1
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Dolenc J, van Gunsteren WF, Prota AE, Steinmetz MO, Missimer JH. Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data. J Chem Inf Model 2019; 59:2218-2230. [PMID: 30855963 DOI: 10.1021/acs.jcim.9b00171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Epothilones are among the most potent chemotherapeutic drugs used for the treatment of cancer. Epothilone A (EpoA), a natural product, is a macrocyclic molecule containing 34 non-hydrogen atoms and a thiazole side chain. NMR studies of EpoA in aqueous solution, unbound as well as bound to αβ-tubulin, and unbound in dimethyl sulfoxide (DMSO) solution have delivered sets of nuclear Overhauser effect (NOE) atom-atom distance bounds, but no structures based on NMR data are present in structural data banks. X-ray diffraction of crystals has provided structures of EpoA unbound and bound to αβ-tubulin. Since both crystal structures derived from X-ray diffraction intensities do not completely satisfy the three available sets of NOE distance bounds for EpoA, molecular dynamics (MD) simulations have been employed to obtain conformational ensembles in aqueous and in DMSO solution that are compatible with the respective NOE data. It was found that EpoA displays a larger conformational variability in DMSO than in water and the two conformational ensembles show little overlap. Yet, they both provide conformational scaffolds that are energetically accessible at physiological temperature and pressure.
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Affiliation(s)
- Jožica Dolenc
- Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institut , CH-5232 Villigen , Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry , Swiss Federal Institute of Technology, ETH , CH-8093 Zurich , Switzerland
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institut , CH-5232 Villigen , Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institut , CH-5232 Villigen , Switzerland.,University of Basel, Biozentrum , CH-4056 Basel , Switzerland
| | - John H Missimer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institut , CH-5232 Villigen , Switzerland
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2
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Woods LM, Arico JW, Frein JD, Sackett DL, Taylor RE. Synthesis and Biological Evaluation of 7-Deoxy-Epothilone Analogues. Int J Mol Sci 2017; 18:E648. [PMID: 28304361 PMCID: PMC5372660 DOI: 10.3390/ijms18030648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/22/2017] [Indexed: 01/27/2023] Open
Abstract
The synthesis of two deoxygenated analogues of potent epothilones is reported in an effort to analyze the relative importance of molecular conformation and ligand-target interactions to biological activity. 7-deoxy-epothilone D and 7-deoxy-(S)-14-methoxy-epothilone D were prepared through total synthesis and shown to maintain the conformational preferences of their biologically active parent congeners through computer modeling and nuclear magnetic resonance (NMR) studies. The significant decrease in observed potency for each compound suggests that a hydrogen bond between the C7-hydroxyl group and the tubulin binding site plays a critical role in the energetics of binding in the epothilone class of polyketides.
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Affiliation(s)
- Laura M Woods
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Joseph W Arico
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey D Frein
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Richard E Taylor
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
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3
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Jiménez VA, Alderete JB, Navarrete KR. Structural insight into epothilones antitumor activity based on the conformational preferences and tubulin binding modes of epothilones A and B obtained from molecular dynamics simulations. J Biomol Struct Dyn 2014; 33:789-803. [DOI: 10.1080/07391102.2014.911702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Verónica A. Jiménez
- Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Universidad Andres Bello Sede Concepción, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Joel B. Alderete
- Facultad de Ciencias Químicas, Departamento de Química Orgánica, Universidad de Concepción, Concepcion, Chile
| | - Karen R. Navarrete
- Facultad de Ciencias Químicas, Departamento de Química Orgánica, Universidad de Concepción, Concepcion, Chile
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4
