Fluorescent lipids: functional parts of fusogenic liposomes and tools for cell membrane labeling and visualization

In this paper a rapid and highly efficient method for controlled incorporation of fluorescent lipids into living mammalian cells is introduced. Here, the fluorescent molecules have two consecutive functions: First, they trigger rapid membrane fusion between cellular plasma membranes and the lipid bilayers of their carrier particles, so called fusogenic liposomes, and second, after insertion into cellular membranes these molecules enable fluorescence imaging of cell membranes and membrane traffic processes. We tested the fluorescent derivatives of the following essential membrane lipids for membrane fusion: Ceramide, sphingomyelin, phosphocholine, phosphatidylinositol-bisphosphate, ganglioside, cholesterol, and cholesteryl ester. Our results show that all probed lipids could more efficiently be incorporated into the plasma membrane of living cells than by using other methods. Moreover, labeling occurred in a gentle manner under classical cell culture conditions reducing cellular stress responses. Staining procedures were monitored by fluorescence microscopy and it was observed that sphingolipids and cholesterol containing free hydroxyl groups exhibit a decreased distribution velocity as well as a longer persistence in the plasma membrane compared to lipids without hydroxyl groups like phospholipids or other artificial lipid analogs. After membrane staining, the fluorescent molecules were sorted into membranes of cell organelles according to their chemical properties and biological functions without any influence of the delivery system.     

Enzymatic methods for glyco(diversification/randomization) of drugs and small molecules

Glyco (randomization/diversification) is a term that encompasses strategies to diversify a core drug scaffold via enzymatic glycosylation to provide sets of analogs wherein the sole diversity element is a carbohydrate. This review covers the influence of glycosylation upon various drug properties, the classes of glycosyl-conjugating enzymes amenable to glyco(randomization/diversification) schemes, approaches to the synthesis of required substrates and specific examples of glycorandomized libraries utilizing both wild-type and engineered enzymes.     

以主族元素为桥的梯形化合物的光电性质

梯形化合物具有大的平面π共轭结构, 不会产生构象扭曲, 可以有效增加π共轭长度, 因而表现出非常好的光电性质. 将主族元素引入到梯形化合物骨架中作为桥接单元不仅可以固定其结构而且由于主族元素和π共轭骨架之间的轨道相互作用, 可以实现对这类化合物光电性质的调节. 采用密度泛函理论对一系列主族元素桥的梯形化合物的结构和光电性质进行了理论研究, 从而可更好地理解和预测这类化合物的性质. 研究发现, 这类化合物的电子结构可以通过引入主族元素进行调节. 由于具有更大的π共轭程度, 四主族元素桥化合物的吸收与双主族元素桥化合物相比有明显的红移, 而且荧光寿命较短. 另外, 通过计算离子化势(IPs)、电子亲和能(EAs)和重组能(λ)考察了这类化合物的电子和空穴注入及传输性质. 研究发现, 四主族元素桥化合物表现出更强的电子和空穴注入能力.     

Novel derivatives of UDP-glucose: concise synthesis and fluorescent properties

A series of novel 5-substituted UDP-glucose derivatives with interesting fluorescent properties and potential applications as sensors for carbohydrate-active enzymes is reported. An efficient synthesis of the target molecules was developed, centred around the Suzuki-Miyaura reaction of (hetero)arylboronic acids with 5-iodo UDP-glucose. Interestingly, the optimised cross-coupling conditions could also be applied successfully to 5-bromo UMP, but not to 5-bromo UDP-glucose.     

Chemical Synthesis of Bioactive Proteins

Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications—transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.     

2-methylindole analogs as cholinesterases and glutathione S-transferase inhibitors: Synthesis,biological evaluation,molecular docking,and pharmacokinetic studies

