Recent applications of affinity interactions in capillary electrophoresis

Study of molecular interactions by nonequilibrium capillary electrophoresis of equilibrium mixtures: Originations, developments, and applications

Molecular interactions play a vital role in regulating various physiological and biochemical processes in vivo. Kinetic capillary electrophoresis (KCE) is an analytical platform that offers significant advantages in studying the thermodynamic and kinetic parameters of molecular interactions. It enables the simultaneous analysis of these parameters within an interaction pattern and facilitates the screening of binding ligands with predetermined kinetic parameters. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was the first proposed KCE method, and it has found widespread use in studying molecular interactions involving proteins/aptamers, proteins/small molecules, and peptides/small molecules. The successful applications of NECEEM have demonstrated its promising potential for further development and broader application. However, there has been a dearth of recent reviews on NECEEM. To address this gap, our study provides a comprehensive description of NECEEM, encompassing its origins, development, and applications from 2015 to 2022. The primary focus of the applications section is on aptamer selection and screening of small-molecule ligands. Furthermore, we discuss important considerations in NECEEM experimental design, such as buffer suitability, detector selection, and protein adsorption. By offering this thorough review, we aim to contribute to the understanding, advancement, and wider utilization of NECEEM as a valuable tool for studying molecular interactions and facilitating the identification of potential ligands and targets.

Pancreatic lipase inhibitory activity of selected pharmaceutical agents

Twenty-five structurally diverse compounds have been tested in vitro for their pancreatic lipase (PL) inhibitory activity. Despite the diversity of tested compounds, the relationship comprising structural attributes of the compounds could be established to correlate with the observed inhibitory activity. Compounds that exerted inhibitory action through surface activity were of different profile from the rest of compounds. When co-incubated with orlistat (OsT), important synergistic effects for some compounds (orphenadrine, gliclazide, cefuroxime and sulfacetamide) were revealed, while antagonistic effects were demonstrated for others (camphor sulfonic acid and dinitro salicylic acid). Docking studies for the most active molecules were performed and molecular interaction forces with the PL active site were identified. The results suggested co-binding of OsT along with the other inhibitor in the binding site in cases of synergistic effect but not in the case of antagonistic effect. These results were additionally supported by affinity capillary electrophoresis. In conclusion, synergistic lipase inhibitory activity between OsT and some other pharmaceutical compounds was demonstrated for the first time, which might help improve the pharmacological effect of OsT.

Moment analysis for reaction kinetics of intermolecular interactions

Moment equations were developed on the basis of the principle of relativity for analyzing elution peak profiles measured by ACE to analytically determine the association (k_a ) and dissociation (k_d ) rate constants of intermolecular interactions. Basic equations representing the mass balance, mass transfer rate, and reaction kinetics in ACE system in a Galilean coordinate system S were transformed to those in another coordinate system S', which imaginarily moved with respect to S. Moment equations for ACE peaks in S' in the time domain were derived from the analytical solution of the modified basic equations in the Laplace domain. Moment equations for ACE peaks in S were derived from those in S' by the inverse Galilean transformation. The moment equations were used for analyzing some ACE data previously published to determine k_a and k_d values. It was demonstrated that the moment equations were effective for extracting the information about affinity kinetics of intermolecular interactions from the elution peak profiles measured by ACE. The moment equations were also used to discuss the influence of mass transfer and reaction kinetics on ACE peak profiles. Some results of the numerical calculations are also indicated in Supporting Information.

Affinity Monolith-Integrated Microchips for Protein Purification and Concentration

Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture.

Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction

Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique.

