Biological Probes Research Articles

Palladium Catalysis Enables Benzylation of α,α‐Difluoroketone Enolates

AbstractA palladium‐catalyzed decarboxylative benzylation reaction of α,α‐difluoroketone enolates is reported, in which the key C(α)−C(sp3) bond is generated by reductive elimination from a palladium intermediate. The transformation provides convergent access to α‐benzyl‐α,α‐difluoroketone‐based products, and should be useful for accessing biological probes.

Palladium Catalysis Enables Benzylation of α,α-Difluoroketone Enolates.

A palladium-catalyzed decarboxylative benzylation reaction of α,α-difluoroketone enolates is reported, in which the key C(α)-C(sp(3) ) bond is generated by reductive elimination from a palladium intermediate. The transformation provides convergent access to α-benzyl-α,α-difluoroketone-based products, and should be useful for accessing biological probes.

The unique chemistry and biology of the piericidins.

The piericidin family of microbial metabolites features a 4-pyridinol core linked with a methylated polyketide side chain. Piericidins are exclusively produced by actinomycetes, especially members of the genus Streptomyces. The close structural similarity with coenzyme Q renders the piericidins important NADH-ubiquinone oxidoreductase (complex I) inhibitors in the mitochondrial electron transport chain. Because of the significant activities of the piericidins, which include insecticidal, antimicrobial and antitumor effects, total syntheses of the piericidins were developed using various synthetic strategies. The biosynthetic origin of this class has also been the subject of investigation. This review covers the isolation and structure determination of the natural piericidins, their chemical modification, the total syntheses of natural and unnatural analogs, their biosynthesis, and reported biological activities together with structure-activity relationships. Given the fundamental biology of this class of metabolites, the piericidin family will likely continue to attract attention as biological probes of important biosynthetic processes.

Fullerenol spin probe containing isoindoline nitroxide and porphyrin groups

ABSTRACTA water-soluble fullerenol containing porphyrin and isoindoline nitroxide groups APTSPP-C60(OH)10-(TMIO)3 was synthesized by the incorporation of 5-(4-amino-phenyl)-10,15,20-tris(4-sulfonatophenyl)-porphyrin (APTSPP) as a tumor-targeting group and 5-formyl-1,1,3,3-tetramethylisoindolin-2-yloxyl (FTMIO) into fullerenol C60(OH)11. This nonmaterial was further characterized by FT-IR, UV, MS, TEM, fluorescence, etc. and its properties in vitro were also evaluated. Electrochemical experiments indicated that APTSPP-C60(OH)10-(TMIO)3 retained similar electrochemical properties and redox reaction mechanisms as 5-carboxy-1,1,3,3-tetramethylisoindolin-2-yloxyl (CTMIO). Electron paramagnetic resonance (EPR) spectra of APTSPP-C60(OH)10-(TMIO)3 exhibited the hyperfine splittings and characteristic spectra of CTMIO, with typical nitroxide g-values and nitrogen isotropic hyperfine coupling constants. In vitro cytotoxicity assay showed APTSPP-C60(OH)10-(TMIO)3 possessed low cytotoxicities to human renal tubular epithelial 293T cells and HepG-2 cells. Therefore APTSPP-C60(OH)10-(TMIO)3 may be considered as a potential candidate for novel biological spin probe using EPR spectroscopy.

Fluorescence in complexes based on quinolines-derivatives: a search for better fluorescent probes

Quinoline-derived fluorescent complexes were designed; synthesized by the reaction of 5-nitro-8-hydroxyquinoline and 5-chloro-8-hydroxyquinoline with Al3+, Mg2+, Zn2+, and Cd2+ salts (1–8); and characterized. The 1H NMR spectra of complexes 1 and 5, containing Al3+, were consistent with an octahedral structure having approximate D3 symmetry, and the results supported the favored facial isomer (fac). Data for complexes 2–4 and 6–8 supported the formation of tetrahedral structures. Intense luminescence was detected for complexes 5–8, even with the naked eye, as indicated by quantum yield values of 0.087, 0.094, 0.051, and 0.021, respectively. Furthermore, in contrast to 5-nitro-8-hydroxyquinoline, the 5-chloro-8-hydroxyquinoline ligand exhibited bands at different energies depending on the coordinated metal, which supported its potential application in ionic and biological probes, as well as in cell imaging.

ChemInform Abstract: Approaches for Modeling Magnetic Nanoparticle Dynamics

AbstractReview: 41 refs.

