Central nicotinic receptors: structure, function, ligands, and therapeutic potential

The growing interest in nicotinic receptors, because of their wide expression in neuronal and non-neuronal tissues and their involvement in several important CNS pathologies, has stimulated the synthesis of a high number of ligands able to modulate their function. These membrane proteins appear to be highly heterogeneous, and still only incomplete information is available on their structure, subunit composition, and stoichiometry. This is due to the lack of selective ligands to study the role of nAChR under physiological or pathological conditions; so far, only compounds showing selectivity between alpha4beta2 and alpha7 receptors have been obtained. The nicotinic receptor ligands have been designed starting from lead compounds from natural sources such as nicotine, cytisine, or epibatidine, and, more recently, through the high-throughput screening of chemical libraries. This review focuses on the structure of the new agonists, antagonists, and allosteric ligands of nicotinic receptors, it highlights the current knowledge on the binding site models as a molecular modeling approach to design new compounds, and it discusses the nAChR modulators which have entered clinical trials.     

Allosteric Molecular Switches in Metabotropic Glutamate Receptors

Metabotropic glutamate receptors (mGlu) are class C G protein-coupled receptors of eight subtypes that are omnipresently expressed in the central nervous system. mGlus have relevance in several psychiatric and neurological disorders, therefore they raise considerable interest as drug targets. Allosteric modulators of mGlus offer advantages over orthosteric ligands owing to their increased potential to achieve subtype selectivity, and this has prompted discovery programs that have produced a large number of reported allosteric mGlu ligands. However, the optimization of allosteric ligands into drug candidates has proved to be challenging owing to induced-fit effects, flat or steep structure-activity relationships and unexpected changes in theirpharmacology. Subtle structural changes identified as molecular switches might modulate the functional activity of allosteric ligands. Here we review these switches discovered in the metabotropic glutamate receptor family..     

Promiscuity and the Conformational Rearrangement of Drug‐Like Molecules: Insight from the Protein Data Bank

Selectivity is a central aspect of lead optimization in the drug discovery process. Medicinal chemists often try to decrease molecular flexibility to improve selectivity, given the common belief that the two are interdependent. To investigate the relationship between polypharmacology and conformational flexibility, we mined the Protein Data Bank and constructed a dataset of pharmaceutically relevant ligands that crystallized in more than one protein target while binding to each co‐crystallized receptor with similar in vitro affinities. After analyzing the molecular conformations of these 100 ligands, we found that 59 ligands bound to different protein targets without significantly changing conformation, suggesting that there is no distinct correlation between conformational flexibility and polypharmacology within our dataset. Ligands crystallized in similar proteins and highly ligand‐efficient compounds with five or fewer rotatable bonds were less likely to adjust conformation when binding.     

Electrostatic phenomena and molecular motion at interfaces of glass/polymer composites

A boundary zone of filler-affected polymeric network is a possible element in the microstructure of composites. The intensity of adsorption potentials for polymeric material on the filler and therefore its surface energy should be an important variable in boundary zone properties. This work has involved the modification of surface energy in a glass filler material through the introduction of externally induced electrostatic charge that is through the creation of a ‘synthetic’ zeta potential on filler particles. The interactions of charged and uncharged glass surfaces with a polymeric matrix were studied by thermally stimulated discharge (TSD), and also by contact angle measurements. The experimental system studied was an aluminosilicate glass as the filler material, and poly(tetraethylene glycol dimethacrylate) as the organic matrix. Contact angle measurements revealed enhanced wettability for the matrix-forming monomer on glass surfaces charged negatively by electric fields. TSD analysis was also carried out on pure polymer, and composite materials containing either uncharged or bipolar filler particles (particles exposed to an external electrical potential). TSD spectra suggest a suppressed level of molecular motion in composites with fillers of high electrostatic surface energy. Also, activation energies calculated from TSD data are higher in bipolar filler composites. The higher activation energies are consistent with the possibility that a less mobile interfacial zone polymerizes around higher surface energy filler particles.     

