Chem Biol 2014; 9:339-46. [PMID: 24245981 PMCID: PMC3944025 DOI: 10.1021/cb400806r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic molecule microarrays, consisting of many different compounds spotted onto a planar surface such as modified glass or cellulose, have proven to be useful tools for the multiplexed analysis of small molecule- and peptide-protein interactions. However, these arrays are technically difficult to manufacture and use with high reproducibility and require specialized equipment. Here we report a more convenient alternative composed of color-encoded beads that display a small molecule protein ligand on the surface. Quantitative, multiplexed assay of protein binding to up to 24 different ligands can be achieved using a common flow cytometer for the readout. This technology should be useful for evaluating hits from library screening efforts, the determination of structure activity relationships, and certain types of serological analyses.
Collapse
Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida , 130 Scripps Way, Jupiter , Florida 33458, United States
| | | |
Collapse
|
18
|
van Domselaar R, de Poot SAH, Bovenschen N. Proteomic profiling of proteases: tools for granzyme degradomics. Expert Rev Proteomics 2014; 7:347-59. [DOI: 10.1586/epr.10.24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
19
|
Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013; 52:9544-9. [DOI: 10.1002/anie.201302161] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Indexed: 01/07/2023]
|
20
|
Li G, Liu Y, Liu Y, Chen L, Wu S, Liu Y, Li X. Photoaffinity Labeling of Small-Molecule-Binding Proteins by DNA-Templated Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302161] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Dixit CK, Kumar A, Kaushik A. Nanosphere lithography-based platform for developing rapid and high sensitivity microarray systems. Biochem Biophys Res Commun 2012; 423:473-7. [PMID: 22683633 DOI: 10.1016/j.bbrc.2012.05.144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
Abstract
A novel gold nanoarray (NA)-based platform was developed for microarray applications. This novel approach is based upon the principle of nanosphere lithography and can be used for one-step antibody immobilization. The developed platform was checked by functionalizing with cysteine followed by capturing biotinylated antibody and detecting it with dye-conjugated steptravidin. An immunoassay was performed with spiked samples containing human fetuin A antigen. The minimum limits of detection (LOD) of human fetuin A for NA-based and conventional microarray platforms were 50 pg/mL and 50 ng/mL, respectively. The developed approach was highly reproducible and unlike conventional microarray approaches the use of a spotting system was omitted because immobilization was controlled and directed on the predefined arrays. This approach could be an ideal alternative for developing microarrays. And, the ease of the strategy also allows the high throughput production of the microarrays.
Collapse
Affiliation(s)
- Chandra K Dixit
- School of Biotechnology, National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | |
Collapse
|
22
|
Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
Collapse
|
23
|
Decoding a PNA encoded peptide library by PCR: the discovery of new cell surface receptor ligands. ACTA ACUST UNITED AC 2012; 18:1284-9. [PMID: 22035797 DOI: 10.1016/j.chembiol.2011.07.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/05/2011] [Accepted: 07/06/2011] [Indexed: 12/18/2022]
Abstract
The ability to screen and identify new ligands for cell surface receptors has been a long-standing goal as it might allow targeting of pharmaceutically relevant receptors, such as integrins or G protein coupled receptors. Here, we present a method to amplify hits from a library of PNA-tagged peptides. To this end, human cells, overexpressing either integrins or the CCR6 receptor, were treated with a 10,000 member PNA-encoded peptide library. Extraction of the PNA tags from the surface of the cells was followed by a PNA-tag to DNA translation and amplification enabling decoding of the tags via microarray hybridization. This approach to ligand discovery facilitates screening for differences in surface-receptor ligands and/or receptor expression between different cell types, and opens up a practical approach to PNA-tag amplification.
Collapse
|
24
|
Serim S, Haedke U, Verhelst SHL. Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 2012; 7:1146-59. [PMID: 22431376 DOI: 10.1002/cmdc.201200057] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Indexed: 11/11/2022]
Abstract
Proteases are important targets for the treatment of human disease. Several protease inhibitors have failed in clinical trials due to a lack of in vivo specificity, indicating the need for studies of protease function and inhibition in complex, disease-related models. The tight post-translational regulation of protease activity complicates protease analysis by traditional proteomics methods. Activity-based protein profiling is a powerful technique that can resolve this issue. It uses small-molecule tools-activity-based probes-to label and analyze active enzymes in lysates, cells, and whole animals. Over the last twelve years, a wide variety of protease activity-based probes have been developed. These synthetic efforts have enabled techniques ranging from real-time in vivo imaging of protease activity to high-throughput screening of uncharacterized proteases. This Review introduces the general principles of activity-based protein profiling and describes the recent advancements in probe design and analysis techniques, which have increased the knowledge of protease biology and will aid future protease drug discovery.
Collapse
Affiliation(s)
- Sevnur Serim
- Center for Integrated Protein Science Munich (CIPS(M)), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | | | | |
Collapse
|
25
|
Reynolds F, Kelly KA. Techniques for molecular imaging probe design. Mol Imaging 2011; 10:407-419. [PMID: 22201532 PMCID: PMC3224676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology--all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.
