Conformational analysis of amphotericin B. I, Isolated molecule

Molecular dynamics of amphotericin B I. Single molecule in vacuum and water

Molecular dynamics simulations were performed for an antifungal polyene antibiotic amphotericin B (AMB). A single molecule of the AMB was modeled in vacuum as well as in water. In the latter case it was surrounded by 354 SPC water molecules and a periodic boundary condition was applied. An amino-sugar mycosamine ring was found to be rigid in the conditions studied. The mean orientation of this ring in relation to a macrolide ring was found to be common in both simulations and similar to that observed in a crystal of N-iodoacetyl derivative. A large flexibility of the amino-sugar orientation was observed in vacuum in contrast to water simulation. Several conformers of the macrolide ring were observed in vacuum as well as in water simulation. Interactions which may force these conformational transitions have been proposed. The structuring of the water molecules around polar and ionizable parts of the AMB molecule were analysed. The influence of the dynamic behavior of the AMB on structures of supramolecular complexes containing this antibiotic is discussed.

Conformational properties of amphotericin B amide derivatives--impact on selective toxicity

Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (phi,psi)=(290 degrees,180 degrees) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model.

Conformational analysis of Amphotericin B

Within a theoretical approach to the problem of antifungal action of Amphotericin B (AmB), a conformational analysis of the neutral and zwitterionic form of this antibiotic in vacuo was performed by the MM2P and AM1 methods. The analysis was carried out with regard to the mutual orientation of the macrolidic and glycosidic fragments of the molecule, which is defined by the phi and psi steric angles. This orientation defines the overall shape of the molecule and is postulated to be important for the antifungal action of the drug. As a result of the MM2P calculations, phi, psi steric energy and population maps were prepared. Several conformers were found on these maps but only two of them (one each for the zwitterionic and the neutral forms of the antibiotic) were previously observed experimentally for isolated molecules. Our other calculated conformers were not observed experimentally but we propose that they may also appear in the AmB channel structure. The results of our conformational analysis were compared with experimental NMR data (nuclear Overhauser effects between selected hydrogen atoms) obtained previously. New structural information obtained for AmB in the present work will be useful for building a molecular model of AmB-target interactions as well as for designing new derivatives of AmB.

Molecular dynamics of amphotericin B. II. Dimer in water

Molecular dynamics simulations were performed for a dimer of the antifungal antibiotic, amphotericin B, in water. In the first step of the work three appropriately selected versions of the dimer structure were taken into consideration. In each version antibiotic molecules were placed antiparallel with polar and ionizable groups outside the hydrophobic core formed by polyene chromophores. During short dynamic simulations versions of the dimer structure were compared in respect of the energy of dimerization. The highest energy was observed for the structure in which polyene chromophores superimposed each other as much as possible and this version was subjected to the main simulation. The analysis of 66 snapshot geometries stored during 33 ps dynamic trajectory allowed us to draw three main conclusions: (i) the relative orientation of the amino-sugar moiety and chromophore as well as conformation of the antibiotic macrolide ring were different in both molecules and could exhibit dynamic changes, (ii) the dimer structure exhibited intrinsic asymmetry which could be responsible for characteristic circular dichroism spectra of the aggregated form of the antibiotic, (iii) relatively high stability of the dimer structure resulted not only from hydrophobic interactions between chromophores but also from hydrogen bonds networks that were observed around polar terminals of antibiotic molecules. Implications of these features of the dimer structure for its susceptibility on the ionic state of carboxyl and/or amino groups are also discussed.

Theoretical study of the self-association of amphotericin B

The aim of this present work is the study of self-association of amphotericin B (AmB) at a molecular levels, because of its importance in the toxicity of this antibiotic. Molecular mechanics calculations have been performed considering different conformations of the polar head of AmB, the two most stable ones we have determined (B and C) and the one issued from the X-ray data. Our calculations have shown that both head-to-head and head-to-tail stable dimers were found within an energy range between -30 and -40 kcal/mol, the very stable head-to-head dimer with the polar head within C conformation having an energy of -46.8 kcal/mol. We have shown that both electrostatic and Van der Waals terms contribute to the total interaction energy but their relative weight depends on the conformation of the polar head and on the head-to-head and head-to-tail structures involved in the dimer. Thus the electrostatic contribution does no particularly stabilize the head-to-tail dimer. Furthermore an explicit calculation of the dipole moment in the ground state of AmB has disproved the current assertion upon the greatest stabilization of head-to-tail dimers by electrostatic dipole-dipole interaction. Among all the dimers we have calculated, we have found a group denoted G1 with a geometrical structure consistent with absorption data, namely a blue-shift of the dimer main absorption band with regard to the monomer one. In this group G1 we have found two isoenergetic (-38.8 kcal/mol) very stable head-to-head and head-to-tail dimers. We have found that, as a rule, the self-association of AmB in dimers is more favourable than the complexation with the cholesterol and, in a less extent, with the ergosterol. It seems that these features could be also observed for some trimers, that we have roughly calculated.