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Canales A, Nieto L, Rodríguez-Salarichs J, Sánchez-Murcia PA, Coderch C, Cortés-Cabrera A, Paterson I, Carlomagno T, Gago F, Andreu JM, Altmann KH, Jiménez-Barbero J, Díaz JF. Molecular recognition of epothilones by microtubules and tubulin dimers revealed by biochemical and NMR approaches. ACS Chem Biol 2014; 9:1033-43. [PMID: 24524625 DOI: 10.1021/cb400673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding of epothilones to dimeric tubulin and to microtubules has been studied by means of biochemical and NMR techniques. We have determined the binding constants of epothilone A (EpoA) and B (EpoB) to dimeric tubulin, which are 4 orders of magnitude lower than those for microtubules, and we have elucidated the conformation and binding epitopes of EpoA and EpoB when bound to tubulin dimers and microtubules in solution. The determined conformation of epothilones when bound to dimeric tubulin is similar to that found by X-ray crystallographic techniques for the binding of EpoA to the Tubulin/RB3/TTL complex; it is markedly different from that reported for EpoA bound to zinc-induced sheets obtained by electron crystallography. Likewise, only the X-ray structure of EpoA bound to the Tubulin/RB3/TTL complex at the luminal site, but not the electron crystallography structure, is compatible with the results obtained by STD on the binding epitope of EpoA bound to dimeric tubulin, thus confirming that the allosteric change (structuring of the M-loop) is the biochemical mechanism of induction of tubulin assembly by epothilones. TR-NOESY signals of EpoA bound to microtubules have been obtained, supporting the interaction with a transient binding site with a fast exchange rate (pore site), consistent with the notion that epothilones access the luminal site through the pore site, as has also been observed for taxanes. Finally, the differences in the tubulin binding affinities of a series of epothilone analogues has been quantitatively explained using the newly determined binding pose and the COMBINE methodology.
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Affiliation(s)
- Angeles Canales
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Dep.
Química Orgánica I, Fac. C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, 28040 Madrid, Spain
| | - Lidia Nieto
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Javier Rodríguez-Salarichs
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de
Estudios
Avanzados de Cuba, Carretera San Antonio
km 1 1/2, Valle Grande, La Lisa, Ciudad Habana CP 17100, Cuba
| | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Claire Coderch
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Alvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Ian Paterson
- University
Chemical Laboratory, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Teresa Carlomagno
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - José M. Andreu
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H405, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Fernando Díaz
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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5
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Sang F, Feng P, Chen J, Ding Y, Duan X, Zhai J, Ma X, Zhang B, Zhang Q, Lin J, Chen Y. Epothilone D and its 9-Methyl analogues: combinatorial syntheses, conformation, and biological activities. Eur J Med Chem 2013; 68:321-32. [PMID: 23994325 DOI: 10.1016/j.ejmech.2013.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/25/2013] [Accepted: 08/02/2013] [Indexed: 01/10/2023]
Abstract
Epothilone D (Epo D) and its 9-Methyl conformational analogues were synthesized through a highly efficient combinatorial approach. The fragment E was synthesized in 11 total steps with 6 longest linear steps, and each aldehyde B was prepared via a 3-step sequence. Starting from the common precursor E and a suitable aldehydes B, each target molecule were obtained in only 4 steps. The 9-(S)-epo D and 9-(R)-epo D demonstrated significant difference in inhibition activities against cancer cell lines and in conformational analysis.
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Affiliation(s)
- Feng Sang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, PR China
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6
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Díaz JF, Andreu JM, Jiménez-Barbero J. The interaction of microtubules with stabilizers characterized at biochemical and structural levels. Top Curr Chem (Cham) 2013; 286:121-49. [PMID: 23563612 DOI: 10.1007/128_2008_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Since the discovery of paclitaxel and its peculiar mechanism of cytotoxicity, which has made it and its analogues widely used antitumour drugs, great effort has been made to understand the way they produce their effect in microtubules and to find other products that share this effect without the undesired side effects of low solubility and development of multidrug resistance by tumour cells. This chapter reviews the actual knowledge about the biochemical and structural mechanisms of microtubule stabilization by microtubule stabilizing agents, and illustrates the way paclitaxel and its biomimetics induce microtubule assembly, the thermodynamics of their binding, the way they reach their binding site and the conformation they have when bound.