A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2

In an attempt to identify novel small-molecule ligands of cyclin-dependent kinase 2 (CDK2) with potential as allosteric inhibitors, we have devised a robust and cost-effective fluorescence-based high-throughput screening assay. The assay is based on the specific interaction of CDK2 with the extrinsic fluorophore 8-anilino-1-naphthalene sulfonate (ANS), which binds to a large allosteric pocket adjacent to the ATP site. Hit compounds that displace ANS directly or indirectly from CDK2 are readily classified as ATP site binders or allosteric ligands through the use of staurosporine, which blocks the ATP site without displacing ANS. Pilot screening of 1453 compounds led to the discovery of 12 compounds with displacement activities (EC(50) values) ranging from 6 to 44 μM, all of which were classified as ATP-site-directed ligands. Four new type I inhibitor scaffolds were confirmed by X-ray crystallography. Although this small compound library contained only ATP-site-directed ligands, the application of this assay to large compound libraries has the potential to reveal previously unrecognized chemical scaffolds suitable for structure-based design of CDK2 inhibitors with new mechanisms of action.     

Ligand‐Biased and Probe‐Dependent Modulation of Chemokine Receptor CXCR3 Signaling by Negative Allosteric Modulators

Over the last decade, functional selectivity (or ligand bias) has evolved from being a peculiar phenomenon to being recognized as an essential feature of synthetic ligands that target G protein‐coupled receptors (GPCRs). The CXC chemokine receptor 3 (CXCR3) is an outstanding platform to study various aspects of biased signaling, because nature itself uses functional selectivity to manipulate receptor signaling. At the same time, CXCR3 is an attractive therapeutic target in the treatment of autoimmune diseases and cancer. Herein we report the discovery of an 8‐azaquinazolinone derivative (N‐{1‐[3‐(4‐ethoxyphenyl)‐4‐oxo‐3,4‐dihydropyrido[2,3‐d]pyrimidin‐2‐yl]ethyl}‐4‐(4‐fluorobutoxy)‐N‐[(1‐methylpiperidin‐4‐yl)methyl]butanamide, 1 b ) that can inhibit CXC chemokine 11 (CXCL11)‐dependent G protein activation over β‐arrestin recruitment with 187‐fold selectivity. This compound also demonstrates probe‐dependent activity, that is, it inhibits CXCL11‐ over CXCL10‐mediated G protein activation with 12‐fold selectivity. Together with a previously reported biased negative allosteric modulator from our group, the present study provides additional information on the molecular requirements for allosteric modulation of CXCR3.     

Charge density effects on polyelectrolyte dynamic rheology

The dynamic rheological properties of an uncharged polymer and charged polyelectrolytes were evaluated in salt‐free water at various concentrations above the entanglement concentration. A poly(acrylic acid) homopolymer was used as the uncharged polymer and was ionized to anionic poly(acrylic acid‐co‐sodium acrylate) at five levels of ionization (0.05, 0.10, 0.15, 0.30, and 0.50). The polymers exhibited a terminal region at a low frequency and a plateau region at a high frequency. The dynamic data for the nonionic parent and all charged polymers could be reduced to a master curve, which indicated a similar distribution of relaxation times for the nonionic and charged polymers. The shear modulus, relaxation time, and zero shear viscosity properties exhibited a concentration and charge density dependence. Higher power‐law exponents for the rheological properties were noted for the nonionic polymer versus the charged derivatives. The number of mechanically active entanglements per number of chains increased with the polymer concentration and charge density. The total number of mechanically active entanglements per number of chains that occurred because of imposing a charge to the nonionic parent did not change with increased concentration, and this indicated a different entanglement mechanism for charged polymers in comparison with their nonionic parent. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Modeling promiscuity based on in vitro safety pharmacology profiling data

This study describes a method for mining and modeling binding data obtained from a large panel of targets (in vitro safety pharmacology) to distinguish differences between promiscuous and selective compounds. Two naïve Bayes models for promiscuity and selectivity were generated and validated on a test set as well as publicly available drug databases. The model shows a higher score (lower promiscuity) for marketed drugs than for compounds in early development or compounds that failed during clinical development. Such models can be used in triaging high‐throughput screening data or for lead optimization.     

