Use In Biological Assays Research Articles

Ranunculin, Protoanemonin, and Anemonin: Pharmacological and Chemical Perspectives.

Ranunculin, a glucoside, serves as a chemotaxonomic marker in Ranunculaceae plants. When these plants are damaged, an enzyme β-glucosidase triggers the conversion of ranunculin into protoanemonin through hydrolysis. Subsequently, protoanemonin undergoes cyclodimerization to form anemonin. The inherent instability of ranunculin and the rapid dimerization of protoanemonin render them unsuitable for use in biological assays. Conversely, anemonin stands out as the optimal molecule for bioassays and demonstrates diverse biological properties, including anti-inflammatory, anti-infective, and anti-oxidant effects. Among these, anemonin exhibits the greatest promise in addressing conditions such as arthritis, cerebral ischemia, and ulcerative colitis. Its potential medical uses are enhanced by its capacity to inhibit nitric oxide synthesis and successfully counteract lipopolysaccharide-induced inflammation. This review describes the chemistry and biological properties of anemonin and its precursors, including discussions on extraction, isolation, synthesis, and investigations into bioactivity and pharmacokinetics.

Advancing botanical safety: A strategy for selecting, sourcing, and characterizing botanicals for developing toxicological tools

Increases in botanical use, encompassing herbal medicines and dietary supplements, have underlined a critical need for an advancement in safety assessment methodologies. However, botanicals present unique challenges for safety assessment due to their complex and variable composition arising from diverse growing conditions, processing methods, and plant varieties. Historically, botanicals have been largely evaluated based on their history of use information, based primarily on traditional use or dietary history. However, this presumption lacks comprehensive toxicological evaluation, demanding innovative and consistent assessment strategies. To address these challenges, the Botanical Safety Consortium (BSC) was formed as an international, cross-sector forum of experts to identify fit-for purpose assays that can be used to evaluate botanical safety. This global effort aims to assess botanical safety assessment methodologies, merging traditional knowledge with modern in vitro and in silico assays. The ultimate goal is to champion the development of toxicity tools for botanicals. This manuscript highlights: 1) BSC's strategy for botanical selection, sourcing, and preparation of extracts to be used in in vitro assays, and 2) the approach utilized to characterize botanical extracts, using green tea and Asian ginseng as examples, to build confidence for use in biological assays.

Fluorescent and Bioluminescent Calcium Indicators with Tuneable Colors and Affinities.

We introduce a family of bright, rhodamine-based calcium indicators with tuneable affinities and colors. The indicators can be specifically localized to different cellular compartments and are compatible with both fluorescence and bioluminescence readouts through conjugation to HaloTag fusion proteins. Importantly, their increase in fluorescence upon localization enables no-wash live-cell imaging, which greatly facilitates their use in biological assays. Applications as fluorescent indicators in rat hippocampal neurons include the detection of single action potentials and of calcium fluxes in the endoplasmic reticulum. Applications as bioluminescent indicators include the recording of the pharmacological modulation of nuclear calcium in high-throughput compatible assays. The versatility and remarkable ease of use of these indicators make them powerful tools for bioimaging and bioassays.

Virus Propagation and Plaque Assay for Dengue Virus.

This chapter describes the methods of propagation and titration for DENV-1 to -4, which are required for most of the experiments using live viruses. DENV does not reach titers as high as those of other viruses or as high as desired for their use in biological assays. Although DENV grows in many different cell lines derived from both vertebrate and invertebrate cells, the most common cell lines used for virus isolation and propagation are mosquito cells C6/36 from Aedes albopictus. Amongst several methods for virus quantification, plaque assay stands out as being very practical and inexpensive. This technique is carried out essentially to estimate virion density in a particular material, being extremely important when evaluating the effect of an antiviral treatment or antibody neutralization capacity, for example. In this assay, viral particles are serially diluted and added onto confluent cell monolayers immersed in a semisolid medium, which is responsible for limiting virus spread throughout the culture. Therefore, regarding the medium consistency, once a virion successfully infects a cell, the newly produced particles can only infect neighboring cells, eventually leading them to death. This phenomenon can be observed as round gaps or plaques in the culture after staining live cells with a crystal violet solution. Then, plaques are counted and used to determine plaque-forming units per milliliter. Here, we describe a protocol established by our group for dengue virus (DENV) titration with porcine kidney (PS) cells.

