The Role of Bile Acids in the Human Body and in the Development of Diseases

Bile acids are specific and quantitatively important organic components of bile, which are synthesized by hepatocytes from cholesterol and are involved in the osmotic process that ensures the outflow of bile. Bile acids include many varieties of amphipathic acid steroids. These are molecules that play a major role in the digestion of fats and the intestinal absorption of hydrophobic compounds and are also involved in the regulation of many functions of the liver, cholangiocytes, and extrahepatic tissues, acting essentially as hormones. The biological effects are realized through variable membrane or nuclear receptors. Hepatic synthesis, intestinal modifications, intestinal peristalsis and permeability, and receptor activity can affect the quantitative and qualitative bile acids composition significantly leading to extrahepatic pathologies. The complexity of bile acids receptors and the effects of cross-activations makes interpretation of the results of the studies rather difficult. In spite, this is a very perspective direction for pharmacology.     

Acid/base controllable molecular recognition

The study of controllable molecular recognition in supramolecular receptors is important for elucidating design strategies that can lead to external control of molecular recognition applications. In this work, we present the design and synthesis of an asymmetric (TTF) tetrathiafulvalene-calix[4]pyrrole receptor and show that its recognition of 1,3,5-trinitrobenzene (TNB) can be controlled by an acid/base input. The new receptor is composed of three identical TTF units and a fourth TTF unit appended with a phenol moiety. Investigation of the host-guest complexation taking place between the TTF-calix[4]pyrrole receptor and the TNB guests was studied by means of absorption and (1)H NMR spectroscopy; this revealed that the conformation of the molecular receptor can be switched between locked and unlocked states by using base and acid as the input. In the unlocked state, the receptor is able to accommodate two TNB guest molecules, whereas the guests are not able to bind to the receptor in the locked state. This work serves to illustrate how external control (acid/base) of a receptor may be used to direct the molecular recognition of guests (TNBs). It has led to a new controllable molecular recognition system that functions as an acid/base switch.     

Synthesis and pharmacological characterization at glutamate receptors of erythro- and threo-tricholomic acid and homologues thereof

The erythro- and threo-amino-(3′-hydroxy-4′,5′-dihydro-isoxazol-5′-yl)-acetic acids, stereoisomers of tricholomic acid, were synthesized along with the corresponding higher homologues erythro- and threo-amino-(3′-carboxy-4′,5′-dihydro-isoxazol-5′-yl)-acetic acids. The target compounds were prepared via the 1,3-dipolar cycloaddition of a suitable nitrile oxide to (±)-2-tert-butoxycarbonylamino-3-buten-1-ol. Such a strategy allowed the synthesis of the two stereoisomeric amino acids in comparable amounts. The pharmacological activity of these compounds was investigated at ionotropic and metabotropic glutamate receptors (iGluRs and mGluRs) by means of receptor binding assays to rat cortical membranes, electrophysiological tests and second messenger assays at cloned receptors expressed in CHO cells. Their pharmacological profiles were compared to those of l-glutamate and of the previously described selective NMDA receptor antagonists 5-(2-amino-2-carboxyethyl)-4,5-dihydroisoxazole-3-carboxylic acids in order to highlight the effect of increasing/reducing the distance between the amino acid moiety and the distal acid group, which represent the two pharmacophoric entities.     

Molecular field analysis and 3D-quantitative structure-activity relationship study (MFA 3D-QSAR) unveil novel features of bile acid recognition at TGR5

Bile acids regulate nongenomic actions through the activation of TGR5, a membrane receptor that is G protein-coupled to the induction of adenylate cyclase. In this work, a training set of 43 bile acid derivatives is used to develop a molecular interaction field analysis (MFA) and a 3D-quantitative structure-activity relationship study (3D-QSAR) of TGR5 agonists. The predictive ability of the resulting model is evaluated using an external set of compounds with known TGR5 activity, and six bile acid derivatives whose unknown TGR5 activity is herein assessed with in vitro luciferase assay of cAMP formation. The results show a good predictive model and indicate a statistically relevant degree of correlation between the TGR5 activity and the molecular interaction fields produced by discrete positions of the bile acid scaffold. This information is instrumental to extend on a quantitative basis the current structure-activity relationships of bile acids as TGR5 modulators and will be fruitful to design new potent and selective agonists of the receptor.     

