Structure and dynamics of cholic acid and dodecylphosphocholine-cholic acid aggregates

Comparative analysis of bile acid composition and metabolism in the liver of Bufo gargarizans aquatic larvae and terrestrial adults

Bile acids are crucial for lipid metabolism and their composition and metabolism differ among species. However, there have been no data on the differences in the composition and metabolism of bile acids between aquatic larvae and terrestrial adults of amphibians. This study explored the differences in composition and metabolism of bile acid between Bufo gargarizans larvae and adults. The results demonstrated that adult liver had a lower total bile acid level and a higher conjugated/total bile acid ratio than larval liver. Meanwhile, histological analysis revealed that the larvae showed a larger cross-sectional area of bile canaliculi lumen compared with the adults. The transcriptomic analysis showed that B. gargarizans larvae synthesized bile acids through both the alternative and the 24-hydroxylase pathway, while adults only synthesized bile acids through the 24-hydroxylase pathway. Moreover, bile acid regulator-related genes FXR and RXRα were highly expressed in adult, whereas genes involved in bile acid synthesis (CYP27A1 and CYP46A1) were highly expressed in larvae. The present study will provide valuable insights into understanding metabolic disorders and exploring novel bile acid-based therapeutics.

Bile Acid Sequestrants Based on Natural and Synthetic Gels

Bile acid sequestrants (BASs) are non-systemic therapeutic agents used for the management of hypercholesterolemia. They are generally safe and not associated with serious systemic adverse effects. Usually, BASs are cationic polymeric gels that have the ability to bind bile salts in the small intestine and eliminate them by excretion of the non-absorbable polymer-bile salt complex. This review gives a general presentation of bile acids and the characteristics and mechanisms of action of BASs. The chemical structures and methods of synthesis are shown for commercial BASs of first- (cholestyramine, colextran, and colestipol) and second-generation (colesevelam and colestilan) and potential BASs. The latter are based on either synthetic polymers such as poly((meth)acrylates/acrylamides), poly(alkylamines), poly(allylamines) and vinyl benzyl amino polymers or biopolymers, such as cellulose, dextran, pullulan, methylan, and poly(cyclodextrins). A separate section is dedicated to molecular imprinting polymers (MIPs) because of their great selectivity and affinity for the template molecules used in the imprinting technique. Focus is given to the understanding of the relationships between the chemical structure of these cross-linked polymers and their potential to bind bile salts. The synthetic pathways used in obtaining BASs and their in vitro and in vivo hypolipidemic activities are also introduced.

Distinctive Weak Interactions Underlie Diverse Nucleation and Small-Angle Scattering Behavior of Aqueous Cholesterol, Cholesteryl Hemisuccinate, and Glycocholic Acid

Increased total cholesterol is a major cause of serious heart ailments leading to an estimated 3 million deaths annually throughout the world. Understanding the flocculation behavior of small lipids is thus quintessential. Nucleation, small-angle scattering, and dynamical behavior of lipids and analogues like cholesterol (CHL), cholesteryl hemisuccinate (CHM), and glycocholic acid (GHL) are studied in water by molecular dynamics simulation. The study shows a distinct aggregation behavior of these physiologically relevant molecules owing to a systematic gradation in their non-bonding interactions with solvents and near neighbors. Spontaneous self-assemblies formed during simulation are observed to have different stability, aggregation patterns, and dynamics depending crucially on the nature of the hydrophobic/hydrophilic tails. With increasing hydrophilicity, in the order CHL < CHM < GHL, the aggregates become breakable and less compact, often interposed by water molecules in the interstitial spaces between the lipids. Small-angle scattering data obtained from our simulations provide insights toward the structural integrity and shape of the aggregates formed. Unique features are noticed while following the time evolution of the packing of the nucleated assemblies from the solution phase in terms of local density and molecular orientation. As hydrophilicity increases from CHL to GHL, the packing becomes progressively erratic with diverse angles between the molecular vectors. Surface electrostatic potential calculation indicates drastic increase in positive surface charge from CHL to CHM, which has strong implication in water and ion transport through membranes. These observations can be further correlated to comprehend the flocculation of cholesterol and bile acids in the human body.

