Screening of the potentially active compounds from Polygonatum sibiricum using RAW264.7 cellular membranes coated magnetic beads fishing followed by HPLC analysis

Target biomolecule-immobilized magnetic beads could be used as a powerful tool for screening active compounds present in natural products. Low damage rates of the target proteins, associated with the availability of diverse automated online approaches for analysis, make it a valuable tool for affinity studies. RAW264.7 cells (a kind of murine macrophage cell line) were used in this study. These cellular membranes were immobilized onto the surface of MBs and were used for screening the active compounds of Polygonatum sibiricum. Combining this technique with HPLC led to the identification of an active compound and its biological activity was confirmed. This is the first report establishing the use of RAW264.7 cellular membrane-coated magnetic bead fishing followed by HPLC analysis for screening active compounds from natural products.     

Screening inhibitors of xanthine oxidase from natural products using enzyme immobilized magnetic beads by high‐performance liquid chromatography coupled with tandem mass spectrometry

In this study, high‐performance liquid chromatography coupled with tandem mass spectrometry was used to assess the results of bioactive compound screening from natural products using immobilized enzyme magnetic beads. We compared three commercial magnetic beads with modified amino, carboxy, and N‐hydroxysuccinimide groups, respectively. Amino magnetic beads performed best for immobilization and were selected for further experiments. Xanthine oxidase was immobilized on amino magnetic beads and applied to screen potential inhibitors in fresh Zingiber officinale Roscoe, extracts of Scutellaria baicalensis Georgi, and Pueraria lobata Ohwi. In total, 12 potential xanthine oxidase ligands were identified from fresh Zingiber root and Scutellaria root extracts, of which eight were characterized and the concentration required for 50% inhibition was determined. Preliminary structure–function relationships were discussed based on these results. A convenient and effective method was therefore developed for the identification of active compounds from complex natural product mixtures.     

FluMag-SELEX as an advantageous method for DNA aptamer selection

Aptamers are ssDNA or RNA oligonucleotides with very high affinity for their target. They bind to the target with high selectivity and specificity because of their specific three-dimensional shape. They are developed by the so-called Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process. We have modified this method in two steps—use of fluorescent labels for DNA quantification and use of magnetic beads for target immobilization. Thus, radioactive labelling is avoided. Immobilization on magnetic beads enables easy handling, use of very small amounts of target for the aptamer selection, rapid and efficient separation of bound and unbound molecules, and stringent washing steps. We have called this modified SELEX technology FluMag-SELEX. With FluMag-SELEX we have provided a methodological background for our objective of being able to select DNA aptamers for targets with very different properties and size. These aptamers will be applied as new biosensor receptors. In this work selection of streptavidin-specific aptamers by FluMag-SELEX is described. The streptavidin-specific aptamers will be used to check the surface occupancy of streptavidin-coated magnetic beads with biotinylated molecules after immobilization procedures.     

Magneto-mechanical trapping systems for biological target detection

We demonstrate a magnetic microsystem capable of detecting nucleic acids via the size difference between bare magnetic beads and bead compounds. The bead compounds are formed through linking nonmagnetic beads and magnetic beads by the target nucleic acids. The system comprises a tunnel magneto-resistive (TMR) sensor, a trapping well, and a bead-concentrator. The TMR sensor detects the stray field of magnetic beads inside the trapping well, while the sensor output depends on the number of beads. The size of the bead compounds is larger than that of bare magnetic beads, and fewer magnetic beads are required to fill the trapping well. The bead-concentrator, in turn, is capable of filling the trap in a controlled fashion and so to shorten the assay time. The bead-concentrator includes conducting loops surrounding the trapping well and a conducting line underneath. The central conducting line serves to attract magnetic beads in the trapping well and provides a magnetic field to magnetize them so to make them detectable by the TMR sensor. This system excels by its simplicity in that the DNA is incubated with magnetic and nonmagnetic beads, and the solution is then applied to the chip and analyzed in a single step. In current experiments, a signal-to-noise ratio of 40.3 dB was obtained for a solution containing 20.8 nM of DNA. The sensitivity and applicability of this method can be controlled by the size or concentration of the nonmagnetic bead, or by the dimension of the trapping well.

