Biological Probes Research Articles

OBTAINING AND RESEARCH OF PALLADIUM COMPLEXES WITH 4-AMINOPIRIDINE

The obtaining and investigation of various complex compounds of the biologically active aromatic heterocyclic ligands with platinum and palladium are of interest due to their potential medical applications. To that end, 4-amino pyridine containing cyclic and exocyclic nitrogen atoms has been used. The main aim of this work is to clarify which nitrogen atom of the ligand composes stronger and more stable bond. As a result of IR-spectroscopic investigation of synthesized complexes, the acquired information demonstrated that the pyridine nitrogen atom of the ligand is protonated and composes outer sphere as monocharged cation. However, tetraacidoanion is formed in the inner sphere. In the alkaline medium the ligand is monodentately coordinated with palladium through nitrogen atom of pyridine. The exocyclic nitrogen atom of the ligand does not participate in the coordination regardless of pH of the medium and stoichiometric ratio of the taken compounds The initial biological probes were accomplished and the correlation between their biological activities, composition and structures of complexes were determined.

Visible-light-mediated multicomponent reaction for secondary amine synthesis.

The widespread presence of secondary amines in agrochemicals, pharmaceuticals, natural products, and small-molecule biological probes has inspired efforts to streamline the synthesis of molecules with this functional group. Herein, we report an operationally simple, mild protocol for the synthesis of secondary amines by three-component alkylation reactions of imines (generated in situ by condensation of benzaldehydes and anilines) with unactivated alkyl iodides catalyzed by inexpensive and readily available Mn2(CO)10. This protocol, which is compatible with a wide array of sensitive functional groups and does not require a large excess of the alkylating reagent, is a versatile, flexible tool for the synthesis of secondary amines.

Biological nanoscale fluorescent probes: From structure and performance to bioimaging

Abstract In recent years, nanomaterials have attracted lots of attention from researchers due to their unique properties. Nanometer fluorescent materials, such as organic dyes, semiconductor quantum dots (QDs), metal nano-clusters (MNCs), carbon dots (CDs), etc., are widely used in biological imaging due to their high sensitivity, short response time, and excellent accuracy. Nanometer fluorescent probes can not only perform in vitro imaging of organisms but also achieve in vivo imaging. This provides medical staff with great convenience in cancer treatment. Combined with contemporary medical methods, faster and more effective treatment of cancer is achievable. This article explains the response mechanism of three-nanometer fluorescent probes: the principle of induced electron transfer (PET), the principle of fluorescence resonance energy transfer (FRET), and the principle of intramolecular charge transfer (ICT), showing the semiconductor QDs, precious MNCs, and CDs. The excellent performance of the three kinds of nano fluorescent materials in biological imaging is highlighted, and the application of these three kinds of nano fluorescent probes in targeted biological imaging is also introduced. Nanometer fluorescent materials will show their significance in the field of biomedicine.

