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Riege D, Herschel S, Fenkl T, Schade D. Small-Molecule Probes as Pharmacological Tools for the Bone Morphogenetic Protein Signaling Pathway. ACS Pharmacol Transl Sci 2023; 6:1574-1599. [PMID: 37974621 PMCID: PMC10644459 DOI: 10.1021/acsptsci.3c00170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
The bone morphogenetic protein (BMP) pathway is highly conserved and plays central roles in health and disease. The quality and quantity of its signaling outputs are regulated at multiple levels, offering pharmacological options for targeted modulation. Both target-centric and phenotypic drug discovery (PDD) approaches were applied to identify small-molecule BMP inhibitors and stimulators. In this Review, we accumulated and systematically classified the different reported chemotypes based on their targets as well as modes-of-action, and herein we illustrate the discovery history of selected candidates. A comprehensive summary of available biochemical, cellular, and in vivo activities is provided for the most relevant BMP modulators, along with recommendations on their preferred use as chemical probes to study BMP-related (patho)physiological processes. There are a number of high-quality probes used as BMP inhibitors that potently and selectively interrogate the kinase activities of distinct type I (16 chemotypes available) and type II receptors (3 chemotypes available). In contrast, only a few high-quality BMP stimulator modalities have been introduced to the field due to a lack of profound target knowledge. FK506-derived macrolides such as calcineurin-sparing FKBP12 inhibitors currently represent the best-characterized chemical tools for direct activation of BMP-SMAD signaling at the receptor level. However, several PDD campaigns succeeded in expanding the druggable space of BMP stimulators. Albeit the majority of them do not entirely fulfill the strict chemical probe criteria, many chemotypes exhibit unique and unrecognized mechanisms as pathway potentiators or synergizers, serving as valuable pharmacological tools for BMP perturbation.
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Affiliation(s)
- Daniel Riege
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Sven Herschel
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Teresa Fenkl
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Dennis Schade
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
- Partner
Site Kiel, DZHK, German Center for Cardiovascular
Research, 24105 Kiel, Germany
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2
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Chemistry revolutionizes genetics and epigenetics. Curr Opin Chem Biol 2023; 72:102247. [PMID: 36549086 DOI: 10.1016/j.cbpa.2022.102247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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3
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Maxson T, Tietz JI, Hudson GA, Guo XR, Tai HC, Mitchell DA. Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc 2016; 138:15157-15166. [PMID: 27797509 DOI: 10.1021/jacs.6b06848] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Natural products (NPs) serve important roles as drug candidates and as tools for chemical biology. However, traditional NP discovery, largely based on bioassay-guided approaches, is biased toward abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new NPs are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based NP screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the NP is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing NPs. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analogue of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor, which have been widely used for over 40 years.
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Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Xiao Rui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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4
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Lee H, Lee JW. Target identification for biologically active small molecules using chemical biology approaches. Arch Pharm Res 2016; 39:1193-201. [DOI: 10.1007/s12272-016-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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5
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Abstract
Withaferin A (WFA), initially identified as a compound that inhibits experimental angiogenesis, has been shown to bind to soluble vimentin (sVim) and other type III intermediate filament (IF) proteins. We review WFA's dose-related activities (Section 1), examining nanomolar concentrations effects on sVim in cell proliferation and submicromolar effects on lamellipodia and focal adhesion formation. WFA effects on polymeric IFs are especially interesting to the study of cell migration and invasion that depend on IF mechanical contractile properties. WFA interferes with NF-κB signaling, though this anti-inflammatory mechanism may occur via perturbation of sVim-protein complexes, and possibly also via targeting IκB kinase β directly. However, micromolar concentrations that induce vimentin cleavage to promote apoptosis may increasingly show off-target effects via targeting other IFs (neurofilaments and keratin) and non-IFs (tubulin, heat-shock proteins, proteasome). Thus, in Section 2, we describe our studies combining cell cultures with animal models of injury to validate relevant type III IF-targeting mechanisms of WFA. In Section 3, we illuminate from investigating myofibroblast differentiation how sVim phosphorylation may govern cell type-selective sensitivity to WFA, offering impetus for exploring vimentin phosphorylation isoforms as targets and biomarkers of fibrosis. These different WFA targets and activities are listed in a summary table.
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Affiliation(s)
- Royce Mohan
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, USA.
| | - Paola Bargagna-Mohan
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut, USA
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6
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Burnette M, Brito-Robinson T, Li J, Zartman J. An inverse small molecule screen to design a chemically defined medium supporting long-term growth of Drosophila cell lines. MOLECULAR BIOSYSTEMS 2014; 10:2713-23. [PMID: 25096480 PMCID: PMC4890965 DOI: 10.1039/c4mb00155a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drosophila cell culture is used as a model system with multiple applications including the identification of new therapeutic targets in screens, the study of conserved signal transduction pathway mechanisms, and as an expression system for recombinant proteins. However, in vitro methods for Drosophila cell and organ cultures are relatively undeveloped. To characterize the minimal requirements for long-term maintenance of Drosophila cell lines, we developed an inverse screening strategy to identify small molecules and synergies stimulating proliferation in a chemically defined medium. In this chemical-genetics approach, a compound-protein interaction database is used to systematically score genetic targets on a screen-wide scale to extract further information about cell growth. In the pilot screen, we focused on two well-characterized cell lines, Clone 8 (Cl.8) and Schneider 2 (S2). Validated factors were investigated for their ability to maintain cell growth over multiple passages in the chemically defined medium (CDM). The polyamine spermidine proved to be the critical component that enables the CDM to support long-term maintenance of Cl.8 cells. Spermidine supplementation upregulates DNA synthesis for Cl.8 and S2 cells and increases MAPK signaling for Cl.8 cells. The CDM also supports the long-term growth of Kc167 cells. Our target scoring approach validated the importance of polyamines, with enrichment for multiple polyamine ontologies found for both cell lines. Future iterations of the screen will enable the identification of compound combinations optimized for specific applications-maintenance and generation of new cell lines or the production and purification of recombinant proteins-thus increasing the versatility of Drosophila cell culture as both a genetic and biochemical model system. Our cumulative target scoring approach improves on traditional chemical-genetics methods and is extensible to biological processes in other species.
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Affiliation(s)
- M Burnette
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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7
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Abstract
Chemical genetics utilizes small molecules to perturb biological processes. Unlike conventional genetics methods, which involve the alteration of genetic information mostly with lasting effects, chemical genetics allows temporary and reversible alterations of biological processes. Furthermore, it enables the alteration of biological processes in a dose-dependent manner, providing an advantage over conventional genetics. In the present chapter, the general procedures of forward chemical genetic screening are described. Forward chemical genetic screening can be performed in three steps. The first step involves the identification of small molecules that induce phenotypic or physiological changes in a biological system from a chemical library. In the second step, cellular targets that interact with the isolated chemical, which are mostly proteins, are identified. Although several methods can be applied in the second step, the most common one is affinity pull-down assay using a target protein that binds to the isolated compound. However, affinity pull-down of a target protein is a formidable barrier in forward chemical genetics. We introduced a tagged chemical library approach that significantly facilitates the identification of target proteins. The third step consists of the validation of the target protein, which should include the assessment of target specificity. This step is critical because small molecules often show pleiotropic effects due to low specificity. The specificity test may include a competition assay using cold competitors and a genetic study using mutants or transgenic lines modified for the cellular target.