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Affiliation(s)
- J F Díaz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain,
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7
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Skjærven L, Codutti L, Angelini A, Grimaldi M, Latek D, Monecke P, Dreyer MK, Carlomagno T. Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring. J Am Chem Soc 2013; 135:5819-27. [DOI: 10.1021/ja4007468] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lars Skjærven
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Luca Codutti
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Andrea Angelini
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Manuela Grimaldi
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
- Department of Biomedical and
Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo 8, 84024 Fisciano (SA), Italy
| | - Dorota Latek
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Peter Monecke
- Sanofi-Aventis Deutschland GmbH R&D LGCR/Structure, Design & Informatics, Industriepark Höchst, Bldg. G838, D-65926 Frankfurt am Main, Germany
| | - Matthias K. Dreyer
- Sanofi-Aventis Deutschland GmbH R&D LGCR/Structure, Design & Informatics, Industriepark Höchst, Bldg. G838, D-65926 Frankfurt am Main, Germany
| | - Teresa Carlomagno
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
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8
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Shi G, Wang Y, Jin Y, Chi S, Shi Q, Ge M, Wang S, Zhang X, Xu S. Structural insight into the mechanism of epothilone A bound to beta-tubulin and its mutants at Arg282Gln and Thr274Ile. J Biomol Struct Dyn 2012; 30:559-73. [DOI: 10.1080/07391102.2012.687522] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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9
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Field JJ, Pera B, Calvo E, Canales A, Zurwerra D, Trigili C, Rodríguez-Salarichs J, Matesanz R, Kanakkanthara A, Wakefield SJ, Singh AJ, Jiménez-Barbero J, Northcote P, Miller JH, López JA, Hamel E, Barasoain I, Altmann KH, Díaz JF. Zampanolide, a potent new microtubule-stabilizing agent, covalently reacts with the taxane luminal site in tubulin α,β-heterodimers and microtubules. CHEMISTRY & BIOLOGY 2012; 19:686-98. [PMID: 22726683 PMCID: PMC3383615 DOI: 10.1016/j.chembiol.2012.05.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 04/26/2012] [Accepted: 05/03/2012] [Indexed: 01/07/2023]
Abstract
Zampanolide and its less active analog dactylolide compete with paclitaxel for binding to microtubules and represent a new class of microtubule-stabilizing agent (MSA). Mass spectrometry demonstrated that the mechanism of action of both compounds involved covalent binding to β-tubulin at residues N228 and H229 in the taxane site of the microtubule. Alkylation of N228 and H229 was also detected in α,β-tubulin dimers. However, unlike cyclostreptin, the other known MSA that alkylates β-tubulin, zampanolide was a strong MSA. Modeling the structure of the adducts, using the NMR-derived dactylolide conformation, indicated that the stabilizing activity of zampanolide is likely due to interactions with the M-loop. Our results strongly support the existence of the luminal taxane site of microtubules in tubulin dimers and suggest that microtubule nucleation induction by MSAs may proceed through an allosteric mechanism.
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Affiliation(s)
- Jessica J. Field
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Benet Pera
- Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Enrique Calvo
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Angeles Canales
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avda Complutense s/n 28040 Madrid, Spain
| | - Didier Zurwerra
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H405, Zürich, Switzerland
| | - Chiara Trigili
- Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Javier Rodríguez-Salarichs
- Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
- Centro de Estudios Avanzados de Cuba. Ciudad Habana, CP. 17100. Cuba
| | - Ruth Matesanz
- Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Arun Kanakkanthara
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - St. John Wakefield
- Department of Pathology, Wellington School of Medicine and Health Sciences, Wellington, New Zealand
| | - A. Jonathan Singh
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Peter Northcote
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - John H. Miller
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Juan Antonio López
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Ernest Hamel
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
| | | | - Karl-Heinz Altmann
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H405, Zürich, Switzerland
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10
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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11
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Orts J, Bartoschek S, Griesinger C, Monecke P, Carlomagno T. An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude. JOURNAL OF BIOMOLECULAR NMR 2012; 52:23-30. [PMID: 22167466 PMCID: PMC3266494 DOI: 10.1007/s10858-011-9590-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/25/2011] [Indexed: 05/31/2023]
Abstract
Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns.
