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Fang WS, Wang SR. Structural studies of taxol analogues for drug discovery. Expert Opin Drug Discov 2008; 3:1109-22. [DOI: 10.1517/17460441.3.9.1109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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52
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Entwistle RA, Winefield RD, Foland TB, Lushington GH, Himes RH. The paclitaxel site in tubulin probed by site-directed mutagenesis of Saccharomyces cerevisiae beta-tubulin. FEBS Lett 2008; 582:2467-70. [PMID: 18570892 DOI: 10.1016/j.febslet.2008.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 06/02/2008] [Indexed: 11/26/2022]
Abstract
Previously, we created a paclitaxel-sensitive strain of Saccharomyces cerevisiae by mutating five amino acid residues in beta-tubulin in a strain that has a decreased level of the ABC multidrug transporters. We have used site-directed mutagenesis to examine the relative importance of the five residues in determining sensitivity of this strain to paclitaxel. We found that the change at position 19 from K (brain beta-tubulin) to A (yeast beta-tubulin) and at position 227 from H (brain beta-tubulin) to N (yeast beta-tubulin) had no effect on the activity of paclitaxel. On the other hand, the changes V23T, D26G and F270Y, drastically reduced sensitivity of AD1-8-tax to paclitaxel. Molecular modeling and computational studies were used to explain the results.
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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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Abstract
Dipolar recoupling techniques in solid-state nuclear magnetic resonance (NMR) consist of radio frequency (rf) pulse sequences applied in synchrony with magic-angle spinning (MAS) that create nonzero average magnetic dipole-dipole couplings under MAS. Stochastic dipolar recoupling (SDR) is a variant in which randomly chosen rf carrier frequency offsets are introduced to cause random phase modulations of individual pairwise couplings in the dipolar spin Hamiltonian. Several aspects of SDR are investigated through analytical theory and numerical simulations: (1) An analytical expression for the evolution of nuclear spin polarization under SDR in a two-spin system is derived and verified through simulations, which show a continuous evolution from coherent, oscillatory polarization exchange to incoherent, exponential approach to equilibrium as the range of random carrier offsets (controlled by a parameter f(max)) increases; (2) in a many-spin system, polarization transfers under SDR are shown to be described accurately by a rate matrix in the limit of large f(max), with pairwise transfer rates that are proportional to the inverse sixth power of pairwise internuclear distances; (3) quantum mechanical interferences among noncommuting pairwise dipole-dipole couplings, which are a complicating factor in solid-state NMR studies of molecular structures by traditional dipolar recoupling methods, are shown to be absent from SDR data in the limit of large f(max), provided that coupled nuclei have distinct NMR chemical shifts.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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Abstract
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Recent research on the chemistry of natural products from the author’s group that led to the receipt of the ACS Ernest Guenther Award in the Chemistry of Natural Products is reviewed. REDOR NMR and synthetic studies established the T-taxol conformation as the bioactive tubulin-binding conformation, and these results were confirmed by the synthesis of compounds which clearly owed their activity or lack of activity to whether or not they could adopt the T-taxol conformation. Similar studies with the epothilones suggest that the current tubulin-binding model needs to be modified. Examples of natural products discovery and biodiversity conservation in Suriname and Madagascar are also presented, and it is concluded that natural products chemistry will continue to make significant contributions to drug discovery.
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Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA.
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Yang J, Paramasivam S, Marulanda D, Cataldi M, Tasayco ML, Polenova T. Magic angle spinning NMR spectroscopy of thioredoxin reassemblies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S73-S83. [PMID: 18157811 DOI: 10.1002/mrc.2092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Differentially isotopically enriched 1-73((13)C,(15)N)/74-108((15)N) and 1-73((15)N)/74-108((13)C,(15)N) Escherichia coli thioredoxin reassemblies prepared by fragment complementation were investigated by high-resolution magic angle spinning solid-state NMR spectroscopy. Nearly complete resonance assignments, secondary and tertiary structure analysis are reported for 1-73((13)C,(15)N)/74-108((15)N) reassembled thioredoxin. Temperature dependence of the dipolar-assisted rotational resonance (DARR) spectra reveals the residues undergoing intermediate timescale motions at temperatures below - 15 degrees C. Analysis of the DARR intensity buildups as a function of mixing time in these reassemblies indicates that at long mixing times medium- and long-range cross-peaks do not experience dipolar truncation, suggesting that isotopic dilution is not required for gaining nontrivial distance restraints for structure calculations.
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Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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56
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Chen L, Kaiser JM, Lai J, Polenova T, Yang J, Rienstra CM, Mueller LJ. J-based 2D homonuclear and heteronuclear correlation in solid-state proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S84-S92. [PMID: 18157839 DOI: 10.1002/mrc.2107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.