IMPEDIMETRIC CLAVMO PEPTIDE-BASED SENSOR DIFFERENTIATES PLOIDY OF CANDIDA SPECIES

Yeast biotechnologies are a cornerstone to modern lifestyle in all spheres of society, as their products are essential for the economy and industrial activities. The life cycle of many yeasts such as Candida alternates between diplophase and haplophase. Both ploidies can exist as stable cultures; however, it has been shown that wild haploid yeast efficiently cross in poor environments, whereas wild diploid species hybridize predominantly in rich nutrient surroundings. Some Candida species have had their ploidy engineered to produce various important biomolecules useful to the detergent, food, pharmaceutical and other industries. Several works show that MALDI-TOF MS has become an ideal platform for ploidy analysis. Recent reports have shown that antimicrobial peptides (AMP) present enhanced hydrophobic interaction towards cell membranes. In this work, the authors explored a modified AMP named Clavanin A (CLAVMO) as an unprecedented bioreceptor capable of differentiating the molecular composition of the cell wall of Candida spp. A thin film of poly(3-thiophene acetic acid) (PTAA) was electropolymerized to avail the covalent immobilization of amino-functionalized titanium dioxide nanoparticles (TiO2NPs) whose electrochemical properties are excellent to provide a discernable redox response. Electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) were used to characterize the biosensor assembly and the biorecognition process. Additionally, MALDI-TOF was employed to confirm ploidy of Candida strains used in this work. Our results suggest that TiO2NPs_CLAVMO biosensor is a suitable biological probe that can be used to detect and differentiate Candida species based on their ploidy. For instance, C. Albicans and C. tropicalis, which are close related species known for being diploid presented higher impedimetric response than haploid species C.krusei and C. glabrata. The proposed biosensor stands out as a useful alternative for highly sensitive differentiation of Candida yeast cells, without the intricacies of MALDI-TOF sample preparation. The biodetection event and its electrochemical evaluation took less than 20 min to perform. The platform showed stability for over a week, a linear detection range between 101-106 CFU mL-1 and limits of detection (LODs) between 2 and 3 CFU mL-1.

Three-Photon Spectroscopy of Porphyrins.

Recent advances in laser technology have made three-photon (3P) microscopy a real possibility, raising interest in the phenomenon of 3P absorption (3PA). Understanding 3PA of organic chromophores is especially important in view of those imaging applications that rely on exogenous probes, whose optical properties can be manipulated and optimized. Here, we present measurements and theoretical analysis of the degenerate 3PA spectra of several phosphorescent metalloporphyrins, which are used in the construction of biological oxygen probes. The effective 3PA cross sections (σ(3)) of these porphyrins near 1700 nm, a new promising biological optical window, were found to be on the order of 1000 GM3 (1 GM3 = 10-83 cm6 s2), therefore being among the highest values reported to date for organic chromophores. To interpret our data, we developed a qualitative four-state model specific for porphyrins and used it in conjunction with quantitative analysis based on the time-dependent density functional theory (TDDFT)/a posteriori Tamm-Dancoff approximation (ATDA)/sum-over-states (SOS) formalism. The analysis revealed that B (Soret) state plays a key role in the enhancement of 3PA of porphyrins in the Q band region, while the low-lying two-photon (2P)-allowed gerade states interfere negatively and diminish the 3PA strength. This study features the first systematic examination of 3PA properties of porphyrins, suggesting ways to improve their performance and optimize them for imaging and other biomedical applications.

Obtaining and Research of Palladium Complexes with 4-aminopiridine

The obtaining and investigation of various complex compounds of the biologically active aromatic heterocyclic ligands with platinum and palladium are of interest due to their potential medical applications. To that end, 4-amino pyridine containing cyclic and exocyclic nitrogen atoms has been used. The main aim of this work is to clarify which nitrogen atom of the ligand composes stronger and more stable bond. For that purpose, the synthesis of palladium salts with ligand has been accomplished within a wide interval of pH (3-12) and temperature (50-800C). The cation-anion and neutral complex compounds have been obtained depending on stoichiometric ratio of the reacting components, temperature and pH and was further studied. As a result of IR-spectroscopic investigation of synthesized complexes, the acquired information demonstrated that the pyridine nitrogen atom of the ligand is protonated and composes outer sphere as monocharged cation. However, tetraacidoanion is formed in the inner sphere. In the alkaline medium the ligand is monodentately coordinated with palladium through nitrogen atom of pyridine. The exocyclic nitrogen atom of the ligand does not participate in the coordination regardless of pH of the medium and stoichiometric ratio of the taken compounds. As a result of investigation of the thermal stability of the complexes it was determined that the neutral complexes are decomposed without melting at higher temperature than cation-anion complexes. It has been found that one of the factors that affects thermal stability is the steric structure of the complexes. The initial biological probes were accomplished and the correlation between their biological activities, composition and structures of complexes were determined. Despite the fact of taking the same medium and ligand, the cation-anion complexes indicate completely different biological activities than neutral ones.

