Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

The 3 ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the Δ G bind of the QPLD model perform much better than the RESP model...

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Veröffentlicht in:	Bioorganic & medicinal chemistry 2008-01, Vol.18 (2), p.542-545
Hauptverfasser:	Zhong, Haizhen, Kirschner, Karl N., Lee, Moses, Bowen, J. Phillip
Format:	Artikel
Sprache:	eng
Schlagworte:	Antineoplastic agents Base Sequence Biological and medical sciences DNA - chemistry DNA - metabolism DNA/duocarmycin complex General aspects Indoles - chemistry Indoles - metabolism Magnetic Resonance Spectroscopy MD simulations Medical sciences MM/GBSA Models, Molecular Pharmacology. Drug treatments Pyrrolidinones - chemistry Pyrrolidinones - metabolism QM-polarized ligand docking (QPLD) RESP charge model Static Electricity Thermodynamics
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Beschreibung
Zusammenfassung:	The 3 ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the Δ G bind of the QPLD model perform much better than the RESP model, with the Δ G bind estimation for QPLD model (−16.11 kcal/mol) versus Δ G bind estimation for RESP model (−10.05 kcal/mol).
ISSN:	0960-894X 0968-0896 1464-3405 1464-3391
DOI:	10.1016/j.bmcl.2007.11.090