Using a pharmacophore representation concept to elucidate molecular similarity of dopamine antagonists

The pharmacophoric concept plays an important role in ligand-based drug design methods to describe the similarity and diversity of molecules, and could also be exploited as a molecular representation scheme. A three-point pharmacophore method was used as a molecular representation perception. This procedure was implemented for dopamine antagonists of the D(2) receptor subtype. The molecular structures of the antagonists included in this analysis were categorized into two structurally distinct classes. Using structural superposition with internal energy minimization, two pharmacophore models were deduced. Based on these two models other D(2) antagonists that fulfil them were derived and studied. This procedure aided the identification of the common 3D patterns present in diverse molecules that act at the same biological target and the extraction of a common molecular framework for the two structural classes. The pharmacophoric information was found to be suitable for guiding superposition of structurally diverse molecules, using a more biologically meaningful selection of the targeting points.     

基于锁核酸的高选择性新型分子信标

通过在分子信标的错配位点修饰锁核酸, 不仅可有效地改善其单碱基错配识别能力, 还可提高检测灵敏度. 因而有望发展成为一种通用的提高分子信标单碱基错配识别能力的方法.     

Capturing molecules with templated materials--analysis and rational design of molecularly imprinted polymers

The creation of synthetic tailor-made receptors capable of recognizing desired molecular targets with high affinity and selectivity is a persistent long-term goal for researchers in the fields of chemical, biological, and pharmaceutical research. Compared to biomacromolecular receptors, these synthetic receptors promise simplified production and processing, less costs, and more robust receptor architectures. During recent decades, molecularly imprinted polymers (MIPs) are widely considered mimics of natural molecular receptors suitable for a diversity of applications ranging from biomimetic sensors, to separations and biocatalysis.A remaining challenge for the next generation of MIPs is the synthesis of deliberately designed and highly efficient receptor architectures suitable for recognizing biologically relevant molecules, for which natural receptors are either not prevalent, or difficult to isolate and utilize. Hence, this review discusses recent advances in synthetic receptor technology for biomolecules (e.g. drugs, amino acids, steroids, proteins, entire cells, etc.) via molecular imprinting techniques. Surface imprinting methods and epitope imprinting approaches have been introduced for protein recognition at imprinted surfaces. Imprinting techniques in aqueous solution or organic-water co-solvents have been introduced avoiding denaturation of biomolecules during MIP synthesis. In addition, improved bioreactivity of entire enzyme or active site mimics generated by molecular imprinting will be highlighted. Finally, the emerging importance of molecular modeling and molecular dynamics studies detailing the intermolecular interactions between the template species, the porogenic solvent molecules, and the involved monomer and cross-linker in the pre-polymerization solution will be addressed yielding a rational approach toward next-generation MIP technology.     

Identification of novel peptides that stimulate human neutrophils

Neutrophils play a key role in innate immunity, and the identification of new stimuli that stimulate neutrophil activity is a very important issue. In this study, we identified three novel peptides by screening a synthetic hexapeptide combinatorial library. The identified peptides GMMWAI, MMHWAM, and MMHWFM caused an increase in intracellular Ca2+ in a concentration-dependent manner via phospholipase C activity in human neutrophils. The three peptides acted specifically on neutrophils and monocytes and not on other non-leukocytic cells. As a physiological characteristic of the peptides, we observed that the three peptides induced chemotactic migration of neutrophils as well as stimulated superoxide anion production. Studying receptor specificity, we observed that two of the peptides (GMMWAI and MMHWFM) acted on formyl peptide receptor (FPR)1 while the other peptide (MMHWAM) acted on FPR2. Since the three novel peptides were specific agonists for FPR1 or FPR2, they might be useful tools to study FPR1- or FPR2-mediated immune response and signaling.     

