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Studies of (−)-Pironetin Binding to α‑Tubulin: Conformation, Docking, and Molecular Dynamics

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journal contribution
posted on 02.05.2014, 00:00 by Angel E. Bañuelos-Hernández, José Alberto Mendoza-Espinoza, Rogelio Pereda-Miranda, Carlos M. Cerda-García-Rojas
A comprehensive conformational analysis for the anticancer agent pironetin (1) was achieved by molecular modeling using density functional theory calculations at the B3PW91/DGTZVP level in combination with calculated and experimental 1H–1H coupling constants comparison. Two solvent-dependent conformational families (L and M) were revealed for the optimum conformations. Docking studies of the pironetin–tubulin complex determined a quantitative model for the hydrogen-bond interactions of pironetin through the αAsn249, αAsn258, and αLys352 amino groups in α-tubulin, which supported the formation of a covalent adduct between the αLys352 and the β carbon atom of the α,β-unsaturated lactone. Saturation-transfer difference NMR spectroscopy confirmed that pironetin binds to tubulin, while molecular dynamics exposed a distortion of the tubulin secondary structure at the H8 and H10 α-helices as well as at the S9 β-sheet, where αLys352 is located. A large structural perturbation in the M-loop geometry between the αIle274 and αLeu285 residues, an essential region for molecular recognition between α–α and β–β units of protofilaments, was also identified and provided a rationale for the pironetin inhibitory activity.