A Review of Target Identification Strategies for Drug Discovery: from Database to Machine-Based Methods

In recent years, target identification has become more efficient than before, and it helped to discover huge amounts of drugs for various diseases. The mystery buried behind was the methods that developed in recent years utilized in the target identification. The advances and research status of database, biological assay and machine-based method in recent years for target identification would be integrated by this review. The various databases help scientists to find information about target property, chemical property or on genome level. The biological assay, such as RNAi, RNA sequencing, DNA microarray, and Gal4/UAS system, is commonly used to identify the target in recent years. The machine-based strategies, such as random forest algorithm and Support Vector Machine (SVM) algorithm, could help scientists identify the target and find compound activity more efficiently. Among the three methods mentioned above, the machine-based methods could have higher efficiency and lower cost while maintaining higher accuracy. Despite the promising properties of machine-based methods, the combination use of biological assay would still be necessary. With wider application of more efficient strategies, target identification, as well as drug discovery process, would gain more rapid development.

Integrating Quantitative Assays with Biologically Based Mathematical Modeling for Predictive Oncology.

SummaryWe provide an overview on the use of biological assays to calibrate and initialize mechanism-based models of cancer phenomena. Although artificial intelligence methods currently dominate the landscape in computational oncology, mathematical models that seek to explicitly incorporate biological mechanisms into their formalism are of increasing interest. These models can guide experimental design and provide insights into the underlying mechanisms of cancer progression. Historically, these models have included a myriad of parameters that have been difficult to quantify in biologically relevant systems, limiting their practical insights. Recently, however, there has been much interest calibrating biologically based models with the quantitative measurements available from (for example) RNA sequencing, time-resolved microscopy, and in vivo imaging. In this contribution, we summarize how a variety of experimental methods quantify tumor characteristics from the molecular to tissue scales and describe how such data can be directly integrated with mechanism-based models to improve predictions of tumor growth and treatment response.

Biological Effects of Propolis on Cancer

Propolis is a special resin and wax material collected from the leaves and shells of trees, buds and shoots of plants by honey bees (Apis mellifera L.). In recent years, many researchers have studied the chemical composition, biological activity and pharmacological properties of propolis. The colour, odour and pharmacological properties of the propolis composition also vary as the composition changes depending on the plant, region, season and bee colony. Flavonoids, aromatic acids, phenolic acids and esters are the main compounds responsible for the biological activity of propolis. A number of studies have been conducted on the use of propolis or its active ingredients in the treatment of cancer. It has been observed that the use of propolis did not cause side effects according to in-vitro and in-vivo studies. Propolis should be extracted with different compounds for use in biological assays. The most commonly used compounds for extraction are ethanol, methanol, oil and water. A number of studies have been carried out showing the antitumor effect of propolis in cell culture and animal tests. The search for new drugs derived from natural products, which may function as chemotherapeutic agents and have low side effects, has increased in recent years. Combination with antioxidant therapy may improve the side effects of chemotherapy on leukocytes, liver and kidney, thus increasing the effect of chemotherapy with dose increase.