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Affiliation(s)
- Julien Orts
- EMBL, Structure and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stefan Bartoschek
- Sanofi-Aventis Deutschland GmbH, R&D LGCR/Parallel Synthesis & Natural Products, Industriepark Hoechst, Bldg. H811, 65926 Frankfurt am Main, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Peter Monecke
- Sanofi-Aventis Deutschland GmbH, R&D LGCR/Structure, Design & Informatics, Industriepark Hoechst, Bldg. G838, 65926 Frankfurt am Main, Germany
| | - Teresa Carlomagno
- EMBL, Structure and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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12
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Dervillez X, Klaukien V, Dürr R, Koch J, Kreutz A, Haarmann T, Stoll M, Lee D, Carlomagno T, Schnierle B, Möbius K, Königs C, Griesinger C, Dietrich U. Peptide ligands selected with CD4-induced epitopes on native dualtropic HIV-1 envelope proteins mimic extracellular coreceptor domains and bind to HIV-1 gp120 independently of coreceptor usage. J Virol 2010; 84:10131-8. [PMID: 20660187 PMCID: PMC2937783 DOI: 10.1128/jvi.00165-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 07/07/2010] [Indexed: 11/20/2022] Open
Abstract
During HIV-1 entry, binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor triggers conformational changes resulting in exposure of new epitopes, the highly conserved CD4-induced (CD4i) epitopes that are essential for subsequent binding to chemokine receptor CCR5 or CXCR4. Due to their functional conservation, CD4i epitopes represent attractive viral targets for HIV-1 entry inhibition. The aim of the present study was to select peptide ligands for CD4i epitopes on native dualtropic (R5X4) HIV-1 envelope (Env) glycoproteins by phage display. Using CD4-activated retroviral particles carrying Env from the R5X4 HIV-1 89.6 strain as the target, we performed screenings of random peptide phage libraries under stringent selection conditions. Selected peptides showed partial identity with amino acids in the extracellular domains of CCR5/CXCR4, including motifs rich in tyrosines and aspartates at the N terminus known to be important for gp120 binding. A synthetic peptide derivative (XD3) corresponding to the most frequently selected phages was optimized for Env binding on peptide arrays. Interestingly, the optimized peptide could bind specifically to gp120 derived from HIV-1 strains with different coreceptor usage, competed with binding of CD4i-specific monoclonal antibody (MAb) 17b, and interfered with entry of both a CCR5 (R5)-tropic and a CXCR4 (X4)-tropic Env pseudotyped virus. This peptide ligand therefore points at unique properties of CD4i epitopes shared by gp120 with different coreceptor usage and could thus serve to provide new insight into the conserved structural details essential for coreceptor binding for further drug development.
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Affiliation(s)
- Xavier Dervillez
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Volker Klaukien
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Ralf Dürr
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Joachim Koch
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Alexandra Kreutz
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Thomas Haarmann
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Michaela Stoll
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Donghan Lee
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Teresa Carlomagno
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Barbara Schnierle
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Kalle Möbius
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Christoph Königs
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Christian Griesinger
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany, Department of Pharmaceutical Chemistry, University of Erlangen-Nuremberg, Germany
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13
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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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14
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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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15
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Mizukoshi Y, Nagasu M, Shimada I, Takahashi H. Precise structural determination of weakly binding peptides by utilizing dihedral angle constraints. JOURNAL OF BIOMOLECULAR NMR 2010; 46:299-305. [PMID: 20229289 DOI: 10.1007/s10858-010-9402-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/24/2010] [Indexed: 05/28/2023]
Abstract
Structural determination of target-bound conformations of peptides is of primary importance for the optimization of peptide ligands and peptide-mimetic design. In the structural determination of weakly binding ligands, transferred nuclear Overhauser effect (TrNOE) methods have been widely used. However, not many distance constraints can be obtained from small peptide ligands by TrNOE, especially for peptides bound to a target molecule in an extended conformation. Therefore, for precise structural determination of weakly binding peptides, additional structural constraints are required. Here, we present a strategy to systematically introduce dihedral angle constraints obtained from multiple transferred cross-correlated relaxation experiments and demonstrate precise structures of weakly binding peptides. As a result, we could determine the bioactive conformations of phage-derived peptide ligands and define their core binding motifs.