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Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
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57
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Huang W, Vega AJ, Gullion T, Polenova T. Internuclear (31)P-(51)V distance measurements in polyoxoanionic solids using rotational echo adiabatic passage double resonance NMR spectroscopy. J Am Chem Soc 2007; 129:13027-34. [PMID: 17918932 PMCID: PMC3985602 DOI: 10.1021/ja073170l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first results establishing rotational echo adiabatic passage double resonance (REAPDOR) experiments for distance measurements between a spin-1/2 (31P) and spin-7/2 (51V) pair in a series of vanadium-substituted polyoxoanionic solids from the Keggin and Wells-Dawson families. We have quantitatively measured 31P-51V distances in monovanadium substituted K4PVW11O40, 1-K7P2VW17O62, and 4-K7P2VW17O62. Numerical simulations of the experimental data yield very good agreement with the averaged P-W/P-V distances determined from the X-ray diffraction measurements in the same or related compounds. REAPDOR is therefore a very sensitive P-V distance probe anticipated to be especially useful in the absence of long-range order. Our results suggest that REAPDOR spectroscopy could be broadly applicable for interatomic distance measurements in other spin-7/2-spin-1/2 nuclear pairs.
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Affiliation(s)
- Wenlin Huang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Alexander J. Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
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58
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Kingston DGI. The shape of things to come: structural and synthetic studies of taxol and related compounds. PHYTOCHEMISTRY 2007; 68:1844-54. [PMID: 17184797 PMCID: PMC1979092 DOI: 10.1016/j.phytochem.2006.11.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/24/2006] [Accepted: 11/01/2006] [Indexed: 05/13/2023]
Abstract
The history of the development of Taxol (paclitaxel) as an anticancer drug is reviewed, and some aspects of the phytochemistry of Taxus species and of the medicinal chemistry of taxol are discussed. The nature of the taxol-tubulin interaction is then described, with an emphasis on studies that led to the discovery and experimental proof of the T-taxol conformation as the tubulin-binding conformation of taxol. The implications of this conformation for future drug development are also briefly covered.
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Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA.
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59
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Thepchatri P, Eliseo T, Cicero DO, Myles D, Snyder JP. Relationship among ligand conformations in solution, in the solid state, and at the Hsp90 binding site: geldanamycin and radicicol. J Am Chem Soc 2007; 129:3127-34. [PMID: 17323946 DOI: 10.1021/ja064863p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unknown effects of a receptor's environment on a ligand's conformation presents a difficult challenge in predicting feasible bioactive conformations, particularly if the receptor is ill-defined. The primary hypothesis of this work is that a structure's conformational ensemble in solution presents viable candidates for protein binding. The experimental solution profile can be achieved with the NAMFIS (NMR analysis of molecular flexibility in solution) method, which deconvolutes the average NMR spectrum of small flexible molecules into individual contributing conformations with varying populations. Geldanamycin and radicicol are structurally different macrocycles determined by X-ray crystallography to bind to a common site on the cellular chaperone heat shock protein 90 (Hsp90). Without benefit of a receptor structure, NAMFIS has identified the bioactive conformers of geldanamycin and radicicol in CDCl3 solution with populations of 4% and 21%, respectively. Conversely, docking the set of NAMFIS conformers into the unliganded proteins with GLIDE followed by MM-GBSA scoring reproduces the experimental crystallographic binding poses.
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Affiliation(s)
- Pahk Thepchatri
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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60
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Ganesh T, Yang C, Norris A, Glass T, Bane S, Ravindra R, Banerjee A, Metaferia B, Thomas SL, Giannakakou P, Alcaraz AA, Lakdawala AS, Snyder JP, Kingston DGI. Evaluation of the tubulin-bound paclitaxel conformation: synthesis, biology, and SAR studies of C-4 to C-3' bridged paclitaxel analogues. J Med Chem 2007; 50:713-25. [PMID: 17263521 PMCID: PMC2585518 DOI: 10.1021/jm061071x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The important anticancer drug paclitaxel binds to the beta-subunit of the alphabeta-tubulin dimer in the microtubule in a stoichiometric ratio, promoting microtubule polymerization and stability. The conformation of microtubule-bound drug has been the subject of intense study, and various suggestions have been proposed. In previous work we presented experimental and theoretical evidence that paclitaxel adopts a T-shaped conformation when it is bound to tubulin. In this study we report additional experimental data and calculations that delineate the allowable parameters for effective paclitaxel-tubulin interactions.
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Affiliation(s)
- Thota Ganesh
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Chao Yang
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Andrew Norris
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Tom Glass
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Susan Bane
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
| | - Rudravajhala Ravindra
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
| | - Abhijit Banerjee
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
| | - Belhu Metaferia
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Shala L. Thomas
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Ana A. Alcaraz
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - James P. Snyder
- Department of Chemistry, Emory University, Atlanta, GA 30322
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
| | - David G. I. Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
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