Tetrodecamycin: An unusual and interesting tetronate antibiotic

The tetrodecamycins are a group of secondary metabolites that are characterized by the presence of a tetronate ring in their structure. Originally discovered for their antibiotic activity against Photobacterium damselae ssp. piscicida, the causative agent of pseudotuberculosis in fish, this family of molecules has also been shown to have potent antibiotic activity against methicillin-resistant Staphylococcus aureus. Due to their small size and highly cyclized nature, they represent an unusual member of the much larger group of bioactive molecules called the tetronates. Herein, we review what is known about the mechanism of action of these molecules and also present a hypothesis for their biosynthesis. A deeper understanding of the tetrodecamycins will provide a more holistic view of the tetronate-family, provide new chemical probes of bacterial biology, and may provide therapeutic lead molecules.

Effects of acute aerobic exercise on neural correlates of attention and inhibition in adolescents with bipolar disorder.

Executive dysfunction is common during and between mood episodes in bipolar disorder (BD), causing social and functional impairment. This study investigated the effect of acute exercise on adolescents with BD and healthy control subjects (HC) to test for positive or negative consequences on neural response during an executive task. Fifty adolescents (mean age 16.54±1.47 years, 56% female, 30 with BD) completed an attention and response inhibition task before and after 20 min of recumbent cycling at ~70% of age-predicted maximum heart rate. 3 T functional magnetic resonance imaging data were analyzed in a whole brain voxel-wise analysis and as regions of interest (ROI), examining Go and NoGo response events. In the whole brain analysis of Go trials, exercise had larger effect in BD vs HC throughout ventral prefrontal cortex, amygdala and hippocampus; the profile of these effects was of greater disengagement after exercise. Pre-exercise ROI analysis confirmed this 'deficit in deactivation' for BDs in rostral ACC and found an activation deficit on NoGo errors in accumbens. Pre-exercise accumbens NoGo error activity correlated with depression symptoms and Go activity with mania symptoms; no correlations were present after exercise. Performance was matched to controls and results survived a series of covariate analyses. This study provides evidence that acute aerobic exercise transiently changes neural response during an executive task among adolescents with BD, and that pre-exercise relationships between symptoms and neural response are absent after exercise. Acute aerobic exercise constitutes a biological probe that may provide insights regarding pathophysiology and treatment of BD.

Photoactivatable Caged Prodrugs of VEGFR-2 Kinase Inhibitors.

In this study, we report on the design, synthesis, photokinetic properties and in vitro evaluation of photoactivatable caged prodrugs for the receptor tyrosine kinase VEGFR-2. Highly potent VEGFR-2 inhibitors 1 and 3 were caged by introduction of a photoremovable protecting group (PPG) to yield the caged prodrugs 4 and 5. As expected, enzymatic and cellular proliferation assays showed dramatically diminished efficacy of caged prodrugs in vitro. Upon ultraviolet (UV) irradiation of the prodrugs original inhibitory activity was completely restored and even distinctly reinforced, as was the case for the prodrug 4. The presented results are a further evidence for caging technique being an interesting approach in the protein kinase field. It could enable spatial and temporal control for the inhibition of VEGFR-2. The described photoactivatable prodrugs might be highly useful as biological probes for studying the VEGFR-2 signal transduction.

Three-Dimensional Graphene Supported Bimetallic Nanocomposites with DNA Regulated-Flexibly Switchable Peroxidase-Like Activity.

A synergistic bimetallic enzyme mimetic catalyst, three-dimensional (3D) graphene/Fe3O4-AuNPs, was successfully fabricated which exhibited flexibly switchable peroxidase-like activity. Compared to the traditional 2D graphene-based monometallic composite, the introduced 3D structure, which was induced by the addition of glutamic acid, and bimetallic anchoring approach dramatically improved the catalytic activity, as well as the catalysis velocity and its affinity for substrate. Herein, Fe3O4NPs acted as supporters for AuNPs, which contributed to enhance the efficiency of electron transfer. On the basis of the measurement of Mott-Schottky plots of graphene and metal anchored hybrids, the catalysis mechanism was elucidated by the decrease of Fermi level resulted from the chemical doping behavior. Notably, the catalytic activity was able to be regulated by the adsorption and desorption of single-stranded DNA molecules, which laid a basis for its utilization in the construction of single-stranded DNA-based colorimetric biosensors. This strategy not only simplified the operation process including labeling, modification, and imprinting, but also protected the intrinsic affinity between the target and biological probe. Accordingly, based on the peroxidase-like activity and its controllability, our prepared nanohybrids was successfully adopted in the visualized and label-free sensing detections of glucose, sequence-specific DNA, mismatched nucleotides, and oxytetracycline.