Synergistic activity of bile salts and their derivatives in combination with conventional antimicrobial agents against Acinetobacter baumannii

ETHNOPHARMACOLOGICAL RELEVANCE

Bile traditionally was used in wound healing, having erodent, antioxidant and antimicrobial potential. Acinetobacter baumannii is a frequent etiological agent of wound infections, exhibiting high level of resistance to conventional antibiotics.

AIM OF THE STUDY

To determine the effect of selected bile acid sodium salts and their 3-dehydro (i.e. 3-oxo) derivatives, as well as their combinations with commercial antibiotics against A. baumanniia, to confirm bile ethnopharmacological application in wound healing from aspect of microbiology.

MATERIALS AND METHODS

The sensitivity of reference and multidrug resistant (MDR) A. baumannii strains to bile salts, their derivatives and conventional antibiotics were examined by a microtiter plate method. The interaction of bile salts/derivatives and antibiotics was examined by a checkerboard method and time kill curve method. The interaction of bile salts with ciprofloxacin in terms of micelles formation was examined by DOSY NMR technique.

RESULTS

The bile salts sodium deoxycholate (Na-DCA) and sodium chenodeoxycholate (Na-CDCA), as well as their derivatives sodium 3-dehydro-deoxycholate (Na-3DH-DCA) and sodium 3-dehydro-chenodeoxycholate (Na-3DH-CDCA), potentiate antibiotic activity and resensitize A. baumannii. The bile salts and their derivatives enhance A. baumannii sensitivity to antibiotics, particularly those that should penetrate cell to exhibit activity. The sodium salts of bile acid derivatives, namely Na-3DH-DCA and Na-3DH-CDCA, showed synergy against both reference and MDR strain in combination with ciprofloxacin or gentamicin, while synergy with gentamicin was obtained in all combinations, regardless of bile salt type and bacterial strains. The synergy with Na-3DH-CDCA was further confirmed by the time-kill curve method, as bacterial number decreased after 12 h. NMR experiment revealed that this bile salt derivative and ciprofloxacin form co-aggregates when bile salts concentration was higher than critical micelle concentrations (CMC), which indicate the possibility that bile salts enhance ciprofloxacin cell penetration by membrane destabilization, contributing to the synergy.

CONCLUSION

The synergistic interactions between bile salts or derivatives with ciprofloxacin and particularly gentamicin represent a promising strategy for the treatment of A. baumannii wound infections.

How to make an undruggable enzyme druggable: lessons from ras proteins

Significant advances have been made toward discovering allosteric inhibitors for challenging drug targets such as the Ras family of membrane-associated signaling proteins. Malfunction of Ras proteins due to somatic mutations is associated with up to a quarter of all human cancers. Computational techniques have played critical roles in identifying and characterizing allosteric ligand-binding sites on these proteins, and to screen ligand libraries against those sites. These efforts, combined with a wide range of biophysical, structural, biochemical and cell biological experiments, are beginning to yield promising inhibitors to treat malignancies associated with mutated Ras proteins. In this chapter, we discuss some of these developments and how the lessons learned from Ras might be applied to similar other challenging drug targets.

Electrophoretic deposition of polymethylmethacrylate and composites for biomedical applications

For the first time, an electrophoretic deposition (EPD) method has been developed for the deposition of polymethylmethacrylate (PMMA) and PMMA-alumina films for biomedical implant applications. The proposed biomimetic approach was based on the use of a bile salt, sodium cholate (NaCh), which served as a multifunctional solubilizing, charging, dispersing and film-forming agent. Investigations revealed PMMA-Ch^- and PMMA-alumina interactions, which facilitated the deposition of PMMA and PMMA-alumina films. This approach allows for the use of a non-toxic water-ethanol solvent for PMMA. The proposed deposition strategy can also be used for co-deposition of PMMA with other functional materials. The PMMA and composite films were tested for biomedical implant applications. The PMMA-alumina films showed statistically improved metabolic results compared to both the bare stainless steel substrate and pure PMMA films. Alkaline phosphatase (ALP) activity affirmed the bioactivity and osteoconductive potential of PMMA and composite films. PMMA-alumina films showed greater ALP activity than both the PMMA-coated and uncoated stainless steel.

