High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors,Evolution, and Discovery

Carbohydrates are attached and removed in living systems through the action of carbohydrate‐active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high‐throughput approaches look at many enzymes at once. Similarly, high‐throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high‐throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence‐activated cell sorting, and metagenomics.     

High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors,Evolution, and Discovery

Carbohydrates are attached and removed in living systems through the action of carbohydrate‐active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high‐throughput approaches look at many enzymes at once. Similarly, high‐throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high‐throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence‐activated cell sorting, and metagenomics.     

Beyond the BET Family: Targeting CBP/p300 with 4‐Acyl Pyrroles

Bromodomain and extra‐terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders. However, non‐BET bromodomains such as those in p300 and CBP are less studied. XDM‐CBP is a highly potent and selective inhibitor for the bromodomains of CBP and p300 derived from a pan‐selective BET BRD‐binding fragment. Along with X‐ray crystal‐structure analysis and thermodynamic profiling, XDM‐CBP was used in screenings of several cancer cell lines in vitro to study its inhibitory potential on cancer cell proliferation. XDM‐CBP is demonstrated to be a potent and selective CBP/p300 inhibitor that acts on specific cancer cell lines, in particular malignant melanoma, breast cancer, and leukemia.     

Detection of LacZ‐Positive Cells in Living Tissue with Single‐Cell Resolution

The LacZ gene, which encodes Escherichia coli β‐galactosidase, is widely used as a marker for cells with targeted gene expression or disruption. However, it has been difficult to detect lacZ‐positive cells in living organisms or tissues at single‐cell resolution, limiting the utility of existing lacZ reporters. Herein we present a newly developed fluorogenic β‐galactosidase substrate suitable for labeling live cells in culture, as well as in living tissues. This precisely functionalized fluorescent probe exhibited dramatic activation of fluorescence upon reaction with the enzyme, remained inside cells by anchoring itself to intracellular proteins, and provided single‐cell resolution. Neurons labeled with this probe preserved spontaneous firing, which was enhanced by application of ligands of receptors expressed in the cells, suggesting that this probe would be applicable to investigate functions of targeted cells in living tissues and organisms.     

Nucleic Acid‐Barcoding Technologies: Converting DNA Sequencing into a Broad‐Spectrum Molecular Counter

The emergence of high‐throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad‐spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non‐traditional applications is the need to append nucleic‐acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic‐acid barcoding of proteinaceous and non‐proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA‐encoded molecules. As commercially available high‐throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.     

Neue Wege in der Biokatalyse: Evolutive Methoden

Biocatalysts are of increasing interest for the preparation of optically active compounds in pharmaceutical, fine chemical and in agricultural business. In the development of industrial applicable biocatalysts under non‐natural conditions, directed evolution is a useful tool which emulates natural processes of diversity generation and selection. Random mutations are introduced in a gene or different genes are recombined to create libraries of new biocatalysts. Selection is performed or high throughput screening procedures are completed by means of laboratory automation to identify optimized catalysts. Repeated cycles of directed evolution allow the in vitromolecular evolution to provide a new biocatalyst with the desired properties like enhanced activity, stability or selectivity in a very rapid manner.     

Tracking Pathogen Infections by Time‐Resolved Chemical Proteomics

Studying the dynamic interaction between host cells and pathogen is vital but remains technically challenging. We describe herein a time‐resolved chemical proteomics strategy enabling host and pathogen temporal interaction profiling (HAPTIP) for tracking the entry of a pathogen into the host cell. A novel multifunctional chemical proteomics probe was introduced to label living bacteria followed by in vivo crosslinking of bacteria proteins to their interacting host‐cell proteins at different time points initiated by UV for label‐free quantitative proteomics analysis. We observed over 400 specific interacting proteins crosslinked with the probe during the formation of Salmonella‐containing vacuole (SCV). This novel chemical proteomics approach provides a temporal interaction profile of host and pathogen in high throughput and would facilitate better understanding of the infection process at the molecular level.     