Tailoring lab-on-fiber SERS optrodes towards biological targets of different sizes

• Three different types of SERS substrates were fabricated by nanosphere lithography. • Performances were compared against different bio-targets (molecule, protein, cell). • A readout system for SERS optrode operation, via optical fiber, was optimized. In this paper, we studied the influence of the geometrical configuration of surface-enhanced Raman scattering (SERS)-active self-assembling gold nanostructures on the interaction with biological targets of different sizes, aiming at large-scope SERS lab-on-fiber optrodes composed of highly efficient SERS substrates integrated onto optical fibre tips. By using nanosphere lithography, we fabricated three types of highly ordered and reproducible SERS-active substrates. To correlate the SERS response to the steric hindrance of the biological target, we experimentally analysed and compared the SERS spectra of three representative biological probes, i.e., ultralow-molecular-weight molecules of biphenyl-4-thiol (BPT, small molecule, 186.27 Da), bovine serum albumin (BSA, medium molecule, 66.5 kDa) and red blood cells (RBCs, diameter <10 μm, complex target). All SERS-active substrates provided the Raman fingerprint of the biological targets, but the SERS intensity was dependent on the substrate geometry and its specific steric interfacing with biological targets. A full three-dimensional numerical analysis was carried out by means of the finite element method to gain insight into the electric field distribution and hot spot distribution of the fabricated structures. By correlating the electric field distribution with the SERS response, we conclude that the most efficient target-based architectures feature not only “intense” but also “accessible” hot spots. Finally, we optimized a Raman readout system for SERS optrode operation with efficient illumination and collection via an optical fibre.

Carbon Nanomaze for Biomolecular Detection with Zeptomolar Sensitivity

AbstractDespite numerous efforts, the accurate determination of trace biomolecules with zeptomolar sensitivity remains elusive. Here, a 3D carbon nanomaze (CAM) electrode for the ultrasensitive detection of trace biomolecules such as nucleic acids, proteins, and extracellular vesicles is reported. The CAM electrode consists of an interlaced carbon fiber array on which intercrossed graphene sheets are vertically tethered in situ, permitting local confinement of trace molecules to increase molecular hybridization efficiency. Furthermore, a self‐assembled DNA tetrahedron array adopts a rigid spatial conformation to guarantee the controllable arrangement of immobilized biological probes, facilitating analytical sensitivity and reproducibility. In a proof‐of‐concept experiment on detecting microRNA‐155, a linearity of 0.1 aM to 100 nM and a sensitivity of 0.023 aM (23 zM) are achieved. With the optimal parameters, the proposed nanoelectrode demonstrates encouraging consistency with quantitative real‐time polymerase chain reaction during clinical sample detection. Through simple functionalization by appending various biomolecular probes of interest, the developed CAM platform with ultrahigh sensitivity can be exploited as a versatile tool in environmental, chemistry, biology, and healthcare fields.

Synthesis of Rhamnolipid Derivatives Containing Ester Isosteres.

Rhamnolipids are biosurfactants with many applications, arising from their inherent biological activity and their potential as bioremediation agents. Herein, we report the synthesis of four rhamnolipid derivatives in which the ester linkage connecting the two lipid chains in the natural compound is replaced with amide, ketone, ether, or hydrocarbon functional groups. Such compounds are anticipated to have enhanced hydrolytic stability and thus be useful probes of rhamnolipid-mediated biology and biotechnology.