If biological targets are present, they link magnetic beads and fluorescent beads. This results in less magnetic beads to be on the surface of magnetic sensor, causing a smaller signal, thus biological targets are detected.     

Preparation and characterization of monodisperse superparamagnetic poly(vinyl alcohol) beads by reverse spray suspension crosslinking

A novel protocol for preparing magnetic poly(vinyl alcohol) (PVA) beads by reverse spray suspension crosslinking was reported. The hydrophilic Fe₃O₄ nanoparticles were mixed with PVA, glutaraldehyde, and water to form aqueous phase. Then the aqueous phase was sprayed into vegetable oil by a pressure of nitrogen gas to form water in oil (W/O) suspension. The magnetic PVA beads were obtained in the presence of hydrochloric acid catalyst. It was found that the magnetic PVA beads obtained good properties when the PVA concentration was 10%, and the oil phase temperature was controlled at 40 °C. The mechanical stirring has little impact on the size of magnetic PVA beads in the process of reverse spray suspension crosslinking. The Cibacron Blue (CB) was coupled on the surface of magnetic PVA beads by surface chemical reaction. The morphology, size, and magnetic properties of the magnetic PVA beads were examined by scanning electron microscopy, laser diffraction, and vibrating sample magnetometer, respectively. Compared with the stirring method, it was found that the size of magnetic PVA beads was monodisperse and their saturation magnetization was much higher. Fourier transform infrared and X‐ray photoelectron spectroscopy experimental results proved that CB molecules were covalently immobilized onto the surface of the magnetic PVA beads. Meanwhile, the protein affinity separation experiments demonstrated that the magnetic PVA beads can potentially be used as a carrier for large‐scale protein separation. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 203–210, 2008     

Systematic identification of the druggable interactions between human protein kinases and naturally occurring compounds in endometriosis

Diverse kinase signaling pathways have been involved in the pathogenesis of endometriosis (EM), which can be modulated either by directly targeting the hub kinases or by indirectly regulating marginal members in the pathways. Here, a systematic kinase–inhibitor interaction profile was created for 8 naturally occurring compounds against 20 human protein kinases. The compounds are all non-sterid that have been reported as pharmacologically active molecular entities potential for EM therapeutics, while the kinases were curated via gene ontology terms enriched from the gene co-citation network with EM. The resulting profile was analyzed at structural, energetic and dynamic levels to identify druggable kinase–compound interactions. The compounds Gossypol, Curcumin and EGCG showed a similar interaction profile across these kinases; they can bind tightly to the top-listed kinases in gene ontology, while the compounds Marrubiin, Apigenin and DIM were predicted to exhibit generally weak affinity for the 20 curated kinases. The JNK kinase, a MAPK family member, was identified as a putative candidate of druggable target for EM therapeutics; the inhibitory activity of eight naturally occurring compounds as well as a sophisticated kinase inhibitor SP600125 against the JNK was tested using enzymatic activity analysis. As might be expected, the Gossypol and EGCG were determined to have high inhibitory activity at namomolar level (IC₅₀ = 55 and 94 nM, respectively), which are comparable with or better than the positive control SP600125 (IC₅₀ = 76 nM), while other tested compounds exhibited weak inhibition (IC₅₀ > 100 nM) or bad potency (IC₅₀ = n.d.) against the kinase.     

Effect of naturally occurring crosslinking junctions on green strength of natural rubber

The effect of the naturally occurring crosslinking junctions on green strength of natural rubber, isolated from Hevea brasiliensis, was investigated by using rubber extracted from Parthenium argentatum Gray (Guayule) as a model. Guayule rubber and natural rubber were characterized through nuclear magnetic resonance spectroscopy and size exclusion chromatography. The non‐rubber components of Guayule rubber and natural rubber were characterized by Kjeldahl method and Fourier transform infrared spectroscopy. It was found that Guayule rubber contains a much higher amount of fatty acids and their esters while it contains no proteins. The gel content, determined by swelling method, was related to a number of naturally occurring crosslinking junctions of Guayule rubber and natural rubber. The outstanding green strength of natural rubber was attributed to the effect of naturally occurring crosslinking junctions, when stress–strain curve and tensile properties of unvulcanized Guayule rubber were compared with those of unvulcanized natural rubber. Copyright © 2016 John Wiley & Sons, Ltd.     

