Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives — A molecular dynamics study
Tài liệu tham khảo
Ritter, 2002, Amphotericin B and its lipid formulations, Mycoses, 45, 34, 10.1111/j.1439-0507.2002.tb04767.x
Kleinberg, 2006, What is the current and future status of conventional amphotericin B?, Int. J. Antimicrob. Agents, 27, S12, 10.1016/j.ijantimicag.2006.03.013
Hartsel, 1996, Amphotericin B: New life for an old drug, Trends Pharmacol. Sci., 17, 445, 10.1016/S0165-6147(96)01012-7
Ellis, 2002, Amphotericin B: spectrum and resistance, J. Antimicrob. Chemother., 49, 7, 10.1093/jac/49.suppl_1.7
Szlinder-Richert, 2001, MFAME, N-methyl-N-D-fructosyl amphotericin B methyl ester, a new amphotericin B derivative of low toxicity: relationship between self-association and effects on red blood cells, Biochim. Biophys. Acta, 1528, 15, 10.1016/S0304-4165(01)00166-0
Borowski, 2000, Novel approaches in the rational design of antifungal agents of low toxicity, Farmaco, 55, 206, 10.1016/S0014-827X(00)00024-0
Cereghetti, 2006, Amphotericin B: 50 years of chemistry and biochemistry, Synthesis (Stuttg.), 914
Grzybowska, 1997, N-methyl-N-D-fructopyranosylamphotericin B methyl ester, new amphotericin B derivative of low toxicity, J. Antibiot., 50, 709, 10.7164/antibiotics.50.709
Zumbuehl, 2007, A novel strategy for bioconjugation: synthesis and preliminary evaluation with amphotericin B, Org. Biomol. Chem., 5, 1339, 10.1039/b701953j
Gale, 1984, Mode of action and resistance mechanisms of polyene macrolides, 425
Bolard, 1986, How do the polyene macrolide antibiotics affect the cellular membrane properties?, Biochim Biophys Acta, 864, 257, 10.1016/0304-4157(86)90002-X
Baginski, 2006, vol. 3, 269
De Kruijff, 1974, Polyene antibiotic-sterol interactions in membranes of acholeplasma laidlawii cells and lecithin liposomes. III. Molecular structure of the polyene antibiotic-cholesterol complexes, Biochim. Biophys. Acta, 339, 57, 10.1016/0005-2736(74)90332-0
Hartsel, 1993, How does amphotericin B work?: studies on model membrane systems, J. Liposome. Res., 3, 377, 10.3109/08982109309150727
Matsuoka, 2005, Dominant formation of a single-length channel by amphotericin B in dimyristoylphosphatidylcholine membrane evidenced by C-13-P-31 rotational echo double resonance, Biochemistry, 44, 704, 10.1021/bi049001k
Kerridge, 1986, Mode of action of clinically important antifungal drugs, Adven. Microb. Physiol., 27, 1, 10.1016/S0065-2911(08)60303-3
Paquet, 2002, The effects of amphotericin B on pure and ergosterol- or cholesterol-containing dipalmitoylphosphatidylcholine bilayers as viewed by H-2 NMR, Chem. Phys. Lipids, 119, 1, 10.1016/S0009-3084(02)00071-3
Teerlink, 1980, The action of pimaricin, etruscomycin and amphotericin B on liposomes with varying sterol content, Biochim. Biophys. Acta, 599, 484, 10.1016/0005-2736(80)90193-5
Cohen, 1998, Amphotericin B toxicity and lethality: a tale of two channels, Int. J. Pharm., 162, 95, 10.1016/S0378-5173(97)00417-1
Fournier, 1998, The structuring effects of amphotericin B on pure and ergosterol- or cholesterol-containing dipalmitoylphosphatidylcholine bilayers: a differential scanning calorimetry study, Biochem. Biophys. Acta, 1373, 76, 10.1016/S0005-2736(98)00083-2
Czub, 2006, Modulation of amphotericin B membrane interaction by cholesterol and ergosterols — a molecular dynamics study, J. Phys. Chem. B, 110, 16743, 10.1021/jp061916g
Czerwinski, 1991, New N-alkyl derivatives of amphotericin B. Synthesis and biological properties, J. Antibiot., 44, 979, 10.7164/antibiotics.44.979
Bolard, 1999
Hac-Wydro, 2005, N-(1-piperidinepropionyl)amphotericin B methyl ester (PAME) — a new derivative of the antifungal antibiotic amphotericin B: Searching for the mechanism of its reduced toxicity, J. Colloid Interface Sci., 287, 476, 10.1016/j.jcis.2005.02.038
Slisz, 2004, Studies of the effects of antifungal cationic derivatives of amphotericin B on human erythrocytes, J Antibiot., 57, 669, 10.7164/antibiotics.57.669
Baginski, 1989, Comparative conformational analysis of cholesterol and ergosterol by molecular mechanics, Eur. Biophys. J., 17, 159, 10.1007/BF00254770
K. Sternal, Molecular properties and interactions of supramolecular systems formed by amphotericin B derivatives: Analysis by computational chemistry methods. - doctoral thesis (Gdansk University of Technology, Gdansk, 2005).
