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Ge Y, Wang G, Jin J, Liu T, Ma X, Zhang Z, Geng T, Song J, Ma X, Zhang Y, Yang D, Ma M. Discovery and Biosynthesis of Pepticinnamins G-M Featuring Three Enzymes-Catalyzed Nonproteinogenic Amino Acid Formation. J Org Chem 2020; 85:8673-8682. [PMID: 32489098 DOI: 10.1021/acs.joc.0c01113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since pepticinnamin E was discovered almost 30 years ago, no other pepticinnamin family of natural products has been reported to date. Here, we report the discovery of pepticinnamins G-I (1-3) from a marine Streptomyces sp. PKU-MA01144 and pepticinnamins J-M (4-7) from several mutants, and these new compounds contain different N-methyl-l-alanine and l-tyrosine residues compared to pepticinnamin E. Genome sequencing, heterologous expression, gene deletion, and reconstitution of enzymatic reaction in vitro identified the biosynthetic gene cluster of 1-7 and first experimentally established the biosynthesis of the nonproteinogenic 2-chloro-3-hydroxy-4-methoxy-l-phenylalanine residue by a biopterin-dependent hydroxylase Pep10, an O-methyltransferase Pep9, and a flavin-dependent halogenase Pep1. The biosynthetic research and heterologous expression system in this study set the stage for pathway engineering for more pepticinnamins generation in the future.
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Affiliation(s)
- Yuanjie Ge
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Guiyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jing Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhongyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Juan Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Xiaojie Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Yingtao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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2
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Lanyon-Hogg T, Ritzefeld M, Sefer L, Bickel JK, Rudolf AF, Panyain N, Bineva-Todd G, Ocasio CA, O'Reilly N, Siebold C, Magee AI, Tate EW. Acylation-coupled lipophilic induction of polarisation (Acyl-cLIP): a universal assay for lipid transferase and hydrolase enzymes. Chem Sci 2019; 10:8995-9000. [PMID: 31762980 PMCID: PMC6855259 DOI: 10.1039/c9sc01785b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/16/2019] [Indexed: 12/12/2022] Open
Abstract
Posttranslational attachment of lipids to proteins is important for many cellular functions, and the enzymes responsible for these modifications are implicated in many diseases, from cancer to neurodegeneration. Lipid transferases and hydrolases are increasingly tractable therapeutic targets, but present unique challenges for high-throughput biochemical enzyme assays which hinder development of new inhibitors. We present Acylation-coupled Lipophilic Induction of Polarisation (Acyl-cLIP) as the first universally applicable biochemical lipidation assay, exploiting the hydrophobic nature of lipidated peptides to drive a polarised fluorescence readout. Acyl-cLIP allows sensitive, accurate, real-time measurement of S- or N-palmitoylation, N-myristoylation, S-farnesylation or S-geranylgeranylation. Furthermore, it is applicable to transfer and hydrolysis reactions, and we demonstrate its extension to a high-throughput screening format. We anticipate that Acyl-cLIP will greatly expedite future drug discovery efforts against these challenging targets.
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Affiliation(s)
- Thomas Lanyon-Hogg
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Markus Ritzefeld
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Lea Sefer
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Jasmine K Bickel
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Amalie F Rudolf
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Nattawadee Panyain
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | | | | | | | - Christian Siebold
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Anthony I Magee
- Molecular Medicine Section , National Heart & Lung Institute , Imperial College London , London , SW7 2AZ , UK
| | - Edward W Tate
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
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3
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Cragg GM, Newman DJ. Natural products: a continuing source of novel drug leads. Biochim Biophys Acta Gen Subj 2013; 1830:3670-95. [PMID: 23428572 DOI: 10.1016/j.bbagen.2013.02.008] [Citation(s) in RCA: 1594] [Impact Index Per Article: 144.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Nature has been a source of medicinal products for millennia, with many useful drugs developed from plant sources. Following discovery of the penicillins, drug discovery from microbial sources occurred and diving techniques in the 1970s opened the seas. Combinatorial chemistry (late 1980s), shifted the focus of drug discovery efforts from Nature to the laboratory bench. SCOPE OF REVIEW This review traces natural products drug discovery, outlining important drugs from natural sources that revolutionized treatment of serious diseases. It is clear Nature will continue to be a major source of new structural leads, and effective drug development depends on multidisciplinary collaborations. MAJOR CONCLUSIONS The explosion of genetic information led not only to novel screens, but the genetic techniques permitted the implementation of combinatorial biosynthetic technology and genome mining. The knowledge gained has allowed unknown molecules to be identified. These novel bioactive structures can be optimized by using combinatorial chemistry generating new drug candidates for many diseases. GENERAL SIGNIFICANCE The advent of genetic techniques that permitted the isolation / expression of biosynthetic cassettes from microbes may well be the new frontier for natural products lead discovery. It is now apparent that biodiversity may be much greater in those organisms. The numbers of potential species involved in the microbial world are many orders of magnitude greater than those of plants and multi-celled animals. Coupling these numbers to the number of currently unexpressed biosynthetic clusters now identified (>10 per species) the potential of microbial diversity remains essentially untapped.