Ligand-Receptor Interactions and Machine Learning in GCGR and GLP-1R Drug Discovery

The large amount of data that has been collected so far for G protein-coupled receptors requires machine learning (ML) approaches to fully exploit its potential. Our previous ML model based on gradient boosting used for prediction of drug affinity and selectivity for a receptor subtype was compared with explicit information on ligand-receptor interactions from induced-fit docking. Both methods have proved their usefulness in drug response predictions. Yet, their successful combination still requires allosteric/orthosteric assignment of ligands from datasets. Our ligand datasets included activities of two members of the secretin receptor family: GCGR and GLP-1R. Simultaneous activation of two or three receptors of this family by dual or triple agonists is not a typical kind of information included in compound databases. A precise allosteric/orthosteric ligand assignment requires a continuous update based on new structural and biological data. This data incompleteness remains the main obstacle for current ML methods applied to class B GPCR drug discovery. Even so, for these two class B receptors, our ligand-based ML model demonstrated high accuracy (5-fold cross-validation Q² > 0.63 and Q² > 0.67 for GLP-1R and GCGR, respectively). In addition, we performed a ligand annotation using recent cryogenic-electron microscopy (cryo-EM) and X-ray crystallographic data on small-molecule complexes of GCGR and GLP-1R. As a result, we assigned GLP-1R and GCGR actives deposited in ChEMBL to four small-molecule binding sites occupied by positive and negative allosteric modulators and a full agonist. Annotated compounds were added to our recently released repository of GPCR data.     

Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase

Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC₅₀=0.29 μM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.     

How and Why Do Cluster Size,Charge State,and Ligands Affect the Course of Metal-Mediated Gas-Phase Activation of Methane?

Recent progress in the gas-phase activation of methane is discussed. We demonstrate that cluster size, charge state, and ligands crucially affect both the reactivity and selectivity of metal-mediated bond activation processes. We outline the important role that relativistic effects and spin densities play and discuss the paradigm of two-state reactivity in thermal reactions. State-of-the-art mass-spectrometry based experiments, in conjunction with electronic structure calculations, permit identification of the elementary steps at a strictly molecular level and thus allow to uncover mechanistic features for four types of reactions: (i) metal-mediated dehydrogenation of methane, (ii) ligand-switch processes of the type ML + CH₄ → M(CH₃) + HL, (iii) hydrogen-atom abstraction as the crucial step in the oxidative coupling of methane, and (iv) the mechanism of the challenging CH₄→CH₃OH conversion.     

吸水链霉菌谷氨酰胺转氨酶两种同源异形体的鉴定及性质分析

目的探讨吸水链霉菌谷氨酰胺转氨酶(transglutaminase,TGase,EC 2.3.2.13)的两种同源异形体成熟酶TGases A和TGases B的分子差异,并进行系统分析和鉴定。方法吸水链霉菌培养上清液经阴离子交换层析和凝胶过滤层析分离纯化后,将纯化产物再经阴离子交换层析,分析纯化产物的分子表面带电性质,通过基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time of flight mass spectrometry,MALDI-TOF-MS)和远紫外圆二色谱(far ultra-violet circular dichroism spectrometry,Far-UV CD)法分析纯化产物的肽段序列及二级结构的差异,并检测成熟酶N-末端氨基酸序列。结果经阴离子交换层析和凝胶过滤层析分离纯化获得TGases的两种成熟酶TGases A和TGases B,均具有酶活性;TGase A和TGase B成熟酶分子具有不同的表面带电性质,酶活分别为(28.33±1.45)U/mg和(22.54±1.77)U/mg;TGases A和TGases B在质荷比(m/z)4 536.481和4 873.393处两个低丰度肽段有差异,但N-末端6个氨基酸序列完全相同;两者二级结构均以α-螺旋为主,但二级结构存在一定差异。结论吸水链霉菌TGases A和TGases B是由同一种酶原活化产生的同源异形体,两者的表面电荷性质、肽段序列及分子二级结构均有差异。     