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Affiliation(s)
- Yumiko Mizukoshi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-41-6, Koto-ku, Tokyo, 135-0064, Japan
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16
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Chen QH, Ganesh T, Jiang Y, Banerjee A, Sharma S, Bane S, Snyder JP, Kingston DGI. Novel epothilone lactones by an unusual diversion of the Grubbs' metathesis reaction. Chem Commun (Camb) 2010; 46:2019-21. [PMID: 20221478 DOI: 10.1039/b926174e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unusual reaction with Grubbs' catalyst during the synthesis of bridged epothilones yielded five-membered internal lactones instead of the expected metathesis products. Three of the lactones have activities comparable to epothilone D.
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Affiliation(s)
- Qiao-Hong Chen
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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17
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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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Affiliation(s)
- Julien Orts
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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18
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Rusinska-Roszak D, Lozynski M. De(side chain) model of epothilone: bioconformer interconversions DFT study. J Mol Model 2009; 15:859-69. [PMID: 19153781 DOI: 10.1007/s00894-008-0428-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 11/17/2008] [Indexed: 10/21/2022]
Abstract
Using ab initio methods, we have studied conformations of the de(sidechain)de(dioxy)difluoroepothilone model to quantify the effect of stability change between the exo and endo conformers of the epoxy ring. The DFT minimization of the macrolactone ring reveals four low energy conformers, although MP2 predicted five stable structures. The model tested with DFT hybride functional (B3LYP/6-31+G(d,p)) exhibits the global minimum for one of the exo forms (C), experimentally observed in the solid state, but unexpectedly with the MP2 electron correlation method for the virtual endo form (W). Using the QST3 technique, several pathways were found for the conversion of the low energy conformers to the other low energy exo representatives, as well as within the endo analog subset. The potential energy relationships obtained for several exo forms suggest a high conformational mobility between three, experimentally observed, conformers. The high rotational barrier, however, excludes direct equilibrium with experimental EC-derived endo form S. The highest calculated transition state for the conversion of the most stable exo M interligand to the endo S form is approximately a 28 kcal/mol above the energy of the former. The two-step interconversion of the exo H conformer to the endo S requires at least 28 kcal/mol. Surprisingly, we found that the transition state energy of the H form to the virtual endo W has the acceptable value of about 9 kcal/mol and the next energy barrier for free interconversion of endo W to endo S is 13 kcal/mol.
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Affiliation(s)
- Danuta Rusinska-Roszak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Pl. M. Sklodowskiej-Curie 2, 60-965 Poznan, Poland
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19
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Chen QH, Ganesh T, Brodie P, Slebodnick C, Jiang Y, Banerjee A, Bane S, Snyder JP, Kingston DGI. Design, synthesis and biological evaluation of bridged epothilone D analogues. Org Biomol Chem 2008; 6:4542-52. [PMID: 19039362 PMCID: PMC2790820 DOI: 10.1039/b814823f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Six epothilone D analogues with a bridge between the C4-methyl and the C12-methyl carbons were prepared in an attempt to constrain epothilone D to its proposed tubulin-binding conformation. Ring-closing metathesis (RCM) was employed as the key step to build the C4-C26 bridge. In antiproliferative assays in the human ovarian cancer (A2780) and prostate cancer (PC3) cell lines, and also in tubulin assembly assay, all these compounds proved to be less active than epothilone D.
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Affiliation(s)
- Qiao-Hong Chen
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
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20
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The Tubulin Binding Mode of MT Stabilizing and Destabilizing Agents Studied by NMR. Top Curr Chem (Cham) 2008; 286:151-208. [DOI: 10.1007/128_2008_22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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21
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Luy B, Frank A, Kessler H. Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9783527621286.ch9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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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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Affiliation(s)
- Máté Erdélyi
- Max-Planck-Institute for Biophysical Chemistry, NMR-Based Structural Biology, Am Fassberg 11, D-37077 Göttingen, Germany
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23
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NMR-Based Strategies to Elucidate Bioactive Conformations of Weakly Binding Ligands. Top Curr Chem (Cham) 2008. [PMID: 23605457 DOI: 10.1007/128_2007_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Key processes in molecular biology are regulated by interactions between biomolecules. Protein-proteinand protein-ligand interactions, e.g., in signal transduction pathways, rely on the subtle interactionsbetween atoms at the binding interface of the involved molecules. Because biomolecules often havemany interacting partners, these interactions are not necessarily strong. The study of molecularrecognition gives insight into the complex network of signaling in life and is the basis of structure-baseddrug design.In the situation where the interaction is weak, one of the traditional methods that can be appliedto obtain structural information (internuclear distances) of the bound ligand is the so-called transferredNOE (trNOE) method. Recently, it became possible to use transferred cross-correlated relaxation (trCCR)to directly measure dihedral angles. The combined use of these two techniques significantly improvesthe precision of the structure determination of ligands weakly bound to macromolecules.The application of these techniques will be discussed in detail for a peptide derived fromIKKβ bound to the protein NEMO that plays an important rolein the NFκB pathway.