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Affiliation(s)
- Gordon M Cragg
- Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
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4
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Tan KT, Guiu-Rozas E, Bon RS, Guo Z, Delon C, Wetzel S, Arndt S, Alexandrov K, Waldmann H, Goody RS, Wu YW, Blankenfeldt W. Design, Synthesis, and Characterization of Peptide-Based Rab Geranylgeranyl Transferase Inhibitors. J Med Chem 2009; 52:8025-37. [DOI: 10.1021/jm901117d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Kirill Alexandrov
- Department of Physical Biochemistry
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St. Lucia, QLD 4072, Australia
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5
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Cragg GM, Grothaus PG, Newman DJ. Impact of natural products on developing new anti-cancer agents. Chem Rev 2009; 109:3012-43. [PMID: 19422222 DOI: 10.1021/cr900019j] [Citation(s) in RCA: 887] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gordon M Cragg
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, NCI-Frederick, Fairview Center, Suite 206, P.O. Box B, Frederick, Maryland 21702-1201, USA
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6
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Guo Z, Wu YW, Tan KT, Bon R, Guiu-Rozas E, Delon C, Nguyen U, Wetzel S, Arndt S, Goody R, Blankenfeldt W, Alexandrov K, Waldmann H. Development of Selective RabGGTase Inhibitors and Crystal Structure of a RabGGTase–Inhibitor Complex. Angew Chem Int Ed Engl 2008; 47:3747-50. [DOI: 10.1002/anie.200705795] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Guo Z, Wu YW, Tan KT, Bon R, Guiu-Rozas E, Delon C, Nguyen U, Wetzel S, Arndt S, Goody R, Blankenfeldt W, Alexandrov K, Waldmann H. Development of Selective RabGGTase Inhibitors and Crystal Structure of a RabGGTase–Inhibitor Complex. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Rawat DS, Krzysiak AJ, Gibbs RA. Synthesis and biochemical evaluation of 3,7-disubstituted farnesyl diphosphate analogues. J Org Chem 2008; 73:1881-7. [PMID: 18225915 DOI: 10.1021/jo701725b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Farnesyl diphosphate (FPP) analogues have proven to be both potent inhibitors of protein-farnesyltransferase (FTase) and valuable probes for the investigation of the function of prenylated proteins. Previously, we have demonstrated that certain 3-substituted and 7-substituted FPP analogues can act as inhibitors of FTase, while others are effective alternative substrates. We have now utilized our vinyl triflate-mediated route to synthesize the first seven FPP variants bearing substituents in both the 3- and 7-positions of the isoprene unit. Despite their exceptional steric bulk with respect to FPP itself, six of the seven analogues bind to FTase. Two of the analogues are potent inhibitors of the enzyme, but a more striking finding is that three FPP variants (4a, 4b, and 4f) are efficient alternative substrates for FTase.
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Affiliation(s)
- Diwan S Rawat
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and Cancer Center, Purdue University, West Lafayette, Indiana 47907, USA
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9
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Krzysiak AJ, Rawat DS, Scott SA, Pais JE, Handley M, Harrison ML, Fierke CA, Gibbs RA. Combinatorial modulation of protein prenylation. ACS Chem Biol 2007; 2:385-9. [PMID: 17530735 PMCID: PMC2922964 DOI: 10.1021/cb700062b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The cell has >60 different farnesylated proteins. Many critically important signal transduction proteins are post-translationally modified with attachment of a farnesyl isoprenoid catalyzed by protein farnesyltransferase (FTase). Recently, it has been shown that farnesyl diphosphate (FPP) analogues can alter the peptide substrate specificity of FTase. We have used combinatorial screening of FPP analogues and peptide substrates to identify patterns in FTase substrate selectivity. Each FPP analogue displays a unique pattern of substrate reactivity with the tested peptides; FTase efficiently catalyzes the transfer of an FPP analogue selectively to one peptide and not another. Furthermore, we have demonstrated that these analogues can enter cells and be incorporated into proteins. These FPP analogues could serve as selective tools to examine the role prenylation plays in individual protein function.
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Affiliation(s)
- Amanda J. Krzysiak
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907
| | | | - Sarah A. Scott
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907
| | - June E. Pais
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Misty Handley
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Marietta L. Harrison
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Carol A. Fierke
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Richard A. Gibbs
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, Indiana 47907
- Corresponding author,
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Brunsveld L, Kuhlmann J, Alexandrov K, Wittinghofer A, Goody RS, Waldmann H. Lipidated ras and rab peptides and proteins--synthesis, structure, and function. Angew Chem Int Ed Engl 2007; 45:6622-46. [PMID: 17031879 DOI: 10.1002/anie.200600855] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Chemical biology can be defined as the study of biological phenomena from a chemical approach. Based on the analysis of relevant biological phenomena and their structural foundation, unsolved problems are identified and tackled through a combination of chemistry and biology. Thus, new synthetic methods and strategies are developed and employed for the construction of compounds that are used to investigate biological procedures. Solid-phase synthesis has emerged as the preferred method for the synthesis of lipidated peptides, which can be chemoselectively ligated to proteins of the Ras superfamily. The generated peptides and proteins have solved biological questions in the field of the Ras-superfamily GTPases that are not amendable to chemical or biological techniques alone.
