Effects of cholesterol concentration on the interaction of cytarabine with lipid membranes: a molecular dynamics simulation study

References

• Abu Lila, A. S., Ishida, T., & Kiwada, H. (2010). Targeting anticancer drugs to tumor vasculature using cationic liposomes. Pharmaceutical Research, 27, 1171–1183. doi:10.1007/s11095-010-0110-110.1007/s11095-010-0110-1
   PubMed Web of Science ®Google Scholar
• Allen, T. M., & Cullis, P. R. (2004). Drug delivery systems: Entering the mainstream. Science, 303, 1818–1822. doi:10.1126/science.109583310.1126/science.1095833
   PubMed Web of Science ®Google Scholar
• Benesch, M., & Urban, C. (2008). Liposomal Cytarabine for leukemic and lymphomatous meningitis: Recent developments. Expert Opinion on Pharmacotherapy, 9, 301–309. doi:10.1517/14656566.9.2.30110.1517/eop.2008.9.issue-2
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690. doi:10.1063/1.44811810.1063/1.448118
   Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. Intermolecular Forces. The Jerusalem Symposia on Quantum Chemistry and Biochemistry, 14, 331–342.10.1007/978-94-015-7658-1
   Web of Science ®Google Scholar
• Boggara, M. B., & Krishnamoorti, R. (2010). Partitioning of nonsteroidal antiinflammatory drugs in lipid membranes: A molecular dynamics simulation study. Biophysical Journal, 98, 586–595. doi:10.1016/j.bpj.2009.10.04610.1016/j.bpj.2009.10.046
   PubMed Web of Science ®Google Scholar
• Boggara, M. B., Mihailescu, M., & Krishnamoorti, R. (2012). Structural association of nonsteroidal anti-inflammatory drugs with lipid membranes. Journal of the American Chemical Society, 134, 19669–19676. doi:10.1021/ja306434210.1021/ja3064342
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. J. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126, 014101–014107. doi:10.1063/1.240842010.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Chiu, S. W., Pandit, S. A., & Scott, H. L. (2009). An improved united atom force field for simulation of mixed lipid bilayers. The Journal of Physical Chemistry B, 113, 2748–2763. doi:10.1021/jp807056c10.1021/jp807056c
   PubMed Web of Science ®Google Scholar
• Darden, T. A., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092. doi:10.1063/1.46439710.1063/1.464397
   Web of Science ®Google Scholar
• Dicko, A., Kwak, S., Frazier, A. A., Mayer, L. D., & Liboiron, B. D. (2010). Biophysical characterization of a liposomal formulation of Cytarabine and daunorubicin. International Journal of Pharmaceutics, 391, 248–259. doi:10.1016/j.ijpharm.2010.02.01410.1016/j.ijpharm.2010.02.014
   PubMed Web of Science ®Google Scholar
• Domínguez, A. R., Hidalgo, D. O., Garrido, R. V., & Sánchez, E. T. (2005). Liposomal Cytarabine (DepoCyte®) for the treatment of neoplastic meningitis. Clinical and Translational Oncology, 7, 232–238. doi:10.1007/BF0271016810.1007/BF02710168
   PubMedGoogle Scholar
• Drummond, D. C., Meyer, O., Hong, K., Kirpotin, D. B., & Papahadjopoulos, D. (1999). Optimizing liposomes for delivery of chemotherapeutic agents to solid tumors. Pharmacological Reviews, 51, 691–744. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10581328
   PubMed Web of Science ®Google Scholar
• Filippov, A., Munavirov, B., Gröbner, G., & Rudakova, M. (2012). Lateral diffusion in equimolar mixtures of natural sphingomyelins with dioleoylphosphatidylcholine. Magnetic Resonance Imaging, 30, 413–421. doi:10.1016/j.mri.2011.12.01010.1016/j.mri.2011.12.010
   PubMed Web of Science ®Google Scholar
• Filippov, A., Orädd, G., & Lindblom, G. (2003). The effect of cholesterol on the lateral diffusion of phospholipids in oriented bilayers. Biophysical Journal, 84, 3079–3086. doi:10.1016/S0006-3495(03)70033-210.1016/S0006-3495(03)70033-2
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Burant, J. C. (2004). Gaussian 03, revision C.02. Wallingford, CT: Gaussian.
