Ion channel screening

Ion channels are attractive targets for drug discovery with recent estimates indicating that voltage and ligand-gated channels account for the third and fourth largest gene families represented in company portfolios after the G protein coupled and nuclear hormone receptor families. A historical limitation on ion channel targeted drug discovery in the form of the extremely low throughput nature of the gold standard assay for assessing functional activity, patch clamp electrophysiology in mammalian cells, has been overcome by the implementation of multi-well plate format cell-based screening strategies for ion channels. These have taken advantage of various approaches to monitor ion flux or membrane potential using radioactive, non-radioactive, spectroscopic and fluorescence measurements and have significantly impacted both high-throughput screening and lead optimization efforts. In addition, major advances have been made in the development of automated electrophysiological platforms to increase capacity for cell-based screening using formats aimed at recapitulating the gold standard assay. This review addresses the options available for cell-based screening of ion channels with examples of their utility and presents case studies on the successful implementation of high-throughput screening campaigns for a ligand-gated ion channel using a fluorescent calcium indicator, and a voltage-gated ion channel using a fluorescent membrane potential sensitive dye.     

Synthetic Methods for the Preparation of Conformationally Restricted Analogues of Nicotine

In the context of naturally occurring nitrogen heterocycles, nicotine is a chiral alkaloid present in tobacco plants, which can target and stimulate nicotinic acetylcholine receptors (nAChRs), a class of ligand-gated ion channels commonly located throughout the human brain. Due to its well-known toxicity for humans, there is considerable interest in the development of synthetic analogues; in particular, conformationally restricted analogues of nicotine have emerged as promising drug molecules for selective nAChR-targeting ligands. In the present mini-review, we will describe the synthesis of the conformationally restricted analogues of nicotine involving one or more catalytic processes. In particular, we will follow a systematic approach as a function of the heteroarene structure, considering: (a) 2,3-annulated tricyclic derivatives; (b) 3,4-annulated tricyclic derivatives; (c) tetracyclic derivatives; and (d) other polycyclic derivatives. For each of them we will also consider, when carried out, biological studies on their activity for specific nAChR subunits.     

Toxins as Tools in Neurochemistry

Neurotoxins have evolved as molecules targeted specifically against molecules with an important function in the nervous system. Because of their selectivity they have been used as probes for detecting and characterizing key proteins of the nerve cell. Ion channels involved in the propagation of the action potential, proteins of presynaptic neurotransmitter exocytosis, and most importantly, neurotransmitter receptors have been and are presently being analyzed, in some cases already at atomic level by a combination of the tools of neurotoxins, molecular biology, and patch clamp electrophysiology. In this review a selection of these toxins is presented, together with their targets in the nervous system. Special emphasis is given to the recent breakthroughs in our understanding of the mechanism of action of tetanus and botulinum toxins and to the neurotoxins ranging from the plant alkaloid strychnine to the peptide toxins from poisonous snakes, which were fundamental in elucidating ligand-gated ion channels like the glycine and nicotinic acetylcholine receptors.     

Simulating ion channel activation mechanisms using swarms of trajectories

Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's “swarms of trajectories” approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function. © 2019 Wiley Periodicals, Inc.     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.     

Molecular dynamics of nicotinic acetylcholine receptor correlating biological functions

The nicotinic acetylcholine receptor (nAChR) that mediates fast intercellular communication in response to neurotransmitters is a paradigm of ligand-gated ion channels. Molecular dynamics (MD) simulations are valuable in understanding membrane protein function at atomic level, providing useful clues for further experimental/theoretical studies. In this brief review, recent progress in MD simulations of the nAChR has been illustrated, mainly focusing on the latest simulation of the whole transmembrane domain of the receptor. On the basis of MD simulations, asymmetrical and asynchronous motions of five subunits were observed both in the ligand binding and transmembrane domains; a closed-to-open conformational shift of the gate was captured in different simulation systems; the contributions from the lipid molecules and other transmembrane segments rather than M2 to the gate switch as well as the conformational change of the whole channel were assessed; the dynamic behavior and related physical/chemical properties of the water molecules and cations within the ion channel were examined; and an experimentally comparable single-channel conductance and ion selectivity were obtained.     