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Affiliation(s)
- Luc Brunsveld
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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11
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Lessmann T, Leuenberger MG, Menninger S, Lopez-Canet M, Müller O, Hümmer S, Bormann J, Korn K, Fava E, Zerial M, Mayer TU, Waldmann H. Natural Product-Derived Modulators of Cell Cycle Progression and Viral Entry by Enantioselective Oxa Diels-Alder Reactions on the Solid Phase. ACTA ACUST UNITED AC 2007; 14:443-51. [PMID: 17462579 DOI: 10.1016/j.chembiol.2007.02.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 01/31/2007] [Accepted: 02/09/2007] [Indexed: 01/12/2023]
Abstract
The underlying frameworks of natural product classes with multiple biological activities can be regarded as biologically selected and prevalidated starting points in vast chemical structure space in the development of compound collections for chemical biology and medicinal chemistry research. For the synthesis of natural product-derived and -inspired compound collections, the development of enantioselective transformations in a format amenable to library synthesis, e.g., on the solid support, is a major and largely unexplored goal. We report on the enantioselective solid-phase synthesis of a natural product-inspired alpha,beta-unsaturated delta-lactone collection and its investigation in cell-based screens monitoring cell cycle progression and viral entry into cells. The screens identified modulators of both biological processes at a high hit rate. The screen for inhibition of viral entry opens up avenues of research for the identification of compounds with antiviral activity.
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Affiliation(s)
- Torben Lessmann
- Abteilung Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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12
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Brunsveld L, Kuhlmann J, Alexandrov K, Wittinghofer A, Goody RS, Waldmann H. Lipidierte Ras- und Rab-Peptide und -Proteine: Synthese, Struktur und Funktion. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600855] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Brunsveld L, Kuhlmann J, Waldmann H. Synthesis of palmitoylated Ras-peptides and -proteins. Methods 2006; 40:151-65. [PMID: 17012027 DOI: 10.1016/j.ymeth.2006.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2006] [Accepted: 04/24/2006] [Indexed: 11/20/2022] Open
Abstract
In this review, an overview is given and details are provided for the synthesis of lipidated Ras (rat-adeno-sarcoma)-peptides and -proteins. The progress made in the synthesis of the lipidated peptides from the Ras superfamily is discussed with special emphasis on the recently developed solid-phase synthesis methods, since these methods have turned out to be the preferred synthesis method for the majority of the required peptides. Solid-phase lipopeptide synthesis has given access to native and modified peptides on a scale that allows peptide-consuming studies like for ligation to proteins and concomitant X-ray crystal structure determination. The access to these peptides has also enabled biological questions concerning these peptides and proteins to be resolved. The review describes different solid-phase methods, which are individually suited for different types of lipopeptides, differing for example in lipidation pattern or amino acid side-chain functionality, and their ligation to proteins. Finally, an example is provided how these peptides can serve to resolve biological aspects of the Ras family GTPases.
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Affiliation(s)
- L Brunsveld
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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14
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Affiliation(s)
- Roland E Dolle
- Department of Chemistry, Adolor Corporation, 700 Pennsylvania Drive, Exton, PA 19341, USA.
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15
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Abstract
Pepticinnamin E is a naturally occurring bisubstrate inhibitor of farnesyltransferase. Based on the structure of the natural product, a compound library was synthesized by variation of eight structural parameters. Following three different routes, a total of 51 analogues was synthesized on the polymeric support in 6-11-step parallel syntheses. Overall yields ranged from 3 to 63%, and the compounds were obtained with >90% purity.
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Affiliation(s)
- Michael Thutewohl
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Str. 11, D-44227, Organische Chemie, Universität Dortmund, Dortmund und Fachbereich 3, Germany
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16
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Thutewohl M, Kissau L, Popkirova B, Karaguni IM, Nowak T, Bate M, Kuhlmann J, Müller O, Waldmann H. Identification of mono- and bisubstrate inhibitors of protein farnesyltransferase and inducers of apoptosis from a pepticinnamin E library. Bioorg Med Chem 2003; 11:2617-26. [PMID: 12757727 DOI: 10.1016/s0968-0896(03)00160-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A library of 51 analogues of the naturally occurring protein farnesyltransferase inhibitor pepticinnamin E was investigated biologically. Several compounds with pronounced inhibitory activity were discovered with the lowest IC(50) value reaching 1 microM. The library contains inhibitors which are competitive to either farnesylpyrophosphate or the peptide substrate and a bisubstrate inhibitor. This activity is supported and rationalized by molecular modelling experiments and different binding modes of the inhibitors deduced from them. Several compounds induced apoptosis in a Ras-transformed tumour cell line, and in one case this correlated with farnesyltransferase-inhibiting activity.
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Affiliation(s)
- Michael Thutewohl
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Str. 11, D-44227 Dortmund und Fachbereich 3, Organische Chemie, Universität Dortmund, Germany
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