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8
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Full kinetics investigation of the formation reaction of phosphonate esters in the gas-phase: a theoretical study. J Mol Model 2014; 20:2103. [PMID: 24633765 DOI: 10.1007/s00894-014-2103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
Abstract
In the present work, the proposed multiple-mechanisms have been investigated theoretically for the reaction between triphenyl phosphite and dimethyl acetylenedicarboxylate in the presence of N-H acid such as aniline for generation of phosphonate esters using ab initio molecular orbital theory in gas phase. The profile of the potential energy surface was constructed at the HF/6-311G(d,p) level of theory. The kinetics of the gas phase reaction was studied by evaluating the reaction path of various mechanisms. Between 12 speculative proposed mechanisms {step₁, step₂ (with four possibilities), step₃ (with three possibilities), and step₄} only the third speculative mechanism was recognized as a desirable mechanism. Theoretical kinetics data involving k and E(a), activation (ΔG(‡), ΔS(‡) and ΔH(‡)), and thermodynamic parameters (ΔG°, ΔS° and ΔH°) were calculated for each step of the various mechanisms. Step₁ of the desirable mechanism was identified as the rate determining step. Comparison of the theoretical desirable mechanism with the rate law that has been previously obtained by UV spectrophotometry experiments indicated that the results are in good agreement.
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9
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Abstract
In recent years, small interference RNAs (siRNAs) have greatly enhanced our understanding of protein functions by allowing knockdown of targeted proteins at the mRNA level. Similarly, in an effort to achieve degradation of targeted proteins at the post-translational level, chimeric small molecules called "PROTACs" (PROteolysis TArgeting Chimeric molecules) have been developed. The PROTAC approach utilizes chimeric small molecules which recruit targeted proteins to the ubiquitin-proteasome pathway, a major intracellular protein degradation system. Unlike conventional small molecules that bind to protein and inhibit its function, the PROTAC approach induces destruction of target protein via the ubiquitin-proteasome system. This article presents a typical strategy for PROTAC design and preparation and biological characterization. Curr. Protoc. Chem Biol. 2:71-87. © 2010 by John Wiley & Sons, Inc.
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10
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Onen-Bayram FE, Durmaz I, Scherman D, Herscovici J, Cetin-Atalay R. A novel thiazolidine compound induces caspase-9 dependent apoptosis in cancer cells. Bioorg Med Chem 2012; 20:5094-102. [PMID: 22867707 DOI: 10.1016/j.bmc.2012.07.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/16/2012] [Accepted: 07/10/2012] [Indexed: 12/13/2022]
Abstract
The forward chemogenomics strategy allowed us to identify a potent cytotoxic thiazolidine compound as an apoptosis-inducing agent. Chemical structures were designed around a thiazolidine ring, a structure already noted for its anticancer properties. Initially, we evaluated these novel compounds on liver, breast, colon and endometrial cancer cell lines. The compound 3 (ALC67) showed the strongest cytotoxic activity (IC(50) ∼5 μM). Cell cycle analysis with ALC67 on liver cells revealed SubG1/G1 arrest bearing apoptosis. Furthermore we demonstrated that cytotoxicity of this compound was due to the activation of caspase-9 involved apoptotic pathway, which is death receptor independent.
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Affiliation(s)
- F Esra Onen-Bayram
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University, Kadıkoy, 34755 Istanbul, Turkey
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11
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Jang ER, Lee NR, Han S, Wu Y, Sharma LK, Carmony KC, Marks J, Lee DM, Ban JO, Wehenkel M, Hong JT, Kim KB, Lee W. Revisiting the role of the immunoproteasome in the activation of the canonical NF-κB pathway. MOLECULAR BIOSYSTEMS 2012; 8:2295-302. [PMID: 22722901 DOI: 10.1039/c2mb25125f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The discovery of NF-κB signaling pathways has greatly enhanced our understanding of inflammatory and immune responses. In the canonical NF-κB pathway, the proteasomal degradation of IκBα, an inhibitory protein of NF-κB, is widely accepted to be a key regulatory step. However, contradictory findings have been reported as to whether the immunoproteasome plays an obligatory role in the degradation of IκBα and activation of the canonical NF-κB pathway. Such results were obtained mainly using traditional gene deletion strategies. Here, we have revisited the involvement of the immunoproteasome in the canonical NF-κB pathway using small molecule inhibitors of the immunoproteasome, namely UK-101 and LKS01 targeting β1i and β5i, respectively. H23 and Panc-1 cancer cells were pretreated with UK-101, LKS01 or epoxomicin (a prototypic inhibitor targeting both the constitutive proteasome and immunoproteasome). We then examined whether these pretreatments lead to any defect in activating the canonical NF-κB pathway following TNFα exposure by monitoring the phosphorylation and degradation of IκBα, nuclear translocation of NF-κB proteins and DNA binding and transcriptional activity of NF-κB. Our results consistently indicated that there is no defect in activating the canonical NF-κB pathway following selective inhibition of the immunoproteasome catalytic subunits β1i, β5i or both using UK-101 and LKS01, in contrast to epoxomicin. In summary, our current results using chemical genetic approaches strongly support that the catalytic activity of the immunoproteasome subunits β1i and β5i is not required for canonical NF-κB activation in lung and pancreatic adenocarcinoma cell line models.
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Affiliation(s)
- Eun Ryoung Jang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, Kentucky 40536-0596, USA
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12
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He W, Brumos J, Li H, Ji Y, Ke M, Gong X, Zeng Q, Li W, Zhang X, An F, Wen X, Li P, Chu J, Sun X, Yan C, Yan N, Xie DY, Raikhel N, Yang Z, Stepanova AN, Alonso JM, Guo H. A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. THE PLANT CELL 2011; 23:3944-60. [PMID: 22108404 PMCID: PMC3246337 DOI: 10.1105/tpc.111.089029] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/08/2011] [Accepted: 10/26/2011] [Indexed: 05/18/2023]
Abstract
The interactions between phytohormones are crucial for plants to adapt to complex environmental changes. One example is the ethylene-regulated local auxin biosynthesis in roots, which partly contributes to ethylene-directed root development and gravitropism. Using a chemical biology approach, we identified a small molecule, l-kynurenine (Kyn), which effectively inhibited ethylene responses in Arabidopsis thaliana root tissues. Kyn application repressed nuclear accumulation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Moreover, Kyn application decreased ethylene-induced auxin biosynthesis in roots, and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE RELATEDs (TAA1/TARs), the key enzymes in the indole-3-pyruvic acid pathway of auxin biosynthesis, were identified as the molecular targets of Kyn. Further biochemical and phenotypic analyses revealed that Kyn, being an alternate substrate, competitively inhibits TAA1/TAR activity, and Kyn treatment mimicked the loss of TAA1/TAR functions. Molecular modeling and sequence alignments suggested that Kyn effectively and selectively binds to the substrate pocket of TAA1/TAR proteins but not those of other families of aminotransferases. To elucidate the destabilizing effect of Kyn on EIN3, we further found that auxin enhanced EIN3 nuclear accumulation in an EIN3 BINDING F-BOX PROTEIN1 (EBF1)/EBF2-dependent manner, suggesting the existence of a positive feedback loop between auxin biosynthesis and ethylene signaling. Thus, our study not only reveals a new level of interactions between ethylene and auxin pathways but also offers an efficient method to explore and exploit TAA1/TAR-dependent auxin biosynthesis.
