Prediction of biological activity for high-throughput screening using binary kernel discrimination

High-throughput screening has made a significant impact on drug discovery, but there is an acknowledged need for quantitative methods to analyze screening results and predict the activity of further compounds. In this paper we introduce one such method, binary kernel discrimination, and investigate its performance on two datasets; the first is a set of 1650 monoamine oxidase inhibitors, and the second a set of 101 437 compounds from an in-house enzyme assay. We compare the performance of binary kernel discrimination with a simple procedure which we call "merged similarity search", and also with a feedforward neural network. Binary kernel discrimination is shown to perform robustly with varying quantities of training data and also in the presence of noisy data. We conclude by highlighting the importance of the judicious use of general pattern recognition techniques for compound selection.     

Virtual screening using binary kernel discrimination: analysis of pesticide data

This paper discusses the use of binary kernel discrimination (BKD) for identifying potential active compounds in lead-discovery programs. BKD was compared with established virtual screening methods in a series of experiments using pesticide data from the Syngenta corporate database. It was found to be superior to methods based on similarity searching and substructural analysis but inferior to a support vector machine. Similar conclusions resulted from application of the methods to a pesticide data set for which categorical activity data were available.     

Virtual screening using binary kernel discrimination: effect of noisy training data and the optimization of performance

Binary kernel discrimination (BKD) uses a training set of compounds, for which structural and qualitative activity data are available, to produce a model that can then be applied to the structures of other compounds in order to predict their likely activity. Experiments with the MDL Drug Data Report database show that the optimal value of the smoothing parameter, and hence the predictive power of BKD, is crucially dependent on the number of false positives in the training set. It is also shown that the best results for BKD are achieved using one particular optimization method for the determination of the smoothing parameter that lies at the heart of the method and using the Jaccard/Tanimoto coefficient in the kernel function that is used to compute the similarity between a test set molecule and the members of the training set.     

Classifying molecules using a sparse probabilistic kernel binary classifier

The central idea of supervised classification in chemoinformatics is to design a classifying algorithm that accurately assigns a new molecule to one of a set of predefined classes. Tipping has devised a classifying scheme, the Relevance Vector Machine (RVM), which is in terms of sparsity equivalent to the Support Vector Machine (SVM). However, unlike SVM classifiers, the RVM classifiers are probabilistic in nature, which is crucial in the field of decision making and risk taking. In this work, we investigate the performance of RVM binary classifiers on classifying a subset of the MDDR data set, a standard molecular benchmark data set, into active and inactive compounds. Additionally, we present results that compare the performance of SVM and RVM binary classifiers.     

Detection of single ion channel activity on a chip using tethered bilayer membranes

Membrane-bound ion channels are promising biological receptors since they allow for the stochastic detection of analytes at high sensitivity. For stochastic sensing, it is necessary to measure the ion currents associated with single ion channel opening and closing events. However, this calls for stability, high reproducibility, and long lifetimes. A critical issue to overcome is the low stability of the ion channel environment, that is, the bilayer membrane. A promising technique to surmount this is to connect the lower part of the membrane to a surface forming a tethered bilayer membrane. By reconstituting the synthetic ion channel, gramicidin A, into a tethered bilayer as part of a microchip design, we have been able to record the activity of single ion channels. The observed activity was compared with that obtained by a conventional electrophysiology method, tip dipping, to confirm its authenticity. These findings allow for the construction of stable biosensors based on ion channels and provide a novel technique for the characterization of ion channel activity.     

Enhancement of antimicrobial activity by synthetic ion channel synergy

Hydraphile synthetic ion channels were found to enhance the cytotoxicity to E. coli and B. subtilis of erythromycin, kanamycin, rifampicin, and tetracycline when co-administered with the antibiotic at sublethal concentrations of channel.     

Retention behavior of high performance ion chromatography using binary eluants

The retention behavior of high performance ion chromatography using binary eluants is given. The relationship between log(t_R) and log(1/[E]) is linear, which has been demonstrated experimentally with mixed anion solution.     

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.     