Matsumori, 2005, Mycosamine orientation of amphotericin B controlling interaction with ergosterol: sterol-dependent activity of conformation-restricted derivatives with an amino-carbonyl bridge, J. Am. Chem. Soc., 127, 10667, 10.1021/ja051597r
Baginski, 1997, Conformational analysis of amphotericin B, Biophys. Chem., 65, 91, 10.1016/S0301-4622(96)02265-X
Torrie, 1977, Nonphysical sampling distributions in Monte Carlo free-energy estimations: umbrella sampling, J. Comput. Phys., 23, 187, 10.1016/0021-9991(77)90121-8
Kumar, 1992, The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method, J. Comput. Chem., 13, 1011, 10.1002/jcc.540130812
Baginski, 1997, Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation, Mol. Pharmacol., 52, 560, 10.1124/mol.52.4.560
Baginski, 2002, Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels, Biochim. Biophys. Acta, 1567, 63, 10.1016/S0005-2736(02)00581-3
Sternal, 2004, Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies, J. Mol. Model., 10, 223, 10.1007/s00894-004-0190-0
Czub, 2006, Comparative molecular dynamics study of lipid membranes containing cholesterol and ergosterol, Biophys. J., 90, 2368, 10.1529/biophysj.105.072801
Szlinder-Richert, 2004, Interaction of amphotericin B and its low toxic derivative, N-methyl-N-D-fructosyl amphotericin B methyl ester, with fungal, mammalian and bacterial cells measured by the energy transfer method, Farmaco, 59, 289, 10.1016/j.farmac.2003.12.007
Kale, 1999, NAMD2: greater scalability for parallel molecular dynamics, J. Comput. Phys., 151, 283, 10.1006/jcph.1999.6201
Mechlinski, 1970, Structure and absolute configuration of the polyene macrolide antibiotic amphotericin B, Tetrahedron Lett., 44, 3873, 10.1016/S0040-4039(01)98612-5
Brooks, 1983, CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211
Baginski, 1997, Distribution of electrostatic potential around amphotericin B and its membrane targets, Theochem. J. Mol. Struct., 389, 139, 10.1016/S0166-1280(96)04585-X
Ryckaert, 1977, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5
Feller, 1995, Constant pressure molecular dynamics simulation: the Langevin piston method, J. Chem. Phys., 103, 4613, 10.1063/1.470648
Feller, 2000, An improved empirical potential energy function for molecular simulations of phospholipids, J. Phys. Chem. B, 104, 7510, 10.1021/jp0007843
Kucerka, 2005, Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles, Biophys. J., 88, 2626, 10.1529/biophysj.104.056606
Saint-Pierre-Chazalet, 1988, Amphotericin B-sterol complex formation and competition with egg phosphatidylcholine: a monolayer study, Biochim. Biophys. Acta, 944, 477, 10.1016/0005-2736(88)90519-6
Czub, 2007, Interactions of amphotericin B derivatives with lipid membranes — a molecular dynamics study, Biochim. Biophys. Acta, 1768, 2616, 10.1016/j.bbamem.2007.06.017
Darden, 1993, Particle mesh Ewald: an N⁎log(N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397
Humphrey, 1996, VMD: Visual molecular dynamics, J. Mol. Graphics, 14, 33, 10.1016/0263-7855(96)00018-5
Baginski, 1993, Theoretical comparison of conformational properties of molecules — conformational probability maps and similarity index, J. Comput. Chem., 14, 478, 10.1002/jcc.540140412
Baginski, 2006, Interaction of amphotericin B and its selected derivatives with membranes: Molecular modeling studies, Chem. Rec., 6, 320, 10.1002/tcr.20096
Zubrzycki, 2000, Molecular dynamics simulations of a fully hydrated dimyristoylphosphatidylcholine membrane in liquid-crystalline phase, J. Chem. Phys., 112, 3437, 10.1063/1.480924
Herve, 1989, The role of the carboxyl and amino groups of polyene macrolides in their interactions with sterols and their selective toxicity. A 31P-NMR study, Biochim. Biophys. Acta, 980, 261, 10.1016/0005-2736(89)90312-X
Xiang, 1994, Substituent contributions to the transport of substituted p-toluic acids across lipid bilayer membranes, J. Pharm. Sci., 83, 1511, 10.1002/jps.2600831027
Xiang, 2002, A computer simulation of functional group contributions to free energy in water and a DPPC lipid bilayer, Biophys. J., 82, 2052, 10.1016/S0006-3495(02)75553-7
Coutinho, 2003, Cooperative partition model of nystatin interaction with phospholipid vesicles, Biophys. J., 84, 3061, 10.1016/S0006-3495(03)70032-0
Aracava, 1981, Effects of amphotericin B on membrane permeability-kinetics of spin probe reduction, Biophys. Chem., 14, 325, 10.1016/0301-4622(81)85034-X
Urbina, 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, Biochim. Biophys. Acta, 1238, 163, 10.1016/0005-2736(95)00117-L
Hsueh, 2005, The effect of ergosterol on dipalmitoylphosphatidylcholine bilayers: a deuterium NMR and calorimetric study, Biophys. J., 88, 1799, 10.1529/biophysj.104.051375
Cheron, 1988, Quantitative structure-activity relationships in amphotericin B derivatives, Biochem. Pharmacol., 37, 827, 10.1016/0006-2952(88)90168-2
Baran, 2002, Molecular modelling of amphotericin B-ergosterol primary complex in water, Biophys. Chem., 95, 125, 10.1016/S0301-4622(01)00252-6