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

• Published in: Journal of organic chemistry Vol. 79; no. 9; pp. 3752 - 3764
• Main Authors: Bañuelos-Hernández, Angel E, Mendoza-Espinoza, José Alberto, Pereda-Miranda, Rogelio, Cerda-García-Rojas, Carlos M
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 02.05.2014
• Subjects: Antineoplastic Agents - chemistry; Binding Sites; Models, Molecular; Molecular Conformation; Pyrones - chemistry; Quantum Theory; Stereoisomerism; Tubulin - chemistry
• ISSN: 0022-3263; 1520-6904
• DOI: 10.1021/jo500420j

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.