Molecular dynamics simulations in drug delivery research: Calcium chelation of G3.5 PAMAM dendrimers

References

• Amsterdam, A., & Jamieson, J. D. (1974). Studies on dispersed pancreatic exocrine cells: I. Dissociation technique and morphologic characteristics of separated cells. The Journal of Cell Biology, 63, 1037–1056.10.1083/jcb.63.3.1037
   Google Scholar
• Astachov, V., Garzoni, M., Danani, A., Choy, K. L., Pavan, G. M., & Fahmi, A. (2016). In situ functionalization of self-assembled dendrimer nanofibers with cadmium sulfide quantum dots through simple ionic-substitution. New Journal of Chemistry, 40, 6325–6331.
   Google Scholar
• Avila-Salas, F., Sandoval, C., Caballero, J., Guiñez-Molinos, S., Santos, L. S., Cachau, R. E., & González-Nilo, F. D. (2012). Study of interaction energies between the PAMAM dendrimer and nonsteroidal anti-inflammatory drug using a distributed computational strategy and experimental analysis by ESI-MS/MS. The Journal of Physical Chemistry B, 116, 2031–2039.10.1021/jp2069122
   Google Scholar
• Barata, T., Teo, I., Lalwani, S., Simanek, E., Zloh, M., & Shaunak, S. (2011). Computational design principles for bioactive dendrimer based constructs as antagonists of the TLR4-MD-2-LPS complex. Biomaterials, 32, 8702–8711.10.1016/j.biomaterials.2011.07.085
   Google Scholar
• Cao, J., Zhang, H., Wang, Y., Yang, J., & Jiang, F. (2013). Investigation on the interaction behavior between curcumin and PAMAM dendrimer by spectral and docking studies. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 108, 251–255.10.1016/j.saa.2013.02.003
   Google Scholar
• Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., … Kollman, P. A. (2014). AMBER 14. San Francisco, CA: University of California.
   Google Scholar
• Castriciano, M. A., Romeo, A., Angelini, N., Micali, N., Guccione, S., & Scolaro, L. M. (2011). Spectroscopic investigation and molecular modeling on porphyrin/PAMAM supramolecular adduct. Photochemistry and Photobiology, 87, 292–301.10.1111/php.2011.87.issue-2
   Google Scholar
• ChemAxon. (2013). Marvin 5.12.4. Cambridge, MA: ChemAxon.
   Google Scholar
• ChemAxon., Berry, I., Ruyts, B. (2012). Future-proofing cheminformatics platforms (pp. 1–16). Retrieved October 31, 2013, from http://www.chemaxon.com/wp-content/uploads/2012/04/Future_proofing_cheminformatics_platforms.pdf
   Google Scholar
• Garzoni, M., Cheval, N., Fahmi, A., Danani, A., & Pavan, G. M. (2012). Ion-selective controlled assembly of dendrimer-based functional nanofibers and their ionic-competitive disassembly. Journal of the American Chemical Society, 134, 3349–3357.10.1021/ja206611s
   Google Scholar
• Hubbard, D., Ghandehari, H., & Brayden, D. J. (2014). Transepithelial transport of PAMAM dendrimers across isolated rat jejunal mucosae in ussing chambers. Biomacromolecules, 15, 2889–2895.10.1021/bm5004465
   Google Scholar
• Hubbard, D., Enda, M., Bond, T., Moghaddam, S. P., Conarton, J., Scaife, C., ... Ghandehari, H. (2015). Transepithelial transport of PAMAM dendrimers across isolated human intestinal tissue. Molecular Pharmaceutics, 12, 4099–4107.10.1021/acs.molpharmaceut.5b00541
   Google Scholar
• Ivanov, A. A., & Jacobson, K. A. (2008). Molecular modeling of a PAMAM-CGS21680 dendrimer bound to an A2A adenosine receptor homodimer. Bioorganic & Medicinal Chemistry Letters, 18, 4312–4315.10.1016/j.bmcl.2008.06.087
   Google Scholar
• Jensen, L. B., Mortensen, K., Pavan, G. M., Kasimova, M. R., Jensen, D. K., Gadzhyeva, V., ... Foged, C. (2010). Molecular characterization of the interaction between siRNA and PAMAM G7 dendrimers by SAXS, ITC, and molecular dynamics simulations. Biomacromolecules, 11, 3571–3577.10.1021/bm101033g
   Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935.10.1063/1.445869
   Google Scholar
• Karatasos, K., Posocco, P., Laurini, E., & Pricl, S. (2012). Poly(amidoamine)-based dendrimer/siRNA complexation studied by computer simulations: Effects of pH and generation on dendrimer structure and siRNA binding. Macromolecular Bioscience, 12, 225–240.10.1002/mabi.v12.2
   Google Scholar
• Lee, I., Majoros, I. J., Williams, C. R., Athey, B. D., & Baker, J. R. (2009). Interactive design strategy for a multi-functional PAMAM dendrimer-based nano-therapeutic using computational models and experimental analysis. Journal of Computational and Theoretical Nanoscience, 6, 54–60.10.1166/jctn.2009.1006
   Google Scholar
• Noach, A. B., Kurosaki, Y., Blom-Roosemalen, M. C., & de Boer, A. G. (1993). Cell-polarity dependent effect of chelation on the paracellular permeability of confluent caco-2 cell monolayers. International Journal of Pharmaceutics., 90, 229–237.10.1016/0378-5173(93)90195-L
   Google Scholar
• Roe, D. R., & Cheatham, 3rd, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9, 3084–3095.10.1021/ct400341p
   Google Scholar
• Shinoda, W., DeVane, R., & Klein, M. L. (2012). Computer simulation studies of self-assembling macromolecules. Current Opinion in Structural Biology, 22, 175–186.10.1016/j.sbi.2012.01.011
   Google Scholar
• Tomita, M., Hayashi, M., & Awazu, S. (1996). Absorption-enhancing mechanism of EDTA, caprate, and decanoylcarnitine in Caco-2 cells. Journal of Pharmaceutical Sciences, 85, 608–611.10.1021/js9504604
   Google Scholar
• Vasumathi, V., & Maiti, P. K. (2010). Complexation of siRNA with dendrimer: A molecular modeling approach. Macromolecules, 43, 8264–8274.10.1021/ma1012495
   Google Scholar
• Vllasaliu, D., Shubber, S., Garnett, M., Alexander, C., Eaton, M., & Stolnik, S. (2012). Evaluation of calcium depletion as a strategy for enhancement of mucosal absorption of macromolecules. Biochemical and Biophysical Research Communications, 418, 128–133.10.1016/j.bbrc.2011.12.146
   Google Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling., 25, 247–260.10.1016/j.jmgm.2005.12.005
   Google Scholar
• Wang, B., Navath, R. S., Menjoge, A. R., Balakrishnan, B., Bellair, R., Dai, H., ... Kannan, R. M. (2010). Inhibition of bacterial growth and intramniotic infection in a guinea pig model of chorioamnionitis using PAMAM dendrimers. International Journal of Pharmaceutics, 395, 298–308.10.1016/j.ijpharm.2010.05.030
   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, 1357–1378.10.1016/j.addr.2006.09.002
   Google Scholar