Affinity Capillary Electrophoresis for Selective Control of Electrophoretic Mobility of Sialic Acid Using Lanthanide-Hexadentate Macrocyclic Polyazacarboxylate Complexes

It is difficult to control the electrophoretic mobility in order to obtain high resolution among saccharides in complex samples. We report herein on a new affinity capillary electrophoresis (ACE) method for an anionic monosaccharide, N-acetylneuraminic acid (Neu5Ac), which is important in terms of pathological diagnosis, using lanthanide-hexadentate macrocyclic polyazacarboxylate complexes (Ln-NOTA) as affinity reagents. It was shown that Ln-NOTA complexes increased the anionic mobility of Neu5Ac by approximately 40% through selective complexation with Neu5Ac. The extent of change in the mobility strongly depended on the type of central metal ion of Ln-NOTA. The stability constant (K) of Lu-NOTA with Neu5Ac was determined by ACE to be log Kb = 3.62 ± 0.04, which is the highest value among artificial receptors for Neu5Ac reported so far. Using this ACE, the Neu5Ac content in a glycoprotein sample, α1-acid glycoprotein (AGP), was determined after acid hydrolysis. Complete separation between Neu5Ac and hydrolysis products was successful by controlling the mobility to determine the concentration of Neu5Ac.

Development of a fraction collection approach in capillary electrophoresis SELEX for aptamer selection

A productive SELEX approach has been developed for generating high affinity aptamer.

Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants

DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.

Theory of end-labeled free-solution electrophoresis: is the end effect important?

In the theory of free-solution electrophoresis of a polyelectrolyte (such as the DNA) conjugated with a "drag-tag," the conjugate is divided into segments of equal hydrodynamic friction and its electrophoretic mobility is calculated as a weighted average of the mobilities of individual segments. If all the weights are assumed equal, then for an electrically neutral drag-tag, the elution time t is predicted to depend linearly on the inverse DNA length 1/M. While it is well-known that the equal-weights assumption is approximate and in reality the weights increase toward the ends, this "end effect" has been assumed to be small, since in experiments the t(1/M) dependence seems to be nearly perfectly linear. We challenge this assumption pointing out that some experimental linear fits do not extrapolate to the free (i.e. untagged) DNA elution time in the limit 1/M→0, indicating nonlinearity outside the fitting range. We show that a theory for a flexible polymer taking the end effect into account produces a nonlinear curve that, however, can be fitted with a straight line over a limited range of 1/M typical of experiments, but with a "wrong" intercept, which explains the experimental results without additional assumptions. We also study the influence of the flexibilities of the charged and neutral parts.

Development of a capillary electrophoresis platform for identifying inhibitors of protein-protein interactions

Methods for identifying chemical inhibitors of protein-protein interactions (PPIs) are often prone to discovery of false positives, particularly those caused by molecules that induce protein aggregation. Thus, there is interest in developing new platforms that might allow earlier identification of these problematic compounds. Capillary electrophoresis (CE) has been evaluated as a method to screen for PPI inhibitors using the challenging system of Hsp70 interacting with its co-chaperone Bag3. In the method, Hsp70 is labeled with a fluorophore, mixed with Bag3, and the resulting bound and free Hsp70 are separated and detected by CE with laser-induced fluorescence detection. The method used a chemically modified CE capillary to prevent protein adsorption. Inhibitors of the Hsp70-Bag3 interaction were detected by observing a reduction in the bound-to-free ratio. The method was used to screen a library of 3443 compounds, and the results were compared to those from a flow cytometry protein interaction assay. CE was found to produce a lower hit rate with more compounds that were reconfirmed in subsequent testing, suggesting greater specificity. This finding was attributed to the use of electropherograms to detect artifacts such as aggregators and to differences in protein modifications required to perform the different assays. Increases in throughput are required to make the CE method suitable for primary screens, but at the current stage of development it is attractive as a secondary screen to test hits found by higher-throughput methods.

Capillary electrophoretic methods in the development of metal-based therapeutics and diagnostics: new methodology and applications

In recent years, capillary electrophoresis (CE) has matured to a standard method in medicinal inorganic chemistry. More and more steps of the drug discovery process are followed by CE. However, not only the number of applications has steadily increased but also the variety of used methodology has significantly broadened and, as compared to a few years ago, a wider scope of separation modes and hyphenated systems has been used. Herein, a summary of the newly utilized CE methods and their applications in metallodrug research in the timeframe 2006-2011 is presented, following related reviews from 2003 and 2007 (Electrophoresis, 2003, 24, 2023-2037; Electrophoresis 2007, 28, 3436-3446). Areas covered include impurity profiling, quality control of pharmaceutical formulations, lipophilicity estimation, interactions between metallodrugs and proteins or nucleotides, and characterization and also quantification of metabolites in biological matrices and real-world samples.

