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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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Rutkowska A, Schultz C. Protein Tango: The Toolbox to Capture Interacting Partners. Angew Chem Int Ed Engl 2012; 51:8166-76. [DOI: 10.1002/anie.201201717] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Indexed: 11/07/2022]
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Itoh Y, Kitaguchi R, Ishikawa M, Naito M, Hashimoto Y. Design, synthesis and biological evaluation of nuclear receptor-degradation inducers. Bioorg Med Chem 2011; 19:6768-78. [PMID: 22014751 DOI: 10.1016/j.bmc.2011.09.041] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/21/2011] [Accepted: 09/22/2011] [Indexed: 12/15/2022]
Abstract
Compounds that regulate the function(s) of nuclear receptors (NRs) are useful for biological studies and as candidate therapeutic agents. Most such compounds are agonists or antagonists. On the other hand, we have developed specific protein degradation inducers, which we designated as SNIPERs (Specific and Nongenetic IAPs-dependent Protein ERasers), for selective degradation of target proteins. SNIPERs are hybrid molecules consisting of an appropriate ligand for the protein of interest, coupled to a ligand for inhibitor of apoptosis proteins (IAPs), which target the bound protein for polyubiquitination and proteasomal degradation. We considered that protein knockdown with SNIPERs would be a promising alternative approach for modulating NR function. In this study, we designed and synthesized degradation inducers targeting retinoic acid receptor (RAR), estrogen receptor (ER), and androgen receptor (AR). These newly synthesized RAR, ER, and AR SNIPERs, 9, 11, and 13, respectively, were confirmed to significantly reduce the levels of the corresponding NRs in live cells.
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Affiliation(s)
- Yukihiro Itoh
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Gaucher-Wieczorek FS, Maillard LT, Badet B, Durand P. Fluorous tagged N-hydroxy phthalimide for the parallel synthesis of O-aryloxyamines. ACTA ACUST UNITED AC 2010; 12:655-8. [PMID: 20831264 DOI: 10.1021/cc100098v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The parallel synthesis of O-aryloxyamines remains an unfulfilled need in the field of medicinal chemistry and fragment-based approaches. To fill this gap a solution-phase two-step process based on (1) a copper-catalyzed cross-coupling of aryl boronic acids with a fluorous tagged N-hydroxyphthalimide, and (2) a supported aminolysis was designed and optimized using Taguchi's method. A library of O-aryloxyamines was synthesized in high yields with high purity and diversity.
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Affiliation(s)
- Florence S Gaucher-Wieczorek
- Centre de recherches de Gif, Institut de Chimie des Substances Naturelles, UPR 2301-CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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Khomutov MA, Mandal S, Weisell J, Saxena N, Simonian AR, Vepsalainen J, Madhubala R, Kochetkov SN. Novel convenient synthesis of biologically active esters of hydroxylamine. Amino Acids 2009; 38:509-17. [DOI: 10.1007/s00726-009-0410-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 09/16/2009] [Indexed: 10/20/2022]
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Corson TW, Aberle N, Crews CM. Design and Applications of Bifunctional Small Molecules: Why Two Heads Are Better Than One. ACS Chem Biol 2008; 3:677-692. [PMID: 19112665 DOI: 10.1021/cb8001792] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Induction of protein--protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein molecules together for enhanced or novel biological effect. The first such bifunctional molecules were the rapamycin- and FK506-based "chemical inducers of dimerization", but the field has since expanded with new molecules and new applications in chemical genetics and cell biology. Examples include coumermycin-mediated gyrase B dimerization, proteolysis targeting chimeric molecules (PROTACs), drug hybrids, and strategies for exploiting multivalency in toxin binding and antibody recruitment. This Review discusses these and other advances in the design and use of bifunctional small molecules and potential strategies for future systems.
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Affiliation(s)
| | | | - Craig M. Crews
- Department of Molecular, Cellular & Developmental Biology
- Departments of Chemistry and Pharmacology, Yale University, New Haven, Connecticut 06511
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George O, Bryant BK, Chinnasamy R, Corona C, Arterburn JB, Shuster CB. Bisphenol A directly targets tubulin to disrupt spindle organization in embryonic and somatic cells. ACS Chem Biol 2008; 3:167-79. [PMID: 18225860 PMCID: PMC3844426 DOI: 10.1021/cb700210u] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
There is increasing concern that animal and human reproduction may be adversely affected by exposure to xenoestrogens that activate estrogen receptors. There is evidence that one such compound, Bisphenol A (BPA), also induces meiotic and mitotic aneuploidy, suggesting that these kinds of molecules may also have effects on cell division. In an effort to understand how Bisphenol A might disrupt cell division, a phenotypic analysis was carried out using sea urchin eggs, whose early embryonic divisions are independent of zygotic transcription. Fertilized Lytechinus pictus eggs exposed to BPA formed multipolar spindles resulting in failed cytokinesis in a dose-dependent, transcriptionally independent manner. By use of novel biotinylated BPA affinity probes to fractionate cell-free extracts, tubulin was identified as a candidate binding protein by mass spectrometry, and BPA promoted microtubule polymerization and centrosome-based microtubule nucleation in vitro but did not appear to display microtubule-stabilizing activity. Treatment of mammalian cells demonstrated that BPA as well as a series of Bisphenol A derivatives induced ectopic spindle pole formation in the absence of centrosome overduplication. Together, these results suggest a novel mechanism by which Bisphenol A affects the nucleation of microtubules, disrupting the tight spatial control associated with normal chromosome segregation, resulting in aneuploidy.