Covalent Allosteric Inhibitors of Akt Generated Using a Click Fragment Approach

Akt is a protein kinase that has been implicated in the progression of cancerous tumours. A number of covalent allosteric Akt inhibitors are known, and based on these scaffolds, a small library of novel potential covalent allosteric imidazopyridine-based inhibitors was designed. The envisaged compounds were synthesised, with click chemistry enabling a modular approach to a number of the target compounds. The binding modes, potencies and antiproliferative activities of these synthesised compounds were explored, thereby furthering the structure activity relationship knowledge of this class of Akt inhibitors. Three novel covalent inhibitors were identified, exhibiting moderate activity against Akt1 and various cancer cell lines, potentially paving the way for future covalent allosteric inhibitors with improved properties.     

Rational Design,Synthesis, Biophysical and Antiproliferative Evaluation of Fluorenone Derivatives with DNA G‐Quadruplex Binding Properties

Molecular modeling studies carried out with experimental DNA models with the sequence d[AG₃(T₂AG₃)₃] suggest that the introduction of a net positive charge onto the side chain of a series of fluorenone carboxamides can improve G‐quadruplex binding. The terminal morpholino moiety was replaced with a novel N‐methylmorpholinium cation starting from two 4‐carboxamide compounds. A different substitution on the fluorenone ring was also investigated and submitted to the same quaternarization process. All compounds were analyzed for their DNA binding properties by competition dialysis methods. In vitro antiproliferative tests were carried out against two different tumor cell lines. Docking experiments were conducted by including all four known human repeat unit G‐quadruplex DNA sequences (27 experimentally determined conformations) against the most active fluorenone derivatives. The results of theoretical, biophysical, and in vitro experiments indicate two novel derivatives as lead compounds for the development of a new generation of G‐quadruplex ligands with greater potency and selectivity.     

Tetrakisphosphates and bispyrophosphates of myo-inositol derivatives as allosteric effectors of human hemoglobin: Synthesis, molecular recognition, and oxygen release

Various 2,5- and 1,4-substituted and unsubstituted myo-inositol tetrakisphosphates and bispyrophosphates were prepared following a general synthetic pathway. All final compounds were tested for their capability to induce oxygen release from human hemoglobin. Most of these proved to be efficient allosteric effectors, with similar affinities for hemoglobin to that of myo-inositol hexakisphosphate, which is one of the best known allosteric effectors of hemoglobin. The efficacy was found to be higher for free phosphates than pyrophosphates. As allosteric Hb effectors, these compounds enable enhanced oxygen release. These effects increase with the strength of Hb binding and correspond primarily to electrostatic interactions. Stereochemical and steric factors also play a significant but secondary role in molecular recognition. In view of the central role played by hypoxia in numerous types of diseases, the exploration of myo-inositol phosphate derivatives represents an important avenue in the search for substances which act on the oxygenation status of tissues and may have significant potential in the discovery and development of novel drug candidates.     

1-Indanone and 1,3-indandione Derivatives as Ligands for Misfolded α-Synuclein Aggregates

The development of imaging agents for in vivo detection of alpha-synuclein (α-syn) pathologies faces several challenges. A major gap in the field is the lack of diverse molecular scaffolds with high affinity and selectivity to α-syn fibrils for in vitro screening assays. Better in vitro scaffolds can instruct the discovery of better in vivo agents. We report the rational design, synthesis, and in vitro evaluation of a series of novel 1-indanone and 1,3-indandione derivatives from a Structure-Activity Relationship (SAR) study centered on some existing α-syn fibril binding ligands. Our results from fibril saturation binding experiments show that two of the lead candidates compounds 8 and 32 bind α-syn fibrils with binding constants (K_d) of 9.0 and 18.8 nM, respectively, and selectivity of greater than 10× for α-syn fibrils compared with amyloid-β (Aβ) and tau fibrils. Our results demonstrate that the lead ligands avidly label all forms of α-syn on PD brain tissue sections, but only the dense core of senile plaques in AD brain tissue, respectively. These results are corroborated by ligand-antibody colocalization data from Syn211, which shows immunoreactivity toward all forms of α-syn aggregates, and Syn303, which displays preferential reactivity toward mature Lewy pathology. Our results reveal that 1-indanone derivatives have desirable properties for the biological evaluation of α-synucleinopathies.     