Diffusion-sensitive optical coherence tomography for real-time monitoring of mucus thinning treatments.

Mucus hydration (wt%) has become an increasingly useful metric in real-time assessment of respiratory health in diseases like cystic fibrosis and COPD, with higher wt% indicative of diseased states. However, available in vivo rheological techniques are lacking. Gold nanorods (GNRs) are attractive biological probes whose diffusion through tissue is sensitive to the correlation length of comprising biopolymers. Through employment of dynamic light scattering theory on OCT signals from GNRs, we find that weakly-constrained GNR diffusion predictably decreases with increasing wt% (more disease-like) mucus. Previously, we determined this method is robust against mucus transport on human bronchial epithelial (hBE) air-liquid interface cultures (R2=0.976). Here we introduce diffusion-sensitive OCT (DS-OCT), where we collect M-mode image ensembles, from which we derive depth- and temporally-resolved GNR diffusion rates. DS-OCT allows for real-time monitoring of changing GNR diffusion as a result of topically applied mucus-thinning agents, enabling monitoring of the dynamics of mucus hydration never before seen. Cultured human airway epithelial cells (Calu-3) with a layer of endogenous mucus were doped with topically deposited GNRs (80×22nm), and subsequently treated with hypertonic saline (HS) or isotonic saline (IS). DS-OCT provided imaging of the mucus thinning response up to a depth of 600μm with 4.65μm resolution, over a total of 8 minutes in increments of ≥3 seconds. For both IS and HS conditions, DS-OCT captured changes in the pattern of mucus hydration over time. DS-OCT opens a new window into understanding mechanisms of mucus thinning during treatment, enabling real-time efficacy feedback needed to optimize and tailor treatments for individual patients.

ChemInform Abstract: The Medicinal Chemist′s Toolbox for Late Stage Functionalization of Drug‐Like Molecules

AbstractReview: [216 refs.

Disc-based microarrays: principles and analytical applications.

The idea of using disk drives to monitor molecular biorecognition events on regular optical discs has received considerable attention during the last decade. CDs, DVDs, Blu-ray discs and other new optical discs are universal and versatile supports with the potential for development of protein and DNA microarrays. Besides, standard disk drives incorporated in personal computers can be used as compact and affordable optical reading devices. Consequently, a CD technology, resulting from the audio-video industry, has been used to develop analytical applications in health care, environmental monitoring, food safety and quality assurance. The review presents and critically evaluates the current state of the art of disc-based microarrays with illustrative examples, including past, current and future developments. Special mention is made of the analytical developments that use either chemically activated or raw standard CDs where proteins, oligonucleotides, peptides, haptens or other biological probes are immobilized. The discs are also used to perform the assays and must maintain their readability with standard optical drives. The concept and principle of evolving disc-based microarrays and the evolution of disk drives as optical detectors are also described. The review concludes with the most relevant uses ordered chronologically to provide an overview of the progress of CD technology applications in the life sciences. Also, it provides a selection of important references to the current literature. Graphical Abstract High density disc-based microarrays.

Iminoboronate-Based Peptide Cyclization That Responds to pH, Oxidation, and Small Molecule Modulators.

As a rich source of therapeutic agents, peptide natural products usually adopt a cyclic or multicyclic scaffold that minimizes structural flexibility to favor target binding. Inspired by nature, chemists have been interested in developing synthetic cyclic and multicyclic peptides that serve as biological probes and potential therapeutics. Herein we describe a novel strategy for peptide cyclization in which intramolecular iminoboronate formation allows spontaneous cyclization under physiologic conditions to yield monocyclic and bicyclic peptides. Importantly the iminoboronate-based cyclization can be rapidly reversed in response to multiple stimuli, including pH, oxidation, and small molecules. This highly versatile strategy for peptide cyclization should find applications in many areas of chemical biology.

One-pot access to l-5,6-dihalotryptophans and l-alknyltryptophans using tryptophan synthase

We report, for the first time, the use of tryptophan synthase in the generation of L-dihalotryptophans and l-alkynyltryptophans. These previously unpublished compounds will be useful tools in the generation of probes for chemical biology, in biosynthetic diversification and as convenient building blocks for synthesis.