Creating Complex Polyacrylamide Hydrogel Structures Using 3D Printing with Applications to Mechanobiology

Due to its favorable physical and chemical properties, including chemical inertness, low fouling by biological molecules, high porosity and permeability, optical transparency, and adjustable elasticity, polyacrylamide has found a wide range of biomedical and non‐biomedical applications. To further increase its versatility, this communication describes a simple method, using readily available reagents and equipment, for 3D printing polyacrylamide hydrogels at a resolution of 100–150 μm to create complex structures. As a demonstration of the application, the method is used for creating a lab‐on‐a‐chip cell culture surface with micropatterned stiffness, which then leads to the discovery of stiffness‐guided collective cell segregation distinct from durotaxis. The present technology is expected to unleash new applications such as the construction of biocompatible elastic medical devices and artificial organs.     

Bioorthogonal Probes for the Study of MDM2‐p53 Inhibitors in Cells and Development of High‐Content Screening Assays for Drug Discovery

To study the behavior of MDM2‐p53 inhibitors in a disease‐relevant cellular model, we have developed and validated a set of bioorthogonal probes that can be fluorescently labeled in cells and used in high‐content screening assays. By using automated image analysis with single‐cell resolution, we could visualize the intracellular target binding of compounds by co‐localization and quantify target upregulation upon MDM2‐p53 inhibition in an osteosarcoma model. Additionally, we developed a high‐throughput assay to quantify target occupancy of non‐tagged MDM2‐p53 inhibitors by competition and to identify novel chemical matter. This approach could be expanded to other targets for lead discovery applications.     

Understanding Interactions between Cellular Matrices and Metal Complexes: Methods To Improve Silver Nanodot‐Specific Staining

Metal complexes are frequently used for biological applications due to their special photophysical and chemical characteristics. Due to strong interactions between metals and biomacromolecules, a random staining of cytoplasm or nucleoplasm by the complexes results in a low signal‐to‐background ratio. In this study, we used luminescent silver nanodots as a model to investigate the major driving force for non‐specific staining in cellular matrices. Even though some silver nanodot emitters exhibited excellent specific staining of nucleoli, labeling with nanodots was problematic owing to severe non‐specific staining. Binding between silver and sulfhydryl group of proteins appeared to be the major factor that enforced the silver staining. The oxidation of thiol groups in cells with hexacyanoferrate(III) dramatically weakened the silver‐cell interaction and consequently significantly improved the efficiency of targeted staining.     

Expressing Forest Origins in the Chemical Composition of Cooperage Oak Woods and Corresponding Wines by Using FTICR‐MS

A non‐targeted, ultra‐high‐resolution mass spectrometric, direct analysis of oak‐wood extracts from two species (Quercus robur L. and Quercus petraea Liebl.) from three French forests, and of a wine aged in barrels derived therefrom has been performed to identify families of metabolites that could discriminate both the species and the geographical origin of woods. From 12 T ultra‐high‐resolution Fourier transform ion cyclotron resonance mass spectra of wood extracts, hundreds of mass signals were identified as possible significant biomarkers of the two species, with phenolic and carbohydrate moieties leading the differentiation between Q. robur and Q. petraea, respectively, as corroborated by both FTMS and NMR data. For the first time, it is shown that oak woods can also be discriminated on the basis of hundreds of forest‐related compounds, and particular emphasis is put on sessile oaks from the Tronçais forest, for which sugars are significantly discriminant. Despite the higher complexity and diversity of wine metabolites, forest‐related compounds can also be detected in wines aged in related barrels. It is only by using these non‐targeted analyses that such innovative results, which reveal specific chemodiversities of natural materials, can be obtained.     

Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures

Optical cross‐reactive sensor arrays (the so‐called chemical “noses/tongues”) have recently been demonstrated as a powerful tool for high‐throughput protein detecting and analysis. Nevertheless, applying this technology to biomarker detection is complicated by the difficulty of non‐selective sensors to operate in biological mixtures. Herein we demonstrate a step toward circumventing this limitation by using self‐assembled fluorescent receptors consisting of two distinct recognition motifs: specific and non‐specific. When combined in an array, binding cooperatively between the specific and non‐specific protein binders enables the system to discriminate among closely related isoform biomarkers even in the presence of serum proteins or within human urine.     

