Characterization of small-molecule–biomacromolecule interactions: From simple to complex

Chemometrics in investigation of small molecule-biomacromolecule interactions: A review

Chemometrics is chemical discipline in which mathematical and statistical methods are coupled with chemical data to extract useful information which cannot be extracted by the use of conventional methods. When experimental techniques are assisted by chemometric methods, very interesting studies will be performed which enable us to obtain valuable information about the system under our study. Chemico-biological interactions are very useful studies which are performed to obtain information about binding of small molecules with biological macromolecules. Recently, these studies have been assisted by chemometric methods to perform advanced studies which can help us to have a deep insight to them. Literature survey showed us that multivariate analysis of the chemico-biological interactions is becoming popular and nowadays, chemometricians are using multivariate chemometric methods for resolving chemico-biological interactions. This article focuses on the works published in the literature to provide a background for those who are interested to work in this field and finally, the results will be discussed and concluded.

Assessment of binding interaction dihydromyricetin and myricetin with bovine lactoferrin and effects on antioxidant activity

The binding interactions of bovine lactoferrin (BLF) with two flavonoids dihydromyricetin (DMY) and myricetin (MY) were investigated by the multi-spectroscopic, microscale thermophoresis (MST) techniques, molecular docking, and then their antioxidant activities were studied by detection of free radical scavenging activity against DPPH. Results of UV-vis and fluorescence spectroscopies showed that DMY/MY and BLF formed the ground state complex through the static quenching mechanism. Moreover, MY with more planar stereochemical structure had higher affinity for BLF than DMY with twisted stereochemical structure, according to the binding constant (K_b), free energy change (ΔG°), dissociation constant (K_d) and donor-acceptor distance (r). Thermodynamic parameters revealed that hydrogen bond and van der Waals force were major forces in the formation of BLF-DMY complex, while hydrophobic interactions played major roles in the formation of BLF-DMY complex. The circular dichroism (CD) study indicated that MY induced more conformational change in BLF than DMY. Furthermore, molecular modeling provided insights into the difference of binding interactions between BLF and two flavonoids. Finally, the radical scavenging activity assays indicated the presence of BLF delayed the decrease in antioxidant capacities of two flavonoids. These results were helpful to understand the binding mechanism and biological effects of non-covalent BLF-flavonoid interaction.

Synthesis of imatinib, a tyrosine kinase inhibitor, labeled with carbon-14

Imatinib (Gleevec) is a multiple tyrosine kinase inhibitor that decreases the activity of the fusion oncogene called BCR-ABL (breakpoint cluster region protein-Abelson murine leukemia viral oncogene homolog) and is clinically used for the treatment of chronic myelogenous leukemia and acute lymphocytic leukemia. Small molecule drugs, such as imatinib, can bind to several cellular proteins including the target proteins in the cells, inducing undesirable effects along with the effects against the disease. In this study, we report the synthetic optimization for 14 C-labeling and radiosynthesis of [14 C]imatinib to analyze binding with cellular proteins using accelerator mass spectroscopy. 14 C-labeling of imatinib was performed by the synthesis of 14 C-labeld 2-aminopyrimidine intermediate using [14 C]guanidine·HCl, which includes an in situ reduction of an inseparable byproduct for easy purification by HPLC, followed by a cross-coupling reaction with aryl bromide precursor. The radiosynthesis of [14 C]imatinib (specific activity, 631 MBq/mmol; radiochemical purity, 99.6%) was achieved in six steps with a total chemical yield of 29.2%.

Isoliquiritigenin Induces Mitochondrial Dysfunction and Apoptosis by Inhibiting mitoNEET in a Reactive Oxygen Species-Dependent Manner in A375 Human Melanoma Cells

The mitochondrial protein mitoNEET is a type of iron-sulfur protein localized to the outer membrane of mitochondria and is involved in a variety of human pathologies including cystic fibrosis, diabetes, muscle atrophy, and neurodegeneration. In the current study, we found that isoliquiritigenin (ISL), one of the components of the root of Glycyrrhiza glabra L., could decrease the expression of mitoNEET in A375 melanoma cells. We also demonstrated that mitoNEET could regulate the content of reactive oxygen species (ROS), by showing that the ISL-mediated increase in the cellular ROS content could be mitigated by the mitoNEET overexpression. We also confirmed the important role of ROS in ISL-treated A375 cells. The increased apoptosis rate and the decreased mitochondrial membrane potential were mitigated by the overexpression of mitoNEET in A375 cells. These findings indicated that ISL could decrease the expression of mitoNEET, which regulated ROS content and subsequently induced mitochondrial dysfunction and apoptosis in A375 cells. Our findings also highlight mitoNEET as a promising mitochondrial target for cancer therapy.