Naturally occurring scaffolds for compound library design: convenient access to bis-aryl 1-azaadamantanes carrying a vicinal amino alcohol motif

The vast majority of scaffolds found in natural products are absent from the currently available compound collections for biological screening. At the same time, scaffolds derived from natural products may have a distinct advantage over non-natural cores in terms of providing compounds endowed with biological activities and should be used extensively in screening library design. We have developed a synthetic approach to merging a naturally occurring 1-azaadamantane core with a vicinal amino alcohol moiety that is also common in natural product chemical space. The synthesis features diastereoselective epoxidation of racemic chiral 2,6-diaryl-4-methylene 1-azaadamantanes with subsequent S_N2-type epoxide opening in aqueous isopropanol.     

Theoretical studies on the structural rearrangement of ligand binding pocket in human vitamin D receptor

The structural rearrangement of the ligand binding domain (LBD) of human Vitamin D receptor (hVDR) complexed with 1α, 25‐dihydroxyvitamin D₃ (natural ligand) and its analogues (denoted as b and c ) was studied by molecular dynamics (MD) simulations. MD simulations revealed that these ligands could induce different structural changes of LBD, in which 1α, 25‐dihydroxyvitamin D₃ only led to a minute change, suggesting that LBD adopted its canonical active conformation upon binding the natural ligand, while b and c could provoke a clear structural rearrangement of the LBD. In complex of hVDR‐LBD/ b , it is found that helix 6 (H6) and subsequent loop 6‐7 shift outward and the last turn of H11 shifts away from H12, which generate a new cavity at the bottom of binding pocket to accommodate the extra butyl group on the side chain of ligand b . As for hVDR‐LBD/ c , the steric exclusion of the second side chain of ligand c makes the N‐terminal of H7 move outsides and C‐terminal of H11 close to H12, expanding the bottom of the pocket. These calculation results agree well the experimental observations. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

New cytotoxic natural products from the mangrove biome: covering the period 2007–2015

Nowadays, the mangrove biome is considered to be a profound resource of natural products usually possessing cytotoxicity of a broader range. Covering the period 2007–2015, a total of 21 new naturally occurring compounds has stood out. For example, xylogranin B and swietephragmin C were found to exhibit very potent cytotoxic activity against the colon HCT-116 cells reaching IC₅₀ values of 0.05 and 0.06 μM, respectively. Bearing in mind the efficacy of the majority compounds in the preliminary in vitro screens, these studies should be expanded to both ex vivo and in vivo screens including the evaluation of the relevant toxicological profiles.     

Recent advances on the synthesis of flavans,isoflavans, and neoflavans

Heterocyclic compounds are the omnipresent structural cores comprising many natural and pharmaceutical products of biological significance. Significantly, heterocyclic compounds are widely distributed in nature, and also have applications in agrochemicals, sanitizers, as dyestuff, as copolymers, etc. Among heterocyles, flavonoids are a class of compounds that are highly interesting and constitute many natural products. In general, all flavanoids contains a basic core of C₆-C₃-C₆ of phenyl-benzopyran backbone. The relative placement of the phenyl group on to the benzopyran core makes further classification into flavanoids, isoflavanoids and neoflavanoids. Flavans (2-aryl chroman) are subclass of anthoxanthanes exhibits a broad spectrum of biological properties such as anti-inflammatory, anti-oxidant, and anti-malarial properties. Some representative naturally occurring products possessing flavan core are apigenin, luteolin, tangeretin, scutellarein, etc. On the other hand, some of the notable isoflavan-based natural products are glabridin and (S)-(−)-equol. Glabridin is isolated from Licorice roots, which regulates paraoxonase (PON₂) levels. While the simple isoflavan (S)-(−)-equol, is produced from soy isoflavone intake. Also, natural products such as dalbergichromene, centchroman, and (+)-myristinin A possess neoflavan (4-aryl-3,4-dihydro-2H-chromenes) core structure. Owing to their broad biological and pharmacological properties, synthetic chemists are fascinated in developing new routes toward their synthesis. As a result, a decent number of reports have been established in the literature. Thus, for the past 5 years of time frame, many new methodologies have been witnessed, for the synthesis of various flavan systems. This review emphasizes most of the significant methods on accomplishing flavans, isoflavans and neoflavans and also focused on their applications to the synthesis of relevant natural as well as biologically active products.     