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Affiliation(s)
- Wenrong He
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Javier Brumos
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Hongjiang Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92507
| | - Yusi Ji
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Meng Ke
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinqi Gong
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qinglong Zeng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Wenyang Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Xinyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Fengying An
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Xing Wen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Pengpeng Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Jinfang Chu
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohong Sun
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cunyu Yan
- National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Nieng Yan
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - De-Yu Xie
- Department of Plant Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Natasha Raikhel
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92507
| | - Zhenbiao Yang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92507
| | - Anna N. Stepanova
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Jose M. Alonso
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Hongwei Guo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
- Address correspondence to
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13
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Kim YK, Lee JS, Bi X, Ha HH, Ng SH, Ahn YH, Lee JJ, Wagner BK, Clemons PA, Chang YT. The binding of fluorophores to proteins depends on the cellular environment. Angew Chem Int Ed Engl 2011; 50:2761-3. [PMID: 21370369 DOI: 10.1002/anie.201007626] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Yun Kyung Kim
- Department of Chemistry, National University of Singapore, Singapore
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14
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Kim YK, Lee J, Bi X, Ha H, Ng SH, Ahn Y, Lee J, Wagner BK, Clemons PA, Chang Y. The Binding of Fluorophores to Proteins Depends on the Cellular Environment. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007626] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yun Kyung Kim
- Department of Chemistry, National University of Singapore, Singapore 11754 (Singapore), Fax: (+65) 6779‐6591 http://ytchang.science.nus.edu.sg
- Korea Institute of Science and Technology (KIST), Life/Health Division, Integrated Omics Center, Seoul (Korea)
| | - Jun‐Seok Lee
- Department of Chemistry, National University of Singapore, Singapore 11754 (Singapore), Fax: (+65) 6779‐6591 http://ytchang.science.nus.edu.sg
- Korea Institute of Science and Technology (KIST), Life/Health Division, Integrated Omics Center, Seoul (Korea)
| | - Xuezhi Bi
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Biopolis, Singapore
| | - Hyung‐Ho Ha
- Department of Chemistry, National University of Singapore, Singapore 11754 (Singapore), Fax: (+65) 6779‐6591 http://ytchang.science.nus.edu.sg
- NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore
| | - Shin Hui Ng
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Biopolis, Singapore
| | - Young‐hoon Ahn
- Department of Pharmacology, Johns Hopkins University, Baltimore, MD (USA)
| | - Jae‐Jung Lee
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Biopolis, Singapore
| | - Bridget K. Wagner
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA (USA)
| | - Paul A. Clemons
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA (USA)
| | - Young‐Tae Chang
- Department of Chemistry, National University of Singapore, Singapore 11754 (Singapore), Fax: (+65) 6779‐6591 http://ytchang.science.nus.edu.sg
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Biopolis, Singapore
- NUS MedChem Program of the Office of Life Sciences, National University of Singapore, Singapore
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15
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Ye S, Wang H, Wu J. Facile Synthesis of 1-(Isoquinolin-1-yl)ureas by Silver Triflate Catalyzed Tandem Reactions of 2-Alkynylbenzaldoximes with Carbodiimides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001040] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Cyrus K, Wehenkel M, Choi EY, Swanson H, Kim KB. Two-headed PROTAC: an effective new tool for targeted protein degradation. Chembiochem 2010; 11:1531-4. [PMID: 20572252 PMCID: PMC3852688 DOI: 10.1002/cbic.201000222] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Indexed: 12/21/2022]
Affiliation(s)
- Kedra Cyrus
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Marie Wehenkel
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Eun-Young Choi
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Hollie Swanson
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Kyung-Bo Kim
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
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17
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Muslin AJ. Phenotypic high-throughput screening in atherosclerosis research: focus on macrophages. J Cardiovasc Transl Res 2010; 3:448-53. [PMID: 20625867 DOI: 10.1007/s12265-010-9205-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 06/21/2010] [Indexed: 10/19/2022]
Abstract
Atherosclerosis is a complex disease characterized by arterial lesions consisting of macrophage foam cells, smooth muscle cells, lymphocytes and other cell types. As atherosclerotic lesions mature, they can rupture and thereby trigger thrombosis that can result in tissue infarction. Macrophage foam cells develop in the subendothelial space when cells take up cholesterol from modified forms of low-density lipoprotein (LDL) and other apolipoprotein B-containing lipoproteins. Current therapies to limit atherosclerosis focus on altering the plasma lipid composition, most commonly by reducing circulating LDL levels. No current therapy is specifically designed to alter the cellular composition of atherosclerotic lesions. To address this deficit, phenotypic high-throughput drug screens have been developed to identify compounds that reduce the uptake of oxidized LDL by macrophages or to identify compounds that increase the efflux of cholesterol from macrophages. Additional phenotypic screens can be envisaged that address cellular processes in active atherosclerotic lesions including macrophage apoptosis and efferocytosis.
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Affiliation(s)
- Anthony J Muslin
- Center for Cardiovascular Research, Washington University School of Medicine, 660 South Euclid Avenue, Box 8086, St. Louis, MO 63110, USA.
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18
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Soleilhac E, Nadon R, Lafanechere L. High-content screening for the discovery of pharmacological compounds: advantages, challenges and potential benefits of recent technological developments. Expert Opin Drug Discov 2010; 5:135-44. [DOI: 10.1517/17460440903544456] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Wu J, Peng Y, Ouyang B, Yuan J, Yang Q, Ding Q. Generation of 3-(1H-Isochromen-1-yl)-1H-indole via Silver Triflate-Catalyzed Tandem Reaction of 2-Alkynylbenzaldehyde with Indole. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)68] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Etzion Y, Muslin AJ. The application of phenotypic high-throughput screening techniques to cardiovascular research. Trends Cardiovasc Med 2009; 19:207-12. [PMID: 20211437 PMCID: PMC2836266 DOI: 10.1016/j.tcm.2009.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In traditional pure protein high-throughput drug screens, also called in vitro screens, individual compounds from a small molecule collection are tested to determine whether they inhibit the enzymatic activity or binding properties of a purified target protein. In contrast, phenotypic high-throughput drug screens, also called chemical genetic or in vivo screens, investigate the ability of individual compounds from a collection to inhibit a biological process or disease model in live cells or intact organisms. In this review, the role of phenotypic screening techniques to identify novel therapeutic agents for the treatment of cardiovascular disease will be discussed.
