Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model.
The 3ns 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 DeltaG(bind) of the QPLD model perform much better than the RESP model, with the DeltaG(bind) estimation for QPLD model (-16.11 kcal/mol) versus DeltaG(bind) estimation for RESP model (-10.05 kcal/mol).
Zhong
Haizhen
H
Center for Drug Discovery, Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
Kirschner
Karl N
KN
Lee
Moses
M
Bowen
J Phillip
JP
D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D000080890:Duocarmycins; D007211:Indoles / Q000737:chemistry / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011760:Pyrrolidinones / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics
D000080890:Duocarmycins; D007211:Indoles; D011760:Pyrrolidinones; D004247:DNA; C058289:duocarmycin A