Molecular dynamics simulations of the interaction of phospholipid bilayers with polycaprolactone

References

• Kwon G, Kataoka K. Block copolymer micelles as long-circulating drug vehicles. Adv Drug Deliv Rev. 1995;16:295–309. doi: 10.1016/0169-409X(95)00031-2
   Web of Science ®Google Scholar
• Ahmed F, Discher DE. Self-porating polymersomes of PEG-PLA and PEG-PCL: hydrolysis-triggered controlled release vesicles. J Control Release. 2004;96:37–53. doi: 10.1016/j.jconrel.2003.12.021
   PubMed Web of Science ®Google Scholar
• Cai S, Vijayan K, Cheng D, et al. Micelles of different morphologies – advantages of worm-like filomicelles of PEO-PCL in paclitaxel delivery. Pharm Res. 2007;24:2099–2109. doi: 10.1007/s11095-007-9335-z
   PubMed Web of Science ®Google Scholar
• Dash TK, Konkimalla VB. Polymeric modification and its implication in drug delivery: poly-ε-caprolactone (PCL) as a model polymer. Mol Pharm. 2012;9:2365–2379. doi: 10.1021/mp3001952
   PubMed Web of Science ®Google Scholar
• Forrest ML, Yanez JA, Remsberg CM, et al. Paclitaxel prodrugs with sustained release and high solubility in poly(ethylene glycol)-b-poly(epsilon-caprolactone) micelle nanocarriers: pharmacokinetic disposition, tolerability, and cytotoxicity. Pharm Res. 2008;25:194–206. doi: 10.1007/s11095-007-9451-9
   PubMed Web of Science ®Google Scholar
• Liu SJ, Chiang FJ, Hsiao CY, et al. Fabrication of balloon-expandable self-lock drug-eluting polycaprolactone stents using micro-injection molding and spray coating techniques. Ann Biomed Eng. 2010;38:3185–3194. doi: 10.1007/s10439-010-0075-6
   PubMed Web of Science ®Google Scholar
• Izquierdo R, Garcia-Giralt N, Rodriguez MT, et al. Biodegradable PCL scaffolds with an interconnected spherical pore network for tissue engineering. J Biomed Mater Res Part A. 2008;85A:25–35. doi: 10.1002/jbm.a.31396
   Web of Science ®Google Scholar
• Rajagopal K, Mahmud A, Christian DA, et al. Curvature-coupled hydration of semicrystalline polymer amphiphiles yields flexible worm micelles but favors rigid vesicles: polycaprolactone-based block copolymers. Macromolecules. 2010;43:9736–9746. doi: 10.1021/ma101316w
   PubMed Web of Science ®Google Scholar
• Qiao C; Zhao J; Jiang S; Ji X; An L; Jiang B. Crystalline morphology evolution in PCL thin films. J Polym Sci Part B: Polym Phys. 2005;43:1303–1309. doi: 10.1002/polb.20422
   Web of Science ®Google Scholar
• Schulz M, Olubummo A, Binder WH. Beyond the lipid-bilayer: interaction of polymers and nanoparticles with membranes. Soft Matter. 2012;8:4849–4864. doi: 10.1039/c2sm06999g
   Web of Science ®Google Scholar
• Nawaz S, Redhead M, Mantovani G, et al. Interactions of PEO–PPO–PEO block copolymers with lipid membranes: a computational and experimental study linking membrane lysis with polymer structure. Soft Matter. 2012;8:6744–6754. doi: 10.1039/c2sm25327e
   Web of Science ®Google Scholar
• Hezaveh S, Samanta S, De Nicola A, et al. Understanding the interaction of block copolymers with DMPC lipid bilayer using coarse-grained molecular dynamics simulations. J Phys Chem B. 2012;116:14333–14345. doi: 10.1021/jp306565e
   PubMed Web of Science ®Google Scholar
• Jeong B, Bae YH, Lee DS, et al. Biodegradable block copolymers as injectable drug-delivery systems. Nature. 1997;388:860–862. doi: 10.1038/42218
   PubMed Web of Science ®Google Scholar
• Geng Y, Dalhaimer P, Cai S, et al. Shape effects of filaments versus spherical particles in flow and drug delivery. Nat Nanotechnol. 2007;2:249–255. doi: 10.1038/nnano.2007.70
   PubMed Web of Science ®Google Scholar