Dimensional distribution control of elongate mineral particles for their use in biological assays

The aim of the present method is to reduce the dimensional variability of asbestos, elongate mineral particles, and other asbestiform minerals for use in biological assays. Here, the pristine mineral sample is filtered through two nylon meshes of different sizes to obtain a narrower dimensional distribution following a power law. Furthermore, we show that anoxic preparation, autoclaving and storage of the mineral prior to addition into biological cultures did not affect the mineral's chemical properties. This approach avoids the use of highly reactive chemicals modifying mineralogical characteristics and surface properties, which can affect to a major extent mineral toxicity as well as interactions between minerals and biological matter or biofluids. The method can be combined with additional selective approaches to further refine the dimensional range of the minerals. The advantages of this protocol over previous methods are:•Exclusive use of distilled water and 2-propanol, thus eliminating chemicals that can modify bulk or surface properties of the studied minerals.•Successful sterilization of the resulting mineral particles for use in biological assays without compromising mineralogical characteristics.•Applicability of this method across various types of asbestos, elongate mineral particles and, potentially, other hazardous minerals.

Automated Glycan Assembly of Plant Cell Wall Oligosaccharides.

Synthetic cell wall oligosaccharides are promising molecular tools for investigating the structure and function of plant cell walls. Their well-defined structure and high purity prevents misinterpretations of experimental data, and the possibility to introduce chemical handles provides means for easier localization and detection. Automated glycan assembly as emerged has a powerful new method for the efficient preparation of oligosaccharide libraries. We recently made use of this technology to prepare a collection of plant cell wall glycans for cell wall research. In this chapter, detailed experimental procedures for the automated synthesis of oligosaccharides that are ready for use in biological assays are described.

Sweet Cherry Extract Targets the Hallmarks of Cancer in Prostate Cells: Diminished Viability, Increased Apoptosis and Suppressed Glycolytic Metabolism

The present work evaluated the anticancer properties of sweet cherry (Prunus avium) extract on human prostate cells. Several sweet cherry cultivars from Fundão (Portugal) were methanol-extracted and their phytochemical composition characterized. The Saco “late harvest” extract was highly-enriched in anthocyanins and selected for use in biological assays. Non-neoplastic (PNT1A) and neoplastic (LNCaP and PC3) human prostate cells were treated with 0–2,000 μg/ml of extract for 48–96 h. Cell viability was evaluated by the MTT assay. Apoptosis, oxidative stress, and glycolytic metabolism were assessed by Western blotting and enzymatic assays. Glucose consumption and lactate production were measured spectrophotometrically. Saco cherry extract diminished the viability of neoplastic and non-neoplastic cells, whereas enhancing apoptosis in LNCaP. Cherry extract-treatment also diminished oxidative damage and suppressed glycolytic metabolism in LNCaP cells. These findings widened the knowledge on the mechanisms by which cherry extract modulate cell physiology, demonstrating their broad action over the hallmarks of cancer.

Abstract 2177: Streptavidin-pHast: A readily conjugatable, pH-sensitive dye to screen for internalization

Abstract Quick and efficient screening of targeting agents that internalize effectively is vital for determining their suitability as potential therapeutics. Some of the most recent successes in the treatment of cancers have been from antibodies to cell surface proteins that are responsible for tumor cell proliferation. Examples are Cetuximab (target: EGFR) approved for colorectal cancer, and Trastuzumab (target: HER2) for breast cancer. These antibodies have more than one effect on the cancer cell, but one of the most important is that, upon binding to the cell surface antigen, the complex is internalized. As such, the down-regulated cell surface protein no longer plays a role in cancer cell division. Here we describe a method for determining internalization of cell surface molecules by targeting agents using a pH-dependent fluorescent reporter cross-linked to streptavidin. Streptavidin is a tetrameric protein (molecular weight 53 kDa in its recombinant form), with each subunit able to bind a single biotin molecule. The bond between streptavidin and biotin is rapid and essentially non-reversible, unaffected by most extremes of pH, organic solvents, and denaturing reagents. It is the strongest known noncovalent biological interaction (Ka = 1015 M-1) between protein and ligand. A variety of molecules, including lectins, proteins, and antibodies, can be biotinylated and reacted with streptavidin-labeled probes or other detection reagents for use in biological assays. The fluorescence from this reporter increases intensity as the pH of its surroundings becomes more acidic, as demonstrated when exposed to the environment inside a cell (thereby providing evidence of internalization). Here we describe methods that can be used to explore candidates as cancer therapeutics in a quick, reliable and reproducible manner. Citation Format: Patrick A. Shramm, Leonardo Ancheta. Streptavidin-pHast: A readily conjugatable, pH-sensitive dye to screen for internalization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2177.

