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Falb M, Amata I, Gabel F, Simon B, Carlomagno T. Structure of the K-turn U4 RNA: a combined NMR and SANS study. Nucleic Acids Res 2010; 38:6274-85. [PMID: 20466811 PMCID: PMC2952850 DOI: 10.1093/nar/gkq380] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/26/2010] [Accepted: 04/27/2010] [Indexed: 11/13/2022] Open
Abstract
K-turn motifs are universal RNA structural elements providing a binding platform for proteins in several cellular contexts. Their characteristic is a sharp kink in the phosphate backbone that puts the two helical stems of the protein-bound RNA at an angle of 60°. However, to date no high-resolution structure of a naked K-turn motif is available. Here, we present the first structural investigation at atomic resolution of an unbound K-turn RNA (the spliceosomal U4-Kt RNA) by a combination of NMR and small-angle neutron scattering data. With this study, we wish to address the question whether the K-turn structural motif assumes the sharply kinked conformation in the absence of protein binders and divalent cations. Previous studies have addressed this question by fluorescence resonance energy transfer, biochemical assays and molecular dynamics simulations, suggesting that the K-turn RNAs exist in equilibrium between a kinked conformation, which is competent for protein binding, and a more extended conformation, with the population distribution depending on the concentration of divalent cations. Our data shows that the U4-Kt RNA predominantly assumes the more extended conformation in the absence of proteins and divalent cations. The internal loop region is well structured but adopts a different conformation from the one observed in complex with proteins. Our data suggests that the K-turn consensus sequence does not per se code for the kinked conformation; instead the sharp backbone kink requires to be stabilized by protein binders.
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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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78
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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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79
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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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80
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Kubicek K, Grimm S, Orts J, Sasse F, Carlomagno T. The Tubulin-Bound Structure of the Antimitotic Drug Tubulysin. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906828] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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81
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Kubicek K, Grimm S, Orts J, Sasse F, Carlomagno T. The Tubulin-Bound Structure of the Antimitotic Drug Tubulysin. Angew Chem Int Ed Engl 2010; 49:4809-12. [DOI: 10.1002/anie.200906828] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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82
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Bartoschek S, Klabunde T, Defossa E, Dietrich V, Stengelin S, Griesinger C, Carlomagno T, Focken I, Wendt KU. Drug design for G-protein-coupled receptors by a ligand-based NMR method. Angew Chem Int Ed Engl 2010; 49:1426-9. [PMID: 20084646 DOI: 10.1002/anie.200905102] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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83
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Stauch B, Simon B, Basile T, Schneider G, Malek N, Kalesse M, Carlomagno T. Elucidation of the Structure and Intermolecular Interactions of a Reversible Cyclic-Peptide Inhibitor of the Proteasome by NMR Spectroscopy and Molecular Modeling. Angew Chem Int Ed Engl 2010; 49:3934-8. [DOI: 10.1002/anie.201000140] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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84
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Stauch B, Simon B, Basile T, Schneider G, Malek N, Kalesse M, Carlomagno T. Elucidation of the Structure and Intermolecular Interactions of a Reversible Cyclic-Peptide Inhibitor of the Proteasome by NMR Spectroscopy and Molecular Modeling. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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85
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Rodríguez-Castañeda F, Coudevylle N, Becker S, Brose N, Carlomagno T, Griesinger C. 1H, 13C and 15N resonance assignments of the Calmodulin-Munc13-1 peptide complex. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:45-48. [PMID: 20013162 PMCID: PMC2862173 DOI: 10.1007/s12104-009-9204-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 12/02/2009] [Indexed: 05/28/2023]
Abstract
Ca(2+)-Calmodulin binding to the variable N-terminal region of the diacylglycerol/phorbol ester-binding UNC13/Munc13 family of proteins modulates the short-term synaptic plasticity characteristics in neurons. Here, we report the sequential backbone and side chain resonance assignment of the Ca(2+)-Calmodulin/Munc13-1(458-492) peptide complex at pH 6.8 and 35 degrees C (BMRB No. 15470).