• Loverde SM, Klein ML, Discher DE. Nanoparticle shape improves delivery: rational coarse grain molecular dynamics (rCG-MD) of taxol in worm-like PEG-PCL micelles. Adv Mater. 2012;24:3823–3830. doi: 10.1002/adma.201103192
   PubMed Web of Science ®Google Scholar
• Laio A, Parrinello M. Escaping free-energy minima. Proc Natl Acad Sci. 2002;99:12562–6. doi: 10.1073/pnas.202427399
   PubMed Web of Science ®Google Scholar
• Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys. 1977;23:187–199. doi: 10.1016/0021-9991(77)90121-8
   Web of Science ®Google Scholar
• Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys. 2008;128:144120:1–144120:13. doi: 10.1063/1.2829861
   Web of Science ®Google Scholar
• Loverde SM. Molecular simulation of the transport of drugs across model membranes. J Phys Chem Lett. 2014;5:1659–1665. doi: 10.1021/jz500321d
   PubMed Web of Science ®Google Scholar
• Drenscko M, Loverde SM. Characterisation of the hydrophobic collapse of polystyrene in water using free energy techniques. Mol Simul. 2017;43:234–241. doi: 10.1080/08927022.2016.1253840
   Web of Science ®Google Scholar
• Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31:671–690.
   PubMed Web of Science ®Google Scholar
• Brooks BR, Brooks III CL, Mackerell Jr. AD, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30:1545–1614. doi: 10.1002/jcc.21287
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935. doi: 10.1063/1.445869
   Web of Science ®Google Scholar
• Lee S, Tran A, Allsopp M, et al. CHARMM36 united atom chain model for lipids and surfactants. J Phys Chem B. 2014;118:547–556. doi: 10.1021/jp410344g
   PubMed Web of Science ®Google Scholar
• Kale L, Skeel R, Bhandarkar M, et al. NAMD2: greater scalability for parallel molecular dynamics. J Comput Phys. 1999;151:283–312. doi: 10.1006/jcph.1999.6201
   Web of Science ®Google Scholar
• Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802. doi: 10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Martyna GJ, Tobias DJ, Klein ML. Constant-pressure molecular-dynamics algorithms. J Chem Phys. 1994;101:4177–4189. doi: 10.1063/1.467468
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald – an n.log(n) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092. doi: 10.1063/1.464397
   Web of Science ®Google Scholar
• Shinoda W, DeVane R, Klein ML. Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B. 2010;114:6836–6849. doi: 10.1021/jp9107206
   PubMed Web of Science ®Google Scholar
• Plimpton S. Fast parallel Algorithms for short-range molecular dynamics. J Comput Phys. 1995;117:1–19. doi: 10.1006/jcph.1995.1039
   Web of Science ®Google Scholar
• Martyna GJ, Klein ML, Tuckerman M. Nose–Hoover chains – the canonical ensemble via continuous dynamics. J Chem Phys. 1992;97:2635–2643. doi: 10.1063/1.463940
   Web of Science ®Google Scholar
• Deserno M, Holm C. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J Chem Phys. 1998;109:7678–7693. doi: 10.1063/1.477414
   Web of Science ®Google Scholar
• Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput. 2010;6:35–47. doi: 10.1021/ct9004432
   PubMed Web of Science ®Google Scholar
• Fiorin G, Klein ML, Hénin J. Using collective variables to drive molecular dynamics simulations. Mol Phys. 2013;111:3345–3362. doi: 10.1080/00268976.2013.813594
   Web of Science ®Google Scholar
• Bussi G, Gervasio FL, Laio A, et al. Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc. 2006;128:13435–13441. doi: 10.1021/ja062463w
   PubMed Web of Science ®Google Scholar
• Ensing B, De Vivo M, Liu ZW, et al. Metadynamics as a tool for exploring free energy landscapes of chemical reactions. Acc Chem Res. 2006;39:73–81. doi: 10.1021/ar040198i
   PubMed Web of Science ®Google Scholar