Stain‐free 3D Nanoscopy of Living Cells

AbstractThe cell is the basis of all life on earth. Therefore, being capable of directly observing and measuring the internal parts of a living cell would open a wealth of possibilities. However, due to the limitation of light used as a biological probe, revealing this internal structure is either strongly limited or requires strong and tedious modifications of observed cells. State‐of‐the art microscopy techniques rely on complicated procedures (risk of errors), which require difficult and time‐consuming preparations, are invasive to the cells (risk of damaging and results falsification), and still give rather limited results. This article presents a novel non‐invasive and tomographic imaging approach for quantitative analysis and differentiation of cell components. Changes in refractive index within the cell itself provide the contrast for labeling various organelles with high precision and at a high resolution. The method can be applied to the 3D examination of living cells and biological samples under various external stimuli or drugs.

Interfacial synthesis of polyethyleneimine-protected copper nanoclusters: Size-dependent tunable photoluminescence, pH sensor and bioimaging

The copper nanoclusters (CuNCs) offer excellent potential as functional biological probes due to their unique photoluminescence (PL) properties. Herein, CuNCs capped with hyperbranched polyethylenimine (PEI) were prepared by the interfacial etching approach. The resultant PEI-CuNCs exhibited good dispersion and strong fluorescence with high quantum yields (QYs, up to 7.5%), which would be endowed for bioimaging system. By changing the reaction temperatures from 25 to 150°C, the size of PEI-CuNCs changed from 1.8 to 3.5nm, and thus tunable PL were achieved, which was confirmed by transmission electron microscopy (TEM) imagings and PL spectra. Besides, PEI-CuNCs had smart absorption characteristics that the color changes from colorless to blue with changing the pH value from 2.0 to 13.2, and thus they could be used as color indicator for pH detection. In addition, the PEI-CuNCs exhibited good biocompatibility and low cytotoxicity to 293T cells through MTT assay. Owing to the positively charged of PEI-CuNCs surface, they had the ability to capture DNA, and the PEI-CuNCs/DNA complexes could get access to cells for efficient gene expression. Armed with these attractive properties, the synthesized PEI-CuNCs are quite promising in biological applications.

Identification of SNAIL1 Peptide-Based Irreversible Lysine-Specific Demethylase 1-Selective Inactivators.

Inhibition of lysine-specific demethylase 1 (LSD1), a flavin-dependent histone demethylase, has recently emerged as a new strategy for treating cancer and other diseases. LSD1 interacts physically with SNAIL1, a member of the SNAIL/SCRATCH family of transcription factors. This study describes the discovery of SNAIL1 peptide-based inactivators of LSD1. We designed and prepared SNAIL1 peptides bearing a propargyl amine, hydrazine, or phenylcyclopropane moiety. Among them, peptide 3, bearing hydrazine, displayed the most potent LSD1-inhibitory activity in enzyme assays. Kinetic study and mass spectrometric analysis indicated that peptide 3 is a mechanism-based LSD1 inhibitor. Furthermore, peptides 37 and 38, which consist of cell-membrane-permeable oligoarginine conjugated with peptide 3, induced a dose-dependent increase of dimethylated Lys4 of histone H3 in HeLa cells, suggesting that they are likely to exhibit LSD1-inhibitory activity intracellularly. In addition, peptide 37 decreased the viability of HeLa cells. We believe this new approach for targeting LSD1 provides a basis for development of potent selective inhibitors and biological probes for LSD1.

Executive Function in Adolescence: A Commentary on Regulatory Control and Depression in Adolescents: Findings From Neuroimaging and Neuropsychological Research

This commentary addresses the manner in which executive control processes and their development is impacted by major depressive episodes during adolescence. Strengths of the articles within this special issue include the breadth of executive functions that were examined, incorporation of biological probes to understand neural mechanisms involved in observed impairments, the use of longitudinal paradigms to assess developmental timing, consideration and modeling of comorbid conditions, and the identification of individual difference factors that may serve as both liabilities and resilience factors. This work is timely; a close examination of negative emotions and how they change during adolescence is needed if we are to fully understand motivation–cognition interactions and how they are impaired by psychopathology.

Identification of an active metabolite of PAR-1 antagonist RWJ-58259 and synthesis of analogues to enhance its metabolic stability.

The discontinuation of PAR-1 antagonist RWJ-58259 beyond use as a biological probe is most likely due to it's short half-life in vivo. However, retention of significant in vivo activity beyond the point where most of the RWJ-58259 had been consumed implies the generation of an active metabolite. Herein we describe the biological activity of a predicted metabolite of RWJ-58259 and the synthesis of analogues designed to enhance the metabolic stability of RWJ-58259.