Recognition and Stabilization of Unsaturated Fatty Acids by a Polyaromatic Receptor

Selective recognition of natural fatty acids is intrinsically difficult owing to the long, flexible, and poorly interactive hydrocarbon chains. Inspired by biological recognition systems, we herein demonstrate the exclusive binding of a monounsaturated fatty acid by an artificial polyaromatic receptor from a mixture of the unsaturated and corresponding saturated substrates (i.e., oleic and stearic acids) in water. The selectivity stems from multiple CH–π/π–π interactions between the host framework and the guest in its roughly coiled conformation. Moreover, competitive binding experiments elucidate higher binding affinities of the receptor for oligo‐ and polyunsaturated fatty acids (e.g., α‐linolenic acid and EPA). Within the receptor, the biosubstrates are remarkably stabilized against air, light, and heat owing to the polyaromatic shielding effect.     

基于框架核酸的细胞表面受体配体相互作用研究进展

细胞表面受体与配体之间的特异性相互作用在细胞生物学过程中起着重要作用。然而,与均相溶液不同,受体分子在细胞膜上的分布是非连续的、动态的,因此细胞表面的受体配体相互作用通常呈现复杂的非线性结合模式。框架核酸作为一类具有确定几何形状的DNA纳米支架,可用于多价配体的偶联,为深入揭示受体配体相互作用机制提供了可靠的工具。利用框架核酸纳米分辨率的可寻址特性,可实现对配体数目、间距及空间构象等参数的精确调控,进而研究细胞表面受体配体的结合特性及影响因素,优化结合条件最终实现高效的分子识别及靶向治疗。本文综述了基于框架核酸的细胞表面受体配体相互作用研究进展,通过探讨细胞表面受体配体相互作用的重要影响因素及生物学应用,对该研究领域的发展前景和未来趋势予以展望。     

Molecular recognition of endocrine disruptors by synthetic and natural 17β-estradiol receptors: a comparative study

A β-estradiol receptor binding mimic was synthesised using molecular imprinting. Bulk polymers and spherical polymer nanoparticles based on methacrylic acid and ethylene glycol dimethacrylate as the functional monomer and crosslinker, respectively, were prepared in acetonitrile. The selectivity was evaluated by radioligand binding assays. The imprinted polymers were very specific to β-estradiol since the control polymers bound virtually none of the radioligand. The bulk polymer was then employed to screen endocrine disrupting chemicals. Structurally related steroids like α-estradiol, estrone and ethynylestradiol showed, respectively, 14.0, 5.0 and 0.7% of relative binding to the β-estradiol polymer, whereas most unrelated chemicals did not bind at all. These results are compared to those obtained with a bioassay using stably transfected yeast cells in culture bearing the human estrogen receptor. The receptor was activated by several estrogen-like chemicals and to a lesser extent by some structurally related chemicals. Figure A molecularly imprinted polymer that was a synthetic receptor for beta-estradiol was used for the screening of endocrine disrupting chemicals that are structurally related or unrelated to beta-estradiol. The results were compared with the recognition of the compounds by the biological estrogen receptor expressed in yeast cells. Related steroids like alpha-estradiol, estrone and ethynylestradiol showed significant binding to the beta-estradiol imprinted polymer, whereas most unrelated chemicals did not bind. The biological receptor was activated by several estrogen-like chemicals, and to a lesser extent by some structurally related chemicals     

A molecular graphics study on structure-action relationships of calcium-antagonistic and agonistic 1,4-dihydropyridines

Summary Based on force field and quantum chemical calculations a hypothesis on the molecular mechanism of Ca channel-modulating 1,4-dihydropyridines (DHPs) has been developed. A careful investigation of the molecular electrostatic fields of the compounds led to the discovery of a unique area of the molecular potentials where Ca agonists and antagonists possess potentials with opposite sign. It is further demonstrated that the molecular potential of a simple receptor site model is reduced by interaction with Ca channel-activating DHPs and on the contrary increased by Ca channel-blocking DHPs. It is concluded that these effects could be the basis for opposite actions of 1,4-dihydropyridine enantiomers at the potential-dependent Ca channels.     