Western blotting using capillary electrophoresis

A microscale Western blotting system based on separating sodium-dodecyl sulfate protein complexes by capillary gel electrophoresis followed by deposition onto a blotting membrane for immunoassay is described. In the system, the separation capillary is grounded through a sheath capillary to a mobile X-Y translation stage which moves a blotting membrane past the capillary outlet for protein deposition. The blotting membrane is moistened with a methanol and buffer mixture to facilitate protein adsorption. Although discrete protein zones could be detected, bands were broadened by ∼1.7-fold by transfer to membrane. A complete Western blot for lysozyme was completed in about one hour with 50 pg mass detection limit from low microgram per milliliter samples. These results demonstrate substantial reduction in time requirements and improvement in mass sensitivity compared to conventional Western blots. Western blotting using capillary electrophoresis shows promise to analyze low volume samples with reduced reagents and time, while retaining the information content of a typical Western blot.

Identifying kinetically stable proteins with capillary electrophoresis

Unlike most proteins, which are in equilibrium with partially and globally unfolded conformations, kinetically stable proteins (KSPs) are trapped in their native conformations and are often resistant to harsh environment. Based on a previous correlation between kinetic stability (KS) and a protein's resistance to sodium dodecyl sulfate (SDS), we show here a simple method to identify KSPs by SDS-capillary electrophoresis (CE). Control non-KSPs were fully denatured by SDS and formed protein:SDS complexes that exhibited similar mobility in CE. In contrast, KSPs bound fewer SDS molecules, and showed a very different migration time and peak pattern in CE, thereby providing some insight about the structural heterogeneity of SDS:protein complexes and the relative KS of the various proteins.

Structural studies of an RNA aptamer containing GGA repeats under ionic conditions using microchip electrophoresis, circular dichroism, and 1D-NMR

Nuclear magnetic resonance (NMR) studies have shown that RNA/DNA oligomers with GGA repeat sequences contain unique G-quadruplex structures in the presence of K(+) or Na(+) ions. In this study, we used microchip electrophoresis to study the structure of an RNA aptamer against bovine prion protein that possessed four GGA-triplet repeats (wt2). We analyzed the structural changes and characterized dimer formation of the aptamer. Mutational, circular dichroism, and one-dimensional NMR studies of wt2 revealed that K(+) ions induce wt2 to assume a thermostable dimer in an intramolecular G-quadruplex with parallel orientation.

High-throughput phase-distribution method to determine drug-cyclodextrin binding constants

A high-throughput method has been developed to measure drug-cyclodextrin binding constants. It measures the distribution ratio of a drug between a polymer film [polyvinyl chloride (PVC) with 67% (w/w) dioctyl sebacate (DOS)] and a cyclodextrin-containing buffer in a 96-well format. Measurements of distribution ratios at several cyclodextrin concentrations lead to binding constants. Binding constants for econazole with six CDs have been determined in one 96-well microplate with four replications of each condition in 10 h. The K(1:1)/10(3) M(-1) values are 3.98 +/- 0.13, 3.90 +/- 0.22, 29.3 +/- 2.2, 0.66 +/- 0.04, 1.78 +/- 0.30, 4.08 +/- 0.50, with (2-hydroxyethyl)-beta-cyclodextrin, (2-hydroxypropyl)-beta-cyclodextrin, 2,6-di-O-methyl-beta-cyclodextrin, heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin, alpha-cyclodextrin, beta-cyclodextrin, respectively. It is likely that 1:2 complexes are also formed in some cases. This method has also been applied to study the binding behavior as a function of the drug concentration and pH. Binding weakens at higher drug concentration which may be due to the self-association of the drug. An acidic environment decreases the binding constant of CD with the basic econazole. The formation of the 1:2 complexes is completely suppressed in acid as well. This protocol is faster than the phase-solubility method. Moreover, the material requirement is up to four orders of magnitude lower.