Interfacing Microbial Styrene Production with a Biocompatible Cyclopropanation Reaction

The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small‐molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non‐native reactivity into metabolic pathways for small‐molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non‐natural phenyl cyclopropanes directly from D ‐glucose in single‐vessel fermentations. This process is the first example of the combination of nonbiological carbene‐transfer reactivity with cellular metabolism for small‐molecule production.     

新冠病毒刺突蛋白及其受体的结构与相互作用

Biochemistry is a branch subject of chemistry, which is the study of chemical structures and processes associated with living organisms. COVID-19 pandemic is a problem for human beings. From the perspective of biochemistry, this paper demonstrates the chemical structure and interactions of SARS-CoV-2's spike protein and its receptor (human angiotensin converting enzyme 2), and summarizes the related research progresses. The authors hope to provide insights for the development of COVID-19 vaccine.     

Enantioselectivity Effects in Clinical Metabolomics and Lipidomics

Metabolomics and lipidomics have demonstrated increasing importance in underlying biochemical mechanisms involved in the pathogenesis of diseases to identify novel drug targets and/or biomarkers for establishing therapeutic approaches for human health. Particularly, bioactive metabolites and lipids have biological activity and have been implicated in various biological processes in physiological conditions. Thus, comprehensive metabolites, and lipids profiling are required to obtain further advances in understanding pathophysiological changes that occur in cells and tissues. Chirality is one of the most important phenomena in living organisms and has attracted long-term interest in medical and natural science. Enantioselective separation plays a pivotal role in understanding the distribution and physiological function of a diversity of chiral bioactive molecules. In this context, it has been the goal of method development for targeted and untargeted metabolomics and lipidomic assays. Herein we will highlight the benefits and challenges involved in these stereoselective analyses for clinical samples.     

Software utilities for the interpretation of mass spectrometric data of glycoconjugates: application to glycosphingolipids of human serum

Glycosphingolipids (GSLs) are major components of the outer leaflet of the cell membrane. These lipids are involved in many cell surface events and show disease‐related expression changes. GSLs could thus serve as useful targets for biomarker discovery. The GSL structure is characterized by two entities: a hydrophilic glycan and a hydrophobic ceramide moiety. Both components exhibit numerous structural variations, the combination of which results in a large diversity of GSL structures that can potentially exist. Mass spectrometry (MS) is a powerful tool for high‐throughput analysis of GSL expression analysis and structural elucidation. Yet, the assignment of GSL structures using MS data is tedious and demands highly specialized expertise. SysBioWare, a software platform developed for MS data evaluation in glycomics, was here applied for the MS analysis of human serum GSLs. The program was tuned to provide automated compositional assignment, supporting a variety of glycan and ceramide structures. Upon in silico fragmentation, the masses of predicted ions arising from cleavages in the glycan as well as the ceramide moiety were calculated, thus enabling structural characterization of both entities. Validation of proposed structures was achieved by matching in silico calculated fragment ions with those of experimental MS/MS data. These results indicate that SysBioWare can facilitate data interpretation and, furthermore, help the user to deal with large sets of data by supporting management of MS and non‐MS data. SysBioWare has the potential to be a powerful tool for high‐throughput glycosphingolipidomics in clinical applications. Copyright © 2010 John Wiley & Sons, Ltd.     

Pseudilins: Halogenated,Allosteric Inhibitors of the Non‐Mevalonate Pathway Enzyme IspD

The enzymes of the non‐mevalonate pathway for isoprenoid biosynthesis have been identified as attractive targets with novel modes of action for the development of herbicides for crop protection and agents against infectious diseases. This pathway is present in many pathogenic organisms and plants, but absent in mammals. By using high‐throughput screening, we identified highly halogenated marine natural products, the pseudilins, to be inhibitors of the third enzyme, IspD, in the pathway. Their activity against the IspD enzymes from Arabidopsis thaliana and Plasmodium vivax was determined in photometric and NMR‐based assays. Cocrystal structures revealed that pseudilins bind to an allosteric pocket by using both divalent metal ion coordination and halogen bonding. The allosteric mode of action for preventing cosubstrate (CTP) binding at the active site was elucidated. Pseudilins show herbicidal activity in plant assays and antiplasmodial activity in cell‐based assays.