Use of the Tubulin Bound Paclitaxel Conformation for Structure-Based Rational Drug Design

Geney, Raphaël; Sun, Liang; Pera, Paula; Bernacki, Ralph J.; Xia, Shujun; Horwitz, Susan Band; Simmerling, Carlos; Ojima, Iwao

doi:10.1016/j.chembiol.2005.01.004

Cited by 73 publications

(128 citation statements)

References 51 publications

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“…33 It is no coincidence that virtually every recent synthetic program attempting to prepare more potent and less resistant taxanes based on biostructural principles has employed the EC structure. 18,20,29,37 Furthermore, the tubulin dimer structure derived from Zn +2 -stabilized sheets has been modeled into the 8 Å resolution microtubule structure determined by cryoelectron microscopy 38 and shown to be entirely consistent with the MT structure. Finally, as we have pointed out previously, 17,20,29 not only is the REDOR geometry derived from lyophilized MTs coincident with the T-Taxol form (Table 2), but bioactivities in situations where MTs are present as soluble dynamic entities can be significantly improved by exploiting the EC structure and bound ligand from stabilized tubulin sheets.…”

Section: Conclusion and Prospectsmentioning

confidence: 99%

Rotational-Echo Double-Resonance NMR Distance Measurements for the Tubulin-Bound Paclitaxel Conformation

et al. 2006

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The important anticancer drug Taxol ® (paclitaxel, PTX) owes its unique activity to its ability to bind to tubulin in a stoichiometric ratio and promote its assembly into microtubules. The conformation of the microtubule-bound drug has been the focus of numerous research efforts, since the inability of polymerized tubulin to form crystals precludes structure proof by X-ray crystallography. Likewise, although the αβ-tubulin dimer structure has been solved by electron crystallography, the 3.7 Å resolution is too low to permit direct determination of either ligand conformation or binding pose. In this study we present experimental results from 2 H{ 19 F} REDOR NMR that provide direct confirmation that paclitaxel adopts a T-shaped conformation when it is bound to tubulin.

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Section: Conclusion and Prospectsmentioning

confidence: 99%

Rotational-Echo Double-Resonance NMR Distance Measurements for the Tubulin-Bound Paclitaxel Conformation

et al. 2006

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“…Following these developments, a T-like conformer with a reorganized C-13 side chain (PTX-NY) was proposed as an alternative binding model. 29,30 However, this conformer is inconsistent with the EC density. 31,32…”

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confidence: 93%

Bridging Converts a Noncytotoxic nor-Paclitaxel Derivative to a Cytotoxic Analogue by Constraining It to the T-Taxol Conformation

et al. 2006

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The synthesis of the bridged A-nor-paclitaxel 4 has been achieved from paclitaxel in a key test of the T-Taxol conformational hypothesis. Although the unbridged A-nor-paclitaxel 3 is essentially non-cytotoxic, the bridged analog 4 is strongly cytotoxic. This result provides strong evidence for the T-Taxol conformation as the bioactive tubulin-binding conformation of paclitaxel.The natural product paclitaxel (PTX) (Taxol™, 1) is a clinically approved drug for several tumor malignancies, 1 and its chemistry and biology have been investigated extensively. 2 It acts by promoting the polymerization of tubulin to stabilized microtubules, leading to apoptotic cell death, 3-456 and its clinical activity is believed to be directly related to this microtubulebinding activity. 6Since the bioactivity of PTX is intimately connected with its tubulin-assembly properties, and since tubulin assembly is initiated by the non-covalent binding of paclitaxel to tubulin, the nature of this binding is a matter of great interest. In one scenario, a knowledge of the tubulinbinding conformation of paclitaxel would enable the design of simple non-taxoid compounds with comparable binding affinity and bioactivity.DKingston@vt.edu. Supporting Information Available Detailed synthetic procedures for the synthesis of the bridged A-nor-paclitaxel 4 and A-nor-baccatin III 5, 1 H and 13 C NMR spectra of compound 4, tubulin-GTP polymerization by compound 3, tubulin binding curves for 1, 3, and 4, and conformational searching, conformer extraction and binding site docking for 3 and 4. This material is available free of charge via the internet at http://pubs.acs.org. Although the taxane ring system of paclitaxel is relatively rigid, the compound has flexible side chains at C2, C4, C10, and notably at C13. As a result, there are many possible conformations available for binding to tubulin. Two different paclitaxel models of the tubulinbinding conformation were proposed based on NMR observables and molecular modeling. A "nonpolar" conformation was put forth on the basis of solution NMR investigations in nonpolar solvents, 7-9 while similar studies in polar solvents were interpreted to favor a bound "polar" conformation. 10 -Although most of the reports assumed a single conformation, deconvolution of PTX in CDCl 3 14 and D 2 O/DMSO-d 6 15 makes it clear that the molecule adopts 9-10 conformations, no one of which achieves a population above 30%. NIH Public AccessA second approach focused on tubulin-bound paclitaxel in the solid state. Application of REDOR NMR provided F-13 C distances of 9.8 and 10.3 Å between the fluorine of a 2-(pfluorobenzoyl)PTX and the C3′ amide carbonyl and C3′ methine carbons, respectively. 16 A related examination reported a distance of 6.5 Å between the fluorines of 2-(pfluorobenzoyl)-3′-(p-fluorophenyl)-10-acetyldocetaxel; and, like the first solid state study, proposed the polar form to be tubulin-bound. 17,18,19The "polar" and "nonpolar" conformations have inspired several elegant synthetic studies designed to generat...

