NMR-based molecular ruler for determining the depth of intercalants within the lipid bilayer

Locating intercalants within lipid bilayers using fluorescence quenching by bromophospholipids and iodophospholipids

In previous work, we have been able to determine the depth of intercalated molecules within the lipid bilayer using the solvent polarity sensitivity of three spectroscopic techniques: the ¹³C NMR chemical shift (δ); the fluorescence emission wavelength (λ_em), and the ESR β-H splitting constants (a_β-H). In the present paper, we use the quenching by a heavy atom (Br or I), situated at a known location along a phospholipid chain, as a probe of the location of a fluorescent moiety. We have synthesized various phospholipids with bromine (or iodine) atoms substituted at various locations along the lipid chain. The latter halolipids were intercalated in turn with various fluorophores into DMPC liposomes, biomembranes and erythrocyte ghosts. The most effective fluorescence quenching occurs when the heavy atom location corresponds to that of the fluorophore. The results show that generally speaking the fluorophore intercalates the same depth independent of which lipid bilayer is used. KBr (or KI) is the most effective quencher when the fluorophore resides in or at the aqueous phase. Presumably because of iodine's larger radius and spin coupling constant, the iodine analogs are far less discriminating in the depth range it quenches.

"Snorkelling" vs. "diving" in mixed micelles probed by means of a molecular bathymeter

A photoactive bathymeter based on a carboxylic acid moiety covalently linked to a signalling methoxynaphthalene (MNP) fluorophore has been designed to prove the concept of "snorkelling" vs. "diving" in mixed micelles (MM). The carboxylic acid "floats" on the MM surface, while the MNP unit sinks deep in MM. The rate constants of MNP fluorescence quenching by iodide, which remains basically in water, consistently decrease with increasing spacer length, revealing different regions. This is associated with the distance MNP should "dive" in MM to achieve protection from aqueous reactants. Unequivocal proof of the exergonic photoinduced electron transfer was obtained from the UV-visible spectral signature of I₃^- upon steady-state photolysis. The applicability of the bathymeter was examined upon testing a family of MNP derivatives. The obtained results were validated by comparison with different lipophilicity tests: (i) a modified version of the K_ow partition coefficient and (ii) the retention factor on thin layer chromatography. This concept could potentially be extended to test drugs or pharmacophores exhibiting any photoactive moiety.

NMR-based molecular ruler for determining the depth of intercalants within the lipid bilayer. Part IV: studies on ketophospholipids

In our companion paper, we described the preparation and intercalation of two homologous series of dicarbonyl compounds, methyl n-oxooctadecanoates and the corresponding n-oxooctadecanoic acids (n=4-16), into DMPC liposomes. (13)C NMR chemical shift of the various carbonyls was analyzed using an E(T)(30) solvent polarity-chemical shift correlation table and the corresponding calculated penetration depth (in Å). An iterative best fit analysis of the data points revealed an exponential correlation between E(T)(30) micropolarity and the penetration depth (in Å) into the liposomal bilayer. However, this study is still incomplete, since the plot lacks data points in the important area of moderately polarity, i.e., in the E(T)(30) range of 51-45.5 kcal/mol. To correct this lacuna, a family of ketophospholipids was prepared in which the above n-oxooctadecanoic acids were attached to the sn-2 position of a phosphatidylcholine with a palmitic acid chain at sn-1. To assist in assignment and detection several derivatives were prepared (13)C-enriched in both carbonyls. The various homologs were intercalated into DMPC liposomes and give points specifically in the missing area of the previous polarity-penetration correlation graph. Interestingly, the calculated exponential relationship of the complete graph was essentially the same as that calculated in the companion paper based on the methyl n-oxooctadecanoates and the corresponding n-oxooctadecanoic acids alone. The polarity at the midplane of such DMPC systems is ca. 33 kcal/mol and is not expected to change very much if we extend the lipid chains. This paper concludes with a chemical ruler that maps the changing polarity experienced by an intercalant as it penetrates the liposomal bilayer.

Use of Ethyl (Benzothiazol-2-ylsulfonyl)acetate for Malonic Ester-type Syntheses of Carboxylic Acids and Esters

A new methodology for the synthesis of substituted carboxylic acids is described. Alkylation of either ethyl (benzothiazol-2-ylsulfonyl)acetate or ethyl 2-(benzothiazol-2-ylsulfonyl)propionate was achieved with alkyl halides and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in dichloromethane solution. These products were then desulfinated and hydrolysed in one-pot under mild conditions to give substituted acetic acids in good-to-excellent yields.

