Crystal structure of chenodeoxycholic acid, ursodeoxycholic acid and their two 3beta,7alpha- and 3beta,7beta-dihydroxy epimers

Gut Microbial Profile Changes in Patients with Gallbladder Stones after UDCA/CDCA Treatment

Background: Ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) are used to treat patients with asymptomatic or mildly symptomatic gallstone disease. This study was conducted to evaluate the efficacy of gallbladder (GB) stone dissolution by UDCA/CDCA and the impact of treatment on gut microbial profiles. Methods: Fifteen treatment-naive patients with GB stones were initially included, but two dropped out during the treatment period. UDCA/CDCA was administered for 6 months. Abdominal ultrasonography was performed to evaluate response to treatment. In addition, fecal samples were collected before and after treatment for gut microbiome profiling. Then, 16S ribosomal RNA gene sequencing was carried out on fecal samples obtained before and after treatment, and results were compared with those of forty healthy controls. Results: Eight (62%) of the thirteen evaluable patients treated with UDCA/CDCA responded to treatment (four achieved complete GB stone resolution and four partial dissolution). Taxonomic compositions of fecal samples at the phylum level showed a significantly lower relative abundance of the Proteobacteria phylum in the pre-UDCA/CDCA group than in the healthy control group (p = 0.024). At the genus level, the relative abundances of five bacteria (Faecalibacterium, Roseburia, Lachnospira, Streptococcus, and Alistipes) differed in the control and pre-UDCA/CDCA group. Interestingly, the abundance of Roseburia was restored after 6 months of UDCA/CDCA treatment. Conclusion: Gut microbial dysbiosis was observed in GB stone patients and partially reversed by UDCA/CDCA treatment, which also effectively dissolved GB stones.

Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis

Numerous repositioned drugs have been sought to decrease the severity of SARS-CoV-2 infection. It is known that among its physicochemical properties, Ursodeoxycholic Acid (UDCA) has a reduction in surface tension and cholesterol solubilization, it has also been used to treat cholesterol gallstones and viral hepatitis. In this study, molecular docking was performed with the SARS-CoV-2 Spike protein and UDCA. In order to confirm this interaction, we used Molecular Dynamics (MD) in "SARS-CoV-2 Spike protein-UDCA". Using another system, we also simulated MD with six UDCA residues around the Spike protein at random, naming this "SARS-CoV-2 Spike protein-6UDCA". Finally, we evaluated the possible interaction between UDCA and different types of membranes, considering the possible membrane conformation of SARS-CoV-2, this was named "SARS-CoV-2 membrane-UDCA". In the "SARS-CoV-2 Spike protein-UDCA", we found that UDCA exhibits affinity towards the central region of the Spike protein structure of - 386.35 kcal/mol, in a region with 3 alpha helices, which comprises residues from K986 to C1032 of each monomer. MD confirmed that UDCA remains attached and occasionally forms hydrogen bonds with residues R995 and T998. In the presence of UDCA, we observed that the distances between residues atoms OG1 and CG2 of T998 in the monomers A, B, and C in the prefusion state do not change and remain at 5.93 ± 0.62 and 7.78 ± 0.51 Å, respectively, compared to the post-fusion state. Next, in "SARS-CoV-2 Spike protein-6UDCA", the three UDCA showed affinity towards different regions of the Spike protein, but only one of them remained bound to the region between the region's heptad repeat 1 and heptad repeat 2 (HR1 and HR2) for 375 ps of the trajectory. The RMSD of monomer C was the smallest of the three monomers with a value of 2.89 ± 0.32, likewise, the smallest RMSF was also of the monomer C (2.25 ± 056). In addition, in the simulation of "SARS-CoV-2 membrane-UDCA", UDCA had a higher affinity toward the virion-like membrane; where three of the four residues remained attached once they were close (5 Å, to the centre of mass) to the membrane by 30 ns. However, only one of them remained attached to the plasma-like membrane and this was in a cluster of cholesterol molecules. We have shown that UDCA interacts in two distinct regions of Spike protein sequences. In addition, UDCA tends to stay bound to the membrane, which could potentially reduce the internalization of SARS-CoV-2 in the host cell.