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“…Tubulin is the major constituent of microtubuli, which facilitate chromosome disjunction during mitosis, and therefore, the affect of tubulin structures is incompatible with functional cell division (19). Hence, it is important to determine whether cytotoxicity can be attributed to tubulin polymerisation as is the case for taxol (20). Alterations in the fine tuned balance of microtubuli polymerisation/de-polymerisation as by taxol were reported to correlate with an increase in the acetylation ONCOLOGY REPORTS 22: 845-852, 2009 level of ·-tubulin (21).…”

Section: Induction Of Caspase-3 and Apoptosis By Extracts Of Hmentioning

confidence: 99%

In vitro anti-neoplastic activity of the ethno-pharmaceutical plant Hypericum adenotrichum Spach endemic to Western Turkey

Özmen

Bauer²,

Gridling³

et al. 2009

Oncol Rep

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Abstract. Hypericum perforatum (St. John's wort) is wellestablished for its antidepressant activity throughout the world and also various other species within this genus are used in different folk medicines. Hyperforin of St. John's wort inhibited growth of cancer cell lines and the use of hypericin (another compound of H. perforatum) in cancer photodynamic therapy is proposed. Therefore, we investigated the anti-cancer properties of H. adenotrichum Spach (Guttiferae), an endemic species in Turkey called 'kantaron', which is used for wound healing and antiseptic effects. Freeze-dried plant was extracted with petroleum ether, dichloromethane, ethyl acetate, and methanol and the bioactivity of these extracts was analysed by proliferation assay, cell death determination, by investigating protein expression profiles specific for cell cycle arrest and apoptosis as well as composition by HPLC. The strongest anti-proliferative activity was determined for the petroleum ether extract with an I p C 50 of ~5.8 μg/ml medium (referring to 1 mg dried plant) which correlated with cyclin D1 suppression and p21 induction. This extract also induced phosphorylation of H2AX, and activated caspase-3 followed by signature-type cleavage of PARP resulting in ~50% apoptosis at 23.2 μg/ml after 24 h of treatment. Neither hyperforin, hypericin, or amentoflavone contributed to these properties. To the best of our knowledge, we report for the first time that the endemic plant H. adenotrichum Spach exhibits potent p53-independent anti-neoplastic properties due to yet unexplored Hypericum constituents. IntroductionSome 60% of all drugs used in Western medicine are derived from natural compounds which served as leads (1). From the 80's up to now pharmaceutical companies collect marine organisms, bacteria, fungi and plants at random to test them in robot-screenings regarding their anti-cancer, anti-inflammatory, anti-bacterial etc. activities. Another approach requests the ancient ethno-botanical knowledge of old civilizations which mostly base on the in depth and long lasting empirical experiences with the locally available natural resources, plants at most.Of the 12,000 plant species in Europe under consideration approximately 11,500 taxa are found in Turkey alone with 33% of these plants endemic. Since numerous ancient civilisations lived in the area, the plant societies were tested for medicinal applications throughout the ages and many plant species are still used in Turkish folk medicine to treat various diseases (2).The rich botanical biodiversity of this region paired with the cultural background was the reason to explore the traditional healing plant Hypericum adenotrichum, one of 43 Hypericum species endemic in Turkey. Within the genus Hypericum various species are used in different folk medicines worldwide and are tested against cancer cell growth.The genus Hypericum is called 'kantaron' in Turkey and H. adenotrichum is used in folk medicine for antispasmodic and antiseptic effects, and wound healing especially burns (2). The use of ...

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Use of the Tubulin Bound Paclitaxel Conformation for Structure-Based Rational Drug Design

Cited by 73 publications

References 51 publications

Rotational-Echo Double-Resonance NMR Distance Measurements for the Tubulin-Bound Paclitaxel Conformation

Rotational-Echo Double-Resonance NMR Distance Measurements for the Tubulin-Bound Paclitaxel Conformation

Bridging Converts a Noncytotoxic nor-Paclitaxel Derivative to a Cytotoxic Analogue by Constraining It to the T-Taxol Conformation

In vitro anti-neoplastic activity of the ethno-pharmaceutical plant Hypericum adenotrichum Spach endemic to Western Turkey

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