Endogenous Stimuli-Responsive DNA Nanostructures Toward Cancer Theranostics

Nanostructures specifically responsive to endogenous biomolecules hold great potential in accurate diagnosis and precision therapy of cancers. In the pool of nanostructures with responsiveness to unique triggers, nanomaterials derived from DNA self-assembly have drawn particular attention due to their intrinsic biocompatibility and structural programmability, enabling the selective bioimaging, and site-specific drug delivery in cancer cells and tumor tissues. In this mini review, we summarize the most recent advances in the development of endogenous stimuli-responsive DNA nanostructures featured with precise self-assembly, targeted delivery, and controlled drug release for cancer theranostics. This mini review briefly discusses the diverse dynamic DNA nanostructures aiming at bioimaging and biomedicine, including DNA self-assembling materials, DNA origami structures, DNA hydrogels, etc. We then elaborate the working principles of DNA nanostructures activated by biomarkers (e.g., miRNA, mRNA, and proteins) in tumor cells and microenvironments of tumor tissue (e.g., pH, ATP, and redox gradient). Subsequently, applications of the endogenous stimuli-responsive DNA nanostructures in biological imaging probes for detecting cancer hallmarks as well as intelligent carriers for drug release in vivo are discussed. In the end, we highlight the current challenges of DNA nanotechnology and the further development of this promising research direction.

The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe.

Pluripotent stem-cell-derived human intestinal organoids (HIOs) are three-dimensional, multicellular structures that model a naive intestinal epithelium in an in vitro system. Several published reports have investigated the use of HIOs to study host-microbe interactions. We recently demonstrated that microinjection of the nonpathogenic Escherichia coli strain ECOR2 into HIOs induced morphological and functional maturation of the HIO epithelium, including increased secretion of mucins and cationic antimicrobial peptides. In the current work, we use ECOR2 as a biological probe to further characterize the environment present in the HIO lumen. We generated an isogenic mutant in the general stress response sigma factor RpoS and employed this mutant to compare challenges faced by a bacterium during colonization of the HIO lumen relative to the germ-free mouse intestine. We demonstrate that the loss of RpoS significantly decreases the ability of ECOR2 to colonize HIOs, although it does not prevent colonization of germ-free mice. These results indicate that the HIO lumen is a more restrictive environment to E. coli than the germ-free mouse intestine, thus increasing our understanding of the HIO model system as it pertains to studying the establishment of intestinal host-microbe symbioses.IMPORTANCE Technological advancements have driven and will continue to drive the adoption of organotypic systems for investigating host-microbe interactions within the human intestinal ecosystem. Using E. coli deficient in the RpoS-mediated general stress response, we demonstrate that the type or severity of microbial stressors within the HIO lumen is more restrictive than those of the in vivo environment of the germ-free mouse gut. This study provides important insight into the nature of the HIO microenvironment from a microbiological standpoint.

Dienone Compounds: Targets and Pharmacological Responses.

The biological responses to dienone compounds with a 1,5-diaryl-3-oxo-1,4-pentadienyl pharmacophore have been studied extensively. Despite their expected general thiol reactivity, these compounds display considerable degrees of tumor cell selectivity. Here we review in vitro and preclinical studies of dienone compounds including b-AP15, VLX1570, RA-9, RA-190, EF24, HO-3867, and MCB-613. A common property of these compounds is their targeting of the ubiquitin–proteasome system (UPS), known to be essential for the viability of tumor cells. Gene expression profiling experiments have shown induction of responses characteristic of UPS inhibition, and experiments using cellular reporter proteins have shown that proteasome inhibition is associated with cell death. Other mechanisms of action such as reactivation of mutant p53, stimulation of steroid receptor coactivators, and induction of protein cross-linking have also been described. Although unsuitable as biological probes due to widespread reactivity, dienone compounds are cytotoxic to apoptosis-resistant tumor cells and show activity in animal tumor models.

Recent Advances in the Synthesis of the Antidepressant Paroxetine.

Paroxetine is a potent inhibitor of serotonin reuptake and is widely prescribed for the treatment of depression and other neurological disorders. The synthesis of paroxetine and the possibility to prepare derivatives with a specific substitution pattern that may allow their use as biological probes is an attractive topic especially for medicinal chemists engaged in neurosciences research. Considering the extensive work that was developed in the last decade on the total synthesis of paroxetine, this review summarizes the most important contributions in this field, organized according to the reagent that was used as a starting material. Most of the methods allowed to prepare paroxetine in 4-9 steps with an overall yield of 9-66%. Despite the progress made in this area, there is still room for improvement, searching for new eco-friendly and sustainable synthetic alternatives.

From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology.

Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.