Crystal structure of a lithium salt of a glucosyl derivative of lithocholic acid

The crystal structure of a Li(+) salt of a glucosyl derivative of lithocholic acid (lithium 3α-(α-d-glucopyranosyl)-5β-cholan-24-oate) has been solved. The crystal belongs to the orthorhombic system, P212121 spatial group, and includes acetone and water in the structure with a 1:1:2 stoichiometry. Monolayers, having a hydrophobic interior and hydrophilic edges, are recognized in the crystal structure. Li(+) is coordinated to three hydroxyl groups of three different glucose residues, with two of them belonging to the same monolayer. A fourth molecule, located in this monolayer, is involved in the coordination of the cation through the carboxylate ion by an electrostatic interaction, thus completing a distorted tetrahedron. All Li(+)-oxygen distances values are very close to the sum of the ionic radius of Li(+) and van der Waals radius of oxygen. Each steroid molecule is linked to other five steroid molecules through hydrogen bonds. Water and acetone are also involved in the hydrogen bond network. A hierarchical organization can be recognized in the crystal, the helical assembly along 21 screw axes being left-handed.

Hydroxylation of lithocholic acid by selected actinobacteria and filamentous fungi

Selected actinobacteria and filamentous fungi of different taxonomy were screened for the ability to carry out regio- and stereospecific hydroxylation of lithocholic acid (LCA) at position 7β. The production of ursodeoxycholic acid (UDCA) was for the first time shown for the fungal strains of Bipolaris, Gibberella, Cunninghamella and Curvularia, as well as for isolated actinobacterial strains of Pseudonocardia, Saccharothrix, Amycolatopsis, Lentzea, Saccharopolyspora and Nocardia genera. Along with UDCA, chenodeoxycholic (CDCA), deoxycholic (DCA), cholic (CA), 7-ketodeoxycholic and 3-ketodeoxycholic acids were detected amongst the metabolites by some strains. A strain of Gibberella zeae VKM F-2600 expressed high level of 7β-hydroxylating activity towards LCA. Under optimized conditions, the yield of UDCA reached 90% at 1g/L of LCA and up to 60% at a 8-fold increased substrate loading. The accumulation of the major by-product, 3-keto UDCA, was limited by using selected biotransformation media.

Crystal structure of head-to-head dimers of cholic and deoxycholic acid derivatives with different symmetric bridges

The crystal structure of three head-to-head dimers (having two cholic acid or deoxycholic acid units) linked at carbon atoms C3 by aromatic or alkyl bridges is studied. An internal coordinates system is necessary for describing the relative orientation in the space of the two bile acid residues. Five angles (three torsion and two common ones) are necessary for defining the relative position of both steroid residues in space. Carbon atoms C3 (which always carries a α-hydroxy group in natural bile acids), and C10 and C13 (which always carry β-methyl groups) of each steroid residue are suitable for this purpose. Furthermore, the distance between each C3 carbon atoms of both steroid residues will allow one to locate the steroids in space. The three dimers selected provide a large range of values for these angles. The packing, hydrogen bond network, and location of guest in the three crystals are discussed.

Ice-like encapsulated water by two cholic acid moieties

Starting from the structure of ice (in which each water molecule is surrounded by other four water molecules forming a tetrahedron with a value of 4.51Å for the edge O-O distance), and the knowledge that this value also corresponds to the O7-O12 distance of the skeleton of cholic acid, it is hypothesized that two steroid cholic acid moieties, with an appropriate steroid-steroid distance and a belly-to-belly orientation, could encapsulate a single water molecule between them. To check this hypothesis two succinyl derivatives of cholic acid (a monomer and the related head-head dimer in which the succinyl group is the linking bridge) were designed. The expected "ice-like" structure is found in the crystal of the dimer. There is a hydrogen bond synergy between those participating in the "ice-like" structure, and those in which the bridge is involved with the O7-H hydroxy group and the side chain of the steroid.