In this study, we aimed to (i) synthesize new 2-methylindole analogs containing various amino structures, pyrrolidine, piperidine, morpholine, and substituted phenyl groups through structural and molecular modifications, (ii) evaluate the pharmaceutical potential of 2-methylindole analogs via assessing enzyme inhibitory activity against glutathione S-transferase (GST), acetylcholinesterase (AChE), and butyrylcholinesterase (BChE), (iii) predict ADMET and pharmacokinetic properties of the synthesized 2-methylindole analogs, (iv) reveal the possible interactions between the synthesized 2-methylindole analogs with GST, AChE, and BChE enzymes using several molecular docking software. In vitro enzyme inhibition assays showed that the synthesized indole analogs exhibited moderate to good inhibitory activities against GST, AChE, and BChE enzymes. Briefly, the inhibitory activities of the analogs 4b and 4i against AChE, 4a and 4b against BChE, and analogs 1 and 4i against GST were detected to be higher or close to the standard inhibitor compounds. The analog 4b was detected to have the best inhibitory activity against both AChE and BChE enzymes with the lowest IC₅₀ values as 0.648 µM for AChE and 0.745 µM for BChE. The analyses of enzyme inhibition relationship with the synthesized analogs could help to design new analogs for the inhibitors of cholinergic and glutathione pathways based on the indole derivatives.     

Racemisation in Chemistry and Biology

The two enantiomers of a compound often have profoundly different biological properties and thus their liability to racemisation in aqueous solutions is an important piece of information. The authors reviewed the available data concerning the process of racemisation in vivo, in the presence of biological molecules (e.g., racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented.     

Ester-Derivatized Indoles as Fluorescent and Infrared Probes for Hydration Environments?

Tryptophan derivatives have long been used as site-specific biological probes. 4-Cyanotryptophan emits in the visible region and is the smallest blue fluorescent amino acid probe for biological applications. Other indole or tryptophan analogs may emit at even longer wavelengths than 4-cyanotryptophan. We performed FTIR, UV-Vis, and steady-state and time-resolved fluorescence spectroscopy on six ester-derivatized indoles in different solvents. Methyl indole-4-carboxylate emits at 450 nm with a long fluorescence lifetime, and is a promising candidate for a fluorescent probe. The ester-derivatized indoles could be used as spectroscopic probes to study local protein environments. Our measurements provide a guide for choosing esterderivatized indoles to use in practice and data for computational modeling of the effect of substitution on the electronic transitions of indole.     

Effects of Substituents on Metastable‐State Photoacids: Design,Synthesis, and Evaluation of their Photochemical Properties

Recently, metastable‐state photoacids have been widely used to control proton transfer in numerous chemical and biological processes as well as applications with visible light. Generally, substituents have a great influence on the photochemical properties of molecules, which will further affect their applications. Yet, the effects of substituents on metastable‐state photoacids have not been studied systematically. In this work, 16 metastable‐state photoacid derivatives were designed and synthesized on the basis of substituents having a large range of σ–π electron–donor–acceptor capabilities. The effects of substituents on the color display [or maximum absorption band(s)], solubility, pK_a values, dark/photoacidity, photosensitivity, and relaxation kinetic(s) were investigated in detail. This study will be helpful for the targeted design and synthesis of promising photoacids and the application of their photocontrolled proton‐release processes in functional materials/devices.     

Rational design of hetero-ring-expanded guanine analogs with enhanced properties for modified DNA building blocks

The properties and modes of recognition of physiological DNAs associated with the four natural nucleobases might be extended, in principle, by the design of non-natural nucleobase derivatives. The goal is an expansion of the genetic alphabet, with the possible outcome of producing new DNAs with improved physical or biological properties. In this work, a new series of hetero-ring-expanded guanine analogs are proposed, and their relevant structural characteristics and electronic properties are determined by density functional theory. The stabilities of the decamer DNA duplexes (dn.dC)10 (where n represents the corresponding expanded guanine analog designed here) are also examined, using molecular dynamics. The simulations show that the designed motifs can form stable DNA-like structures. We determined the pairing energies for the Watson-Crick (WC) hydrogen-bonded dimers between the expanded G-analogs and the natural C, and found that the pairing energies are close to those of the natural GC pair. The calculated adiabatic ionization potentials (IPs) of the size-expanded guanine analogs and their base pairs, and the corresponding vertical ionization potentials, show that some are distinctly smaller than the corresponding natural versions. The HOMO-LUMO energy gaps for most of the size-expanded guanine analogs and their WC base pairs are considerably lower than those of the corresponding natural base and base pairs. Thus, the expanded G bases may be considered as DNA genetic motifs, and they may serve as building blocks for potential biological applications and the development of molecular electronic devices.     