Magnetic bead-based approach to monitoring of cigarette smoke-induced DNA oxidation damage and screening of natural protective compounds

Cigarette smoking can damage DNA and induce spontaneous mutagenesis or carcinogenesis. Here, we describe a novel strategy for in situ monitoring of cigarette smoke-induced DNA oxidation damage and offer a method for screening natural compounds that protect DNA against tobacco smoke. The present protocol takes advantage of a fast and simple magnetic separation/mixing method and a highly sensitive chemiluminescence (CL) ELISA. The DNA immobilized on the magnetic beads was oxidized by the smoke in the absence or presence of natural compounds, and then oxidative DNA was conveniently held by magnetic force, whereas the complex tobacco smoke matrix and any remaining compounds were completely eliminated by extensive washing, and possible interferences were thus removed and oxidative damage was then sensitively monitored by CL ELISA. A library of 32 natural products was then screened and three were found to protect DNA from oxidative damage and thus may be promising compounds for the development of new drugs. Moreover, the protection effect of these three natural compounds against DNA oxidation damage was successfully classified by directly spiking them in the reference cigarettes. In addition, the potential to screen a mixture in a complex sample matrix, such as crude extracts, was also demonstrated, and hence the proposed technique can screen compounds within a complex matrix and enhance the screening throughput.     

Specific peptides as alternative to antibody ligands for biomagnetic separation of Clostridium tyrobutyricum spores

Nowadays, the reference method for the detection of Clostridium tyrobutyricum in milk is the most-probable-number method, a very time-consuming and non-specific method. In this work, the suitability of the use of superparamagnetic beads coated with specific antibodies and peptides for bioseparation and concentration of spores of C. tyrobutyricum has been assessed. Peptide or antibody functionalized nanoparticles were able to specifically bind C. tyrobutyricum spores and concentrate them up to detectable levels. Moreover, several factors, such as particle size (200 nm and 1 μm), particle derivatization (aminated and carboxylated beads), coating method, and type of ligand have been studied in order to establish the most appropriate conditions for spore separation. Results show that concentration of spore is favored by a smaller bead size due to the wider surface of interaction in relation to particle volume. Antibody orientation, related to the binding method, is also critical in spore recovery. However, specific peptides seem to be a better ligand than antibodies, not only due to the higher recovery ratio of spores obtained but also due to the prolonged stability over time, allowing an optimal recovery of spores up to 3 weeks after bead coating. These results demonstrate that specific peptides bound to magnetic nanoparticles can be used instead of traditional antibodies to specifically bind C. tyrobutyricum spores being a potential basis for a rapid method to detect this bacterial target.     