双分子层膜人工离子通道的合成

离子通道(ion channels)是由细胞膜上的一类特殊亲水性蛋白质构成的微孔道,它的主要功能就是传输离子跨膜,相当于细胞的通气孔。其结构与功能的异常往往引起上千种疾病,统称为离子通道病,这种疾病目前不能靠常规的仪器来检查,在确诊上有一定的难度。因此通过化学手段合成人工离子通道来模拟生物体内细胞膜上的离子通道的结构与功能,对于深入研究这些疾病并发现特异性治疗药物均具有十分重要的理论和实际意义。本论文就近三十年来人们设计合成的不同种类人工离子通道进行了综述,介绍了其研究进展并总结了各种人工离子通道的分子结构设计以及在膜上传输离子行为,展望了其在模拟天然离子通道功能的同时在生物医药以及生命科学等领域的应用前景。     

Spider venoms: a rich source of acylpolyamines and peptides as new leads for CNS drugs

Advances in NMR and mass spectrometry as well as in peptide biochemistry coupled to modern methods in electrophysiology have permitted the isolation and identification of numerous products from spider venoms, previously explored due to technical limitations. The chemical composition of spider venoms is diverse, ranging from low molecular weight organic compounds such as acylpolyamines to complex peptides. First, acylpolyamines (< 1000 Da) have an aromatic moiety linked to a hydrophilic lateral chain. They were characterized for the first time in spider venoms and are ligand-gated ion channel antagonists, which block mainly postsynaptic glutamate receptors in invertebrate and vertebrate nervous systems. Acylpolyamines represent the vast majority of organic components from the spider venom. Acylpolyamine analogues have proven to suppress hippocampal epileptic discharges. Moreover, acylpolyamines could suppress excitatory postsynaptic currents inducing Ca+ accumulation in neurons leading to protection against a brain ischemic insult. Second, short spider peptides (< 6000 Da) modulate ionic currents in Ca2+, Na+, or K+ voltage-gated ion channels. Such peptides may contain from three to four disulfide bridges. Some spider peptides act specifically to discriminate among Ca2+, Na+, or K+ ion channel subtypes. Their selective affinities for ion channel subfamilies are functional for mapping excitable cells. Furthermore, several of these peptides have proven to hyperpolarize peripheral neurons, which are associated with supplying sensation to the skin and skeletal muscles. Some spider N-type calcium ion channel blockers may be important for the treatment of chronic pain. A special group of spider peptides are the amphipathic and positively charged peptides. Their secondary structure is alpha-helical and they insert into the lipid cell membrane of eukaryotic or prokaryotic cells leading to the formation of pores and subsequently depolarizing the cell membrane. Acylpolyamines and peptides from spider venoms represent an interesting source of molecules for the design of novel pharmaceutical drugs.     

Lighting Up the Plasma Membrane: Development and Applications of Fluorescent Ligands for Transmembrane Proteins

Despite the fact that transmembrane proteins represent the main therapeutic targets for decades, complete and in-depth knowledge about their biochemical and pharmacological profiling is not fully available. In this regard, target-tailored small-molecule fluorescent ligands are a viable approach to fill in the missing pieces of the puzzle. Such tools, coupled with the ability of high-precision optical techniques to image with an unprecedented resolution at a single-molecule level, helped unraveling many of the conundrums related to plasma proteins’ life-cycle and druggability. Herein, we review the recent progress made during the last two decades in fluorescent ligand design and potential applications in fluorescence microscopy of voltage-gated ion channels, ligand-gated ion channels and G-coupled protein receptors.     

The tethered agonist approach to mapping ion channel proteins--toward a structural model for the agonist binding site of the nicotinic acetylcholine receptor