Synthesis of α-glycosidase hybrid nano-flowers and their application for enriching and screening α-glycosidase inhibitors

To rapidly and accurately screen compounds present in traditional Chinese herbal medicines for α-glycosidase inhibitors, we synthesized a novel nano-affinity material to enable the targeted screening of α-glycosidase inhibitors.

An insight to the binding of ellagic acid with human serum albumin using spectroscopic and isothermal calorimetry studies

Ellagic acid (EA), a natural polyphenol evidence several pharmacological benefits. The binding profile of EA with human serum albumin (HSA) has been explored and investigated by Isothermal titration calorimetry (ITC), circular dichroism (CD) spectroscopy, time-correlated single-photon counting (TCSPC), absorbance spectroscopy, steady-state fluorescence spectroscopy, and modelling studies. The ITC data analysis revealed the binding Constant (K_a), ΔH, ΔS and ΔG values to be 15.5×10⁴M⁻¹, −116.2±18.1 Kcal mol⁻¹, −366 cal mol⁻¹K⁻¹ and −7.13 Kcal mol⁻¹ respectively with a unique binding site at HSA. EA effectively quenched the intrinsic fluorescence of HSA by static quenching, whereas TCSPC data also revealed association of dynamic quenching also. Thermodynamic analysis confirmed that hydrophobic and mainly hydrogen bonding interaction played important role in stabilizing the HSA-EA complex. It further dictates the binding reaction to be enthalpy driven. The secondary structure of HSA was altered upon binding with EA. CD spectroscopic data indicated the fraction of alpha helicity to be decreased from 52% to 40% upon binding to EA. This study will provide an insight on evaluation of this bioactive interaction during transport and releasing efficiency at the target site in human physiological system since HSA is the most important carrier protein in blood serum.

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A single state binding mode of Human Serum Albumin with Ellagic Acid is proposed.

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Fluoresence quenching of HSA with Ellagic acid is validated in this study.

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Number of binding sites of HSA is characterized using Molecular Docking and ITC study.

Fluorescent DNA-Protected Silver Nanoclusters for Ligand-HIV RNA Interaction Assay

Studying ligand-biomacromolecule interactions provides opportunities for creating new compounds that can efficiently regulate specific biological processes. Ribonucleic acid (RNA) molecules have become attractive drug targets since the discovery of their roles in modulating gene expression, while only a limited number of studies have investigated interactions between ligands and functional RNA molecules, especially those based on nanotechnology. DNA-protected silver nanoclusters (AgNCs) were used to investigate ligand-RNA interactions for the first time in this study. The anthracycline anticancer drug mitoxantrone (MTX) was found to quench the fluorescence of AgNCs. After adding human immunodeficiency virus trans-activation responsive region (TAR) RNA or Rev-response element (RRE) RNA to AgNCs-MTX mixtures, the fluorescence of the AgNCs recovered due to interactions between MTX with RNAs. The binding constants and number of binding sites of MTX to TAR and RRE RNA were determined through theoretical calculations. MTX-RNA interactions were further confirmed in fluorescence polarization and mass spectrometry experiments. The mechanism of MTX-based fluorescence quenching of the AgNCs was also explored. This study provides a new strategy for ligand-RNA binding interaction assay.

Leishmanicidal effect of Spiranthera odoratíssima (Rutaceae) and its isolated alkaloid skimmianine occurs by a nitric oxide dependent mechanism

Leishmaniasis is one of the neglected diseases. High cost, systemic toxicity, and diminished efficacy due to development of resistance by the parasites has a negative impact on the current treatment options. Thus, the search for a new, effective and safer anti-leishmanial drug becomes of paramount importance. Compounds derived from natural products may be a better and cheaper source in this regard. This study evaluated the in vitro anti-leishmanial activity of Spiranthera odoratíssima (Rutaceae) fractions and isolated compounds, using promastigote and amastigote forms of different Leishmania species. J774 A.1 macrophage was used as the parasite host cell for the in vitro assays. Evaluations of cytoxicity, nitric oxide (NO), interleukin-10 and in silico analysis were carried out. In vitro experiments showed that the fruit hexanic fraction (Fhf) and its alkaloid skimmianine (Skm) have a significant (P<0·001) effect against L. braziliensis. This anti-L. braziliensis activity of Fhf and Skm was due to increased production of NO and attenuation of IL-10 production in the macrophages at concentrations ranging from 1·6 to 40·0 μg/ml. The in silico assay demonstrated significant interaction between Skm and amino acid residues of NOS2. Skm is thus a promising drug candidate for L. braziliensis due to its potent immunomodulatory activity.