Biological activities from andiroba (Carapa guianensis Aublet.) and its biotechnological applications: A systematic review

Carapa guianensis is a tree from Meliaceae family traditionally known as andiroba that has a wide range of biological properties, including therapeutic effects, antioxidant activities, insecticidal and repellent effects that can be used in biotechnological approaches to medicine, agriculture, and cosmetic products. Therefore, we aim to explore the biological activities exhibited by this species and their respective biotechnological applications of interest. For this, a systematic review was carried out following the PRISMA guidelines dated from 1993 to 2022 through the Scopus, Web of Science and Agricultural Research Database (Base de Dados da Pesquisa Agropecuária - BDPA), screened for biological activity/bioactive compounds. A total of 129 studies were included in the PRISMA flow analysis. Biological properties and major bioactive compounds, as well as biotechnological approaches could be identified. The biological activity from C. guianensis could be observed in different vegetative parts through diverse methods of extractions. These activities are mainly due to the unsaturated fatty acids and bioactive compounds, such as the limonoids and a small fraction of phenolic compounds. Gedunin-type limonoids, like gedunin and its derivatives, represent the class of compounds that show the highest bioactivities in different applications.     

Analytical methods for the determination of mixtures of bisphenols and derivatives in human and environmental exposure sources and biological fluids. A review

Bisphenol A (BPA) is ubiquitous in humans and the environment. Its potential adverse effects through genomic and non-genomic pathways have fostered BPA replacement by bisphenol analogs that, unfortunately, exert similar adverse effects. Many of these analogs, as well as their derivatives, have already found in humans and the environment and major concerns have arisen over their low dose- and mixture-related effects. This review aims to discuss the characteristics of the main analytical methods reported so far for the determination of mixtures of bisphenol analogs and/or derivatives in human and environmental exposure sources and biological fluids. Approaches followed for removal of background contamination, sample preparation and separation and detection of mixtures of bisphenols and derivatives are critically discussed. Sample treatment is matrix-dependent and common steps include analyte isolation, removal of interferences, evaporation of the extracts and solvent reconstitution. Separation and quantification has been almost exclusively carried out by liquid chromatography tandem mass spectrometry (LC-MS/MS) or gas chromatography mass spectrometry (GC–MS), in the last case prior derivatization, but LC-fluorescence detection has also found some applications. Main characteristics, advantages and drawbacks of these methods will be comparatively discussed. Although at an early stage, some approaches for the assessment of the risk to mixtures of bisphenols, mainly based on the combination of chemical target analysis and toxicity evaluation, have been already applied and they will be here presented. Current knowledge gaps hindering a reliable assessment of human and environmental risk to mixtures of bisphenols and derivatives will be outlined.     

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.     

Bioinspired catalysis at the crossroads between biology and chemistry: A remarkable example of an electrocatalytic material mimicking hydrogenases

There is an increasing need for new, efficient and cheap chemical catalysts, as part of the emerging “green” chemistry field. Living organisms provide a wealth of fascinating enzymes, with exceptional catalytic efficiencies and selectivities, which can be either directly exploited in biotechnological synthetic systems or imitated by chemists. The bioinspired catalysis approach exploits the basic chemical principles on which a biological enzyme active site is built in order to generate original functional analogs of this site. This is illustrated here with a molecular electrode material inspired from hydrogenases, metalloenzymes involved in hydrogen metabolism, and displaying exceptional electrocatalytic properties for hydrogen production and oxidation, thus with potential applications for electrolyzer and fuel cell technologies.     

Biomimetic Assembly Lines Producing Natural Product Analogs: Strategies from a Versatile Manifold to Skeletally Diverse Scaffolds

Biosynthetic assembly lines have evolved in nature, adopting divergent processes to produce a vast number of secondary metabolites. Inspired by these biogenetic processes, this account introduces recent investigations by my research group to formulate a synthetic strategy for establishing a biomimetic assembly line. With the aim not only to construct natural product‐relevant scaffolds within 5–7 steps, but also to systematically diversify skeletal and stereochemical properties and functional groups, divergent synthetic processes exploiting a versatile manifold have been developed. This approach allows for cost‐effective production of skeletally diverse and biologically active natural product analogs inaccessible by other means. Discovery of several lead candidates for a neglected tropical disease is a proof‐of‐concept of this synthetic approach.     