BACKGROUND: The integral membrane proteins of neurons and other excitable cells are generally resistant to high resolution structural tools. Structure-function studies, especially those enhanced by the nonsense suppression methodology for unnatural amino acid incorporation, constitute one of the most powerful probes of ion channels and related structures. The nonsense suppression methodology can also be used to incorporate functional side chains designed to deliver novel structural probes to membrane proteins. In this vein, we sought to generalize a potentially powerful tool - the tethered agonist approach - for mapping the agonist binding site of ligand-gated ion channels. RESULTS: Using the in vivo nonsense suppression method for unnatural amino acid incorporation, a series of tethered quaternary ammonium derivatives of tyrosine have been incorporated into the nicotinic acetylcholine receptor. At three sites a constitutively active receptor results, but the pattern of activation as a function of chain length is different. At position alpha149, there is a clear preference for a three-carbon tether, while at position alpha93 tethers of 2-5 carbons are comparably effective. At position gamma55/delta57 all tethers except the shortest one can activate the receptor. Based on these and other data, a model for the receptor binding site can be developed by analogy to the acetylcholine esterase crystal structure. CONCLUSION: Through the use of nonsense suppression techniques, the tethered agonist approach has been made into a general tool for probing receptor structures. When applied to the nicotinic receptor, the method places new restrictions on developing models for the agonist binding site.     

Optochemical genetics

Transmembrane receptors allow a cell to communicate with its environment in response to a variety of input signals. These can be changes in the concentration of ligands (e.g. hormones or neurotransmitters), temperature, pressure (e.g. acoustic waves or touch), transmembrane potential, or light intensity. Many important receptors have now been characterized in atomic detail and our understanding of their functional properties has markedly increased in recent years. As a consequence, these sophisticated molecular machines can be reprogrammed to respond to unnatural input signals. In this Review, we show how voltage-gated and ligand-gated ion channels can be endowed with synthetic photoswitches, and how the resulting artificial photoreceptors can be used to optically control neurons with exceptional temporal and spatial precision. They work well in animals and might find applications in the restoration of vision and the optical control of other sensations. The combination of synthetic photoswitches and receptor proteins contributes to the field of optogenetics and adds a new functional dimension to chemical genetics. As such, we propose to call it "optochemical genetics".     

The role of bioactive compounds on the promotion of neurite outgrowth

Neurite loss is one of the cardinal features of neuronal injury. Apart from neuroprotection, reorganization of the lost neuronal network in the injured brain is necessary for the restoration of normal physiological functions. Neuritogenic activity of endogenous molecules in the brain such as nerve growth factor is well documented and supported by scientific studies which show innumerable compounds having neurite outgrowth activity from natural sources. Since the damaged brain lacks the reconstructive capacity, more efforts in research are focused on the identification of compounds that promote the reformation of neuronal networks. An abundancy of natural resources along with the corresponding activity profiles have shown promising results in the field of neuroscience. Recently, importance has also been placed on understanding neurite formation by natural products in relation to neuronal injury. Arrays of natural herbal products having plentiful active constituents have been found to enhance neurite outgrowth. They act synergistically with neurotrophic factors to promote neuritogenesis in the diseased brain. Therefore use of natural products for neuroregeneration provides new insights in drug development for treating neuronal injury. In this study, various compounds from natural sources with potential neurite outgrowth activity are reviewed in experimental models.     

Potential analytical applications of gated artificial ion channels

Biosensors based on natural ion channels combine a biological recognition mechanism with a physical transduction technique in a very selective and sensitive manner. This kind of molecular sensor will contribute to drug screening and environmental screening. Key information about channel gating, ion transport, and molecular mechanism is provided by the patch-clamp technique, commonly used for electrophysiological analysis. Here we report the synthesis of light-gated artificial ion channels, necessary constituents for construction of biosensors based on natural ion channels. The artificial gated ion channels described here are based on calix[4]resorcinarene. Opening and closing of the artificial ion channel is achieved by azo groups, which work like a lid. Azo groups alter their conformation on irradiation with light, and are chemically quite stable. Addition of a gate function will enhance the potential of synthetic channels to be used in sensors as molecular switches.Dedicated to the memory of Wilhelm Fresenius     

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein

Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.     

Electron impact ionization of haloalkanes in helium nanodroplets

Electron impact (EI) mass spectra of a selection of C1-C3 haloalkanes in helium nanodroplets have been recorded to determine if the helium solvent can significantly reduce molecular ion fragmentation. Haloalkanes were chosen for investigation because their EI mass spectra in the gas phase show extensive ion fragmentation. There is no evidence of any major softening effect in large helium droplets ( approximately 60 000 helium atoms), but some branching ratios are altered. In particular, channels requiring C-C bond fission or concerted processes leading to the ejection of hydrogen halide molecules are suppressed by helium solvation. Rapid cooling by the helium is not sufficient to account for all the differences between the helium droplet and gas phase mass spectra. It is also suggested that the formation of a solid "snowball" of helium around the molecular ion introduces a cage effect, which enhances those fragmentation channels that require minimal disruption to the helium cage for products to escape.     