LIQUID-LIQUID EXTRACTION OF Ag(I), Hg(II), Au(III) AND Pd(II) BY SOME OLIGOTHIA MACROCYCLIC LIGANDS INCORPORATING AROMATIC AND HETEROAROMATIC SUBUNITS*

ABSTRACT

A series of hydrophobic tri- to hexa-dentate sulfur containing macrocyclic ligands incorporating aromatic and heteroaromatic subunits have been studied with respect to their extraction properties toward Ag(I), Hg(II), Au(III), and Pd(II) in aqueous//organic systems. The stoichiometry of extracted species and their extraction constants have been determined. The different ligands are compared with structure related open-chain compounds. The influence of substitution, solvent, and anion on the extraction equilibrium is also discussed providing a basis for future design of selective extractants and for die development of improved separation methods. The extractability of the various metal ions strongly depends on the nature and the number of donor atoms of the corresponding ligands and on the properties of the metal ion itself. In some cases, simple open-chain ligands show extraction properties comparable to the present macrocycles. A trithia crown with incorporated benzo subunit highly prefers Ag(I) to Hg(II). Furthermore a distinct selectivity for Au(ni) and Hg(II) over Pd(II) with pyridine substituted macrocycles was found.     

Physicochemical Properties of Zwitterionic Drugs in Therapy

In solution, amphoteric compounds exist in anionic, uncharged, zwitterionic and cationic forms. The importance of zwitterionic drugs is currently under-represented in the literature. Herein, the acid-base parameters, lipophilicity and solubility of such compounds are discussed to deepen the molecular-level understanding of their pharmacokinetic and pharmacodynamic behaviour. Our recent studies show there are many drug molecules, including thyroid hormones and 5-hydroxytryptophan, the precursor of the neurotransmitter serotonin, for which the contribution of the zwitterionic microspecies to the overall lipophilicity exceeds that of the uncharged one, which is of higher individual lipophilicity, but occurs in much lower concentration. The second part of the minireview highlights the most important zwitterionic compounds in therapy, grouped into therapeutic classes. The importance of the charge of the molecules is emphasized in their binding to the target molecules.     

Initiation of cationic polymerization by tetramethylene zwitterions from tetracyanocyclobutanes

The initiating ability of tetramethylene zwitterions formed from cyclobutane adducts of donor olefins with TCNE was investigated. Polar solvents increased the ability of vinyl ether-TCNE cyclobutane adducts to initiate the cationic polymerization of N-vinylcarbazole. The concept of charge separation in the tetramethylene zwitterions was also investigated.     

Structure–Activity Relationships of Quinoxaline‐Based 5‐HT3A and 5‐HT3AB Receptor‐Selective Ligands

Until recently, discriminating between homomeric 5‐HT₃A and heteromeric 5‐HT₃AB receptors was only possible with ligands that bind in the receptor pore. This study describes the first series of ligands that can discriminate between these receptor types at the level of the orthosteric binding site. During a recent fragment screen, 2‐chloro‐3‐(4‐methylpiperazin‐1‐yl)quinoxaline (VUF10166) was identified as a ligand that displays an 83‐fold difference in [³H]granisetron binding affinity between 5‐HT₃A and 5‐HT₃AB receptors. Fragment hit exploration, initiated from VUF10166 and 3‐(4‐methylpiperazin‐1‐yl)quinoxalin‐2‐ol, resulted in a series of compounds with higher affinity at either 5‐HT₃A or 5‐HT₃AB receptors. These ligands reveal that a single atom is sufficient to change the selectivity profile of a compound. At the extremes of the new compounds were 2‐amino‐3‐(4‐methylpiperazin‐1‐yl)quinoxaline, which showed 11‐fold selectivity for the 5‐HT₃A receptor, and 2‐(4‐methylpiperazin‐1‐yl)quinoxaline, which showed an 8.3‐fold selectivity for the 5‐HT₃AB receptor. These compounds represent novel molecular tools for studying 5‐HT₃ receptor subtypes and could help elucidate their physiological roles.