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Affiliation(s)
- Yoram Etzion
- Center for Cardiovascular Research, Washington University School of Medicine, 660 South Euclid Avenue, Box 8086, St. Louis, MO 63110, FAX: 314-747-3545, Phone: 314-747-3525
| | - Anthony J. Muslin
- Center for Cardiovascular Research, Washington University School of Medicine, 660 South Euclid Avenue, Box 8086, St. Louis, MO 63110, FAX: 314-747-3545, Phone: 314-747-3525
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21
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Nandy JP, Prakesch M, Khadem S, Reddy PT, Sharma U, Arya P. Advances in Solution- and Solid-Phase Synthesis toward the Generation of Natural Product-like Libraries. Chem Rev 2009; 109:1999-2060. [DOI: 10.1021/cr800188v] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jyoti P. Nandy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael Prakesch
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Shahriar Khadem
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - P. Thirupathi Reddy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Utpal Sharma
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Prabhat Arya
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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22
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Schneekloth AR, Pucheault M, Tae HS, Crews CM. Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics. Bioorg Med Chem Lett 2008; 18:5904-8. [PMID: 18752944 DOI: 10.1016/j.bmcl.2008.07.114] [Citation(s) in RCA: 376] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 07/24/2008] [Accepted: 07/28/2008] [Indexed: 10/21/2022]
Abstract
We have developed a heterobifunctional all-small molecule PROTAC (PROteolysis TArgeting Chimera) capable of inducing proteasomal degradation of the androgen receptor. This cell permeable PROTAC consists of a non-steroidal androgen receptor ligand (SARM) and the MDM2 ligand known as nutlin, connected by a PEG-based linker. The SARM-nutlin PROTAC recruits the androgen receptor to MDM2, which functions as an E3 ubiquitin ligase. This leads to the ubiquitination of the androgen receptor, and its subsequent degradation by the proteasome. Upon treatment of HeLa cells with 10microM PROTAC for 7h, we were able to observe a decrease in androgen receptor levels. This degradation is proteasome dependent, as it is mitigated in cells pre-treated with 10microM epoxomicin, a specific proteasome inhibitor. These results have implications for the potential study and treatment of various cancers with increased androgen receptor levels.
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Affiliation(s)
- Ashley R Schneekloth
- Department of Chemistry, Yale University, PO Box 208103, New Haven, CT 06520-8103, USA
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23
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Thompson J, Winoto A. During negative selection, Nur77 family proteins translocate to mitochondria where they associate with Bcl-2 and expose its proapoptotic BH3 domain. ACTA ACUST UNITED AC 2008; 205:1029-36. [PMID: 18443228 PMCID: PMC2373836 DOI: 10.1084/jem.20080101] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Apoptosis accompanying negative selection is a central but poorly understood event in T cell development. The Nur77 nuclear steroid receptor and Bim, a proapoptotic BH3-only member of the Bcl-2 family, are two molecules implicated in this process. However, how they relate to each other and how Nur77 induces apoptosis remain unclear. In thymocytes, Nur77 has been shown to induce cell death through a transcriptional-dependent pathway, but in cancer cell lines, Nur77 was reported to induce apoptosis through conversion of Bcl-2 into a killer protein at the mitochondria. Whether this Nur77 transcriptional-independent pathway actually occurs in vivo remains controversial. Using an optimized fractionation protocol for thymocytes, here we report that stimulation of CD4+CD8+ thymocytes results in translocation of Nur77 and its family member Nor-1 to the mitochondria, leading to their association with Bcl-2 and exposure of the Bcl-2 proapoptotic BH3 domain. In two T cell receptor transgenic models of negative selection, F5 and HY, a conformational change of the Bcl-2 molecule in the negatively selected T cell population was similarly observed. Thus, the Nur77 family and Bim pathways converge at mitochondria to mediate negative selection.
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Affiliation(s)
- Jennifer Thompson
- Cancer Research Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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24
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Lee H, Puppala D, Choi EY, Swanson H, Kim KB. Targeted degradation of the aryl hydrocarbon receptor by the PROTAC approach: a useful chemical genetic tool. Chembiochem 2008; 8:2058-62. [PMID: 17907127 DOI: 10.1002/cbic.200700438] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hyosung Lee
- Department of Pharmaceutical Sciences, University of Kentucky, 725 Rose Street, Lexington, KY 40536-0082, USA
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25
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A novel immobilization strategy using oligonucleotide as linker for small molecule microarrays construction. Biosens Bioelectron 2008; 23:1694-700. [PMID: 18346888 DOI: 10.1016/j.bios.2008.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/04/2008] [Accepted: 02/06/2008] [Indexed: 11/24/2022]
Abstract
A novel immobilization method based on oligonucleotide as linker has been developed for small molecule microarrays (SMMs) construction. The oligonucleotide tail was employed as a linker in solid-phase synthesis. Small molecules could be easily conjugated at the 5' end of the oligonucleotide, previously modified with a functional group. Being a reactive species, the oligonucleotide was activated by UV irradiation, for the attachment of the conjugate to the slide surface. The method was successfully applied to structurally distinct small molecules, including biotin, antibiotic and drug. This immobilization strategy showed high efficiency, 1.1fmol of small molecules in the spotting solution per spot gave a detectable signal (mean S/N=10.9). The results suggest that it is very promising for exploring interaction between small molecules and proteins, and high throughput detecting the chemical compounds.
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26
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Wehenkel M, Hong JT, Kim KB. Proteasome modulators: essential chemical genetic tools for understanding human diseases. MOLECULAR BIOSYSTEMS 2008; 4:280-6. [DOI: 10.1039/b716221a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Lee J, Wu X, Pasca di Magliano M, Peters EC, Wang Y, Hong J, Hebrok M, Ding S, Cho CY, Schultz PG. A Small-Molecule Antagonist of the Hedgehog Signaling Pathway. Chembiochem 2007; 8:1916-9. [PMID: 17886323 DOI: 10.1002/cbic.200700403] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jongkook Lee
- Dept. of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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28
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Ahn YH, Chang YT. Tagged small molecule library approach for facilitated chemical genetics. Acc Chem Res 2007; 40:1025-33. [PMID: 17547366 DOI: 10.1021/ar700030k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical genetics is a powerful method which utilizes small molecule regulators to reveal the molecular basis of diverse biological processes. However, the current chemical genetic approach sometimes meets a serious bottleneck during the process of target identification. One faces difficulty in conjugating the active compound to an affinity matrix without losing or reducing its activity that leads to laborious structure-activity relationship (SAR) studies. To facilitate this process, we have developed a tagged triazine library containing a built-in linker that provides a straightforward transition from phenotypic screening to target identification. A strategy for constructing a tagged library and applications with a streamlined target identification and subsequent mechanistic study are discussed in this Account.