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Affiliation(s)
- Olivia George
- Department of Biology, New Mexico State University, Las Cruces NM, 88003
- the Marine Biological Laboratory, Woods Hole MA 02543
| | - Bj K. Bryant
- Department of Biochemistry and Chemistry, New Mexico State University, Las Cruces NM, 88003
| | - Ramesh Chinnasamy
- Department of Biochemistry and Chemistry, New Mexico State University, Las Cruces NM, 88003
| | - Cesear Corona
- Department of Biochemistry and Chemistry, New Mexico State University, Las Cruces NM, 88003
| | - Jeffrey B. Arterburn
- Department of Biochemistry and Chemistry, New Mexico State University, Las Cruces NM, 88003
| | - Charles B. Shuster
- Department of Biology, New Mexico State University, Las Cruces NM, 88003
- the Marine Biological Laboratory, Woods Hole MA 02543
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Rickert EL, Trebley JP, Peterson AC, Morrell MM, Weatherman RV. Synthesis and characterization of bioactive tamoxifen-conjugated polymers. Biomacromolecules 2007; 8:3608-12. [PMID: 17929966 PMCID: PMC2528197 DOI: 10.1021/bm070413t] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macromolecular conjugates of tamoxifen could perhaps be used to circumvent some of the limitations of the extensively used breast cancer drug. To test the feasibility of these conjugates, a 4-hydroxytamoxifen analogue was conjugated to a diaminoalkyl linker and then conjugated to activated esters of a poly(methacrylic acid) polymer synthesized by atom transfer radical polymerization. A polymer conjugated to the 4-hydroxytamoxifen analogue with a six-carbon linker showed high affinity for both estrogen receptor alpha and estrogen receptor beta and potent antagonism of the estrogen receptor in cell-based transcriptional reporter assays. These results suggest that the conjugation of 4-hydroxytamoxifen to a polymer results in a macromolecular conjugate that can display ligand in a manner that can be recognized by estrogen receptor and still act as a potent antiestrogen in cells.
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Affiliation(s)
- Emily L. Rickert
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907
| | | | - Anton C. Peterson
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907
| | | | - Ross V. Weatherman
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907
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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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Inverarity IA, Hulme AN. Marked small molecule libraries: a truncated approach to molecular probe design. Org Biomol Chem 2007; 5:636-43. [PMID: 17285172 DOI: 10.1039/b616494c] [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] [Indexed: 11/21/2022]
Abstract
A truncated approach to the design of molecular probes from small molecule libraries is outlined, based upon the incorporation of a bioorthogonal marker. The applicability of this strategy to small molecule chemical genetics screens has been demonstrated using analogues of the known stress activated protein kinase (SAPK) pathway activator, anisomycin. Compounds marked with a propargyl group have shown activation of the SAPK pathways comparable to that induced by their parent structures, as demonstrated by immunoblot assays against the downstream target JNK1/2. The considerable advantages of this new approach to molecular probe design have been illustrated through the rapid development of a functionally active fluorescent molecular probe, through coupling of the marked analogues to fluorescent azides using the copper(i)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction. Active molecular probes generated in this study were used to investigate cellular uptake through FACS analysis and confocal microscopy.
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Affiliation(s)
- Iain A Inverarity
- School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh, UKEH9 3JJ
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Synthesis of peptidomimetic-spirostane hybrids via Ugi reaction: a versatile approach for the formation of peptide–steroid conjugates. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.06.050] [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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Abstract
Biotin (1), a water-soluble B series vitamin, distributes widely in microorganisms, plants, and animals. Biosynthesis of 1 involves five steps sequence starting from pimelic acid. The last step, a transformation from dethiobiotin (DTB) to 1, includes an iron clusters-mediated radical process. The compound 1 is a cofactor of carboxylation enzymes and plays crucial roles in the metabolism of fatty acids, sugars, and alpha-amino acids. In addition to the increasing application to feed additives, recent reports have revealed that 1 enhances insulin secretion in animals, suggesting it for a promising therapeutic candidate for an anti-diabetes drug. The remarkably strong affinity of 1 with avidin and streptavidin has been extensively applied for such technologies as photoaffinity labeling. Among the number of approaches to 1 so far developed in 50 years, a synthesis using L-cysteine and thiolactone as a starting material and a key intermediate, respectively, represents one of the best routes leading to 1, because of short steps, high yield, use of inexpensive reagents, and ease of operation.
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Affiliation(s)
- Masahiko Seki
- Tanabe Seiyaku Co., Ltd., 3-2-10, Dosho-Machi, Osaka 541-8505, Japan.
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Maillard LT, Benohoud M, Durand P, Badet B. A New Supported Reagent for the Parallel Synthesis of Primary and Secondary O-Alkyl Hydroxylamines through a Base-Catalyzed Mitsunobu Reaction. J Org Chem 2005; 70:6303-12. [PMID: 16050691 DOI: 10.1021/jo050722e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The growing field of applications of O-alkyl hydroxylamines in medicinal chemistry and chemical biology has motivated the search for a parallel synthesis. A solid-phase approach based on the alkylation by alcohols of a new supported N-hydroxyphthalimide reagent using a Mitsunobu reaction followed by methylaminolysis has been optimized. This study points out the importance of the linker and a specific base effect for the Mitsunobu reaction. A large variety of alcohols can be used to give with moderate to high yields diverse O-alkyl hydroxylamines in high purity.
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Affiliation(s)
- Ludovic T Maillard
- Institut de Chimie des Substances Naturelles, UPR 2301-CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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