Specific GABA(A) agonists and partial agonists

The GABA(A) receptor system is implicated in a number of neurological and psychiatric diseases, making GABA(A) receptor ligands interesting as potential therapeutic agents. Only a few different classes of structures are currently known as ligands for the GABA recognition site on the hetero-pentameric GABA(A) receptor complex, reflecting the very strict structural requirements for GABA(A) receptor recognition and activation. Within the series of compounds showing agonist activity at the GABA(A) receptor site that have been developed, most of the ligands are structurally derived from the GABA(A) agonists muscimol, THIP, or isoguvacine, which we developed in the initial stages of the project. Using recombinant GABA(A) receptors, functional selectivity was demonstrated for a number of compounds, including THIP, showing highly subunit-dependent potency and maximal response. In light of the interest in partial GABA(A) receptor agonists as potential therapeutics, structure-activity studies of a number of analogs of 4-PIOL, a low-efficacy partial GABA(A) agonist derived from THIP, have been performed. In this connection, a series of GABA(A) ligands has been developed that exhibit pharmacological profiles from moderately potent low-efficacy partial GABA(A) agonist activity to potent and selective antagonist effects. Very little information is available on direct-acting GABA(A) receptor agonists in clinical studies. However, the results of clinical studies on the effect of the partial GABA(A) agonist THIP on human sleep patterns show that the functional consequences of a direct-acting agonist are different from those seen after the administration of GABA(A) receptor modulators, such as benzodiazepines and barbiturates.     

Binding of small guest molecules to multivalent receptors

The complexation of phenol derivatives, aromatic carboxylic acids, and n-octylgalactopyranoside by hydrogen-bonded exo-receptors is described. The receptors are formed by self-assembly of differently functionalized calix[4]arene dimelamines with 5,5-diethyl barbiturate or butyl cyanurate. The multivalent complementary recognition site of the receptors is used very efficiently to complex multiple guests. A 1:6 binding mode was observed for phenol derivatives forming single hydrogen bonds with all six recognition sites of an ureido functionalized receptor assembly, while 1:3 complexation was observed for phenol derivatives which form two hydrogen bonds with two different ureido recognition sites of the same receptor. Aromatic carboxylic acids are complexed in a 1:6 ratio by receptors having six amino recognition sites. The complexation of n-octylgalactopyranoside by Gly-L-Ser functionalized receptors is also described, indicating that it is possible to use small peptidic fragments to complex biologically important molecules.     

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.     

Artificial receptors that provides a preorganized hydrophobic environment: a biomimetic approach to dopamine recognition in water

[structure: see text] The recognition of dopamine in water has been achieved with tripodal oxazoline-based artificial receptors, capable of providing a preorganized hydrophobic environment by rational design, which mimics a hydrophobic pocket predicted for a human D2 receptor. The receptors show an amphiphilic nature owing to the presence of hydrophilic sulfonate groups at the periphery of the tripodal oxazoline ligands, which seems to contribute in forming the preorganized hydrophobic environment. The artificial receptors recognized dopamine hydrochloride in water with reasonable selectivity among various organoammonium guests examined. The observed binding behavior of the receptors was explained by evoking guest inclusion in the preorganized hydrophobic pocket-like environment and not by simple ion-pairing interactions. The rationally predicted 1:1 inclusion binding mode was supported by binding studies such as with a reference receptor that cannot provide a similar binding pocket, Job and VT-NMR experiments, electrospray ionization mass analysis, and guest selectivity data. This study implies that an effective hydrophobic environment can be generated even from an acyclic, small molecular artificial receptor. Such a preorganized hydrophobic environment, as being utilized in biological systems, can be effectively used as a complementary binding force for the recognition of organoammonium guests such as dopamine hydrochloride in water.     

