Paper Citing NAMD - Abstract
Spiegel, Katrin; Magistrato, Alessandra; Maurer, Patrick; Ruggerone, Paolo; Rothlisberger, Ursula; Carloni, Paolo; Reedijk, Jan; Klein, Michael L.
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:38-49, JAN 15 2008
Azole-bridged diplatinum compounds are promising new anticancer drugs designed to induce small distortions upon DNA alkylation, able to circumvent resistance problems of existing platinum drugs. Hybrid quantum classical (QM/MM) molecular dynamics (MD) simulations of different azole-bridged platinum drugs have recently revealed the nature of the local deformations at the DNA binding site. However, the description of global slow converging rearrangements cannot be addressed by QM/MM MD due to the short time scale accessible. Extensive classical MD simulations are therefore mandatory to describe accurately the structural distortions in the DNA double helix. This issue is now addressed by developing a new set of accurate force field parameters of the platinated moiety via a recently proposed force matching procedure of the classical forces to ab initio forces obtained from QM/MM trajectories. The accuracy of our force field parameters is validated by comparison of structural properties from classical MD and hybrid QM/MM simulations. The structural characteristics of the Pt-lesion are well reproduced during classical MD compared with QM/MM simulations and available experimental data. The global distortions in the DNA duplex upon binding of dinuclear Pt-compounds are very small and rather opposite to those induced by cisplatin. Thus, the force match approach significantly extends the potentialities of molecular simulations in the study of anticancer drugs and of the interactions with their biological targets. (C) 2007 Wiley Periodicals, Inc.