Influence of intramolecular hydrogen bond of templates on molecular recognition of molecularly imprinted polymers

Three molecularly imprinted polymers (MIPs) were prepared corresponding to three structurally related template compounds 4-hydroxybenzoic acid (4-HBA), gentisic acid (GA) and salicylic acid (SA) that differ in intramolecular hydrogen bonding ability using acrylamide (AA) as a functional monomer. HPLC method was used to evaluate the binding performances of the MIPs to the templates and several analogues. The results showed that the difference in their molecular recognition ability was pronounced. The highest molecular recognition ability was observed for 4-HBA-imprinted polymer. It was proved that the hydrogen bond interaction between the functional monomer and the template (4-HBA) played a major role in the recognition process and Scatchard analysis showed that two classes of binding sites were formed in 4-HBA-imprinted polymer. Their dissociation constants were estimated to be 1.76×10⁻⁴ and 1.40×10⁻³ mol l⁻¹, respectively. But for GA- or SA-imprinted polymer the molecular recognition ability was not improved compared to the blank polymer (BP). By comparison of the structures of the three templates, it was concluded that the molecular recognition ability will decrease when the template itself is able to form intramolecular hydrogen bond in the molecular imprinting process. This study will be helpful for us to understand the molecular recognition mechanism of MIPs and of instructive significance for the prediction of the selectivity of MIPs.     

The computational design of test compounds with potentially specific biological activity: Histamine-H2 agonists derived from 5-HT/H2 antagonists

Summary The previously proposed models for the recognition and activation of 5-HT and histamine-H₂ receptors, which were employed to explain the antagonist activity of LSD at both of these receptors, as well as the selective antagonism for H₂ receptors by SKF-10856 and 9,10-dihydro-LSD, are used herein to design a compound to test the H₂-receptor model. The design strategy attempts to construct a compound with potentially selective H₂ agonism. The design scheme maintains features which were previously used to explain selective recognition of SKF-10856 and 9,10-dihydro-LSD as well as reintroduces the chemical features proposed to be responsible for H₂ activation. The existence of the H₂ recognition and activation features in the proposed compound is verified, in a previously proposed model, by computational studies of the molecular electrostatic potentials and shifts in the tautomeric preference.The majority of the work was conducted in the Department of Medicinal Chemistry, Berlex Laboratories, Inc., Cedar Knolls, NJ 07927, U.S.A.     

功能化核酸适体的筛选及分子识别应用

核酸适体是从寡核苷酸文库中筛选获得的一段单链寡核苷酸. 由于能与多种靶标分子高特异性结合, 核酸适体已发展成为一种新兴的分子识别工具, 广泛应用于生物医学等领域. 天然核酸文库有限的化学组成限制了核酸适体的结构和功能, 进而限制了其在分子识别中的应用. 功能化核酸适体通过引入特定的化学官能团使核酸序列具有更丰富的构象和功能, 增强其分子识别能力. 然而, 功能化核酸很难与核酸扩增方法兼容, 因而难以使用传统筛选方法进行功能化核酸的筛选. 因此, 优化筛选方法对于获得具有优异性能的功能化核酸适体至关重要. 本综述总结了功能化核酸适体的筛选方法, 并介绍了其作为分子识别工具在生物医学领域中的应用.     

Differential modulation of cellular death and survival pathways by conjugated bile acids

Background  

The liver-derived McNtcp.24 cells transport bile acids and show distinctive responses to the two classes of conjugated bile acids. Whereas taurine-conjugated bile acids are non-toxic, glycine-conjugated bile acids efficiently induce apoptosis. The aim of this study was to determine if the differential sensitivity is limited to cells that normally transport bile acids and if bile acid binding proteins could reduce bile acid-mediated apoptosis. The apical sodium/bile acid co-transporter (asbt) was expressed in Chinese hamster ovary (CHO) cells to establish active bile acid transport in a non-liver-derived cell model (CHO.asbt). A high-affinity bile acid binder was expressed in McNtcp.24 cells.     