Use of biological detection methods to assess dioxin-like compounds in sediments of Bohai Bay, China

Bohai Bay, in the western region of northeastern China's Bohai Sea, receives water from large rivers containing various pollutants including dioxin-like compounds (DLCs). This study used the established zebrafish (Danio rerio) model, its known developmental toxicity endpoints and sensitive molecular analyses to evaluate sediments near and around an industrial effluent site in Bohai Bay. The primary objective was to assess the efficacy of rapid biological detection methods as an addition to chemical analyses. Embryos were exposed to various concentrations of sediment extracts as well as a 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) positive control. Exposure to sediment extract nearest the discharge site (P1) resulted in the most severe- and highest rates of change in embryos and larvae, suggesting that DLC contaminated sediment probably did not occur much beyond it. P1 extract resulted in concentration dependent increases in mortality and pericardial edema. Its highest concentration caused up-regulation of P-450 (CYP)-1A1(CYP1A) mRNA expression at 72 h post fertilization (hpf), an increase in its expression in gill arches as observed by whole mount in situ hybridization, and an increased signal in the Tg(cyp1a: mCherry) transgenic line. The pattern and magnitude of response was very similar to that of TCDD and supported the presence of DLCs in these sediment samples. Follow-up chemical analysis confirmed this presence and identified H7CDF, O8CDF and O8CDD as the main components in P1 extract. This study validates the use of biological assays as a rapid, sensitive, and cost-effective method to evaluate DLCs and their effects in sediment samples. Additionally, it provides support for the conclusion that DLCs have limited remobilization capacity in marine sediments.

Luciferase Advisor: High-Accuracy Model To Flag False Positive Hits in Luciferase HTS Assays.

Firefly luciferase is an enzyme that has found ubiquitous use in biological assays in high-throughput screening (HTS) campaigns. The inhibition of luciferase in such assays could lead to a false positive result. This issue has been known for a long time, and there have been significant efforts to identify luciferase inhibitors in order to enhance recognition of false positives in screening assays. However, although a large amount of publicly accessible luciferase counterscreen data is available, to date little effort has been devoted to building a chemoinformatic model that can identify such molecules in a given data set. In this study we developed models to identify these molecules using various methods, such as molecular docking, SMARTS screening, pharmacophores, and machine learning methods. Among the structure-based methods, the pharmacophore-based method showed promising results, with a balanced accuracy of 74.2%. However, machine-learning approaches using associative neural networks outperformed all of the other methods explored, producing a final model with a balanced accuracy of 89.7%. The high predictive accuracy of this model is expected to be useful for advising which compounds are potential luciferase inhibitors present in luciferase HTS assays. The models developed in this work are freely available at the OCHEM platform at http://ochem.eu .

English

Research on natural products is facing significant difficulty. The analysis "high-throughput screening" has limited effectiveness in their evaluation. This report on in vitro screening of pharmacological activity of the drugs candidate molecule by evaluating a single target. The presence of many substances in a natural extract makes this process unprecise. The zebrafish (Danio rerio, ZF) is well suited to high-throughput applications owing to its high fecundity, rapid extrauterine development and transparency during organogenesis. This fact promotes increase in the relevance of their use in biological assays, which is hard to be matched in vitro. Tests based on ZF can aid in the isolation of bioactive molecules from plant extracts, which was identified in a large-scale screening. This increases the biological relevance of such findings. Another decisive factor for the use of ZF as an experimental model, for widespread testing, is the few extracts or the isolated compounds required for tests. Therefore, the growing number of publications and innovative models created for the research shows a lot of diseases with this species, revealing the importance of ZF as an experimental model for the screening of natural products. Key words: Danio rerio, experimental models, natural products.

