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Nicolaou KC, Rhoades D, Wang Y, Totokotsopoulos S, Bai R, Hamel E. Synthesis and Biological Evaluation of Novel Epothilone B Side Chain Analogues. ChemMedChem 2015; 10:1974-9. [PMID: 26447977 DOI: 10.1002/cmdc.201500401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/10/2022]
Abstract
The design, synthesis, and biological evaluation of a series of epothilone analogues with novel side chains equipped with an amino group are described. Their design facilitates potential conjugation to selective drug delivery systems such as antibodies. Their synthesis proceeded efficiently via Stille coupling of a readily available vinyl iodide and heterocyclic stannanes. Cytotoxicity studies and tubulin binding assays revealed two of these analogues to be more potent than epothilones A-D and the anticancer agent ixabepilone, currently in clinical use.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
| | - Derek Rhoades
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yanping Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Sotirios Totokotsopoulos
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ruoli Bai
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Ernest Hamel
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
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Entwistle RA, Rizk RS, Cheng DM, Lushington GH, Himes RH, Gupta ML. Differentiating between models of epothilone binding to microtubules using tubulin mutagenesis, cytotoxicity, and molecular modeling. ChemMedChem 2012; 7:1580-6. [PMID: 22807375 DOI: 10.1002/cmdc.201200286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Indexed: 11/08/2022]
Abstract
Microtubule stabilizers are powerful antimitotic compounds and represent a proven cancer treatment strategy. Several classes of compounds in clinical use or trials, such as the taxanes and epothilones, bind to the same region of β-tubulin. Determining how these molecules interact with tubulin and stabilize microtubules is important both for understanding the mechanism of action and enhancing chemotherapeutic potential, for example, minimizing side effects, increasing solubility, and overcoming resistance. Structural studies using non-polymerized tubulin or stabilized polymers have produced different models of epothilone binding. In this study we used directed mutagenesis of the binding site on Saccharomyces cerevisiae β-tubulin to analyze interactions between epothilone B and its biologically relevant substrate, dynamic microtubules. Five engineered amino acid changes contributed to a 125-fold increase in epothilone B cytotoxicity independent of inherent microtubule stability. The mutagenesis of endogenous β-tubulin was done in otherwise isogenic strains. This facilitated the correlation of amino acid substitutions with altered cytotoxicity using molecular mechanics simulations. The results, which are based on the interaction between epothilone B and dynamic microtubules, most strongly support the binding mode determined by NMR spectroscopy-based studies. This work establishes a system for discriminating between potential binding modes and among various compounds and/or analogues using a sensitive biological activity-based readout.
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Affiliation(s)
- Ruth A Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045-7534, USA
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Coderch C, Klett J, Morreale A, Díaz JF, Gago F. Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β-Tubulin. ChemMedChem 2012; 7:836-43. [DOI: 10.1002/cmdc.201200065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/02/2012] [Indexed: 01/08/2023]
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Zhan W, Jiang Y, Banerjee A, Brodie PJ, Bane S, Kingston DGI, Liotta DC, Snyder JP. C6-C8 bridged epothilones: consequences of installing a conformational lock at the edge of the macrocycle. Chemistry 2011; 17:14792-804. [PMID: 22127984 PMCID: PMC3248799 DOI: 10.1002/chem.201102630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Indexed: 11/08/2022]
Abstract
A series of conformationally restrained epothilone analogues with a short bridge between the methyl groups at C6 and C8 was designed to mimic the binding pose assigned to our recently reported EpoA-microtubule binding model. A versatile synthetic route to these bridged epothilone analogues has been successfully devised and implemented. Biological evaluation of the compounds against A2780 human ovarian cancer and PC3 prostate cancer cell lines suggested that the introduction of a bridge between C6-C8 reduced potency by 25-1000 fold in comparison with natural epothilone D. Tubulin assembly measurements indicate these bridged epothilone analogues to be mildly active, but without significant microtubule stabilization capacity. Molecular mechanics and DFT energy evaluations suggest the mild activity of the bridged epo-analogues may be due to internal conformational strain.