   Google Scholar
• Gregoriadis, G., & Florence, A. T. (1993). Liposomes in drug delivery. Drugs, 45, 15–28. doi:10.2165/00003495-199345010-0000310.2165/00003495-199345010-00003
   PubMed Web of Science ®Google Scholar
• Hess, B. (2002). Determining the shear viscosity of model liquids from molecular dynamics simulations. The Journal of Chemical Physics, 116, 209–217. doi:10.1063/1.142136210.1063/1.1421362
   Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., & van der Spoel, D. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447. doi:10.1021/ct700301q10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hockney, R. W., Goel, S. P. J., & Eastwood, J. W. (1974). Quite high resolution computer models of a plasma. Journal of Computational Physics, 14, 148–158. doi:10.1016/0021-9991(74)90010-210.1016/0021-9991(74)90010-2
   Web of Science ®Google Scholar
• Hofsass, C., Lindahl, E., & Edholm, O. (2003). Molecular dynamics simulations of phospholipid bilayers with cholesterol. Biophysical Journal, 84, 2192–2206. doi:10.1016/S0006-3495(03)75025-510.1016/S0006-3495(03)75025-5
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38. doi:10.1016/0263-7855(96)00018-510.1016/0263-7855(96)00018-5
   PubMed Web of Science ®Google Scholar
• Jämbeck, J. P. M., & Lyubartsev, A. P. (2012). An extension and further validation of an all-atomistic force field for biological membranes. Journal of Chemical Theory and Computation, 8, 2938–2948. doi:10.1021/ct300342n10.1021/ct300342n
   PubMed Web of Science ®Google Scholar
• Kahya, N., Schwille, P., & Fluoresc, J. (2006). How phospholipid–cholesterol interactions modulate lipid lateral diffusion, as revealed by fluorescence correlation spectroscopy. Journal of Fluorescence, 16, 671–678. doi:10.1007/s10895-006-0108-610.1007/s10895-006-0108-6
   PubMed Web of Science ®Google Scholar
• Kirby, C., Clarke, J., & Gregoriadis, G. (1980). Cholesterol content of small unilamellar liposomes controls phospholipid loss to high density lipoproteins in the presence of serum. FEBS Letters, 111, 324–328. doi:10.1016/0014-5793(80)80819-210.1016/0014-5793(80)80819-2
   PubMed Web of Science ®Google Scholar
• Lian, T., & Ho, R. J. Y. (2001). Trends and developments in liposome drug delivery systems. Journal of Pharmaceutical Sciences, 90, 667–680. doi:10.1002/jps.102310.1002/(ISSN)1520-6017
   PubMed Web of Science ®Google Scholar
• Liu, A., & Qi, X. (2012). Molecular dynamics simulations of DOPC lipid bilayers: The effect of Lennard–Jones parameters of hydrocarbon chains. Biomedical & Life Sciences, 2, 78–82. doi:10.4236/cmb.2012.23007
   Google Scholar
• MacCallum, J. L., & Tieleman, D. P. (2006). Computer simulation of the distribution of hexane in a lipid bilayer: Spatially resolved free energy, entropy, and enthalpy profiles. Journal of the American Chemical Society, 128, 125–130. doi:10.1021/ja053509910.1021/ja0535099
   PubMed Web of Science ®Google Scholar
• Marrink, S. J., & Berendsen, H. J. C. (1996). Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. The Journal of Physical Chemistry, 100, 16729–16738. doi:10.1021/jp952956f10.1021/jp952956f
   Web of Science ®Google Scholar
• McMullen, T. P. W., & McElhaney, R. N. (1996). Physical studies of cholesterol–phospholipid interactions. Current Opinion in Colloid & Interface Science, 1, 83–90. doi:10.1016/S1359-0294(96)80048-3
   Web of Science ®Google Scholar
• Mitragotri, S. (2002). A theoretical analysis of permeation of small hydrophobic solutes across the stratum corneum based on scaled particle theory. Journal of Pharmaceutical Sciences, 91, 744–752. doi:10.1002/jps.1004810.1002/(ISSN)1520-6017