Collapse
Affiliation(s)
- Fred Reynolds
- Robert M. Berne Cardiovascular Research Center and Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | | |
Collapse
|
26
|
Abstract
Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology—all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.
Collapse
Affiliation(s)
- Fred Reynolds
- From the Robert M. Berne Cardiovascular Research Center and the Department of Biomedical Engineering, University of Virginia, Charlottesville, VA. Reprints not available
| | - Kimberly A. Kelly
- From the Robert M. Berne Cardiovascular Research Center and the Department of Biomedical Engineering, University of Virginia, Charlottesville, VA. Reprints not available
| |
Collapse
|
27
|
Sahu B, Sacui I, Rapireddy S, Zanotti KJ, Bahal R, Armitage BA, Ly DH. Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility. J Org Chem 2011; 76:5614-27. [PMID: 21619025 PMCID: PMC3175361 DOI: 10.1021/jo200482d] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity toward DNA and RNA and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol ("miniPEG", R-MP) unit at the γ-backbone transforms a randomly folded PNA into a right-handed helix. Synthesis of optically pure (R-MP)γPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-l-serine. Once synthesized, (R-MP)γPNA oligomers are preorganized into a right-handed helix, hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology, and medicine, as well as in other disciplines, including drug discovery and molecular engineering.
Collapse
Affiliation(s)
- Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Kimberly J. Zanotti
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| |
Collapse
|
28
|
Abstract
The use of classical genetic and molecular biology methods along with the sequencing of many genomes has proven crucial for elucidating complex biological processes. Despite being invaluable tools, their limitations have led to a search for more versatile alternatives and, thus, to the use of small molecules. Chemical genetics is a rapidly emerging field that uses small-molecule techniques to probe biological systems and is composed of three parts: natural product or small-molecule libraries, phenotypic screening and target identification. Currently, the biggest hurdle in the overall process of chemical genetics is target identification. Efforts to overcome this obstacle have led to advances in the areas of affinity chromatography, yeast haploinsufficiency, complementary DNA (cDNA) overexpression, DNA microarray, small-molecule microarray and RNA interference (RNAi) technologies. While these technologies continue to undergo further optimization, they have been integral in the identification and/or confirmation of many cellular targets and have seen an increase in applications to the drug-development process.
Collapse
|
29
|
Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
Collapse
Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
|
32
|
Daguer JP, Ciobanu M, Alvarez S, Barluenga S, Winssinger N. DNA-templated combinatorial assembly of small molecule fragments amenable to selection/amplification cycles. Chem Sci 2011. [DOI: 10.1039/c0sc00574f] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
33
|
Diezmann F, Seitz O. DNA-guided display of proteins and protein ligands for the interrogation of biology. Chem Soc Rev 2011; 40:5789-801. [DOI: 10.1039/c1cs15054e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
34
|
Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du S, Madrid M, Ly DH. Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. J Am Chem Soc 2010; 132:10717-27. [PMID: 20681704 DOI: 10.1021/ja907225d] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.
Collapse
Affiliation(s)
- Joanne I Yeh
- Department of Structural Biology, University of Pittsburgh Medical School 1036 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA.
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Park Y, Choi Y, Mitra D, Kang T, Lee LP. Study of microscale hydraulic jump phenomenon for hydrodynamic trap-and-release of microparticles. APPLIED PHYSICS LETTERS 2010; 97:154101. [PMID: 21057671 PMCID: PMC2973986 DOI: 10.1063/1.3479052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/17/2010] [Indexed: 05/30/2023]
Abstract
Easy trap-and-release of microparticles is necessary to study biological cellular behavior. The hydraulic jump phenomenon inspired us to conceive a microfluidic device for the hydrodynamic trap-and-release of microparticles. A sudden height increase in a microfluidic channel leads to a dramatic decrease in flow velocity, allowing effective trapping of the microparticles by energy conversion. The trapped particles can be released by stronger inertial force based on simply increasing the flow velocity. We present a systematic, numerical study of trap-and-release of the microparticles using multiphase Navier-Stokes equations. Effect of geometry flow velocity, particle diameter, and adhesion force on trap-and-release was studied.
Collapse
|
36
|
Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
37
|
Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
Collapse
Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
| |
Collapse
|
38
|
Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
39
|
Collet BYM, Nagashima T, Yu MS, Pohl NLB. Fluorous-based Peptide Microarrays for Protease Screening. J Fluor Chem 2009; 130:1042-1048. [PMID: 20161483 DOI: 10.1016/j.jfluchem.2009.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As ever more protease sequences are uncovered through genome sequencing projects, efficient parallel methods to discover the potential substrates of these proteases becomes crucial. Herein we describe the first use of fluorous-based microarrays to probe peptide sequences and begin to define the scope and limitations of fluorous microarray technologies for the screening of proteases. Comparison of a series of serine proteases showed that their ability to cleave peptide substrates in solution was maintained upon immobilization of these substrates onto fluorous-coated glass slides. The fluorous surface did not serve to significantly inactivate the enzymes. However, addition of hydrophilic components to the peptide sequences could induce lower rates of substrate cleavage with enzymes such as chymotrypsin with affinities to hydrophobic moieties. This work represents the first step to creating robust protease screening platforms using noncovalent microarray interface that can easily incorporate a range of compounds on the same slide.