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86
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Bülow L, Nickeleit I, Girbig AK, Brodmann T, Rentsch A, Eggert U, Sasse F, Steinmetz H, Frank R, Carlomagno T, Malek N, Kalesse M. Synthesis and Biological Characterization of Argyrin F. ChemMedChem 2010; 5:832-6. [DOI: 10.1002/cmdc.201000080] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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87
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Jehle S, Falb M, Kirkpatrick JP, Oschkinat H, Rossum BJV, Althoff G, Carlomagno T. Intermolecular Protein−RNA Interactions Revealed by 2D 31P−15N Magic Angle Spinning Solid-State NMR Spectroscopy. J Am Chem Soc 2010; 132:3842-6. [DOI: 10.1021/ja909723f] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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88
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Bartoschek S, Klabunde T, Defossa E, Dietrich V, Stengelin S, Griesinger C, Carlomagno T, Focken I, Wendt K. Drug Design for G-Protein-Coupled Receptors by a Ligand-Based NMR Method. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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89
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Orts J, Griesinger C, Carlomagno T. The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 200:64-73. [PMID: 19592283 DOI: 10.1016/j.jmr.2009.06.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 06/04/2009] [Indexed: 05/21/2023]
Abstract
During the process of drug discovery, INPHARMA can be used to derive the structure of receptor/lead compound complexes binding to each other with a K(d) in the microM to mM range. To be successful, the methodology needs adjustment of various parameters that depend on the physical constants of the binding event and on the receptor size. Here we present a thorough theoretical analysis of the INPHARMA interligand NOE effect in dependence of experimental parameters and physical constants. This analysis helps the experimentalist to choose the correct experimental parameters and consequentially to achieve optimal performance of the methodology.
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90
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Kirkpatrick JP, Li P, Carlomagno T. Probing mutation-induced structural perturbations by refinement against residual dipolar couplings: application to the U4 spliceosomal RNP complex. Chembiochem 2009; 10:1007-14. [PMID: 19308925 DOI: 10.1002/cbic.200800786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Confident interpretation of biochemical experiments performed with mutated proteins relies on verification of the integrity of the mutant structures. We present a simple and rapid refinement protocol for comparing the structures of mutated and wild-type proteins. Our approach involves measurement of residual dipolar couplings, and only requires assignment of the backbone resonances of the mutant species. We demonstrate application of the protocol to a mutant of the 15.5K protein, a core component of the U4 spliceosomal ribonucleoprotein (RNP) complex. Confirmation of the unperturbed structure of the mutated protein prompted re-examination of a previous mutagenesis study and indicated that the interpretation of mutant binding affinities in terms of direct interfacial contacts should be applied with caution.
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91
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Li P, Kirkpatrick J, Carlomagno T. An efficient strategy for the determination of the three-dimensional architecture of ribonucleoprotein complexes by the combination of a few easily accessible NMR and biochemical data: intermolecular recognition in a U4 spliceosomal complex. J Mol Biol 2009; 388:283-98. [PMID: 19281818 DOI: 10.1016/j.jmb.2009.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/02/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022]
Abstract
Ribonucleoprotein (RNP) complexes are involved in several cellular processes, including RNA processing, transcription and translation. RNP structures are often dynamic in nature, undergoing significant remodeling during the course of their function. Visualization of the three-dimensional arrangement of single components in the complex and characterization of the intermolecular interactions are essential for understanding the mechanisms of operation. Crystallization either is not always achievable for these highly dynamic RNP particles or requires trimming the complex to a stable, well-structured core that lacks the flexible, regulatory domains. Alternative techniques that can provide structural information for complexes in solution under native conditions, where they retain their natural dynamic properties, are needed. In this study, we explored the possibility of using a combination of NMR, biochemical data and molecular modeling to generate an accurate high-resolution model of RNP complexes. We applied this strategy to the ternary hPrp31 (human Prp31)-15.5K-U4 5'-SL (stem-loop) spliceosomal complex, which, due to its large size and instability and because of the difficulty in obtaining isotopically labeled hPrp31, is not amenable to complete structure determination by NMR. We designed a protocol where the protein-protein interaction surface is defined for 15.5K by NMR data, while the relative orientations of the U4 RNA and the hPrp31 protein are described by mutational and cross-linking data. Using these data in a restrained ensemble docking protocol, we obtained a model for the ternary complex that reveals a novel rationale for the hierarchical assembly of the complex. Comparison of the docking model with the crystal structure recently obtained for a trimmed version of the complex reveals the high accuracy of the docking model, even down to an atomic level. This work shows that the architecture of large RNP complexes is within reach by NMR investigation in solution even for those cases where a traditional structural determination cannot be performed.