Ligand Fishing with Cellular Membrane-Coated Magnetic Beads: A New Method for the Screening of Potentially Active Compounds from Natural Products

Ligand fishing with target biomolecule-immobilized magnetic beads (MBs) has been established and developed for nearly 10 years. Advantages of this technique, such as the ease of operation, associated with a diversity of automated online approaches, make it a valuable tool for affinity studies. However, transmembrane proteins have not been used as the target biomolecules in the assay, since they are usually not available in a purified and bioactive form. In addition, few publications have reported the use of this method for screening active compounds derived from natural products. In this work, for the first time, cellular membrane-coated MBs, which to a large extent maintain the activity of the transmembrane proteins, were used for the fishing assay. We demonstrated application of red blood cell membrane-coated MBs for fishing potential active components from a natural product (Angelica dahurica). The potential active compounds, such as imperatorin, bergapten, and pabulenol, were detected. The result correlated well with cell membrane chromatography (CMC) coupled with HPLC. Comparisons of the developed MBs fishing assay with the CMC method showed the noteworthy advantages of the fishing technique regarding the consumption of cellular membranes, buffers as well as length of operation time.     

Covalent attachment of the plant natural product naringenin to small glass and ceramic beads

Background  

Natural products have numerous medicinal applications and play important roles in the biology of the organisms that accumulate them. Few methods are currently available for identifying proteins that bind to small molecules, therefore the discovery of cellular targets for natural products with pharmacological activity continues to pose a significant challenge in drug validation. Similarly, the identification of enzymes that participate in the biosynthesis or modification of natural products remains a formidable bottleneck for metabolic engineering. Flavonoids are one large group of natural products with a diverse number of functions in plants and in human health. The coupling of flavonoids to small ceramic and glass beads provides a first step in the development of high-throughput, solid-support base approaches to screen complex libraries to identify proteins that bind natural products.     

Volatile profiling reveals intracellular metabolic changes in <Emphasis Type="Italic">Aspergillus parasiticus</Emphasis>: <Emphasis Type="Italic">veA</Emphasis> regulates branched chain amino acid and ethanol metabolism

Background  

Filamentous fungi in the genus Aspergillus produce a variety of natural products, including aflatoxin, the most potent naturally occurring carcinogen known. Aflatoxin biosynthesis, one of the most highly characterized secondary metabolic pathways, offers a model system to study secondary metabolism in eukaryotes. To control or customize biosynthesis of natural products we must understand how secondary metabolism integrates into the overall cellular metabolic network. By applying a metabolomics approach we analyzed volatile compounds synthesized by Aspergillus parasiticus in an attempt to define the association of secondary metabolism with other metabolic and cellular processes.     

Synthesis of Chiral Benzofuran-Derived β-Amino Esters Induced by N-tert-Butanesulfinamide

The benzofuran skeleton is commonly found in a wide variety of natural products that display a wide range of biological activities. For this reason, benzofuran has a high potential for use as a scaffold in both chemical and pharmaceutical syntheses of natural products. This work describes the development of a novel asymmetric synthetic method of benzofuran-derived β-amino esters via K₂CO₃-promoted domino reactions of ortho-hydroxyl aromatic N-tert-butylsulfinyl imines and diethyl bromomalonate. A small library of target compounds was prepared under optimized reaction conditions in moderate to good yields with high distereoselective and enantioselective properties. The newly generated chiral carbon center was of an (S)-configuration as determined by x-ray diffraction.     

Biosynthetic origins of C-P bond containing tripeptide K-26

[reaction: see text] Primary metabolic precursors for K-26, a naturally occurring tripeptide phosphonic acid from Actinomyces sp. K-26, are investigated by heavy-atom isotope labeled substrate incorporation experiments. A highly sensitive selected reaction monitoring (SRM)-based method for isotopic incorporation estimation in natural products is reported. The incorporation of heavy-atom isotope labeled tyrosine compounds into the (R)-1-amino-2-(4-hydroxyphenyl)-ethylphosphonic acid moiety of compound K-26 suggests a new mechanism of biosynthesis of phosphonate functionality in natural products.     

(2E)-4,4-Dimethoxy-2-butenal in the Synthesis of Conjugated Dienes and Dienals

Using (2E)-4,4-dimethoxy-2-butenal as starting compound, methods were developed for synthesis of (2E,4E)- and (2E,4Z)-dimethoxyalkadienes. Deacetalization of the latter gives with high yield the corresponding dienals which are naturally occurring compounds and also synthons for preparation of conjugated dienes as key compounds for building up other natural products.