Isolation and analysis of ginseng: advances and challenges

Ginseng occupies a prominent position in the list of best-selling natural products in the world. Because of its complex constituents, multidisciplinary techniques are needed to validate the analytical methods that support ginseng's use worldwide. In the past decade, rapid development of technology has advanced many aspects of ginseng research. The aim of this review is to illustrate the recent advances in the isolation and analysis of ginseng, and to highlight new applications and challenges. Emphasis is placed on recent trends and emerging techniques.

Traditional Chinese medicine and separation science

Traditional Chinese medicines (TCMs) are getting more and more popular nowadays in the whole world for improving health condition of human beings as well as preventing and healing diseases. TCM is a multi-component system with components mostly unknown, and only a few compounds are responsible for the pharmaceutical and/or toxic effects. The large numbers of other components in the TCM make the screening and analysis of the bioactive components extremely difficult. So, separation and analysis of the desired chemical components in TCM are very important subjects for modernization research of TCM. Thus, many novel separation techniques with significant advantages over conventional methods were introduced and applied to separation and analysis of the chemical constituents in TCM. This review presents just a brief outline of the applications of different separation methods for the isolation and analysis of TCM constituents.

Recent developments in CE and CEC of peptides

The article brings a comprehensive survey of recent developments and applications of high-performance capillary electromigration methods, zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography, to analysis, preparation, and physicochemical characterization of peptides. New approaches to the theoretical description and experimental verification of electromigration behavior of peptides and to methodology of their separations, such as sample preparation, adsorption suppression, and detection, are presented. Novel developments in individual CE and CEC modes are shown and several types of their applications to peptide analysis are presented: conventional qualitative and quantitative analysis, purity control, determination in biomatrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid and sequence analysis, and peptide mapping of proteins. Some examples of micropreparative peptide separations are given and capabilities of CE and CEC techniques to provide important physicochemical characteristics of peptides are demonstrated.

Screening and identification of permeable components in a combined prescription of Danggui Buxue decoction using a liposome equilibrium dialysis system followed by HPLC and LC-MS

A new method, i.e., liposome equilibrium dialysis followed by HPLC and LC-MS analysis, has been developed for the screening of permeable components in combined prescriptions of Danggui Buxue decoction (CPDBD). Multiple permeable components were simultaneously predicted by comparison of chromatograms of CPDBD extract before and after interaction with liposome membranes. A diode-array detector (DAD) and an evaporative light scattering detector (ELSD) were used, and the permeable compounds were identified by comparison with the available reference compounds and confirmed by on-line LC-MS. About fifteen compounds in a CPDBD extract were found to interact with liposome membranes. They were identified as calycosin-7-O-beta-D-glucoside (1), senkyunolide I or H (2), ononin (3), (6alphaR,11alphaR)-9,10-dimethoxypterocarpan-3-O-beta-D-glucoside (4), (3R)-2'-hydroxy-3',4'-dimethoxyisoflavan-7-O-beta-D-glucoside (5), calycosin (6), astragaloside IV (7), isoastragaloside II (8), formononetin (9), (6alphaR, 11alphaR),-3-hydroxy-9,10-dimethoxypterocarpan (10), (3R)-7,2'-dihydroxy-3',4'-dimethoxyisoflavan (11), astragaloside I (12), isoastragaloside I (13), E-ligustilide (14), and Z-ligustilide (15), respectively. Among all permeable components, 1, 3, 6, and 9 (flavonoids), 2, 14, and 15 (phthalides), and 7 (saponins) have been considered as major bioactive components in CPDBD. Therefore, this new method appears useful as a first step in the screening of bioactive components in natural products including Traditional Chinese Medicines (TCMs).

Analysis of interaction property of bioactive components in Danggui Buxue Decoction with protein by microdialysis coupled with HPLC–DAD–MS

Interaction of a commonly used combined prescription of Danggui Buxue Decoction (CPDBD) with protein was studied by microdialysis coupled with HPLC-DAD-MS. Nine compounds in CPDBD were unequivocally identified by comparing with their t(R), MS data and UV spectra with those of reference compounds, and simultaneously quantified. Microdialysis recoveries and binding degrees of 20 compounds in CPDBD with bovine serum albumin (BSA) were determined. Recoveries of microdialysis sampling ranged from 66.9 to 91.5% with RSD below 3.0%, and the binding degrees of those to BSA ranged from 6.3 to 59.8% (0.3mM BSA) and from 6.9 to 86.6% (0.6mM BSA). The results were determined at pH 7.4 and the influence of different pH value was investigated. Furthermore, the binding degrees of eight reference compounds were determined separately under the same conditions, indicating a significant effect of the interaction of compounds with each other on their binding degrees to BSA. By comparing their binding degrees with BSA with those of proven active compounds in CPDBD, i.e. chlorogenic acid (3), ferulic acid (6), ononin (12) and calycosin (16), other five compounds were found to possess potential activities, which were tentatively identified as calycosin-7-O-beta-D-glucoside-6-O-malonate (9), senkyunolide I or H (10), formononetin-7-O-beta-D-glucoside-6-O-malonate (17), and two unknown compounds.