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Affiliation(s)
- Young-Hoon Ahn
- Department of Chemistry, New York University, New York, New York 10003, USA
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29
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O'Keefe SJ, Mudgett JS, Cupo S, Parsons JN, Chartrain NA, Fitzgerald C, Chen SL, Lowitz K, Rasa C, Visco D, Luell S, Carballo-Jane E, Owens K, Zaller DM. Chemical genetics define the roles of p38alpha and p38beta in acute and chronic inflammation. J Biol Chem 2007; 282:34663-71. [PMID: 17855341 DOI: 10.1074/jbc.m704236200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The p38 MAP kinase signal transduction pathway is an important regulator of proinflammatory cytokine production and inflammation. Defining the roles of the various p38 family members, specifically p38alpha and p38beta, in these processes has been difficult. Here we use a chemical genetics approach using knock-in mice in which either p38alpha or p38beta kinase has been rendered resistant to the effects of specific inhibitors along with p38beta knock-out mice to dissect the biological function of these specific kinase isoforms. Mice harboring a T106M mutation in p38alpha are resistant to pharmacological inhibition of LPS-induced TNF production and collagen antibody-induced arthritis, indicating that p38beta activity is not required for acute or chronic inflammatory responses. LPS-induced TNF production, however, is still completely sensitive to p38 inhibitors in mice with a T106M point mutation in p38beta. Similarly, p38beta knock-out mice respond normally to inflammatory stimuli. These results demonstrate conclusively that specific inhibition of the p38alpha isoform is necessary and sufficient for anti-inflammatory efficacy in vivo.
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Affiliation(s)
- Stephen J O'Keefe
- Department of Immunology, Merck Research Laboratories, Rahway, New Jersey 07065, USA.
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30
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Bargagna-Mohan P, Hamza A, Kim YE, Ho YK(A, Mor-Vaknin N, Wendschlag N, Liu J, Evans RM, Markovitz DM, Zhan CG, Kim KB, Mohan R. The tumor inhibitor and antiangiogenic agent withaferin A targets the intermediate filament protein vimentin. ACTA ACUST UNITED AC 2007; 14:623-34. [PMID: 17584610 PMCID: PMC3228641 DOI: 10.1016/j.chembiol.2007.04.010] [Citation(s) in RCA: 241] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/30/2007] [Accepted: 04/19/2007] [Indexed: 11/22/2022]
Abstract
The natural product withaferin A (WFA) exhibits antitumor and antiangiogenesis activity in vivo, which results from this drug's potent growth inhibitory activities. Here, we show that WFA binds to the intermediate filament (IF) protein, vimentin, by covalently modifying its cysteine residue, which is present in the highly conserved alpha-helical coiled coil 2B domain. WFA induces vimentin filaments to aggregate in vitro, an activity manifested in vivo as punctate cytoplasmic aggregates that colocalize vimentin and F-actin. WFA's potent dominant-negative effect on F-actin requires vimentin expression and induces apoptosis. Finally, we show that WFA-induced inhibition of capillary growth in a mouse model of corneal neovascularization is compromised in vimentin-deficient mice. These findings identify WFA as a chemical genetic probe of IF functions, and illuminate a potential molecular target for withanolide-based therapeutics for treating angioproliferative and malignant diseases.
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Affiliation(s)
| | - Adel Hamza
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | | | - Yik Khuan (Abby) Ho
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Nirit Mor-Vaknin
- Department of Internal Medicine, Division of Infectious Diseases
| | | | - Junjun Liu
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Robert M. Evans
- Department of Pathology, University of Colorado Health Sciences Center, Denver, CO 80045, USA
| | - David M. Markovitz
- Department of Internal Medicine, Division of Infectious Diseases
- Cellular and Molecular Biology Program, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Royce Mohan
- Department of Ophthalmology and Visual Sciences
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Correspondence:
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31
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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32
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Fonrose X, Ausseil F, Soleilhac E, Masson V, David B, Pouny I, Cintrat JC, Rousseau B, Barette C, Massiot G, Lafanechère L. Parthenolide inhibits tubulin carboxypeptidase activity. Cancer Res 2007; 67:3371-8. [PMID: 17409447 DOI: 10.1158/0008-5472.can-06-3732] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microtubules are centrally involved in cell division, being the principal components of mitotic spindle. Tubulin, the constituent of microtubules, can be cyclically modified on its alpha-subunit by enzymatic removal of the COOH-terminal tyrosine residue by an ill-defined tubulin carboxypeptidase (TCP) and its readdition by tubulin tyrosine ligase (TTL). We and others have previously shown that suppression of TTL and resulting accumulation of detyrosinated tubulin are frequent in human cancers of poor prognosis. Explanations for the involvement of TTL and detyrosinated tubulin in tumor progression arise from the recent discovery that tubulin detyrosination leads to CAP-Gly protein mislocalization, which correlates with defects in spindle positioning during mitosis. Impaired control of spindle positioning is one factor favoring tumor invasiveness. Thus, TCP could be a target for developing novel therapeutic strategies against advanced stages of cancers. Inhibitors of TCP, by reversing abnormal detyrosinated tubulin accumulation in tumor cells, could impair tumor progression. TCP has never been isolated and this has hampered search of specific inhibitors. In this article, we describe a cell-based assay of TCP activity and its use to screen a library of natural extracts for their inhibitory potency. This led to the isolation of two sesquiterpene lactones. We subsequently found that parthenolide, a structurally related compound, can efficiently inhibit TCP. This inhibitory activity is a new specific property of parthenolide independent of its action on the nuclear factor-kappaB pathway. Parthenolide is also known for its anticancer properties. Thus, TCP inhibition could be one of the underlying mechanisms of these anticancer properties.
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Affiliation(s)
- Xavier Fonrose
- Centre de Criblage pour Molécules Bio-Actives, institut de Recherches en Technologies et Sciences pour le Vivant, Commissariat à l'Energie Atomique-Grenoble, Grenoble, France
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33
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Kim YK, Chang YT. Tagged library approach facilitates forward chemical genetics. MOLECULAR BIOSYSTEMS 2007; 3:392-7. [PMID: 17533452 DOI: 10.1039/b702321a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Forward chemical genetics has been highlighted as a new method for the study of various biological pathways using exogenous ligands. However, limited success in the field has demonstrated that, in many cases, it is not feasible to determine the protein targets of small-molecule probes. Identifying protein targets is an integral part of forward chemical genetics and is also the most challenging. Over the past decade, several biochemical and genetic methods have been developed to facilitate target identification processes. Even so, one of the major difficulties is that these methods require the chemical modification of active compounds, with a significant amount of structure-activity relationship (SAR) study to ensure that the small-molecule tags do not compromise bioactivity. In this article, we will highlight a new strategy for small molecule libraries that have built-in linkers in order to avoid this well-known problem and demonstrate their successful use in forward chemical genetics.