The Fluidity of Phosphocholine and Maltoside Micelles and the Effect of CHAPS

The dynamics of phosphocholine and maltoside micelles, detergents frequently used for membrane protein structure determination, were investigated using electron paramagnetic resonance of spin probes doped into the micelles. Specifically, phosphocholines are frequently used detergents in NMR studies, and maltosides are frequently used in x-ray crystallography structure determination. Beyond the structural and electrostatic differences, this study aimed to determine whether there are differences in the local chain dynamics (i.e., fluidity). The nitroxide probe rotational dynamics in longer chain detergents is more restricted than in shorter chain detergents, and maltoside micelles are more restricted than phosphocholine micelles. Furthermore, the micelle microviscosity can be modulated with mixtures, as demonstrated with mixtures of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate with n-dodecylphosphocholine, n-tetradecylphosphocholine, n-decyl-β-D-maltoside, or n-dodecyl-β-D-maltoside. These results indicate that observed differences in membrane protein stability in these detergents could be due to fluidity in addition to the already determined structural differences.

Characterization of the self-assembly and size dependent structural properties of dietary mixed micelles by molecular dynamics simulations

The bile salts and phospholipids are secreted by the gallbladder to form dietary mixed micelles in which the solvation of poorly absorbed lipophilic drugs and nutraceuticals take place. A comprehensive understanding of the micellization and structure of the mixed micelles are crucial to design effective delivery systems for such substances. In this study, the evolution of the dietary mixed micelle formation under physiologically relevant concentrations and the dependence of structural properties on micelle size were investigated through coarse-grained molecular dynamics simulations. The MARTINI force field was used to model cholate and POPC as the representative bile salt and phospholipid, respectively. The micellization behavior was similar under both fasted and fed state concentrations. Total lipids concentration and the micelle size did not affect the internal structure of the micelles. All the micelles were slightly ellipsoidal in shape independent of their size. The extent of deviation from spherical geometry was found to depend on the micellar POPC/cholate ratio. We also found that the surface and core packing density of the micelles increased with micelle size. The former resulted in more perpendicular alignments of cholates with respect to the surface, while the latter resulted in an improved alignment of POPC tails with the radial direction and more uniform core density.

Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification

Membrane proteins represent a considerable fraction of pharmaceutical drug targets. A computational technique to identify ligand binding pockets in these proteins is therefore of great importance. We recently reported such a technique called pMD-membrane that utilizes small molecule probes to detect ligand binding sites and surface hotspots on membrane proteins based on probe-based molecular dynamics simulation. The current work extends pMD-membrane to a diverse set of small organic molecular species that can be used as cosolvents during simulation of membrane proteins. We also describe a projection technique for globally quantifying probe densities on the protein surface and introduce a technique to construct surface topography maps directly from the probe-binding propensity of surface residues. The map reveals surface patterns and geometric features that aid in filtering out high probe density hotspots lacking pocketlike characteristics. We demonstrate the applicability of the extended pMD-membrane and the new analysis tool by exploring the druggability of full-length G12D, G12V, and G13D oncogenic K-Ras mutants bound to a negatively charged lipid bilayer. Using data from 30 pMD-membrane runs conducted in the presence of a 2.8 M cosolvent made up of an equal proportion of seven small organic molecules, we show that our approach robustly identifies known allosteric ligand binding sites and other reactive regions on K-Ras. Our results also show that accessibility of some pockets is modulated by differential membrane interactions.