Trp-Lys-Tyr-Met-Val-Met stimulates phagocytosis via phospho-lipase D-dependent signaling in mouse dendritic cells

Dendritic cells (DCs) play a key role in activating the immune response against invading pathogens as well as dying cells or tumors. Although the immune response can be initiated by the phagocytic activity by DCs, the molecular mechanism involved in this process has not been fully investigated. Trp-Lys-Tyr-Met-Val-Met-NH(2) (WKYMVM) stimulates the activation of phospholipase D (PLD) via Ca(2+) increase and protein kinase C activation in mouse DC cell line, DC2.4. WKYMVM stimulates the phagocytic activity, which is inhibited in the presence of N-butanol but not t-butanol in DC2.4 cells. Furthermore, the addition of phosphatidic acid, an enzymatic product of PLD activity, enhanced the phagocytic activity in DC2.4 cells. Since at least two of formyl peptide receptor (FPR) family (FPR1 and FPR2) are expressed in DC2.4 as well as in mouse bone marrow-derived dendritic cells, this study suggests that the activation of FPR family by WKYMVM stimulates the PLD activity resulting in phagocytic activity in DC2.4 cells.     

模板分子中作用基团的数目及位置对印迹聚合物印迹效应的影响

为了研究模板分子中作用基团的数目和位置对印迹聚合物印迹效应的影响, 分别以含有羟基数目和位置不同的羟基苯甲酸化合物3,4,5-三羟基苯甲酸(3,4,5-THBA), 3,4-二羟基苯甲酸(3,4-DHBA), 2,4-二羟基苯甲酸(2,4-DHBA)和3-羟基苯甲酸(3-HBA)为模板分子, 以丙烯酰胺为功能单体, 乙二醇二甲基丙烯酸酯为交联剂和乙腈(MeCN)为致孔剂, 采用非共价本体聚合方法制备了对应的印迹聚合物, 用色谱法评价了其分子识别性能. 结果表明, 制备的印迹聚合物对相应的模板分子均具有印迹效应, 在流动相H₂O/MeCN(体积比1/99)中, 各印迹聚合物对相应的模板分子3,4,5-THBA, 3,4-DHBA, 2,4-DHBA和3-HBA的印迹因子分别为5.51, 5.55, 2.60和2.03. 通过与同样条件下制备的龙胆酸(GA)、水杨酸(SA)和对-羟基苯甲酸(4-HBA)印迹聚合物对其模板分子印迹效应的比较发现, 模板分子中作用基团数目越多, 印迹效率越高; 模板分子中作用基团-COOH和-OH的相对位置对印迹效率影响很大, 当-COOH和-OH在苯环上处于对位时的印迹效率, 高于其处于间位的印迹效率; 当-COOH和-OH在苯环上处于邻位时, 由于形成分子内氢键会降低其印迹效率. 实验还发现, 3,4-DHBA的印迹聚合物可以实现其结构类似物3,4,5-THBA和2,4-DHBA的基线分离, 为生物活性组分3,4,5-THBA的分离和测定提供了依据.     

Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor

The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists (‘beta-blockers’) thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor–ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular fragments in ligands and the analysis of their interactions with receptors separately. A series of beta-blockers, based on phenylethanolamines and phenoxypropanolamines, were docked to the beta2-adrenoceptor binding site in the crystal structure. Hydrophobic complementarity between the ligand and the receptor was calculated using the PLATINUM web-server (http://model.nmr.ru/platinum). Based on the analysis of the hydrophobic match for molecular fragments of beta-blockers, we have developed a new scoring function which efficiently predicts dissociation constant (pKd) with strong correlations (r ²～ 0.8) with experimental data.