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Affiliation(s)
- Yun Kyung Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
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34
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Coffinier Y, Szunerits S, Jama C, Desmet R, Melnyk O, Marcus B, Gengembre L, Payen E, Delabouglise D, Boukherroub R. Peptide immobilization on amine-terminated boron-doped diamond surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:4494-7. [PMID: 17367174 DOI: 10.1021/la063440y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This paper reports on the formation and characterization of semicarbazide termination on aminated boron-doped diamond (BDD) surfaces, and further preparation of peptide microarray through site-specific alpha-oxo semicarbazone ligation. Hydrogen-terminated BDD electrodes were first aminated using NH3 plasma treatment and then reacted with triphosgene and Fmoc-protected hydrazine to yield a protected semicarbazide termination. Subsequent deprotection and chemical reaction with glyoxylyl peptides led to the covalent immobilization of the peptides on the surface through site-specific ligation. The resulting surfaces were characterized using X-ray photoelectron spectroscopy (XPS) and fluorescence measurements.
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Affiliation(s)
- Yannick Coffinier
- Institut de Recherche Interdisciplinaire (IRI, FRE2963) and Institut d'Electronique, de Microélectronique et de Nanotechnologie (IEMN), Cité Scientifique, Avenue Poincaré - BP. 60069, 59652 Villeneuve d'Ascq, France
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35
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Hong J, Lee J, Min KH, Walker JR, Peters EC, Gray NS, Cho CY, Schultz PG. Identification and characterization of small-molecule inducers of epidermal keratinocyte differentiation. ACS Chem Biol 2007; 2:171-5. [PMID: 17348628 DOI: 10.1021/cb600435t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An essential function of the human epidermis is the maintenance of a protective barrier against the environment. As a consequence, keratinocytes, which make up this layer of the skin, undergo an elaborate process of self-renewal, terminal differentiation, and cell death. Misregulation of these processes can lead to several human diseases, including psoriasis and basal cell and squamous cell carcinomas. To identify novel regulators of keratinocyte differentiation, a cell-based screen of small-molecule libraries was carried out for molecules that induce terminal differentiation of normal human epidermal keratinocytes. One class of molecules was identified, the 2-(3,4,5-trimethoxyphenylamino)-pyrrolo[2,3-d]pyrimidines, which were shown to induce differentiation of epidermal progenitor cells to terminally differentiated keratinocytes. These molecules serve as useful mechanistic probes of the cellular differentiation programs that regulate the formation and homeostasis of the epidermis and may lead to novel therapeutic approaches for the treatment of skin hyperproliferative disorders.
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36
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Adams DS, Levin M. Inverse drug screens: a rapid and inexpensive method for implicating molecular targets. Genesis 2007; 44:530-40. [PMID: 17078061 PMCID: PMC3142945 DOI: 10.1002/dvg.20246] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Identification of gene products that function in some specific process of interest is a common goal in developmental biology. Although use of drug compounds to probe biological systems has a very long history in teratology and toxicology, systematic hierarchical drug screening has not been capitalized upon by the developmental biology community. This "chemical genetics" approach can greatly benefit the study of embryonic and regenerative systems, and we have formalized a strategy for using known pharmacological compounds to implicate specific molecular candidates in any chosen biological phenomenon. Taking advantage of a hierarchical structure that can be imposed on drug reagents in a number of fields such as ion transport, neurotransmitter function, metabolism, and cytoskeleton, any assay can be carried out as a binary search algorithm. This inverse drug screen methodology is much more efficient than exhaustive testing of large numbers of drugs, and reveals the identity of a manageable number of specific molecular candidates that can then be validated and targeted using more expensive and specific molecular reagents. Here, we describe the process of this loss-of-function screen and illustrate its use in uncovering novel bioelectrical and serotonergic mechanisms in embryonic patterning. This technique is an inexpensive and rapid complement to existing molecular screening strategies. Moreover, it is applicable to maternal proteins, and model species in which traditional genetic screens are not feasible, significantly extending the opportunities to identify key endogenous players in biological processes.
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Affiliation(s)
| | - Michael Levin
- Correspondence to: Michael Levin, Center for Regenerative and Developmental Biology, Forsyth Institute and Developmental Biology Department, Harvard School of Dental Medicine, 140 The Fenway, Boston, MA 02115.
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37
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Kishore Kumar G, Saenz D, Lokesh G, Natarajan A. Microwave-assisted cleavage of phosphate, phosphonate and phosphoramide esters. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.06.126] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Gagna CE, Lambert WC. Novel drug discovery and molecular biological methods, via DNA, RNA and protein changes using structure-function transitions: Transitional structural chemogenomics, transitional structural chemoproteomics and novel multi-stranded nucleic acid microarray. Med Hypotheses 2006; 67:1099-114. [PMID: 16828979 DOI: 10.1016/j.mehy.2006.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 04/30/2006] [Accepted: 05/03/2006] [Indexed: 11/22/2022]
Abstract
Nucleic acids and proteins are dynamic molecules that undergo structural changes which control gene expression. The authors have developed two novel techniques, viz., transitional structural chemogenomics and transitional structural chemoproteomics. Transitional structural chemogenomics is used to regulate gene expression, employing ultrasensitive small-molecule drugs targeted toward nucleic acids. Gene expression can be regulated by using chemicals to target transitional changes in the helical conformations of single-stranded (ss-) and double-stranded (ds-) DNA (e.g., B- to Z-DNA), and RNA (e.g., A- to Z-RNA). This method also targets alternative types of ds- and ss-DNA and RNA (e.g., cruciform DNA), and other multi-stranded nucleic acids (e.g., triplex-DNA). Our second technique, transitional structural chemoproteomics, targets a protein before, during or after post-translational modifications which alters its structure and function. Both a proteins' structured and unstructured regions are targeted. These two novel methods represent the next step in the evolution of chemical genomics and chemical proteomics. They allow for two approaches to regulate gene expression, viz., turning genes "on", "off" or variable control (e.g., dimmer switch). This article also discusses the confusion that exists between the term chemical genomics and other related subdisciplines, such as chemical proteomics. Additionally, we have developed a novel multi-stranded DNA, RNA and plasmid microarray which immobilizes intact nondenatured ds-DNA, alternative, and other multiple-stranded nucleic acids onto a substrate surface. This technique represents the next generation of nucleic acid microarrays, which will enhance the characterization of nucleic acids and the drug discovery process. These three novel techniques allow for a multifaceted approach that will greatly enhance the success of molecular biology, the "omics" and drug discovery. They represent the next era of gene expression tools.