Computational Models of the Gastrointestinal Environment. 1. The Effect of Digestion on the Phase Behavior of Intestinal Fluids

Improved models of the gastrointestinal environment have great potential to assist the complex process of drug formulation. Molecular dynamics (MD) is a powerful method for investigating phase behavior at a molecular level. In this study we use multiple MD simulations to calculate phase diagrams for bile before and after digestion. In these computational models, undigested bile is represented by mixtures of palmitoyl-oleoylphosphatidylcholine (POPC), sodium glycodeoxycholate (GDX), and water. Digested bile is modeled using a 1:1 mixture of oleic acid and palmitoylphosphatidylcholine (lysophosphatidylcholine, LPC), GDX, and water. The computational phase diagrams of undigested and digested bile are compared, and we describe the typical intermolecular interactions that occur between phospholipids and bile salts. The diffusion coefficients measured from MD simulation are compared to experimental diffusion data measured by DOSY-NMR, where we observe good qualitative agreement. In an additional set of simulations, the effect of different ionization states of oleic acid on micelle formation is investigated.

Interaction of Biologically Active Flavins inside Bile Salt Aggregates: Molecular Level Investigation

In this work we have studied the photophysics of biologically active flavin molecule lumichrome (LCM) in different bile-salt aggregates. With alteration of the functional groups of the bile salts, the photophysics of confined fluorophore is largely affected and shows difference in their spectral behavior. This study also reveals the selective prototropic species of LCM present in bile salt aggregates. In the presence of the bile salt aggregates, LCM molecule shows excitation and emission wavelength-dependent emission properties, indicating switch over of the structural change of different prototropic form of the LCM molecule. The observation of higher rotational relaxation time in NaDC aggregates compared to NaTC aggregates clearly reflects that NaDC aggregates are more rigid due to its greater hydrophobicity and large in size, which is capable to bind the guest molecule more into their nanoconfined medium. Moreover, due to less acidic nature, NaDC aggregates have more ability to accept hydrogen bond from the LCM molecule and show the selective formation of isoalloxazine N10 anion (A1 monoanionic form) of LCM.

pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins

Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.

Water confined in self-assembled ionic surfactant nano-structures

We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on the structural features of the absorbed fluid. On increasing the hydration level under ambient conditions, the model exhibits a series of three distinct phases: lamellar, cylindrical and micellar. We characterize the different structures in terms of diffraction patterns and neutron scattering static structure factors. We demonstrate that the rate of variation of the nano-metric sizes of the self-assembled water domains shows peculiar changes in the different phases. We also analyse in depth the structure of the water/confining matrix interfaces, the implications of their tunable degree of curvature, and the properties of water molecules in different restricted environments. Finally, we compare our results with experimental data and their impact on a wide range of important scientific and technological domains, where the behavior of water at the interface with soft materials is crucial.

Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates

In this article, we have investigated the effect of hydrophilic 1-butyl-3-methylimidazolium tetrafluoroborate on the aggregation properties of sodium deoxycholate (NaDC).

New polyfluorothiopropanoyloxy derivatives of 5β-cholan-24-oic acid designed as drug absorption modifiers

A series of final six propanoyloxy derivatives of 5β-cholan-24-oic acid (tridecafluoroctylsulfanyl- and tridecafluoroctylsulfinylethoxycarbonylpropanoyloxy derivatives) as potential drug absorption promoters (skin penetration enhancers, intestinal absorption promoters) was generated by multistep synthesis. Structure confirmation of all generated compounds was accomplished by (1)H NMR, (13)C NMR, IR and MS spectroscopy methods. All the prepared compounds were analyzed using RP-TLC, and their lipophilicity (RM) was determined. The hydrophobicity (log P), solubility (logS), polar surface area (PSA) and molar volume (MV) of the studied compounds were also calculated. All the target compounds were tested for their in vitro transdermal penetration effect and as potential intestinal absorption enhancers. The cytotoxicity of all the evaluated compounds was evaluated against normal human skin fibroblast cells. Their anti-proliferative activity was also assessed against human cancer cell lines: T-lymphoblastic leukaemia cell line and breast adenocarcinoma cell line. One compound showed high selective cytotoxicity against human skin fibroblast cells and another compound possessed high cytotoxicity against breast adenocarcinoma cell line and skin fibroblast cells. Only one compound expressed anti-proliferative effect on leukaemia and breast adenocarcinoma cells without affecting the growth of normal cells, which should be promising in potential development of new drugs. Most of the target compounds showed minimal anti-proliferative activity (IC50>37μM), indicating they would have moderate cytotoxicity when administered as chemical absorption modifiers. The relationships between the lipophilicity/polarity and the chemical structure of the studied compounds as well as the relationships between their chemical structure and penetration enhancement effect are discussed in this article.