Capillary electrophoresis applied to proteomic analysis

In the postgenomic era, proteomics has become a dominant field for identifying and quantifying the complex protein machinery of the cell. The expression levels, posttranslational modifications, and specific interactions of proteins control the biology of such processes as development, differentiation, and signal transduction. Studies of the proteins involved in these processes often lead to a better understanding of biology and of human disease. Powerful separation techniques and sensitive detection methods enable researchers to untangle these complicated networks of processes. CE coupled with either MS or LIF are two of the techniques that make this possible. This review will cover proven CE-based methods for proteomics on the cell and tissue level and their application in biological and clinical studies, relevant new developments in enabling technology such as microfluidic CE-MS demonstrated on model systems, and comment on the future of CE in proteomics.

Optimization of capillary electrophoresis conditions for a glucagon competitive immunoassay using response surface methodology

The capillary electrophoresis (CE) conditions for a competitive immunoassay of glucagon were optimized for highest sensitivity of the immunoassay and resolution of the electrophoretic peaks using a Box-Behnken design. Injection time, voltage ramp time, and separation voltage were varied between three levels and two responses, bound-to-free (B/F) ratio of the immunoassay peaks and resolution between the peaks, were measured. Analysis of variance was applied to fit a predictive model, and a desirability function was used to simultaneously optimize both responses. A 10-s injection, 1.6-min ramp time, and a 22-kV separation voltage were the conditions found when high B/F was given more emphasis than high resolution. To test the model, calibration curves of a glucagon immunoassay were measured at the optimum and least optimum CE conditions. Optimal conditions increased the sensitivity of the immunoassay by 388% compared to the least optimum conditions while maintaining adequate resolution.

Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography-mass spectrometry for solution-based ligand screening against multiple proteins

We present herein a novel bioseparation/chemical analysis strategy for protein-ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography-mass spectrometry (LC-MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC-MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5s, and on-line prepare the "clean" sample to be directly compatible with the LC-MS analysis. The improvement in performance of this 2D-TFC/LC-MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC-MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation.

Capillary separation: micellar electrokinetic chromatography

Micellar electrokinetic chromatography (MEKC), a separation mode of capillary electrophoresis (CE), has enabled the separation of electrically neutral analytes. MEKC can be performed by adding an ionic micelle to the running solution of CE without modifying the instrument. Its separation principle is based on the differential migration of the ionic micelles and the bulk running buffer under electrophoresis conditions and on the interaction between the analyte and the micelle. Hence, MEKC's separation principle is similar to that of chromatography. MEKC is a useful technique particularly for the separation of small molecules, both neutral and charged, and yields high-efficiency separation in a short time with minimum amounts of sample and reagents. To improve the concentration sensitivity of detection, several on-line sample preconcentration techniques such as sweeping have been developed.

Development of aptamer-based affinity assays using temperature gradient focusing: minimization of the limit of detection

A method is described for an aptamer-based affinity assay using a combination of two nonconventional techniques, temperature gradient focusing (TGF) and field-amplified continuous sample injection TGF (FACSI-TGF), with fluorescence detection. Human immunodeficiency virus reverse transcriptase (HIVRT) is used as the protein target for the assay. The TGF and FACSI-TGF assays are compared to similar results obtained with conventional CE. A range of starting aptamer concentrations are used to determine the optimal LOD for human immunodeficiency virus reverse transcriptase (HIVRT) using each approach. The results indicate that the LODs for HIVRT obtained with TGF and FACSI-TGF are comparable to or even lower than the LODs obtained with conventional CE in spite of the inferior detector used for the TGF and FACSI-TGF assays (arc lamp and low-cost CCD for TGF versus LIF with PMT for CE). It is hypothesized that this is due to the greater reproducibility of the TGF and FACSI-TGF techniques since they do not employ a defined sample injection. The lowest LOD achieved with the new aptamer assay approach is more than an order of magnitude lower than that reported for a similar CE-based aptamer assay for the same target.