Fabrication of highly insulating tethered bilayer lipid membrane using yeast cell membrane fractions for measuring ion channel activity

A tethered bilayer lipid membrane (tBLM) was fabricated on a gold electrode using 1,2-dipalmitoyl-sn-glycero-phosphothioethanol as a tethering lipid and the membrane fractions of Saccharomyces pombe yeast cells to deposit the upper leaflet. The membrane fractions were characterized using transmission electron microscopy and dynamic light scattering and found to be similar in size to small unilamellar vesicles of synthetic lipids. The dynamics of membrane-fraction deposition and rupture on the tethering-lipid layer were measured using quartz crystal microgravimetry. The electrochemical properties of the resulting tBLM were characterized using electrical impedance spectroscopy and cyclic voltammetry. The tBLM's electrical resistance was greater than 1 MOmegacm(2), suggesting a defect-free membrane. The suitability of tBLM produced using membrane fractions for measuring ion-channel activities was shown by a decrease in membrane resistance from 1.6 to 0.43 MOmegacm(2) following addition of gramicidin. The use of membrane fractions to form high-quality tBLM on gold electrodes suggests a new approach to characterize membrane proteins, in which the upper leaflet of the tBLM is deposited, and overexpressed membrane proteins are incorporated, in a single step. This approach would be especially useful for proteins whose activity is lost or altered during extraction, purification, and reconstitution, or whose activities are strongly influenced by the lipid composition of the bilayer.     

Synthetic ion channel activity documented by electrophysiological methods in living cells

Hydraphiles are synthetic ion channels that use crown ethers as entry portals and that span phospholipid bilayer membranes. Proton and sodium cation transport by these compounds has been demonstrated in liposomes and planar bilayers. In the present work, whole cell patch clamp experiments show that hydraphiles integrate into the membranes of human embryonic kidney (HEK 293) cells and significantly increase membrane conductance. The altered membrane permeability is reversible, and the cells under study remain vital during the experiment. Control compounds that are too short (C(8)-benzyl channel) to span the bilayer or are inactive owing to a deficiency in the central relay do not induce similar conductance increases. Control experiments confirm that the inactive channel analogues do not show nonspecific effects such as activation of native channels. These studies show that the combination of structural features that have been designed into the hydraphiles afford true, albeit simple, channel function in live cells.     

Analysis of dihydropyridine calcium channel blockers using negative ion photoionization mass spectrometry

The fragmentation of dihydropyridine calcium-channel antagonists are compared by electrospray ionization (ESI) and atmospheric pressure photonization (APPI). The results demonstrate that in ESI the preferred ionization process is in positive mode, with the mass spectra of [M+H]+ showing base peak ions probably formed by loss of alcohols from carboxyl groups. Conversely, in APPI, a high intense peak is observed in negative mode due to deprotonated molecule [M-H]- after two serial 1, 2-hydride shifts leading to a rearranged deprotonated molecule [M-H]-. These ions undergo another 1,2-hydride shifts to produce a nitro-phenyl product ion of m/z 122. The APPI is also used to develop a method for the quantitation of dihydropyridines (e.g., nifedipine) in human plasma.     

Spatial distribution of ion channel activity in biological membranes: the role of noise

A new approach is proposed to model a collective ion channel dynamics. We have assumed that ion channels create a two-component spatio-temporal interaction field. Every channel at its current spatial location in membrane contributes permanently to this field with its state (open or closed) and coupling strength to other channels. This field is described by a reaction-diffusion equation, the transition of ion channel from closed to open state (and vice versa) is described by a master equation, and migration of channels in membrane is described by a set of Langevin equations coupled by the interaction field. Within this model, we have investigated critical conditions for spatial distribution of ion channel activity.     

A light-gated synthetic ion channel

A gated synthetic ion channel with beta-cyclodextrin as the pore and azobenzene as the gate is reported. Irradiation converts a tethered trans-azobenzene to cis-azobenzene which likely transforms the channel from a self-inclusion complex to a dissociated structure. This transformation results in an increase in anion transport and a decrease in cation transport across a phospholipid vesicle membrane.     