对十四烷氧基亚胺衍生物对CN-的高选择性“双响应”识别

设计并合成了一种新型长链烷氧基亚胺衍生物R,系统研究了受体R对10种阴离子的紫外可见(UV?Vis)及裸眼识别性能。结果表明,该受体对F^-、Ac^-和CN^-表现出良好的UV?Vis识别能力,且在H2O/DMSO(1∶1,V/V)体系中可对CN^-实现单一裸眼识别。受体R识别CN^-的检出限可达7.02μmol·L^-1,并制备了受体R对阴离子的检测试纸。Job曲线表明受体与阴离子以1∶2的比例结合。最后利用UV?Vis滴定、核磁滴定、质谱及理论计算推测了CN^-离子的识别机理,在CN^-离子核磁滴定中发现了“反应型”与“氢键型”双响应识别现象,而在F^-的核磁滴定中发生去质子化过程。     

A novel fluorescent and colorimetric anion sensor based on thiourea derivative in competitive media

A novel and simple fluorescent receptor bearing thiourea moiety as recognition site was described. The recognition behavior of the receptor toward different anions was investigated in DMSO/H(2)O (95:5 v/v) and dry DMSO through two various channels: the colorless-yellow color change and a remarkable enhancement of the fluorescence. And the enhancement of the fluorescence was attributed to an anion-induced increase of the rigidity of the host molecule.     

Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide

Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.     

Diarylurea-linked zinc porphyrin dimer as a dual-mode artificial receptor: supramolecular control of complexation-facilitated photoinduced electron transfer

A novel porphyrinic receptor 1 in which two zinc porphyrins are bridged by two diarylurea linkers was developed for recognition of a viologen derivative (hexyl viologen, HV). The electronic absorption spectra as well as the 1H NMR experiments revealed that the HV molecule was bound to the cleft in 1 mainly through carbonyl dipole-charge interactions to afford a 1:1 complex. From the steady-state fluorescence spectroscopic study, the photoinduced electron transfer (PET) from 1 to HV was extremely facilitated by the receptor-substrate complexation. The receptor 1 also formed a 1:1 complex with 1,4-diazabicyclo[2.2.2]octane (DABCO) through two Zn-N coordination interactions, and, using DABCO as an inhibitor, we suppressed the PET reaction via the substrate exchange.     

Multipoint recognition of catecholamines by hydrindacene-based receptors accompanied by the complexation-induced conformational switching

The molecular recognition of catecholamines by hydrindacene-based receptors 1 and 2, as well as the durene-based receptor 3, and the guest-induced conformational changes are reported. These receptors selectively bind adrenaline and dopamine salts through the guests' ammonium group and 3-hydroxyl group on the aromatic ring. In the case of adrenaline, an additional hydrogen bond with a benzylic hydroxyl group is formed. In 2 % CD3CN/CDCl3, the association constants are of the order of 10(4) M(-1), which is much larger than with guests without the 3-hydroxyl groups (10(3) M(-1)). The two amide groups of receptor 1 can rotate freely around the C(aromatic)--C(amide) bond, whereas the tert-amide in 2 changes between two stable conformations at a slow enough rate to allow detection by (1)H NMR spectroscopy. In the absence of a guest molecule, the syn-conformer is less stable than the anti-conformer. On complex formation with adrenaline, the syn-conformer becomes dominant due to an intramolecular dipole-reversal effect in addition to multipoint hydrogen bonding.     

A new series of 2-alkoxy(aralkoxy)-[1,2,4]triazolo[1,5-a]quinazolin-5-ones as adenosine receptor antagonists

This research was carried out to study the pharmacological activity of a newly synthesized series of 2-alkoxy-[1,2,4]triazolo[1,5-a]quinazolin-5-ones as adenosine receptor antagonists. These compounds have been tested in radioligand binding assays on cloned Chinese hamster ovary (CHO) cells transfected with A(1), A(2A), A(2B) and A(3) receptors. In particular, among the triazoloquinazolines (1-11), the dialkoxy derivative (7b) was found to have the highest affinity at A(1) subtype receptor, and its radioligand binding activity together with 1,3-dipropyl-8-cyclopentylxanthine (DPCPX) was studied. Finally, the structure-activity relationship (SAR) studies on the titled compounds provide some new insights about steric hindrance and lipophilic requirements for anchoring to the adenosine receptors recognition site.     