Molecular insight into affinities of drugs and their metabolites to lipid bilayers

The penetration properties of drug-like molecules on human cell membranes are crucial for understanding the metabolism of xenobiotics and overall drug distribution in the human body. Here, we analyze partitioning of substrates of cytochrome P450s (caffeine, chlorzoxazone, coumarin, ibuprofen, and debrisoquine) and their metabolites (paraxanthine, 6-hydroxychlorzoxazone, 7-hydroxycoumarin, 3-hydroxyibuprofen, and 4-hydroxydebrisoquine) on two model membranes: dioleoylphosphatidylcholine (DOPC) and palmitoyloleoylphophatidylglycerol (POPG). We calculated the free energy profiles of these molecules and the distribution coefficients on the model membranes. The drugs were usually located deeper in the membrane than the corresponding metabolites and also had a higher affinity to the membranes. Moreover, the behavior of the molecules on the membranes differed, as they seemed to have a higher affinity to the DOPC membrane than to POPG, implying they have different modes of action in human (mostly PC) and bacterial (mostly PG) cells. As the xenobiotics need to pass through lipid membranes on their way through the body and the effect of some drugs might depend on their accumulation on membranes, we believe that detailed information of penetration phenomenon is important for understanding the overall metabolism of xenobiotics.

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from "pulling" coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives.

Using fluorescence to locate intercalants within the lipid bilayer of liposomes, bioliposomes and erythrocyte ghosts

In previous work, we have shown the utility of the "NMR technique" in locating intercalants within the lipid bilayer. We describe herein the development of a more sensitive and complementary "fluorescence technique" for this purpose and its application to liposomes, bioliposomes and erythrocyte ghosts. This technique is based on the observation in selected compounds of an excellent correlation between the emission wavelength (λ(em)) and Dimroth-Reichardt E(T)(30) polarity parameter for the solvent in which the fluorescence emission spectrum was obtained.

A reinvestigation of the reaction of coumarins with superoxide in the liposomal bilayer: correlation between depth and reactivity

Afri et al. reported in this journal (Free Radic. Biol. Med.32:605-618; 2002) that a direct relationship exists between the depth of alkanoylcoumarins 1 within the liposomal lipid bilayer and the rate at which they undergo superoxide-mediated saponification. These results were based on a correlation between the (13)C NMR chemical shift of polarizable carbonyl carbons and the E(T)(30) polarity they sense. Subsequent studies challenged these results, however, demonstrating that, in conjugated ketones and aldehydes, charge separation influences the E(T)(30) polarity measured. To elucidate whether this is true for conjugated esters such as coumarins as well, the nonconjugated analogs 3,4-dihydrocoumarins 11 and 15 were intercalated within DMPC liposomal bilayers and their relative locations within the liposomal bilayer were determined. The length of the alkyl chain substituted at C-4 and C-10 influences the depth of the substrates within the liposome. The location of these 3,4-dihydrocoumarins corresponds well with the conjugated analog coumarin 1-confirming the validity of the abovementioned results of Afri et al. The lack of substantial charge separation in the coumarin 1 system presumably results from the "swamping-out" effect of the ester oxygen. Instead of 1,3-delocalization of charge, typical of conjugated systems, delocalization of the nonbonding pair on the ester oxygen predominates.

NMR-based molecular ruler for determining the depth of intercalants within the lipid bilayer Part II. The preparation of a molecular ruler

We have previously shown how the location of an intercalant within the lipid bilayer can be qualitatively determined by using the excellent correlation that exists between the 13C NMR chemical shift of a polarizable carbon (e.g., the carbonyl or nitronyl carbon) and the polarity (using the Dimroth-Reichardt's ET(30) parameter) of the microenvironment in which that carbon resides. In a companion paper, we have determined criteria for reporter molecules that will assist us in converting this qualitative polarity data into quantitative Angstrom values. In the present paper, we report on our initial success in quantitatively mapping of the DMPC bilayer by linking two or more vertical points within a bilayer by both distance (in Angstroms) and ET(30) polarity. The results correlated well with the values obtained using the "parallax method" of Erwin London.