Benchmarking of Force Fields for Molecule鈥揗embrane Interactions

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• 作者：Mark茅ta Palonc媒ov谩 ; Gabin Fabre ; Russell H. DeVane ; Patrick Trouillas ; Karel Berka ; Michal Otyepka
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2014
• 出版时间：September 9, 2014
• 年：2014
• 卷：10
• 期：9
• 页码：4143-4151
• 全文大小：556K
• ISSN：1549-9626

文摘

Studies of drug鈥搈embrane interactions witness an ever-growing interest, as penetration, accumulation, and positioning of drugs play a crucial role in drug delivery and metabolism in human body. Molecular dynamics simulations complement nicely experimental measurements and provide us with new insight into drug-membrane interactions; however, the quality of the theoretical data dramatically depends on the quality of the force field used. We calculated the free energy profiles of 11 molecules through a model dimyristoylphosphatidylcholine (DMPC) membrane bilayer using five force fields, namely Berger, Slipids, CHARMM36, GAFFlipids, and GROMOS 43A1-S3. For the sake of comparison, we also employed the semicontinuous tool COSMOmic. High correlation was observed between theoretical and experimental partition coefficients (log K). Partition coefficients calculated by all-atomic force fields (Slipids, CHARMM36, and GAFFlipids) and COSMOmic differed by less than 0.75 log units from the experiment and Slipids emerged as the best performing force field. This work provides the following recommendations (i) for a global, systematic and high throughput thermodynamic evaluations (e.g., log K) of drugs COSMOmic is a tool of choice due to low computational costs; (ii) for studies of the hydrophilic molecules CHARMM36 should be considered; and (iii) for studies of more complex systems, taking into account all pros and cons, Slipids is the force field of choice.