Solubility of polycyclic aromatics in binary solvent mixtures using activity coefficient models

Polycyclic aromatic hydrocarbons (PAHs) precipitation is one of the major problems in the hydrocracking units. In this investigation, pyrene and phenanthrene were selected because they were found to be in higher concentrations in the feed to hydrocracking units. Their solubilities were investigated in toluene solvent mixture of iso-octane and heptane over a temperature range from 293 to 323 K. The experimental solubility data were used to predict the interaction parameters for seven different solid–liquid equilibrium models. The following activity coefficient models were used; Wilson, NIBS/Redlich–Kister, UNIQUAC, modified UNIFAC, modified UNIFAC (Dortmund), Flory–Huggins and Sheng. The interaction parameters were expressed as a second-order polynomial function in temperature. In order to test the models, the average absolute deviation percentage (AADP) was used. The overall AADP was found to range from approximately 7 to 14%. The models can be arranged according to their accuracy in a descending order based on AADP as follows: NIBS/Redlich–Kister, Wilson, UNIQUAC, Sheng, Flory–Huggins, modified UNIFAC (Dortmund) and finally modified UNIFAC. All models used in this work gave reasonable results; however, the group contribution models can also be used as a predictive tool for the solubility measurement of pyrene and phenanthrene in other solvents containing the same groups of the solvents used in this study.     

Prediction of CNS activity of compound libraries using substructure analysis

An in silico ADME/Tox prediction tool based on substructural analysis has been developed. The tool called SUBSTRUCT has been used to predict CNS activity. Data sets with CNS active and nonactive drugs were extracted from the World Drug Index (WDI). The SUBSTRUCT program predicts CNS activity as good as a much more complicated artificial neural network model. SUBSTRUCT separates the data sets with approximately 80% accuracy. Substructural analysis also shows surprisingly large differences in substructure profiles between CNS active and nonactive drugs.     

Influence of binary/ternary complex of imprint ion on the preconcentration of uranium(VI) using ion imprinted polymer materials

Ion imprinted polymer (IIP) materials were prepared for uranyl ion (imprint ion) by forming binary (5,7-dichloroquinoline-8-ol (DCQ) or 4-vinylpyridine (VP)) or ternary (5,7-dichloroquinoline-8-ol and 4-vinylpyridine) complexes in 2-methoxy ethanol (porogen) and copolymerizing in the presence of styrene and divinyl benzene as functional and crosslinking monomers, respectively and 2,2′-azobisisobutyronitrile as initiator. IIP particles were obtained by leaching the imprint ion in these polymer materials with 50% (v/v) hydrochloric acid, filtering, drying in an oven at 50 °C and grinding. Control polymer particles were also prepared under identical conditions. The above synthesized polymer particles were characterized by IR, CHN, X-ray diffraction, and pore size analyses. These leached polymer particles can now pick up uranyl ions from dilute aqueous solutions. The IIP particles obtained with ternary complex of uranyl ion alone gave quantitative enrichment of traces of uranyl ions from dilute aqueous solutions. The optimal pH for quantitative enrichment is 4.5-7.5 and eluted completely with 10 ml of 1.0 M HCl. The retention capacity of uranyl IIP particles was found to be 34.05 mg of uranyl ion per gram of polymer. Further, the percent extraction, distribution ratio, and selectivity coefficients of uranium and other selected inorganic ions were also evaluated. Five replicate determinations of 25 μg of uranium present in 1.0 l of aqueous solution gave a mean absorbance of 0.036 with a relative standard deviation of 2.50%. The detection limit corresponding to three times the standard deviation of the blank was found to be 5 μg l⁻¹.     

Prediction of ternary phase equilibria from binary data

The two-parameter UNIQUAC equation is modified to give better results of vapor—liquid and liquid—liquid equilibria for a variety of binary systems. The proposed equation is easily extended to a multicomponent system without including any ternary (or multicomponent) parameters. The good capability of the equation in data reduction is shown by many illustrative examples for various kinds of strongly nonideal binary and ternary mixtures.     

Synthesis and ion conductance behavior of a tetrameric alamethicin ion channel

[structure: see text] A porphyrin-tethered construct, containing four full-length alamethicin monomers, has been synthesized and characterized. The ion conductance data of the assembly in 1 M HCl display long-lived, albeit noisy, channels that appear to be voltage-independent multiples of only one conductance state. The noise in the data is consistent with the molecular modeling studies, which indicate that the side chain of glutamine 7 of alamethicin does not fit well into the narrow pore of a parallel four-helix bundle.