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Affiliation(s)
- Weiqiang Zhan
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta GA 30322 (USA), Fax: (+1) 404-712-8670
| | - Yi Jiang
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta GA 30322 (USA), Fax: (+1) 404-712-8670
| | - Abhijit Banerjee
- Department of Chemistry, State University of New York, Binghamton, NY 13902-6016 (USA)
| | - Peggy J. Brodie
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (USA)
| | - Susan Bane
- Department of Chemistry, State University of New York, Binghamton, NY 13902-6016 (USA)
| | - David G. I. Kingston
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (USA)
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta GA 30322 (USA), Fax: (+1) 404-712-8670
| | - James P. Snyder
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta GA 30322 (USA), Fax: (+1) 404-712-8670
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Erdélyi M, Navarro-Vázquez A, Pfeiffer B, Kuzniewski CN, Felser A, Widmer T, Gertsch J, Pera B, Díaz JF, Altmann KH, Carlomagno T. The binding mode of side chain- and C3-modified epothilones to tubulin. ChemMedChem 2010; 5:911-20. [PMID: 20432490 DOI: 10.1002/cmdc.201000050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The tubulin-binding mode of C3- and C15-modified analogues of epothilone A (Epo A) was determined by NMR spectroscopy and computational methods and compared with the existing structural models of tubulin-bound natural Epo A. Only minor differences were observed in the conformation of the macrocycle between Epo A and the C3-modified analogues investigated. In particular, 3-deoxy- (compound 2) and 3-deoxy-2,3-didehydro-Epo A (3) were found to adopt similar conformations in the tubulin-binding cleft as Epo A, thus indicating that the 3-OH group is not essential for epothilones to assume their bioactive conformation. None of the available models of the tubulin-epothilone complex is able to fully recapitulate the differences in tubulin-polymerizing activity and microtubule-binding affinity between C20-modified epothilones 6 (C20-propyl), 7 (C20-butyl), and 8 (C20-hydroxypropyl). Based on the results of transferred NOE experiments in the presence of tubulin, the isomeric C15 quinoline-based Epo B analogues 4 and 5 show very similar orientations of the side chain, irrespective of the position of the nitrogen atom in the quinoline ring. The quinoline side chain stacks on the imidazole moiety of beta-His227 with equal efficiency in both cases, thus suggesting that the aromatic side chain moiety in epothilones contributes to tubulin binding through strong van der Waals interactions with the protein rather than hydrogen bonding involving the heteroaromatic nitrogen atom. These conclusions are in line with existing tubulin polymerization and microtubule-binding data for 4, 5, and Epo B.
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Affiliation(s)
- Máté Erdélyi
- NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Kumar A, Heise H, Blommers MJJ, Krastel P, Schmitt E, Petersen F, Jeganathan S, Mandelkow EM, Carlomagno T, Griesinger C, Baldus M. Interaction of Epothilone B (Patupilone) with Microtubules as Detected by Two-Dimensional Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kumar A, Heise H, Blommers MJJ, Krastel P, Schmitt E, Petersen F, Jeganathan S, Mandelkow EM, Carlomagno T, Griesinger C, Baldus M. Interaction of Epothilone B (Patupilone) with Microtubules as Detected by Two-Dimensional Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2010; 49:7504-7. [DOI: 10.1002/anie.201001946] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Dietrich SA, Lindauer R, Stierlin C, Gertsch J, Matesanz R, Notararigo S, Díaz JF, Altmann KH. Epothilone analogues with benzimidazole and quinoline side chains: chemical synthesis, antiproliferative activity, and interactions with tubulin. Chemistry 2010; 15:10144-57. [PMID: 19697384 DOI: 10.1002/chem.200901376] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of epothilone B and D analogues bearing isomeric quinoline or functionalized benzimidazole side chains has been prepared by chemical synthesis in a highly convergent manner. All analogues have been found to interact with the tubulin/microtubule system and to inhibit human cancer cell proliferation in vitro, albeit with different potencies (IC(50) values between 1 and 150 nM). The affinity of quinoline-based epothilone B and D analogues for stabilized microtubules clearly depends on the position of the N-atom in the quinoline system, while the induction of tubulin polymerization in vitro appears to be less sensitive to N-positioning. The potent inhibition of human cancer cell growth by epothilone analogues bearing functionalized benzimidazole side chains suggests that these systems might be conjugated with tumor-targeting moieties to form tumor-targeted prodrugs.
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Affiliation(s)
- Silvia Anthoine Dietrich
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Chemistry and Applied Biosciences, HCI H405, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
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Altmann KH, Pfeiffer B, Arseniyadis S, Pratt BA, Nicolaou KC. The chemistry and biology of epothilones--the wheel keeps turning. ChemMedChem 2008; 2:396-423. [PMID: 17340668 DOI: 10.1002/cmdc.200600206] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Karl-Heinz Altmann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H 405, 8093 Zürich, Switzerland.
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Alhamadsheh MM, Gupta S, Hudson RA, Perera L, Tillekeratne LMV. Total synthesis and selective activity of a new class of conformationally restrained epothilones. Chemistry 2008; 14:570-81. [PMID: 17955508 PMCID: PMC2712887 DOI: 10.1002/chem.200701143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Stereoselective total syntheses of two novel conformationally restrained epothilone analogues are described. Evans asymmetric alkylation, Brown allylation, and a diastereoselective aldol reaction served as the key steps in the stereoselective synthesis of one of the two key fragments of the convergent synthetic approach. Enzyme resolution was employed to obtain the second fragment as a single enantiomer. The molecules were assembled by esterification, followed by ring-closing metathesis. In preliminary cytotoxicity studies, one of the analogues showed strong and selective growth inhibitory activity against two leukemia cell lines over solid human tumor cell lines. The precise biological mechanism of action and high degree of selectivity of this analogue remain to be examined.