New propanoyloxy derivatives of 5β-cholan-24-oic acid as drug absorption modifiers

A series of final twelve propanoyloxy derivatives of 5β-cholan-24-oic acid (O-propanoyl derivatives of cholic acid) as potential drug absorption modifiers (skin penetration enhancers, intestinal absorption promoters) was generated by multistep synthesis. Structure confirmation of all generated compounds was accomplished by 1H NMR, 13C NMR, IR and MS spectroscopy methods. All the prepared compounds were analyzed using RP-TLC, and their lipophilicity (RM) was determined. The hydrophobicity (log P), solubility (log S), polar surface area (PSA) and molar volume (MV) of the studied compounds were also calculated. All the target compounds were tested for their in vitro transdermal penetration effect and as potential intestinal absorption enhancers. The cytotoxicity of all the evaluated compounds was evaluated against normal human skin fibroblast cells. Their anti-proliferative activity was also assessed against human cancer cell lines: T-lymphoblastic leukemia cell line and breast adenocarcinoma cell line. One compound showed selective cytotoxicity against human skin fibroblast cells and another compound possessed the highest cytotoxicity against all the tested cell lines. Only one compound expressed anti-proliferative effect on leukemia cancer cells without affecting the growth of normal cells, which should be promising in potential development of new drugs. Most of the target compounds showed minimal anti-proliferative activity (IC50>37 μM), indicating they would have moderate cytotoxicity when administered as chemical absorption modifiers. The relationships between the lipophilicity/polarity and the chemical structure of the studied compounds as well as the relationships between their chemical structure and enhancement effect are discussed in this article.

Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles

Non-steroidal anti-inflammatory drugs (NSAIDs) are frequently used to treat chronic pain and inflammation. However, prolonged use of NSAIDs has been known to result in Gastrointestinal (GI) ulceration/bleeding, with a bile-mediated mechanism underlying their toxicity to the lower gut. Bile acids (BAs) and phosphatidylcholines (PCs), the major components of bile, form mixed micelles to reduce the membrane disruptive actions of monomeric BAs and simple BA micelles. NSAIDs are suspected to alter the BA/PC balance in the bile, but the molecular interactions of NSAID-BA or NSAID-BA-PC remain undetermined. In this work, we used a series of all-atom molecular dynamics simulations of cholic acid (CA), ibuprofen (IBU) and dodecylphosphocholine (DPC) mixtures to study the spontaneous aggregation of CA and IBU as well as their adsorption on a DPC micelle. We found that the size of CA-IBU mixed micelles varies with their molar ratio in a non-linear manner, and that micelles of different sizes adopt similar shapes but differ in composition and internal interactions. These observations are supported by NMR chemical shift changes, NMR ROESY crosspeaks between IBU and CA, and dynamic light scattering experiments. Smaller CA-IBU aggregates were formed in the presence of a DPC micelle due to the segregation of CA and IBU away from each other by the DPC micelle. While the larger CA-IBU aggregates arising from higher IBU concentrations might be responsible for NSAID-induced intestinal toxicity, the absence of larger CA-IBU aggregates in the presence of DPC micelles may explain the observed attenuation of NSAID toxicity by PCs.

New micellar morphologies from amphiphilic block copolymers: disks, toroids and bicontinuous micelles

This review discusses recent advances of the self-assembly of amphiphilic block copolymers into novel micellar architectures in dilute solutions. The formation of multi-compartment, disk-like, toroidal and bicontinuous micelles and the macromolecular architectures that give rise to these morphologies are reviewed and discussed.