烯醇-酮互变异构型亚胺衍生物对Co2+的高选择性识别

设计合成了新型烯醇-酮互变异构型亚胺衍生物R, 考察了受体R对18种阳离子的紫外光谱及裸眼识别性能. 结果表明, 该受体对Co²⁺, Fe²⁺和Ni²⁺表现出良好的紫外光谱识别能力, 且可实现对Co²⁺相对明显的裸眼单一识别. Job曲线表明, 受体R与Co²⁺形成了1:1型金属配合物, 且检出限可达4.14×10^-7 mol/L. 制备了受体R裸眼比色识别试纸; 根据理论计算及核磁滴定实验结果阐述了Co²⁺离子识别过程中烯醇-酮互变异构机理.     

ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric,steric, and substructure searching of three-dimensional molecular structures

Summary ALADDIN is a computer program for the design or recognition of compounds that meet geometric, steric, and substructural criteria. ALADDIN searches a database of three-dimensional structures, marks atoms that meet substructural criteria, evaluates geometric criteria, and prepares a number of files that are input for molecular modification and coordinate generation as well as for molecular graphics. Properties calculated from the three-dimensional structure are described by either properties calculated from the molecule itself or from the molecule as compared to a reference molecule and associated surfaces. ALADDIN was used to design analogues to probe a bioactive conformation of a small molecule and a peptide, to test alternative superposition rules for receptor mapping of the D2 dopamine receptor, to recognize unexpected D2 dopamine agonist activity of existing compounds, and to design compounds to fit a binding site on a protein of known structure. We have found that series designed by ALADDIN show much more subtle variation in shape than do those designed by traditional methods and that compounds can be designed to be very close matches to the objective.     

一种长链烷氧基苯腙衍生物对氟离子的高选择性识别

设计并合成了一种新型长链烷氧基酰腙衍生物1-(2,4-二硝基苯基)-2-(4-(十四烷氧基)亚苄基)肼R,系统研究了受体R对9种阴离子(F^-、Cl^-、Br^-、I^-、HSO^-₄、NO^-₃、ClO^-₄、H₂PO^-₄、Ac^-)的紫外-可见吸收光谱(UV-Vis)及裸眼识别性能。 结果表明,该受体在二甲基亚砜(DMSO)体系中对F^-、Ac^-和H₂PO^-₄表现出良好的UV-Vis及裸眼识别能力。 此外,在H₂O/DMSO(体积比1∶9)体系中可对F^-实现单一UV-Vis及裸眼识别,且检出限可达7.02×10^-7 mol/L,同时制备了受体R对阴离子的检测试纸,Job曲线表明受体与阴离子形成1∶1型配合物。 F^-离子的识别机理为“氢键型”响应识别现象。     

Conformational and electronic study of dopamine interacting with the D2 dopamine receptor

We report an exhaustive conformational and electronic study on dopamine (DA) interacting with the D₂ dopamine receptor (D₂DR). For the first time, the complete surface of the conformational potential energy of the complex DA/D₂DR is reported. Such a surface was obtained through the use of QM/MM calculations. A detailed study of the molecular interactions that stabilize and destabilize the different molecular complexes was carried out using two techniques: Quantum Theory of Atoms in Molecules computations and nuclear magnetic shielding constants calculations. A comparative study of the behavior of DA in the gas phase, aqueous solution, and in the active site of D₂DR has allowed us to evaluate the degree of deformation suffered by the ligand and, therefore, analyze how rustic are the lock-key model and the induced fit theory in this case. Our results allow us to propose one of the conformations obtained as the “biologically relevant” conformation of DA when it is interacting with the D₂DR.     