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Affiliation(s)
- Claude E Gagna
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Newark, NJ 07103, USA
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39
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40
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Won J, Kim M, Kim N, Ahn JH, Lee WG, Kim SS, Chang KY, Yi YW, Kim TK. Small molecule-based reversible reprogramming of cellular lifespan. Nat Chem Biol 2006; 2:369-74. [PMID: 16767085 DOI: 10.1038/nchembio800] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/15/2006] [Indexed: 01/04/2023]
Abstract
Most somatic cells encounter an inevitable destiny, senescence. Little progress has been made in identifying small molecules that extend the finite lifespan of normal human cells. Here we show that the intrinsic 'senescence clock' can be reset in a reversible manner by selective modulation of the ataxia telangiectasia-mutated (ATM) protein and ATM- and Rad3-related (ATR) protein with a small molecule, CGK733. This compound was identified by a high-throughput phenotypic screen with automated imaging. Employing a magnetic nanoprobe technology, magnetism-based interaction capture (MAGIC), we identified ATM as the molecular target of CGK733 from a genome-wide screen. CGK733 inhibits ATM and ATR kinase activities and blocks their checkpoint signaling pathways with great selectivity. Consistently, siRNA-mediated knockdown of ATM and ATR induced the proliferation of senescent cells, although with lesser efficiency than CGK733. These results might reflect the specific targeting of the kinase activities of ATM and ATR by CGK733 without affecting any other domains required for cell proliferation.
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Affiliation(s)
- Jaejoon Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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41
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Ho A, Kim YE, Lee H, Cyrus K, Baek SH, Kim KB. SAR studies of 2-methoxyestradiol and development of its analogs as probes of anti-tumor mechanisms. Bioorg Med Chem Lett 2006; 16:3383-7. [PMID: 16650989 DOI: 10.1016/j.bmcl.2006.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 04/05/2006] [Accepted: 04/05/2006] [Indexed: 11/20/2022]
Abstract
The major estrogen metabolite 2-methoxyestradiol (2ME) has been shown to target tumor cells without severe side effects and is currently being evaluated in clinical trials for several types of cancer. Despite its promise for use in clinical setting, the mechanism(s) by which 2ME exerts its anti-tumor activity is not clearly defined at this time. Employing organic chemistry tools, we synthesized 2ME analogs with which 2ME affinity column was prepared, enabling us to detect a protein that selectively interacts with 2ME. This 2ME analog will be useful as a probe to identify the biological target(s) of 2ME and study their functions in tumor cells.
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Affiliation(s)
- Abby Ho
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, USA
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Kell DB. Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest. FEBS J 2006; 273:873-94. [PMID: 16478464 DOI: 10.1111/j.1742-4658.2006.05136.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The newly emerging field of systems biology involves a judicious interplay between high-throughput 'wet' experimentation, computational modelling and technology development, coupled to the world of ideas and theory. This interplay involves iterative cycles, such that systems biology is not at all confined to hypothesis-dependent studies, with intelligent, principled, hypothesis-generating studies being of high importance and consequently very far from aimless fishing expeditions. I seek to illustrate each of these facets. Novel technology development in metabolomics can increase substantially the dynamic range and number of metabolites that one can detect, and these can be exploited as disease markers and in the consequent and principled generation of hypotheses that are consistent with the data and achieve this in a value-free manner. Much of classical biochemistry and signalling pathway analysis has concentrated on the analyses of changes in the concentrations of intermediates, with 'local' equations - such as that of Michaelis and Menten v=(Vmax x S)/(S+K m) - that describe individual steps being based solely on the instantaneous values of these concentrations. Recent work using single cells (that are not subject to the intellectually unsupportable averaging of the variable displayed by heterogeneous cells possessing nonlinear kinetics) has led to the recognition that some protein signalling pathways may encode their signals not (just) as concentrations (AM or amplitude-modulated in a radio analogy) but via changes in the dynamics of those concentrations (the signals are FM or frequency-modulated). This contributes in principle to a straightforward solution of the crosstalk problem, leads to a profound reassessment of how to understand the downstream effects of dynamic changes in the concentrations of elements in these pathways, and stresses the role of signal processing (and not merely the intermediates) in biological signalling. It is this signal processing that lies at the heart of understanding the languages of cells. The resolution of many of the modern and postgenomic problems of biochemistry requires the development of a myriad of new technologies (and maybe a new culture), and thus regular input from the physical sciences, engineering, mathematics and computer science. One solution, that we are adopting in the Manchester Interdisciplinary Biocentre (http://www.mib.ac.uk/) and the Manchester Centre for Integrative Systems Biology (http://www.mcisb.org/), is thus to colocate individuals with the necessary combinations of skills. Novel disciplines that require such an integrative approach continue to emerge. These include fields such as chemical genomics, synthetic biology, distributed computational environments for biological data and modelling, single cell diagnostics/bionanotechnology, and computational linguistics/text mining.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, Faraday Building, The University of Manchester, UK.
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43
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Du A, Zhao B, Miao J, Yin D, Zhang S. Safrole oxide induces apoptosis by up-regulating Fas and FasL instead of integrin β4 in A549 human lung cancer cells. Bioorg Med Chem 2006; 14:2438-45. [PMID: 16326105 DOI: 10.1016/j.bmc.2005.11.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 11/11/2005] [Accepted: 11/11/2005] [Indexed: 11/26/2022]
Abstract
Previously, we found that 3,4-(methylenedioxy)-1-(2',3'-epoxypropyl)-benzene (safrole oxide) induced a typical apoptosis in A549 human lung cancer cells by activating caspase-3, -8, and -9. In this study, we further investigated which upstream pathways were activated by safrole oxide during the apoptosis. Immunofluorescence assay combined with laser scanning confocal microscopy revealed that both Fas and Fas ligand (FasL) were up-regulated by the small molecule. In addition, Fas protein distribution was altered, showing a clustering distribution instead of a homogeneous one. Subsequently, Western blot analysis confirmed the up-regulations of Fas and its membrane-binding form of FasL (m-FasL), as well as P53 protein. Conversely, safrole oxide hardly affected integrin beta4 subunit expression or distribution, which was reflected from the data obtained by immunofluorescence assay combined with laser scanning confocal microscopy. The results suggested that Fas/FasL pathway might be involved in safrole oxide-induced apoptosis of A549 cells, while integrin beta4 might be irrelevant to the apoptosis. Nevertheless, we first found the strong expression of integrin beta4 in A549 cells. The study first suggested that safrole oxide might be used as a small molecular promoter of Fas/FasL pathway to elicit apoptosis in A549 cells, which would lay the foundation for us to insight into the new strategies for lung cancer therapy.
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Affiliation(s)
- AiYing Du
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
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Yokota Y, Bargagna-Mohan P, Ravindranath PP, Kim KB, Mohan R. Development of withaferin A analogs as probes of angiogenesis. Bioorg Med Chem Lett 2006; 16:2603-7. [PMID: 16513346 PMCID: PMC3222585 DOI: 10.1016/j.bmcl.2006.02.039] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 02/11/2006] [Accepted: 02/15/2006] [Indexed: 11/29/2022]
Abstract
The natural product withaferin A (WFA) is a potent angiogenesis inhibitor and it targets the ubiquitin-proteasome pathway in vascular endothelial cells. We generated a biotinylated affinity analog WFA-LC(2)B for use as a probe to study angiogenesis. WFA-LC(2)B inhibits angiogenic sprouting in vitro and it causes levels of ubiquitinated proteins to increase in tumor necrosis factor-alpha-treated human umbilical vein endothelial cells, confirming the retention of WFA's biological activity. We show that WFA-LC(2)B forms protein adducts in endothelial cells which are competed by free WFA in vivo. This WFA-LC(2)B analog will be useful to isolate the biological target of WFA.