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92
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Carlomagno T, Amata I, Williamson JR, Hennig M. NMR assignments of HIV-2 TAR RNA. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:167-169. [PMID: 19636896 DOI: 10.1007/s12104-008-9112-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 09/08/2008] [Indexed: 05/28/2023]
Abstract
We report nearly complete assignment for all (1)H, (13)C, (31)P, and (15)N resonances in the 30-nucleotide stem-loop HIV-2 TAR RNA located at the 5' end of all viral mRNAs.
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93
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Orts J, Tuma J, Reese M, Grimm S, Monecke P, Bartoschek S, Schiffer A, Wendt K, Griesinger C, Carlomagno T. Crystallography-Independent Determination of Ligand Binding Modes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801792] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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94
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Orts J, Tuma J, Reese M, Grimm S, Monecke P, Bartoschek S, Schiffer A, Wendt K, Griesinger C, Carlomagno T. Crystallography-Independent Determination of Ligand Binding Modes. Angew Chem Int Ed Engl 2008; 47:7736-40. [DOI: 10.1002/anie.200801792] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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95
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Orts J, Grimm SK, Griesinger C, Wendt KU, Bartoschek S, Carlomagno T. Specific Methyl Group Protonation for the Measurement of Pharmacophore-Specific Interligand NOE Interactions. Chemistry 2008; 14:7517-20. [DOI: 10.1002/chem.200800880] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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96
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Nickeleit I, Zender S, Sasse F, Geffers R, Brandes G, Sörensen I, Steinmetz H, Kubicka S, Carlomagno T, Menche D, Gütgemann I, Buer J, Gossler A, Manns MP, Kalesse M, Frank R, Malek NP. Argyrin a reveals a critical role for the tumor suppressor protein p27(kip1) in mediating antitumor activities in response to proteasome inhibition. Cancer Cell 2008; 14:23-35. [PMID: 18598941 DOI: 10.1016/j.ccr.2008.05.016] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 02/14/2008] [Accepted: 05/20/2008] [Indexed: 12/21/2022]
Abstract
A reduction in the cellular levels of the cyclin kinase inhibitor p27(kip1) is frequently found in many human cancers and correlates directly with patient prognosis. In this work, we identify argyrin A, a cyclical peptide derived from the myxobacterium Archangium gephyra, as a potent antitumoral drug. All antitumoral activities of argyrin A depend on the prevention of p27(kip1) destruction, as loss of p27(kip1) expression confers resistance to this compound. We find that argyrin A exerts its effects through a potent inhibition of the proteasome. By comparing the cellular responses exerted by argyrin A with siRNA-mediated knockdown of proteasomal subunits, we find that the biological effects of proteasome inhibition per se depend on the expression of p27(kip1).
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97
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Farès C, Hassfeld J, Menche D, Carlomagno T. Simultaneous Determination of the Conformation and Relative Configuration of Archazolide A by Using Nuclear Overhauser Effects,J Couplings, and Residual Dipolar Couplings. Angew Chem Int Ed Engl 2008; 47:3722-6. [DOI: 10.1002/anie.200800225] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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98
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Farès C, Hassfeld J, Menche D, Carlomagno T. Simultaneous Determination of the Conformation and Relative Configuration of Archazolide A by Using Nuclear Overhauser Effects,J Couplings, and Residual Dipolar Couplings. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800225] [Citation(s) in RCA: 18] [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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99
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Höfer P, Parigi G, Luchinat C, Carl P, Guthausen G, Reese M, Carlomagno T, Griesinger C, Bennati M. Field Dependent Dynamic Nuclear Polarization with Radicals in Aqueous Solution. J Am Chem Soc 2008; 130:3254-5. [DOI: 10.1021/ja0783207] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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100
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Erdélyi M, Pfeiffer B, Hauenstein K, Fohrer J, Gertsch J, Altmann KH, Carlomagno T. Conformational preferences of natural and C3-modified epothilones in aqueous solution. J Med Chem 2008; 51:1469-73. [PMID: 18271516 DOI: 10.1021/jm7013452] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational properties of the microtubule-stabilizing agent epothilone A ( 1a) and its 3-deoxy and 3-deoxy-2,3-didehydro derivatives 2 and 3 have been investigated in aqueous solution by a combination of NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The tubulin-bound conformation of epothilone A ( 1a), as previously proposed on the basis of solution NMR data, was found to represent a significant fraction of the ensemble of conformations present for the free ligands in aqueous solution.
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