Abstract
The complex marine natural product halichondrin B was compared with NSC 707389 (E7389), a structurally simplified, synthetic macrocyclic ketone analog, which has been selected for clinical trials in human patients. NSC 707389 was invariably more potent than halichondrin B in its interactions with tubulin. Both compounds inhibited tubulin assembly, inhibited nucleotide exchange on β-tubulin, and were noncompetitive inhibitors of the binding of radiolabeled vinblastine and dolastatin 10 to tubulin. Neither compound seemed to induce an aberrant tubulin assembly reaction, as occurs with vinblastine (tight spirals) or dolastatin 10 (aggregated rings and spirals). We modeled the two compounds into a shared binding site on tubulin consistent with their biochemical properties. Of the two tubulin structures available, we selected for modeling the complex of a stathmin fragment with two tubulin heterodimers with two bound colchicinoid molecules and a single bound vinblastine between the two heterodimers (Nature (Lond)435:519-522, 2005). Halichondrin B and NSC 707389 fit snugly between the two heterodimers adjacent to the exchangeable site nucleotide. Fitting the compounds into this site, which was also close to the vinblastine site, resulted in enough movement of amino acid residues at the vinblastine site to cause the latter compound to bind less well to tubulin. The model suggests that halichondrin B and NSC 707389 most likely form highly unstable, small aberrant tubulin polymers rather than the massive stable structures observed with vinca alkaloids and antimitotic peptides.
Footnotes
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↵2 The designations of protein secondary structural features are as in PDB entry 1Z2B.
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↵1 Further details of the modeling studies, including coordinates, can be obtained from R. Gussio (gussio{at}ncifcrf.gov).
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↵3 The amino acid residue numbers used for β-tubulin follow the convention in Nogales et al. (1998), which maximized sequence alignment with α-tubulin rather than the actual sequence established by sequencing the polypeptide chain (Krauhs et al., 1981).
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This work was partially supported by National Cancer Institute contract number NO-1-CO-12400.
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ABBREVIATIONS: NCI, National Cancer Institute; NSC 707389, CA index: 11,15:18,21:24,28-triepoxy-7,9-ethano-12,15-methano-9H,15H-furo[3,2-i]furo[2′,3′:5,6]pyrano[4,3-b][1,4]dioxacyclopentacosin-5-(4H)-one, 2-[(2S)-3-amino-2-hydroxypropyl]hexacosahydro-3-methoxy-26-methyl-20,27-bis(methylene)-, (2R,3R,3aS,7R,8aS,9S,10aR,11S,12R,13aR,13bS,15S,18S,21S,24S,26R,28R,29aS)-, methanesulfonate (salt); PDB, Protein Data Bank; MES, 4-morpholineethanesulfonate; HPLC, high-performance liquid chromatography; TP-TF, tetrahydropyrantetrahydrofuran.
- Received May 16, 2006.
- Accepted August 29, 2006.
- The American Society for Pharmacology and Experimental Therapeutics
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