Theoretical study of the complexation of amphotericin B with sterols

The aim of this present work was the study of the intermolecular complexes between amphotericin B (AmB) and either cholesterol or ergosterol. In such complexes the intermolecular interaction energy mainly proceeds from both Van der Waals and H-bonding (via water molecules) forces. Our calculations have shown that the Van der Waals forces slightly favor the AmB-ergosterol complex. Several relative positions of the sterol with regard to AmB lead to energy minima: sterol may be either in contact with the AmB polar head or repelled towards the end of the macrolide ring. It appeared that the role played by some water molecules was to maintain the sterol close to the AmB polar head.

Structures of amphotericin B-cholesterol complex

The structures of amphotericin B-cholesterol complex that forms a channel in a lipid membrane were analysed by molecular mechanics calculations. The symmetric complex consisting of eight rigid antibiotic and cholesterol molecules was considered. The presence of a continuous set of low-energy states of the complex with different values of the channel diameter was shown. These states are characterized by significant tilt of the amphotericin planes to the radial axis of the channel and by strong interaction between the charged ammonium and carboxyl groups of the antibiotic. Changes of the channel diameter may result in changes in pore permeability.

Computational analysis of conformational behavior of cholecystokinin fragments. I-CCK4, CCK5, CCK6 and CCK7 molecules

A conformational analysis has been performed on several peptide fragments (CCK4 to CCK7) of the cholecystokinin neuromodulator. The Monte-Carlo Metropolis method was used to explore the conformational space of all these flexible units and different electric charge distributions were introduced in order to mimic pH effects. Results agree reasonably well with experimental data from NMR and fluorescence experiments. The CCK4 fragment displays a peculiar conformational behavior when compared to all other longer peptides with short range interaction between the Trp and Phe aromatic side-chains. Several H-bonded conformers including C- or beta-turns are found for CCK5 to CCK7. These findings are correlated to the central and peripheral actions of these compounds and hypotheses concerning the best possible templates for each one are discussed.

Phase behaviour of amphotericin B multilamellar vesicles

Because side effect profiles and key physical properties of liposomal amphotericin B reflect the molecular nature of the hydrated preparations, effort has been directed toward understanding this nature. We describe here an examination by differential scanning calorimetry in the region of the main transition of the phase behaviour of amphotericin B multilamellar liposomes used investigationally for patient treatment. Liposomes were composed of 7:3 dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (7:3 DMPC/DMPG) containing up to 33 mol% drug. Preparations in which pure DMPC or pure 1-oleoyl-2-stearoylphosphatidylcholine (OSPC) was substituted for 7:3 DMPC/DMPG were subjected to the same measurements for comparison. The DSC-derived partial phase diagrams were similar to those previously recorded using EPR spectroscopy for unsonicated liposomes of 7:3 DMPC/DMPG containing amphotericin B, and for mixtures with different pure saturated and unsaturated phosphatidylcholines (Grant, C.W.M., et al. (1989) Biochim. Biophys. Acta 984, 11-20). Fluidization onset temperatures for liposome host matrices were relatively unaffected by drug compared to the temperatures of completion. This effect was particularly marked for the unsaturated phospholipid matrix. Partial phase diagrams were interpreted as demonstrating that amphotericin B has a tendency to separate into a rigid phase within the membrane. This is consistent with molecular modelling considerations which suggest that amphotericin B may exist as oligomers in a phospholipid matrix. Drug-induced alterations of DSC melting profiles for the phospholipid bilayers studied were less extensive than those reported for partially sonicated preparations of 7:3 DMPC/DMPG (Janoff, A.S., et al. (1989) Proc. Natl. Acad. Sci. USA 85, 6122-6126). Melting profiles obtained did not change upon further sample incubation, suggesting that the hydrated preparation represented a thermodynamically stable form.