Carbosilane glycodendrimers

Glycodendrimers fascinate both carbohydrate chemists and biologists because of their ability to recognize lectins and enhance carbohydrate-protein interactions. These characteristics make glycodendrimers a valuable tool in glycoscience and chemical biology. Many glycodendrimers have been described to date; this tutorial review focuses specifically on carbosilane glycodendrimers. We present methodologies for synthesizing parent carbosilane dendrimers and describe their use in biological assays. We also describe representative functionalizations of parent carbosilane dendrimers at terminal positions which are necessary for chemical ligation with carbohydrate ligands. This is followed by a description of all coupling reactions between carbohydrate and carbosilane dendrimer functionalities used in the synthesis of carbosilane glycodendrimers. The major emphasis of this review is the use of carbosilane glycodendrimers as medical agents against Shiga toxins, dengue viruses, relapsing fever Borrelia, and hemagglutinin and neuraminidase of influenza viruses, as well as on the relationship between dendrimer structure and these biological activities. The last two sections introduce recent attempts to use carbosilane glycodendrimers as new versatile and widely-applicable lectin sensors, and the use of carbosilane glycodendrimers as a novel drug carrier in an active targeting drug delivery system. This review article will be of interest to scientists in the areas of organic chemistry, chemical biology, carbohydrate chemistry, heteroatom chemistry, and organosilicon chemistry.

Antibacterial activity of (-)-cubebin isolated from Piper cubeba and its synthetic derivatives against microorganisms that cause endodontic infections

The aim of this study was the obtainment of (-)-cubebin 1, its semisynthetic derivatives and the subsequent evaluation of their antibacterial activity. It was used for the synthesis of: (-)-O-methylcubebin 2, (-)-O-benzylcubebin 3, (-)-O-acetylcubebin 4, (-)-O-(N,N-dimethylamino-ethyl)-cubebin 5, (-)-hinokinin 6 and (-)-6.6'-dinitrohinokinin 7. The evaluation of the antibacterial activity have been done by broth microdilution technique for determination of the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) against Porphyromonas gingivalis, Prevotella nigrescens, Actinomyces naeslundii, Bacteroides fragilis and Fusobacterium nucleatum. From this study, it was possible to make an analysis regarding the relationship between structure and antimicrobial activity of derivatives against microorganisms that cause endodontic infections. Among the results presented in both trials, the most promising were MIC=50mg/mL against P. gingivalis by 2 and 3, and MIC=100µg/mL against B. fragilis by 6. The cytotoxicity assays demonstrated that 1 does not display toxicity, as well as its derivatives, which contributes to its direct use in biological assays. Sponsors: CNPq, FAPESP and CAPES

Adverse effects in risk assessment: Modeling polychlorinated biphenyls and thyroid hormone disruption outcomes in animals and humans

There is a growing need for quantitative approaches to extrapolate relationships between chemical exposures and early biological perturbations from animals to humans given increasing use of biological assays to evaluate toxicity pathways. We have developed such an approach using polychlorinated biphenyls (PCBs) and thyroid hormone (TH) disruption as a case study. We reviewed and identified experimental animal literature from which we developed a low-dose, linear model of PCB body burdens and decrements in free thyroxine (FT4) and total thyroxine (TT4), accounting for 33 PCB congeners; extrapolated the dose–response from animals to humans; and compared the animal dose–response to the dose–response of PCB body burdens and TH changes from eleven human epidemiological studies. We estimated a range of potencies for PCB congeners (over 4 orders of magnitude), with the strongest for PCB 126. Our approach to developing toxic equivalency models produced relative potencies similar to the toxicity equivalency factors (TEFs) from the World Health Organization (WHO). We generally found that the dose–response extrapolated from the animal studies tends to under-predict the dose–response estimated from human epidemiological studies. A quantitative approach to evaluating the relationship between chemical exposures and TH perturbations, based on animal data can be used to assess human health consequences of thyroid toxicity and inform decision-making.

