Sanna Nico, Chillemi Giovanni, Gontrani Lorenzo, Grandi Andrea, Mancini Giordano, Castelli Silvia, Zagotto Giuseppe, Zazza Costantino, Barone Vincenzo, Desideri Alessandro
CASPUR, Consortium for Supercomputing in Research, Via dei Tizii 6, 00185 Roma, Italy.
J Phys Chem B. 2009 Apr 23;113(16):5369-75. doi: 10.1021/jp809801y.
The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.
喜树碱(CPT)的紫外-可见吸收光谱已在pH 5.3的水溶液中记录,此时不同CPT形式之间的平衡向内酯形式偏移。含时密度泛函理论(TD-DFT)计算仅在加入与喜树碱分子特定部分相互作用的明确水分子后,才能显著重现实验光谱。分子动力学(MD)模拟对嵌入865个水分子的CPT施加边界周期性条件,其力场源自DFT计算,结果表明实验光谱归因于具有不同溶剂化模式的CPT分子的贡献。对于几种CPT衍生物,包括临床相关的SN-38和拓扑替康药物,也观察到了类似的溶剂效应。TD-DFT/MD计算与实验数据之间的定量一致性使我们能够识别诊断药物环境的特定光谱特征,并开发可用于监测药物与DNA/蛋白质相互作用的程序。