Enzyme-directed assembly and manipulation of organic nanomaterials

Enzymes are the prime protagonists in the chemistry of living organisms. As such, chemists and biologists have long been fascinated by the array of highly selective transformations possible under biological conditions that are facilitated by enzyme-catalyzed reactions. Moreover, enzymes are involved in replicating, repairing and transmitting information in a highly selective and organized fashion through detection and signal amplification cascades. Indeed, because of their selectivity and potential for use outside of biological systems, enzymes have found immense utility in various biochemical assays and are increasingly finding applications in the preparation of small molecules. By contrast, the use of enzymatic reactions to prepare and build supramolecular and nanoscale materials is relatively rare. In this article, we seek to highlight efforts over the past 10 years at taking advantage of enzymatic reactions to assemble and manipulate complex soft, organic materials on the nanoscale. It is tantalizing to think of these processes as mimics of natural systems where enzymes are used in the assembly and transformation of the most complex nanomaterials known, for example, virus capsid assemblies and the myriad array of nanoscale biomolecular machinery.     

Coarse‐grained molecular dynamics simulations of protein–ligand binding

Coarse‐grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. We chose two protein–ligand systems, the levansucrase–sugar (glucose or sucrose), and LinB–1,2‐dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand‐binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse‐grained (CG) ligand molecules revealed potential ligand‐binding sites on the protein surfaces other than the real ligand‐binding sites. The ligands bound most strongly to the real ligand‐binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase–sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand‐binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein–ligand binding processes. © 2014 Wiley Periodicals, Inc.     

Chemoinformatic analysis of a supertargeted combinatorial library of styryl molecules

Styryl dyes are fluorescent, lipophilic cations that have been used as specific labeling probes of mitochondria in living cells. For specific applications such as epifluorescence microscopy or flow cytometry, it is often desirable to synthesize fluorescent derivatives with optimized excitation, emission, and localization properties. Here, we present a chemoinformatic strategy suitable for multiparameter analysis of a combinatorial library of styryl molecules supertargeted to mitochondria. The strategy is based on a simple additive model relating the spectral and subcellular localization characteristics of styryl compounds to the two chemical building blocks that are used to synthesize the molecules. Using a cross-validation approach, the additive model predicts with a high degree of confidence the subcellular localization and spectral properties of the styryl product, from numerical scores that are independently associated with the individual building blocks of the molecule. The fit of the data indicates that more complex, nonadditive interactions between the two building blocks play a minor role in determining the molecule's optical or biological properties. Moreover, the observed additive relationship allows mechanistic inferences to be made regarding the structure-property relationship observed for this particular class of molecules. It points to testable, mechanistic hypotheses about how chemical structure, fluorescence, and localization properties are related.     

Labeling Cell Surface GPIs and GPI‐Anchored Proteins through Metabolic Engineering with Artificial Inositol Derivatives

Glycosylphosphatidylinositol (GPI) anchoring of proteins to the cell surface is important for various biological processes, but GPI‐anchored proteins are difficult to study. An effective strategy was developed for the metabolic engineering of cell‐surface GPIs and GPI‐anchored proteins by using inositol derivatives carrying an azido group. The azide‐labeled GPIs and GPI‐anchored proteins were then tagged with biotin on live cells through a click reaction, which allows further elaboration with streptavidin‐conjugated dyes or other molecules. The strategy can be used to label GPI‐anchored proteins with various tags for biological studies.     

Cyclodextrins as Protective Agents of Protein Aggregation: An Overview

Cyclodextrins are extensively used in different fields (e.g., catalysis, chromatography, pharma, supramolecular chemistry, bioorganic chemistry, and bioinorganic chemistry), and their applications have been widely reviewed. Their main application in the field of pharmaceutical is as a drug carrier. This review overviews, for the first time, the use of cyclodextrins and their derivatives as antiaggregant agents in a number of proteins (e.g., amyloid‐β, insulin, recombinant human growth hormone, prion protein, transthyretin, and α‐synuclein) and some multimeric enzymes. There are many diseases that are correlated to protein misfolding and amyloid formation processes affecting numerous organs and tissues. There are over 30 different amyloid proteins and a number of corresponding diseases. Alzheimer's disease is the most common neurodegenerative disease. Treatment of these diseases is still a goal to reach, and many molecules are studied in this perspective. Cyclodextrins have also been studied, and they show great potential; as such, further studies could be very promising. This review aims to be a stimulus for the design of new cyclodextrin derivatives to obtain multifunctional systems with antiaggregant activity.