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Affiliation(s)
- Mamoun M. Alhamadsheh
- Department of Medicinal and Biological Chemistry, College of Pharmacy, The University of Toledo, Toledo, OH 43606 (USA), Fax: (+1)419-530-7946
| | - Shuchi Gupta
- Department of Medicinal and Biological Chemistry, College of Pharmacy, The University of Toledo, Toledo, OH 43606 (USA), Fax: (+1)419-530-7946
| | - Richard A. Hudson
- Department of Medicinal and Biological Chemistry, College of Pharmacy, The University of Toledo, Toledo, OH 43606 (USA), Fax: (+1)419-530-7946
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (USA)
| | - L. M. Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy, The University of Toledo, Toledo, OH 43606 (USA), Fax: (+1)419-530-7946
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11
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Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents. Top Curr Chem (Cham) 2008; 286:279-328. [PMID: 23563616 DOI: 10.1007/128_2008_20] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tubulin targeting agents constitute an important class of anticancer drugs. By acting either as microtubule stabilizers or destabilizers, they disrupt microtubule dynamics, thus inducing mitotic arrest and, ultimately, cell death by apoptosis. Three different binding sites, whose exact location on tubulin has been experimentally detected, have been identified so far for antimitotic compound targeting microtubules, namely the taxoid, the colchicine and the vinka alkaloid binding site. A number of ligand- and structure-based molecular modeling studies in this field has been reported over the years, aimed at elucidating the binding modes of both stabilizing and destabilizing agent, as well as the molecular features responsible for their efficacious interaction with tubulin. Such studies are described in this review, focusing on information provided by different modeling approaches on the structural determinants of antitubulin agents and the interactions with the binding pockets on tubulin emerged as fundamental for antitumor activity.To describe molecular modeling approaches applied to date to molecules known to bind microtubules, this paper has been divided into two main parts: microtubule destabilizing (Part 1) and stabilizing (Part 2) agents. The first part includes structure-based and ligand-based approaches to study molecules targeting colchicine (1.1) and vinca alkaloid (1.2) binding sites, respectively. In the second part, the studies performed on microtubule-stabilizing antimitotic agents (MSAA) are described. Starting from the first representative compound of this class, paclitaxel, molecular modeling studies (quantitative structure-activity relationships - QSAR - and structure-based approaches), performed on natural compounds acting with the same mechanism of action and temptative common pharmacophoric hypotheses for all of these compounds, are reported.
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Reese M, Sánchez-Pedregal VM, Kubicek K, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solution. Angew Chem Int Ed Engl 2007; 46:1864-8. [PMID: 17274084 DOI: 10.1002/anie.200604505] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcel Reese
- Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany
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Lange A, Schupp T, Petersen F, Carlomagno T, Baldus M. High-Resolution Solid-State NMR Structure of an Anticancer Agent. ChemMedChem 2007; 2:522-7. [PMID: 17315255 DOI: 10.1002/cmdc.200600299] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We demonstrate that solid-state NMR methods can be used to rapidly determine the high-resolution 3D structure of Epothilone B in the polycrystalline state. The solid-state NMR structures exhibit an average heavy atom RMSD to the mean structure of 0.14 A. The 3D-structural analysis leads to stereospecific assignments and provides insight into the influence of intermolecular interactions upon ssNMR chemical-shift parameters. Our results pave the way to the study of ligand-microtubule interactions in a noncrystalline and insoluble environment at atomic level.
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Affiliation(s)
- Adam Lange
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Reese M, Sánchez-Pedregal V, Kubicek K, Meiler J, Blommers M, Griesinger C, Carlomagno T. Structural Basis of the Activity of the Microtubule-Stabilizing Agent Epothilone A Studied by NMR Spectroscopy in Solution. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604505] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sánchez-Pedregal VM, Kubicek K, Meiler J, Lyothier I, Paterson I, Carlomagno T. The Tubulin-Bound Conformation of Discodermolide Derived by NMR Studies in Solution Supports a Common Pharmacophore Model for Epothilone and Discodermolide. Angew Chem Int Ed Engl 2006; 45:7388-94. [PMID: 17036370 DOI: 10.1002/anie.200602793] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Víctor M Sánchez-Pedregal
- Abteilung NMR-basierte Strukturbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany
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Sánchez-Pedregal VM, Kubicek K, Meiler J, Lyothier I, Paterson I, Carlomagno T. The Tubulin-Bound Conformation of Discodermolide Derived by NMR Studies in Solution Supports a Common Pharmacophore Model for Epothilone and Discodermolide. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602793] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping. Angew Chem Int Ed Engl 2006; 44:4172-5. [PMID: 15929149 DOI: 10.1002/anie.200500503] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA Method: Protein-Mediated Interligand NOEs for Pharmacophore Mapping. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500503] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Heinz DW, Schubert WD, Höfle G. Lange gesucht - die bioaktive Konformation von Epothilon und seine Bindung im Tubulin. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200462241] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Heinz DW, Schubert WD, Höfle G. Much Anticipated-The Bioactive Conformation of Epothilone and Its Binding to Tubulin. Angew Chem Int Ed Engl 2005; 44:1298-301. [PMID: 15714588 DOI: 10.1002/anie.200462241] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dirk W Heinz
- Division of Structural Biology, Gesellschaft für Biotechnologische, Forschung, 38124 Braunschweig, Germany.
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