   PubMed Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). SETTLE – An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13, 952–962. doi:10.1002/jcc.54013080510.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Ohvo-Rekila, H., Ramstedt, B., Leppimaki, P., & Slotte, J. P. (2002). Cholesterol interactions with phospholipids in membranes. Progress in Lipid Research, 41, 66–97. doi:10.1016/S0163-7827(01)00020-010.1016/S0163-7827(01)00020-0
   PubMed Web of Science ®Google Scholar
• Ollila, S., Róg, T., Karttunen, M., & Vattulainen, I. (2007). Role of sterol type on lateral profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol. Journal of Structural Biology, 159, 311–323. doi:10.1016/j.jsb.2007.01.01210.1016/j.jsb.2007.01.012
   PubMed Web of Science ®Google Scholar
• Pandit, S. A., Bostick, D., & Berkowitz, M. L. (2004). Complexation of phosphatidylcholine lipids with cholesterol. Biophysical Journal, 86, 1345–1356. doi:10.1016/S0006-3495(04)74206-X10.1016/S0006-3495(04)74206-X
   PubMed Web of Science ®Google Scholar
• Pandit, S. A., Vasudevan, S., Chiu, S. W., Mashl, R. J., Jakobsson, E., & Scott, H. L. (2004). Sphingomyelin-cholesterol domains in phospholipid membranes: Atomistic simulation. Biophysical Journal, 87, 1092–1100. doi:10.1529/biophysj.104.04193910.1529/biophysj.104.041939
   PubMed Web of Science ®Google Scholar
• Papahadjopoulos, D., Jacobson, K., & Isac, T. (1973). Phase transitions in phospholipid vesicles. Fluorescence polarization and permeability measurements concerning the effect of temperature and cholesterol. Biochimica et Biophysica Acta (BBA) – Biomembranes, 311, 330–348. doi:10.1016/0005-2736(73)90314-310.1016/0005-2736(73)90314-3
   PubMed Web of Science ®Google Scholar
• Petrache, H. I., Tristram-Nagle, S., Gawrisch, K., Harries, D., Parsegian, V. A., & Nagle, J. F. (2004). Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt. Biophysical Journal, 86, 1574–1586. doi:10.1016/S0006-3495(04)74225-310.1016/S0006-3495(04)74225-3
   PubMed Web of Science ®Google Scholar
• Pourmousa, M., Wong-ekkabut, J., Patra, M., & Karttunen, M. (2013). Molecular dynamic studies of transportan interacting with a DPPC lipid bilayer. The Journal of Physical Chemistry B, 117, 230–241. doi:10.1021/jp310255r10.1021/jp310255r
   PubMed Web of Science ®Google Scholar
• Róg, T., Murzyn, K., Gurbiel, R., Kitamura, K., Kusumi, A., & Pasenkiewicz-Gierula, M. (2004). Effects of phospholipid unsaturation on the structure and dynamics of the hydrocarbon core of the membrane. A molecular simulation study. Journal of Lipid Research, 45, 326–336. doi:10.1194/jlr.M300187-JLR200
   PubMed Web of Science ®Google Scholar
• Róg, T., & Pasenkiewicz-Gierula, M. (2001). Cholesterol effect on the phospholipid condensation and packing in the bilayer: A molecular simulation study. FEBS Letters, 502, 68–71. doi:10.1016/S0014-5793(01)02668-010.1016/S0014-5793(01)02668-0
   PubMed Web of Science ®Google Scholar
• Róg, T., & Pasenkiewicz-Gierula, M. (2004). Non-polar interactions between cholesterol and phospholipids: A molecular dynamics simulation study. Biophysical Chemistry, 107, 151–164. doi:10.1016/j.bpc.2003.09.00210.1016/j.bpc.2003.09.002
   PubMed Web of Science ®Google Scholar
• Schuettelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D: Biological Crystallography, 60, 1355–1363. doi:10.1107/S090744490401167910.1107/S0907444904011679
   PubMed Web of Science ®Google Scholar
