title: Analysis of the binding mode of laulimalide to microtubules: Establishing a laulimalide-tubulin pharmacophore.
abstract: Laulimalide (LA) is a microtubule-stabilizing agent, currently in preclinical studies. However, studying the binding of this species and successfully synthesizing potent analogues have been challenging. The LA binding site is located between tubulin protofilaments, and therefore LA is in contact with two adjacent [Formula: see text]-tubulin units. Here, an improved model of the binding mode of LA in microtubules is presented, using the newly available crystal structure pose and an extended tubulin heterodimer complex, as well as molecular dynamics simulations. With this model, a series of LA analogues developed by Mooberry and coworkers are also analyzed in order to establish important pharmacophores in LA binding and cytotoxicity. In the side chain, [Formula: see text]-[Formula: see text] interactions are important contributors to LA binding, as are water-mediated hydrogen bonds. An intramolecular hydrogen bond is correlated with high cytotoxicity, and is dependent on macrocycle conformation. Therefore, while the epoxide and olefin groups in the macrocycle do not engage in specific interactions with the protein, they are essential contributions to an active macrocycle conformation, and therefore potency. Calculations reveal that a balance in binding affinity is important for LA activity, where the more potent compounds have larger interactions with the adjacent tubulin unit than the less-active analogs. Several modifications are suggested for the rational design of LA analogues that should not disrupt the active macrocycle conformation.
authors.affiliation: a Department of Chemistry , University of Alberta , 11227 Saskatchewan Drive, Edmonton , Alberta , Canada T6G 2G2 .
authors.forename: Cassandra D M
authors.initials: CD
authors.lastname: Churchill
authors.affiliation: a Department of Chemistry , University of Alberta , 11227 Saskatchewan Drive, Edmonton , Alberta , Canada T6G 2G2 .
authors.forename: Mariusz
authors.initials: M
authors.lastname: Klobukowski
authors.affiliation: b Department of Oncology , Cross Cancer Institute , 11560 University Avenue, Edmonton , Alberta , Canada T6G 1Z2 .
authors.forename: Jack A
authors.initials: JA
authors.lastname: Tuszynski
mesh_terms: D000970:Antineoplastic Agents / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D018942:Macrolides / Q000737:chemistry* / Q000378:metabolism; D008870:Microtubules / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D055503:Protein Multimerization
chemical_list: D000970:Antineoplastic Agents; D008024:Ligands; D018942:Macrolides; C117305:laulimalide
keywords: cytotoxicity; isolaulimalide; laulimalide; microtubule; rational drug design; tubulin heterodimer