Affinity chromatography with immobilized DNA stationary phase for biological fingerprinting analysis of traditional Chinese medicines

A stationary phase for high performance affinity chromatography with immobilization of DNA onto silica gel was prepared and characterized. The effect of the ionic strength, concentration of Mg2+, EDTA and CH3CN in the mobile phase on the retention of alkaloids were investigated. With this stationary phase, biological fingerprinting analysis of traditional Chinese medicines (TCMs) Coptis chinensis Franch and Rheum palmatum L. was performed with both one-dimensional (1-D) and two-dimensional (2-D) chromatography. The 1-D chromatography was performed with isocratic and gradient elution and 2-D chromatography was developed with immobilized DNA column combined with silica monolithic ODS column. It was found that 7 compounds in Coptis chinensis Franch including berberine, palmatine and jatrorrhizine, 14 compounds in Rheum palmatum L. including aloe-emodin, rhein, emodin, chrysophannol-8-O-glucophranoside and physionl-8-O-glucophranoside were active in binding to the immobilized DNA.

Functionalized Magnetic Nanoparticles for Small-Molecule Isolation, Identification, and Quantification

Functionalized magnetic nanoparticles (MNPs) were synthesized to serve as laser desorption/ionization elements as well as solid-phase extraction probes for simultaneous enrichment and detection of small molecules in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. Two laser-absorbing matrices were each conjugated onto MNP to give MNP@matrix which provided high ionization efficiency and background-free detection in MS leading to unambiguous identification of target small molecules in a complex mixture. MNP@matrix was demonstrated to serve as a general matrix-free additive in MALDI-TOF MS analysis of structurally distinct small molecules. Also, MNP@matrix provides a simple, rapid, and reliable quantitative assay for small molecules by mass without either the use of an internal standard or an isotopic labeling tag. Furthermore, the affinity extraction of small molecules from complex biofluid was achieved by probe protein-conjugated MNP@matrix without laborious purification. We demonstrated that a nanoprobe-based assay is a cost-effective, rapid, and accurate platform for robotic screening of small molecules.

Biological fingerprinting analysis of the interactome of a kinase inhibitor in human plasma by a chemiproteomic approach

In this study, a gel free chemiproteomic method based on chromatography was developed and applied for the biological fingerprinting analysis of complex biological system. p-Aminobenzamidine (ABA), an inhibitor of trypsin-like serine proteases, was immobilized for characterizing their interacting proteins in human plasma. By the proteomic analysis method, 214 proteins were identified with obvious affinity to the immobilized ABA. By searching the sequences of above proteins with consensus patterns of the two active sites, seven proteins belong to trypsin-like serine protease group were found. Based on the Gene Ontology annotation, the identified trypsin-like serine proteases have the function of catalytic activity and calcium ion binding, and are mainly involved in the biological process of blood coagulation. Eight more other proteins related to calcium ion binding and blood coagulation were found. Nearly all of these proteins cannot be identified by directly analyzing the plasma sample demonstrating the chemiproteomics a useful approach to characterize interacting proteins in the low abundance range.

Bioanalytical interaction studies executed by preincubation affinity capillary electrophoresis

The versatility of CE is beneficial for the study of many types of molecular interactions, because different experimental designs can be made to suit the characteristics of a particular interaction. A very versatile starting point is the preequilibration type of affinity CE that has been used extensively for characterizing biomolecular interactions in the last 15 years. We review this field here and include a comprehensive overview of the existing preincubation ACE modes including their advantages and limitations as well as the methodological developments and applications within the bioanalytical field.

Comprehensive two-dimensional HPLC to study the interaction of multiple components inRheum palmatum L. with HSA by coupling a silica-bonded HSA column to a silica monolithic ODS column

A mode of comprehensive 2-D LC was developed by coupling a silica-bonded HSA column to a silica monolithic ODS column. This system combined the affinity property of the HSA column and the high-speed separation ability of the monolithic ODS column. The affinity chromatography with HSA-immobilized stationary phase was applied to study the interaction of multiple components in traditional Chinese medicines (TCMs) with HSA according to their affinity to protein in the first dimension. Then the unresolved components retained on the HSA column were further separated on the silica monolithic ODS column in the second dimension. By hyphenating the 2-D separation system to diode array detector and MS detectors, the UV and molecular weight information of the separated compounds can also be obtained. The developed separation system was applied to analysis of the extract of Rheum palmatum L., a number of low-abundant components can be separated on a single peak from the HSA column after normalization of peak heights. Six compounds were preliminarily identified according to their UV and MS spectra. It showed that this system was very useful for biological fingerprinting analysis of the components in TCMs and natural products.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.