• Senior, J. H. (1987). Fate and behavior of liposomes in vivo: A review of controlling factors. Critical Reviews in Therapeutic Drug Carrier Systems, 3, 123–193. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3542245
   PubMed Web of Science ®Google Scholar
• Simons, K., & Ikonen, E. (2000). How cells handle cholesterol. Science, 290, 1721–1726. doi:10.1126/science.290.5497.172110.1126/science.290.5497.1721
   PubMed Web of Science ®Google Scholar
• Smondyrev, A. M., & Berkowitz, M. L. (2001a). Effects of oxygenated sterol on phospholipid bilayer properties: A molecular dynamics simulation. Chemistry and Physics of Lipids, 112, 31–39. doi:10.1016/S0009-3084(01)00160-810.1016/S0009-3084(01)00160-8
   PubMed Web of Science ®Google Scholar
• Smondyrev, A. M., & Berkowitz, M. L. (2001b). Molecular dynamics simulation of the structure of dimyristoylphosphatidylcholine bilayers with cholesterol, ergosterol, and lanosterol. Biophysical Journal, 80, 1649–1658. doi:10.1016/S0006-3495(01)76137-110.1016/S0006-3495(01)76137-1
   PubMed Web of Science ®Google Scholar
• Stępniewski, M., Kepczynski, M., Jamróz, D., Nowakowska, M., Rissanen, S., Vattulainen, I., & Róg, T. (2012). Interaction of hematoporphyrin with lipid membranes. The Journal of Physical Chemistry B, 116, 4889–4897. doi:10.1021/jp300899b10.1021/jp300899b
   PubMed Web of Science ®Google Scholar
• Tielaman, D. P., Marrink, S. J., & Berendsen, H. J. C. (1997). A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems. Biochimica et Biophysica Acta (BBA) – Reviews on Biomembranes, 1331, 235–270. doi:10.1016/S0304-4157(97)00008-710.1016/S0304-4157(97)00008-7
   PubMed Web of Science ®Google Scholar
• Tieleman, D. P. (2006). Computer simulations of transport through membranes: Passive diffusion, pores, channels and transporters. Clinical and Experimental Pharmacology and Physiology, 33, 893–903. doi:10.1111/j.1440-1681.2006.04461.x10.1111/cep.2006.33.issue-10
   PubMed Web of Science ®Google Scholar
• Tu, K. C., Klein, M. L., & Tobias, D. J. (1998). Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer. Biophysical Journal, 75, 2147–2156. doi:10.1016/S0006-3495(98)77657-X10.1016/S0006-3495(98)77657-X
   PubMed Web of Science ®Google Scholar
• Urbina, J. A., Pekerar, S., Le, H., Patterson, J., Montez, B., & Oldfield, E. (1995). Molecular order and dynamics of phosphatidylcholine bilayer membranes in the presence of cholesterol, ergosterol and lanosterol: A comparative study using 2H-, 13C- and 31P-NMR spectroscopy. Biochimica et Biophysica Acta (BBA) – Biomembranes, 1238, 163–176. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/754813110.1016/0005-2736(95)00117-L
   PubMed Web of Science ®Google Scholar
• Wang, W. S., Tzeng, C. H., Chiou, T. J., Liu, J. H., Hsieh, R. K., Yen, C. C., & Chen, P. M. (1997). High-dose Cytarabine and Mitoxantrone as salvage therapy for refractory non-Hodgkin’s lymphoma. Japanese Journal of Clinical Oncology, 27, 154–157. doi:10.1093/jjco/27.3.15410.1093/jjco/27.3.154
   PubMed Web of Science ®Google Scholar
• Xiang, T. X., & Anderson, B. D. (2006). Liposomal drug transport: A molecular perspective from molecular dynamics simulations in lipid bilayers. Advanced Drug Delivery Reviews, 58, 1357–1378. doi:10.1016/j.addr.2006.09.00210.1016/j.addr.2006.09.002
   PubMed Web of Science ®Google Scholar
• Yeagle, P. L., Albert, A. D., Boesze-Battaglia, K., Young, J., & Frye, J. (1990). Cholesterol dynamics in membranes. Biophysical Journal, 57, 413–424. doi:10.1016/S0006-3495(90)82558-310.1016/S0006-3495(90)82558-3
   PubMed Web of Science ®Google Scholar