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Affiliation(s)
- Yasuno Yokota
- Department of Ophthalmology and Visual Science, University of Kentucky, Lexington, KY 40536, USA
| | - Paola Bargagna-Mohan
- Department of Ophthalmology and Visual Science, University of Kentucky, Lexington, KY 40536, USA
| | - Padma P. Ravindranath
- Department of Ophthalmology and Visual Science, University of Kentucky, Lexington, KY 40536, USA
| | - Kyung B. Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Royce Mohan
- Department of Ophthalmology and Visual Science, University of Kentucky, Lexington, KY 40536, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Corresponding author. Tel.: +1 859 323 4764; fax: +1 859 257 9700;
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Choi Y, Shimogawa H, Murakami K, Ramdas L, Zhang W, Qin J, Uesugi M. Chemical Genetic Identification of the IGF-Linked Pathway that Is Mediated by STAT6 and MFP2. ACTA ACUST UNITED AC 2006; 13:241-9. [PMID: 16638529 DOI: 10.1016/j.chembiol.2005.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 12/22/2005] [Accepted: 12/28/2005] [Indexed: 10/24/2022]
Abstract
Insulin-like growth factor 2 (IGF2) is a potent mitogen whose deregulation plays a role in developing liver, breast, and prostate cancers. Here, we take a small-molecule approach to investigate molecular pathways that modulate IGF2 signaling, by using chromeceptin, a synthetic molecule that selectively impairs the viability and growth of IGF2-overexpressing hepatocellular carcinoma cells. Affinity purification revealed that chromeceptin binds to multifunctional protein 2 (MFP-2), a seemingly multifunctional enzyme implicated in peroxisomal beta-oxidation. The small molecule-protein interaction stimulates the expression of IGF binding protein 1 (IGFBP-1) and suppressor of cytokine signaling-3 (SOCS-3), two cellular attenuators of the IGF signals, through activation of signal transducers and activators of transcription 6 (STAT6). The results underline the importance of STATs in IGF/insulin regulation, and they implicate a new pathway for STAT6 activation that is amenable to small-molecule intervention.
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Affiliation(s)
- Yongmun Choi
- TheVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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46
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Gough JD, Crews CM. Probing protein function with small molecules. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:61-74. [PMID: 16708999 DOI: 10.1007/978-3-540-37635-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The interface of chemistry and biology offers many opportunities to explore different aspects of cell biology. The emerging field of chemical genetics is providing the chemical means to understand biological systems not easily accessible using classical genetic manipulations. In this article, we will discuss how natural product mode of action studies and novel bio-organic manipulation of intracellular protein levels are proving useful in the exploration of cell biology.
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Affiliation(s)
- J D Gough
- Department of Molecular, Cell and Development Biology, New Haven, CT 06520-8103, USA
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47
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Du A, Zhao B, Yin D, Zhang S, Miao J. Safrole oxide induces apoptosis by activating caspase-3, -8, and -9 in A549 human lung cancer cells. Bioorg Med Chem Lett 2006; 16:81-3. [PMID: 16242324 DOI: 10.1016/j.bmcl.2005.09.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2005] [Revised: 09/02/2005] [Accepted: 09/20/2005] [Indexed: 11/15/2022]
Abstract
Previously we found that 3,4-(methylenedioxy)-1-(2',3'-epoxypropyl)-benzene (safrole oxide) induced a typical apoptosis in A549 human lung cancer cells. In this study, we further investigated which caspases were activated by safrole oxide during the apoptosis. The data showed that the activity of caspase-3, -8, and -9 was significantly enhanced by the compound, which suggested that safrole oxide might be used as a caspase promoter to initiate lung cancer cell apoptosis.
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Affiliation(s)
- Aiying Du
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
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48
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Phillips CI, Bogyo M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cell Microbiol 2005; 7:1061-76. [PMID: 16008574 DOI: 10.1111/j.1462-5822.2005.00554.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques that have made a significant impact on the resolution of complex proteomes. In addition, we highlight recent developments in the field of chemical proteomics, a branch of proteomics aimed at functionally profiling a proteome. These techniques include the development of activity-based probes and activity-based protein profiling methods as well as the use of synthetic small molecule libraries to screen for pharmacological tools to perturb basic biological processes. This review will focus on the applications of these technologies to the field of microbiology.
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Affiliation(s)
- Carolyn I Phillips
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA
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Kodadek T, Bachhawat-Sikder K. Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads. MOLECULAR BIOSYSTEMS 2005; 2:25-35. [PMID: 16880920 DOI: 10.1039/b514349g] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many methods have been published by which combinatorial libraries may be screened for compounds capable of manipulating the function(s) of a target protein. One of the simplest approaches is to identify compounds in a library that bind the protein of interest, since these binding events usually occur on functionally important surfaces of the protein. These protein-binding compounds could also be of utility as protein capture agents in the construction of protein-detecting microarrays or related analytical devices and as reagents for the affinity purification of proteins from complex mixtures. In this article, we provide optimized methods for screening libraries of molecules displayed on the beads on which they were synthesized. This is a particularly convenient format for library screening for laboratories with limited budgets and modest robotics capabilities.
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Affiliation(s)
- Thomas Kodadek
- Department of Internal Medicine, Division of Translational Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9185, USA.
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50
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Mandal AK, Hines J, Kuramochi K, Crews CM. Developing microcolin A analogs as biological probes. Bioorg Med Chem Lett 2005; 15:4043-7. [PMID: 15993592 PMCID: PMC2507739 DOI: 10.1016/j.bmcl.2005.06.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 06/05/2005] [Accepted: 06/06/2005] [Indexed: 11/18/2022]
Abstract
Three microcolin A and B analogs have been synthesized. Their biological activity profiles were evaluated against several cell lines, revealing the existence of a structural determinant whose role in mediating the antiproliferative effect of the microcolins has heretofore gone unrecognized. While previously described as potent immunosuppressive natural products, we found that these microcolin analogs possessed no selective cytotoxicity when comparing immune cell versus nonimmune cell proliferation. In addition, the amino-terminus of microcolin A has been modified to incorporate a biotinylated polyethylene glycol linker. The biological activity of this biotinylated microcolin A analog was determined. This affinity reagent was shown to retain limited biological activity and thus can serve as a useful probe for elucidating the mechanism of action of microcolin A.
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Affiliation(s)
- Amit K. Mandal
- Department of Molecular, Cell, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - John Hines
- Department of Molecular, Cell, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Kouji Kuramochi
- Department of Molecular, Cell, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Craig M. Crews
- Department of Molecular, Cell, and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
- Department of Chemistry, Yale University, New Haven, CT 06520-8103, USA
- Department of Pharmacology, Yale University, New Haven, CT 06520-8103, USA
- Corresponding author. Tel.: +1 203 432 9364; fax: +1 203 432 6161; e-mail: , URL:http://www.yale.edu/crews
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