Pharmacophore model for bile acids recognition by the FPR receptor

Formyl-peptide receptors (FPRs) belong to the family A of the G-protein coupled receptor superfamily and include three subtypes: FPR, FPR-like-1 and FPR-like-2. They have been involved in the control of␣many inflammatory processes promoting the recruitment and infiltration of leukocytes in regions of inflammation through the molecular recognition of chemotactic factors. A large number of structurally diverse chemotypes modulate the activity of FPRs. Newly identified antagonists include bile acids deoxycholic acid (DCA) and chenodeoxycholic acid (CDCA). The molecular recognition of these compounds at FPR receptor was computationally investigated using both ligand- and structure-based approaches. Our findings suggest that all antagonists bind at the first third of the seven helical bundles. A closer inspection of bile acid interaction reveals a number of unexploited anchor points in the binding site that may be used to aid the design of new potent and selective bile acids derivatives at FPR.     

A benzimidazole-based fluorescent sensor for Cu2+ and its complex with a phosphate anion formed through a Cu2+ displacement approach

A benzimidazole-based imine linked receptor was synthesized for fluorescent recognition of Cu²⁺ in a CH₃CN/H₂O (8:2, v/v) solvent system. The receptor offers an opportunity for the selective estimation of Cu²⁺ in the presence of another metal ion at equimolar concentration. The Cu²⁺ complex with the receptor acted as a sensor for a phosphate anion, and the phosphate recognition event restored the fluorescence intensity of the receptor.     

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.     

Ion-pair recognition by a heteroditopic triazole-containing receptor

A new heteroditopic calix[4]diquinone triazole containing receptor capable of recognising both cations and anions through Lewis base and C-H hydrogen-bonding modes, respectively, of the triazole motif has been prepared. This ion-pair receptor cooperatively binds halide/monovalent-cation combinations in an aqueous mixture, with selectivity trends being established by (1)H?NMR and UV/Vis spectroscopy. Cation binding by the calix[4]diquinone oxygen and triazole nitrogen donors enhances the strength of the halide complexation at the isophthalamide recognition site of the receptor. Conversely, anions bound in the receptor's isophthalamide cavity enhance cation recognition. (1)H?NMR investigations in solution suggest that the receptor's triazole motifs are capable of coordinating simultaneously to both cation and anion guest species. Solid-state X-ray crystallographic structural analysis of a variety of receptor ion-pair adducts further demonstrates the dual cation-anion binding role of the triazole group.     

间苯二甲酰腙分子钳的合成及阴离子识别研究

设计合成了3种新型间苯二甲酰腙类化合物,利用UV-Vis及¹H NMR考察了其与F^-、Cl^-、Br^-、I^-、CH₃COO^-、HSO₄^-、H₂PO4-、ClO4-阴离子的相互作用。结果表明,主体分子4a(双对硝基苯并呋喃甲醛间苯二甲酰腙)在DMSO溶液中对F-和CH₃COO-有显著识别效果,溶液颜色由黄色变为深黄色和棕红色。通过¹H NMR滴定及质子溶剂效应进一步证明,主体分子与阴离子之间是以氢键作用方式相结合。Job曲线表明,主客体间形成1：1型氢键络合物。基于实验结果,探讨了主客体间形状和大小匹配对识别能力的影响以及主客体之间的识别模式。     

An Artificial Receptor for Dimethyl Aspartate

[trans-5,15-Bis(2,7-dihydroxy-1-naphthyl)-2,3,7,8,12,13,17,18-octaethylporphyrinato]zinc(II) (1), a trifunctionalized porphyrin host, was prepared as a receptor for amino acid derivatives, particularly those having a hydrogen-bonding site in the side chain. The free energy changes for the binding of Leu-OMe, Asp-OMe, and Glu-OMe to 1 were -5.8 kcal/mol, -6.6 kcal/mol, and -5.9 kcal/mol, showing a selectivity for Asp-OMe. (1)H NMR titration experiments indicated that three simultaneous attractive interactions, one coordination interaction, and two hydrogen-bonding interactions, are operating in the host-guest complex. The preference for Asp-OMe over Glu-OMe was found to originate from the favorable enthalpy term for Asp-OMe. The free energy change, the enthalpy change, and the entropy change were determined and split into contributions arising from coordination interaction and from hydrogen-bonding interactions by use of reference hosts. Comparison of enthalpy and entropy changes suggests that the host-guest complex becomes more ordered as the number of recognition pairs increases.