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24
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Jiménez-Barbero J, Canales A, Northcote PT, Buey RM, Andreu JM, Díaz JF. NMR determination of the bioactive conformation of peloruside A bound to microtubules. J Am Chem Soc 2007; 128:8757-65. [PMID: 16819869 DOI: 10.1021/ja0580237] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here on the determination of the conformation of Peloruside A bound to biochemically stabilized microtubules, by using TR-NOESY NMR experiments. As a previous step, the conformation of the free molecule in water solution has also been deduced. Despite the large size of the ring, Peloruside A mainly adopts two conformations in water solution. A conformational selection process takes place, and the microtubules-bound conformer is one of those present in the water solution, different than that existing in chloroform medium. A model of the binding mode to tubulin has also been proposed, by docking the bioactive conformation of peloruside, which involves the alpha-tubulin monomer, in contrast with taxol, which binds to the beta-monomer.
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Affiliation(s)
- Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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25
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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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26
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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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27
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Takahashi H, Shimada I. Pairwise NMR experiments for the determination of protein backbone dihedral angle Phi based on cross-correlated spin relaxation. JOURNAL OF BIOMOLECULAR NMR 2007; 37:179-85. [PMID: 17237977 DOI: 10.1007/s10858-006-9108-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 10/05/2006] [Accepted: 10/16/2006] [Indexed: 05/13/2023]
Abstract
Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Phi. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond JNCalpha coupling evolution and generate the N(i)-Calpha(i) or C'(i-1)-Calpha(i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15N- and 13C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Phi angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Psi, we can determine high resolution structures of peptides that bind weakly to large target molecules.
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Affiliation(s)
- Hideo Takahashi
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi 2-41-6, Koto-ku, Tokyo, 135-0064, Japan.
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28
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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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29
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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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30
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Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules. Z PHYS CHEM 2006. [DOI: 10.1524/zpch.2006.220.5.567] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Bold G, Wojeik S, Caravatti G, Lindauer R, Stierlin C, Gertsch J, Wartmann M, Altmann KH. Structure-Activity Relationships in Side-Chain-Modified Epothilone Analogues—How Important is the Position of the Nitrogen Atom? ChemMedChem 2006; 1:37-40. [PMID: 16892331 DOI: 10.1002/cmdc.200500051] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guido Bold
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, Basel, Switzerland
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32
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Abstract
The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.
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Affiliation(s)
- Teresa Carlomagno
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology, Am Fassberg, 11-D 37077 Göttingen, Germany.
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33
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Pineda O, Farràs J, Maccari L, Manetti F, Botta M, Vilarrasa J. Computational comparison of microtubule-stabilising agents laulimalide and peloruside with taxol and colchicine. Bioorg Med Chem Lett 2005; 14:4825-9. [PMID: 15341932 DOI: 10.1016/j.bmcl.2004.07.053] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 07/05/2004] [Accepted: 07/23/2004] [Indexed: 10/26/2022]
Abstract
Microtubule-stabilising agents laulimalide and peloruside have been compared with tubulin-interacting drugs paclitaxel and colchicine by different computational approaches. Docking and QSAR-based programs point to a favourable interaction with the beta tubulin paclitaxel binding site, although an additional, preferred binding site has been found at the alpha subunit of tubulin. All together provides a plausible rationalisation of the singular binding features of these microtubule stabilisers and paves the way for future structural studies.
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Affiliation(s)
- Oriol Pineda
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, EU
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