Industry Development of Derivative Functionalized Gold Nanomaterials and Their Application in Chemiluminescence Bioanalysis: Based on the Industrial Practice of China's Central Yunnan Urban Agglomeration

Electrochemiluminescence biosensor is an analytical method combining electrochemiluminescence technology with biosensor. Using nanomaterials as electrochemical luminescence sensor platform can not only immobilize a large number of biomolecules but also improve the performance of the sensor to realize the supersensitive detection of biomacromolecules. Although these methods have high sensitivity for bioanalysis, there are still some shortcomings which limit the practical application. Therefore, this paper discusses the development of functional gold nanomaterials industry and its application in chemiluminescence bioanalysis. In this paper, two methods of synthesizing luminescent functional gold nanomaterials at room temperature were studied by using chemiluminescent reagents as reducing agent and protective agent. Based on luminescent functionalized gold nanoparticles, immunoassay and DNA bioanalysis probes were constructed, and their applications in chemiluminescence and electrochemiluminescence bioanalysis were discussed. Finally, the simulation results show that the relative deviation between the experimental results and the existing clinical methods is less than 17%. The sensor has good stability and selectivity and can be used for the determination of CEA in human serum. The gold nanomaterials synthesized by further research have excellent chemiluminescence activity and can be used to label biomolecules and prepare biological probes. This article aims to explore the application of chemical methods in the transformation of new industries, to achieve breakthroughs in new products in industrial innovation, and to achieve the cross-fusion of management science and engineering disciplines and chemical disciplines. The industrial development of derivative functionalized gold nanomaterials has broad application prospects in biological analysis.

Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential.

Protein kinases represent a very pharmacologically attractive class of targets; however, some members of the family still remain rather unexplored. The biology and therapeutic potential of cdc-like kinases (CLKs) have been explored mainly over the last decade and the first CLK inhibitor, compound SM08502, entered clinical trials only recently. This review summarizes the biological roles and therapeutic potential of CLKs and their heretofore published small-molecule inhibitors, with a focus on the compounds’ potential to be utilized as quality chemical biology probes.

The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli

The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli. These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.

Fluorophosphonate-Based Degrader Identifies Degradable Serine Hydrolases by Quantitative Proteomics.

Novel chemical biology probes linking a serine hydrolase-directed fluorophosphonate warhead and cereblon-binding pomalidomide were assessed for the degradation of serine hydrolases. A quantitative proteomics approach to detect degraded proteins revealed that, despite the engagement of ∼40 serine hydrolases, degradation was achieved for only a single serine hydrolase, lysophospholipase II (LYPLA2).

Characterization of Conformationally Constrained Benzanilide Scaffolds for Potent and Selective HDAC8 Targeting.

Histone deacetylases (HDACs) are an attractive therapeutic target for a variety of human diseases. Currently, all four FDA-approved HDAC-targeting drugs are nonselective, pan-HDAC inhibitors, exhibiting adverse side effects at therapeutic doses. Although selective HDAC inhibition has been proposed to mitigate toxicity, the targeted catalytic domains are highly conserved. Herein, we describe a series of rationally designed, conformationally constrained, benzanilide foldamers which selectively bind the catalytic tunnel of HDAC8. The series includes benzanilides, MMH371, MMH409, and MMH410, which exhibit potent in vitro HDAC8 activity (IC50 = 66, 23, and 66 nM, respectively) and up to 410-fold selectivity for HDAC8 over the next targeted HDAC. Experimental and computational analyses of the benzanilide structure docked with human HDAC8 enzyme showed the adoption of a low-energy L-shaped conformer that favors HDAC8 selectivity. The conformationally constrained HDAC8 inhibitors present an alternative biological probe for further determining the clinical utility and safety of pharmacological knockdown of HDAC8 in diseased cells.

How Gain Layer Design Determines Performance of Nanoparticle-Based Spaser

Spaser nanoparticles, with ultranarrow spectral line width, small size and good biocompatibility, offer a bright prospect as potential biological probes. Sadly, over ten years since the first demon...