Cotinine-conjugated aptamer/anti-cotinine antibody complexes as a novel affinity unit for use in biological assays

Aptamers are synthetic, relatively short (e.g., 20-80 bases) RNA or ssDNA oligonucleotides that can bind targets with high affinity and specificity, similar to antibodies, because they can fold into unique, three-dimensional shapes. For use in various assays and experiments, aptamers have been conjugated with biotin or digoxigenin to form complexes with avidin or anti-digoxigenin antibodies, respectively. In this study, we developed a method to label the 5' ends of aptamers with cotinine, which allows formation of a stable complex with anti-cotinine antibodies for the purpose of providing another affinity unit for the application in biological assays using aptamers. To demonstrate the functionality of this affinity unit in biological assays, we utilized two well-known aptamers: AS1411, which binds nucleolin, and pegaptanib, which binds vascular endothelial growth factor. Cotinine-conjugated AS1411/anti-cotinine antibody complexes were successfully applied to immunoblot, immunoprecipitation, and flow cytometric analyses, and cotinine-conjugated pegaptanib/anti-cotinine antibody complexes were used successfully in enzyme immunoassays. Our results show that cotinine-conjugated aptamer/anti-cotinine antibody complexes are an effective alternative and complementary technique for aptamer use in multiple assays and experiments.

The Androgen Receptor and Its Use in Biological Assays: Looking Toward Effect-Based Testing and Its Applications

Steroid abuse is a growing problem among amateur and professional athletes. Because of an inundation of newly and illegally synthesized steroids with minor structural modifications and other designer steroid receptor modulators, there is a need to develop new methods of detection which do not require prior knowledge of the abused steroid structure. The number of designer steroids currently being abused is unknown because detection methods in general are only identifying substances with a known structure. The detection of doping is moving away from merely checking for exposure to prohibited substance toward detecting an effect of prohibited substances, as biological assays can do. Cell-based biological assays are the next generation of assays which should be utilized by antidoping laboratories; they can detect androgenic anabolic steroid and other human androgen receptor (hAR) ligand presence without knowledge of their structure and assess the relative biological activity of these compounds. This review summarizes the hAR and its action and discusses its relevance to sports doping and its use in biological assays.

Dispersion stabilization of silver nanoparticles in synthetic lung fluid studied under in situ conditions

The dispersion stabilization of silver nanoparticles (AgNPs) in synthetic lung fluid was studied to interrogate the effects on colloidal stability due to the principal constituents of the fluid. The colloidal stability of 20 nm citrate-AgNPs dispersed in the presence of each constituent of the synthetic lung fluid (individually, the complete fluid, and without additives) was observed during titration of increasing sodium chloride concentration. A variety of complementary in situ measurement techniques were utilized, including dynamic light scattering, ultraviolet-visible absorption spectroscopy, atomic force microscopy, and small-angle X-ray scattering, which provided a collective set of information that enabled far better understanding of the dispersion behavior in the fluid than any one technique alone. It was observed that AgNPs continued to adsorb bovine serum albumin (BSA) protein from the synthetic lung fluid solution as the sodium chloride concentration increased, until a maximum BSA coating was achieved prior to reaching the physiological sodium chloride concentration of 154 mmol L−1. BSA was determined to be the constituent of the synthetic lung fluid that is required to provide colloidal stability at high salt loadings, though the phospholipid constituent exerts a subtle effect. Additionally, as AgNPs are a distinctly different class of nanoparticles apart from the carbon nanotubes and titanium dioxide nanoparticles initially reported to be dispersible using this fluid, this work also demonstrates the broad applicability of synthetic lung fluid in providing stable dispersions for engineered nanoparticles for use in biological assays.