Collapse
Affiliation(s)
- Beatrice Y M Collet
- Department of Chemistry and the Plant Sciences Institute, Gilman Hall, Iowa State University, Ames, IA, 50011-3111
| | | | | | | |
Collapse
|
40
|
High quality protein microarray using in situ protein purification. BMC Biotechnol 2009; 9:72. [PMID: 19698181 PMCID: PMC2746808 DOI: 10.1186/1472-6750-9-72] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 08/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC). This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. RESULTS Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG) coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST) composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents protein solubility and denaturation problems caused by buffer exchange steps and freeze-thaw cycles, which are associated with resin-based purification, intermittent protein storage and deposition on microarrays. CONCLUSION An optimized platform for in situ protein purification on microarray slides using His-tagged recombinant proteins is a desirable tool for the screening of novel protein functions and protein-protein interactions. In the context of immunoproteomics, such protein microarrays are complimentary to approaches using non-recombinant methods to discover and characterize bacterial antigens.
Collapse
|
41
|
Prins L, Scrimin P. “Covalent Capture”: Verschmelzung von kovalenter und nichtkovalenter Synthese. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803583] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
42
|
Prins L, Scrimin P. Covalent Capture: Merging Covalent and Noncovalent Synthesis. Angew Chem Int Ed Engl 2009; 48:2288-306. [DOI: 10.1002/anie.200803583] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
43
|
Abstract
Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.
Collapse
Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
| | | | | |
Collapse
|
44
|
Jonkheijm P, Weinrich D, Schröder H, Niemeyer CM, Waldmann H. Chemical strategies for generating protein biochips. Angew Chem Int Ed Engl 2008; 47:9618-47. [PMID: 19025742 DOI: 10.1002/anie.200801711] [Citation(s) in RCA: 427] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.
Collapse
Affiliation(s)
- Pascal Jonkheijm
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology and Faculty of Chemistry, Chemical Biology, Technical University of Dortmund, Otto Hahn Strasse 11, 44227 Dortmund, Germany
| | | | | | | | | |
Collapse
|
45
|
Jonkheijm P, Weinrich D, Schröder H, Niemeyer C, Waldmann H. Chemische Verfahren zur Herstellung von Proteinbiochips. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801711] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
46
|
Abstract
Hepatocellular carcinoma (HCC) typically has poor prognosis, because it is often diagnosed at an advanced stage. Heterogeneous phenotypic and genetic traits of affected individuals and a wide range of risk factors have classified it a complex disease. HCC is not amenable to standard chemotherapy and is resistant to radiotherapy. In most cases, surgical resection and liver transplantation remain the only curative treatment options. Therefore, development of novel, effective therapies is of prime importance. Extensive research over the past decade has identified a number of molecular biomarkers as well as cellular networks and signaling pathways affected in liver cancer. Recent studies using a combination of "omics" technologies, microRNA studies, combinatorial chemistry, and bioinformatics are providing new insights into the gene expression and protein profiles during various stages of the disease. In this review, we discuss the contribution of these newer approaches toward an understanding of molecular mechanisms of HCC and for the development of novel cancer therapeutics.
Collapse
Affiliation(s)
- Rajagopal N Aravalli
- Department of Radiology, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN, USA.
| | | | | |
Collapse
|
47
|
Collard D, Takeuchi S, Fujita H. MEMS technology for nanobio research. Drug Discov Today 2008; 13:989-96. [PMID: 18835363 DOI: 10.1016/j.drudis.2008.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 10/21/2022]
Abstract
Micro- and nanotechnology have gathered 20 years of increasing research efforts. This research activity began and developed with the design and the fabrication of micro- and nanomechanisms, sensors and actuators, which range from 10nm to 100mum. More recent trends focus on the transfer of this technology know-how towards nanobiological topics and very wide range applications can be addressed. Among them, this review proposes various examples that include MEMS tweezers for molecular direct handling and characterization, single molecular characterization in femto-L chambers and dynamic microarray for cell positioning. The micromachined devices are described with bio-oriented experiences that are relevant to foresee their future contribution to drug discovery.
Collapse
Affiliation(s)
- Dominique Collard
- Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
| | | | | |
Collapse
|
48
|
Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem 2008; 77:383-414. [PMID: 18366325 DOI: 10.1146/annurev.biochem.75.101304.124125] [Citation(s) in RCA: 933] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomic strategy to characterize enzyme function directly in native biological systems on a global scale. Here, we review the basic technology of ABPP, the enzyme classes addressable by this method, and the biological discoveries attributable to its application.
Collapse
Affiliation(s)
- Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | | | | |
Collapse
|
49
|
Uttamchandani M, Li J, Sun H, Yao SQ. Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics. Chembiochem 2008; 9:667-75. [DOI: 10.1002/cbic.200700755] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
50
|
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.
Collapse
Affiliation(s)
- Sebastian Charbonnier
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | | | | |
Collapse
|