Formation of tubules by p-tert-butylphenylamide derivatives of chenodeoxycholic and ursodeoxycholic acids in aqueous solution

The formation of tubules by p-tert-butylphenylamide derivatives of chenodeoxycholic and ursodeoxycholic acids in aqueous solution is investigated. The critical aggregation concentrations of the new surfactants are much lower than those of ursodeoxycholate and chenodeoxycholate, indicating the enhanced surfactant properties resulting by the presence of the hydrophobic p-tert-butylphenyl group. The molecular areas at the air-water interface suggest the formation of monolayer films with molecules upright oriented. The shape of the aggregates was investigated by TEM. The main structure present in solution corresponds to tubules. The estimated value for the wall thickness of tubules suggests that a bilayer structure is formed. Host of positively charged latex beads by tubules suggests that their inner and outer surfaces are negatively charged. The acid form of the chenodeoxycholate derivative was recrystallized from toluene and its crystal structure analyzed.

Microwave assisted synthesis and solid-state characterization of lithocholyl amides of isomeric aminopyridines

Microwave (MW) assisted synthesis and solid state structural characterizations of novel lithocholyl amides of 2-, 3-, and 4-aminopyridine are reported. It is shown that the MW technique is a proper method in the preparation of N-lithocholyl amides of isomeric aminopyridines. It offers many advantages compared to conventional heating. The molecular and crystal structures as well as the polymorphic and hydrated forms of prepared conjugates with their thermodynamic stabilities have been characterized by means of high resolution liquid- and solid-state NMR spectroscopy, single crystal and powder X-ray diffraction, and thermogravimetric analysis. Owing to the many biological functions of bile acids and amino substituted nitrogen heterocycles, knowledge of the crystal packing of these novel conjugates may have relevance for potential pharmaceutical applications.

Supramolecular structures generated by a p-tert-butylphenylamide derivative of deoxycholic acid. From planar sheets to tubular structures through helical ribbons

The formation of supramolecular structures initiated by a p-tert-butylphenylamide derivative of deoxycholic acid (Na-t-butPhDC) is investigated. At 1.18 mM concentration of Na-t-butPhDC and 37 degrees C, initial flat ribbons are observed which self-transform into helical ribbons (with a mean pitch angle of 47 +/- 6 degrees) which finally originate molecular tubes with an external diameter of 241 +/- 28 nm. Most of the molecular tubes show helical markings with a pitch angle value of 45 +/- 4 degrees, in full agreement with predictions of simple models based on chiral elastic properties of the membrane. A lateral association mechanism is proposed to account for the growth of the external diameter (from 225 +/- 32 to 546 +/- 59 nm) of tubes with time at 3.99 mM.

Influence of the solvent ability to form hydrogen bonds in the crystal structure of ([3beta,5beta,7alpha,12alpha]-3[(norbornyl-2-acetyl)-amino]-7,12-dihydroxycholan-24-oic acid (a norbornyl derivative of cholic acid)

A norbornyl-2-acetyl derivative of cholic acid ([3beta,5beta,7alpha,12alpha]-3[(norbornyl-2-acetyl)-amino]-7,12-dihydroxycholan-24-oic acid -NbCH2CA-) was synthesized and recrystallized in two dipolar aprotic solvents (acetone, DMSO) and in one protic solvent (2-propanol). In DMSO and acetone the crystals are orthorhombic, P2(1)2(1)2(1) (all their parameters being very similar) while in 2-propanol the crystal is monoclinic, P2(1). The inclusion complexes with the solvent have a 1:1 stochiometry with DMSO and acetone and 1:2 with 2-propanol. All solvents are forming a hydrogen bond with the amide bond of the bridge between the norbornyl residue and the steroid nucleus of the bile acid. In DMSO and acetone the beta side of the steroid groups lies in the same region facilitating hydrophobic interactions, and the molecules are disposed in an antiparallel orientation (the methyl groups having a beta interdigitation) forming bilayers. The width of the bilayers is 9.231 A and 8.859 A in DMSO and acetone, respectively. A lamellar structure is also evident for the crystal in 2-propanol (the width being 11.908 A), but the packing is different from the previous one since a sliding between the steroid groups is observed and the methyl groups are not interdigitated. Four different hydrogen bonds are established by every steroid molecule in the NbCH2CA/DMSO (or acetone) crystal. This hydrogen bond network interconnects the hydrophilic regions of the lamellar structure. The hydrogen bond network of the NbCH2CA:2-propanol crystal is different because of the different abilities of 2-propanol to form hydrogen bonds. The side chain has a ttti conformation in the two orthorhombic crystals, and a tgtg one in the monoclinic crystal.