High pressure effects in anaesthesia and narcosis

There is growing interest in determining the effects of high pressure on biological functions. Studies of brain processes under hyperbaric conditions can give a unique insight into phenomena such as nitrogen narcosis, inert gas anaesthesia, and pressure reversal of the effects of anaesthetic and narcotic agents. Such research may shed light on the action of anaesthetics, which remains poorly understood, and on the nature of consciousness itself. Various studies have established the behavioural response of organisms to hyperbaric conditions, in the presence or absence of anaesthetic agents. At the molecular level, X-ray crystallography has been used to investigate the incorporation of species like Xe in hydrophobic pockets within model ion channels that may account for pressure effects on neuronal transmission. New magnetic resonance imaging techniques are providing tomographic three-dimensional images that detail brain structure and function, and that can be correlated with behavioural studies and psychological test results. Such whole organ techniques are linked to the molecular scale via voltage-sensitive dye (VSD) imaging studies on brain slices that provide time-resolved images of the dynamic formation and interconnection of inter-neuronal complexes. The VSD experiments are readily adapted to in situ studies under high pressure conditions. In this tutorial review we review the current state of knowledge of hyperbaric effects on brain processes: anaesthesia and narcosis, recent studies at the molecular level via protein crystallography at high pressure in a Xe atmosphere, and we also present some preliminary results of VSD imaging of brain slices under hyperbaric conditions.     

Mimicking/Extracting Structure and Functions of Natural Products: Synthetic Approaches that Address Unexplored Needs in Chemical Biology

Natural products are often attractive and challenging targets for synthetic chemists, and many have interesting biological activities. However, synthetic chemists need to be more than simply suppliers of compounds to biologists. Therefore, we have been seeking ways to actively apply organic synthetic methods to chemical biology studies of natural products and their activities. In this personal review, I would like to introduce our work on the development of new biologically active compounds inspired by, or extracted from, the structures of natural products, focusing on enhancement of functional activity and specificity and overcoming various drawbacks of the parent natural products.     

Cellular targets of natural products

Natural products have evolved, at least in part, to bind to biological macromolecules, particularly proteins. As a result, natural products are able to interact with many specific targets within the cell. Indeed for many years this has been central in the drug development process. Today, however, natural products are finding increasing use as probes to interrogate biological systems as part of chemical genomics and related research. In order to demonstrate the utility of natural products in these efforts, the biological activities of many of the major classes of natural products is discussed, according to the cellular organelle and localisation of their specific molecular targets. Emphasis is given to newly discovered compounds and activities that either provide interesting insights into a specific biological function, or that form the basis for potentially new therapeutic approaches.     

Study of the effect of ion channel modulators on photosynthetic oxygen evolution

Various ion channel activities can be recorded by electrophysiological methods in the outer and inner envelope membranes of chloroplasts as well as in the thylakoid membrane. However, most of these channels are poorly characterized from a pharmacological point of view. Furthermore, the molecular identity has been determined only for a few of them, preventing an understanding of their role in plant physiology. By allowing specific ion fluxes across plastidial membranes, these ion channels may either directly or indirectly regulate photosynthesis, as has been hypothesized earlier. We have determined the effect of various ion channel modulators [indole-3-acetic acid, 5-nitro-2-(3-phenylpropylamino)-benzoate, (-)-epigallocatechin-3-gallate, p-chlorophenoxyacetic acid, Konig's polyanion, Cs+, Gd3+, 4-aminopyridine, tetraethylammonium chloride, charybdotoxin, nimodipine, and cyclosporin A] on the efficiency of photosynthetic oxygen evolution in intact chloroplasts, broken chloroplasts, and isolated thylakoids. The data may improve our understanding of chloroplast ion channels and identifies inhibitors which may be exploited for electrophysiological studies.