title: Localization of the antimitotic peptide and depsipeptide binding site on beta-tubulin.
abstract: Several naturally occurring peptides and depsipeptides which include the cryptophycins, dolastatin 10, hemiasterlin, and phomopsin A have been found to be potent antimitotic agents, causing cell death at picomolar or low nanomolar concentrations. These compounds inhibit microtubule growth, modulate the dynamics of microtubules, and induce the self-association of tubulin dimers into single-walled rings and spirals. These peptides exhibit mutual competitive inhibition in binding to beta-tubulin, while noncompetitively inhibiting the binding of vinblastine and vincristine to beta-tubulin. Despite the abundance of biochemical information, the details of their molecular interactions with tubulin are not known. In this study, using a combination of molecular dynamics simulations and molecular docking studies, a common binding site for cryptophycin 1, cryptophycin 52, dolastatin 10, hemiasterlin, and phomopsin A on beta-tubulin has been identified. Application of these same methods to alpha-tubulin indicated no interaction between alpha-tubulin and any of the peptides. On the basis of the docking results, a model for the mechanism of microtubule disruption and formation of aberrant nonmicrotubule structures is proposed. Both the active site and mechanism of microtubule depolymerization predictions are in good agreement with experimental findings.
authors.affiliation: Department of Chemical Engineering, Washington University, St. Louis, Missouri 63130, USA.
authors.forename: Arpita
authors.initials: A
authors.lastname: Mitra
authors.forename: David
authors.initials: D
authors.lastname: Sept
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000970:Antineoplastic Agents / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D047630:Depsipeptides / Q000378:metabolism*; D007769:Lactams / Q000378:metabolism; D007783:Lactones / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009183:Mycotoxins / Q000378:metabolism; D009842:Oligopeptides / Q000378:metabolism; D010455:Peptides / Q000378:metabolism*; D010456:Peptides, Cyclic / Q000378:metabolism; D017354:Point Mutation; D011485:Protein Binding / Q000235:genetics; D011487:Protein Conformation; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014404:Tubulin / Q000235:genetics / Q000378:metabolism*
chemical_list: D000970:Antineoplastic Agents; D047630:Depsipeptides; D007769:Lactams; D007783:Lactones; D008024:Ligands; D009183:Mycotoxins; D009842:Oligopeptides; D010455:Peptides; D010456:Peptides, Cyclic; D020033:Protein Isoforms; D029701:Saccharomyces cerevisiae Proteins; D014404:Tubulin; C088419:cryptophycin; C035753:phomopsin; C467070:hemiasterlin; C064570:dolastatin 10; C114033:cryptophycin 52