Fluorescence imaging of drug target proteins using chemical probes

Fluorescence imaging can provide valuable information on the expression,distribution,and activity of drug target proteins.Chemical probes are useful small-molecule tools for fluorescence imaging with high structural flexibility and biocompatibility.In this review,we briefly introduce two classes of fluorescent probes for the visualization of drug target proteins.Enzymatically activatable probes make use of the specific enzymatic transformations that generally produce a fluorogenic response upon reacting with target enzymes.Alternatively,specific imaging can be conferred with a ligand that drives the probes to target proteins,where the labeling relies on noncovalent binding,covalent inhibition,or traceless labeling by ligand-directed chemistry.

Recent advances in target identification by natural product based chemical probes

Natural products have been extensively used to treat diseases throughout human history. These are mainly because natural products normally target biological macromolecules selectively. Target identification could help us to develop new therapeutic agents and discover new biological pathways underlying human diseases. Herein, we highlight some recent examples of using natural products and their derivatives as chemical probes to identify the molecular targets and elucidate mode of action.

Small-molecule chemical probes for the potential therapeutic targets in alcoholic liver diseases

Alcoholic liver disease(ALD)encompasses a range of conditions resulting from prolonged and excessive alcohol consumption,causing liver damage such as alcoholic fatty liver,inflammation,fibrosis,and cirrhosis.Alcohol consumption contributes to millions of deaths each year.So far,the effective treatments for ALD are limited.To date,the most effective treatment for ALD is still prevention by avoiding excessive alcohol consumption,and only few specialized medicines are in the market for the treatment of patients suffering from ALD.Small molecules targeting various pathways implicated in ALD pathogenesis can potentially be used for effective therapeutics development.In this review,we provide a concise overview of the latest research findings on potential therapeutic targets,specifically emphasizing small-molecule interventions for the treatment and prevention of ALD.

Polyvinyl alcohol–potassium iodide gel probe to monitor the distribution of reactive species generation around atmospheric-pressure plasma jet

This study proposes polyvinyl alcohol–potassium iodide(PVA–KI)as a novel gel chemical probe.The probe uses the reactions among PVA,KI,water,borax,and oxidative species to visualize the distribution of reactive species.This method provides information regarding the distribution of reactive species by coloration on the gel surface.The effects of the surrounding gas phase on the distribution and diffusion of the reactive species are also investigated using the PVA–KI gel probe.Further,the relationship between the irradiation distance and reactive species diffusion is determined on the surface of the PVA–KI probe with and without plastic shielding.Adjusting the irradiation distance appropriately leads to an increase in the modified area as detected by the PVA–KI gel probe analysis.The relative concentration distributions of the reactive species are also obtained from visualized color distributions measured using a colorimeter.Furthermore,reactive species generation by long-scale line plasma is confirmed by the color reaction on the PVA–KI gel surface,with a greater area being covered by an atmospheric-pressure pulsed microwave line plasma source.

Chemical probe systems for assessing liquid–liquid mixing efficiencies of reactors

Liquid-liquid mixing,including homogeneous and heterogeneous mixing,widely exists in the chemical industry.How to quantitatively characterize the mixing performance is important for reactor assessment and development.As a convenient and direct method for mixing characterization,the chemical probe method uses some special test reactions to characterize the mixing results.Here,the working principle and selection requirements of this method are introduced,and some common chemical probe systems for homogeneous and heterogeneous mixing processes are reviewed.The characteristics and applications of these systems are illustrated.Finally,the development of the new system is proposed.

Biochemical reactions in metabolite-protein interaction

Active endogenous metabolites regulate the viability of cells. This process is controlled by a series ofinteractions between small metabolites and large proteins. Previously, several studies had reported thatmetabolite regulates the protein functions, such as diacylglycerol to protein kinase C, lactose regulationof the lac repressor, and HIF-1α stabilization by 2-hydroxyglutarate. However, decades old traditionalbiochemical methods are insufficient to systematically investigate the bio-molecular reactions for a high-throughput discovery. Here, we have reviewed an update on the recently developed chemical proteomicscalled activity-based protein profiling （ABPP）. ABPP is able to identify proteins interacted eithercovalently or non-covalently with metabolites significantly. Thus, ABPP will facilitate the characteriza-tion of specific metabolite regulating; proteins in human disease progression.

Intracellular RNA Labeling Technologies for the Analysis of RNA Biology

As a cornerstone of the central dogma of molecular biology,RNA plays vital roles in living organisms.Over the past few decades,many RNA labeling technologies have been developed to elucidate the biological function of RNA.These technologies have signifi-cantly advanced our understanding of RNA secondary structure,localization,and turnover.Additionally,taking advantage of these innovative RNA labeling approaches,plenty of tool kits have been devised for the regulation of RNA-related biological process,such as gene expression and gene editing.In this review,we primarily focus on an array of intracellular RNA labeling methods,encom-passing chemical probes-based labeling,metabolic labeling,and proximity-dependent labeling.We also provide a brief overview of their applications in the research of RNA biology.Finally,the perspectives of RNA labeling are also discussed.

Comparative and integrative analysis of RNA structural profiling data： current practices and emerging questions

Background： Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transeriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. Results： We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. Conclusions： To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.

Discovery of CECR2 Bromodomain Inhibitors with High Selectivities over BPTF Bromodomain

Cat's eye syndrome chromosome candidate 2 bromodomain(CECR2 BRD)and Bromodomain PHD transcription factor bromodomain(BPTF BRD)are the same subfamily proteins,both of which are highly conserved in sequence and binding pockets.Challenges remain in the development of small molecules to inhibit one of the two bromodomains(BRDs),in view of each subtype may possess unique physiological and pathological functions.There is still a lack of effective selective inhibitors of CECR2 BRD,which makes it difficult to fully understand the pathogenesis of CECR2-BRD in diseases,especially cancers.Herein,we report our efforts to discover a series of highly selective CECR2 BRD inhibitors over BPTF BRD based on TP-248.Structure-based molecular optimization led to the discovery of DC-CEi-26,whose IC_(50) for CECR2 BRD was 96.7±14.9 nmol/L and selectivity was up to 590×over BPTF BRD.DC-CEi-26 showed weak potencies for other classic BRDs in different subfamily,which may serve as a chemical probe for CECR2 BRD biological research.

Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy

DNA-encoded chemical library(DEL)represents an emerging drug discovery technology to construct com-pound libraries with abundant chemical combinations.While drug-like small molecule DELs facilitate the discovery of binders against targets with defined pockets,macrocyclic DELs harboring extended scaffolds enable targeting of the protein–protein interaction(PPI)interface.We previously demonstrated the design of the first-generation DNA-encoded multiple display based on a constant macrocyclic scaffold,which harvested binders against difficult targets such as tumor necrosis factor-α(TNF-α).Here,we developed a novel strategy which utilized four orthogonal amine-protecting groups on DNA,to explore larger chem-ical combinations on the same constant macrocyclic scaffold,following the parallel paradigm to mimic the versatile antibody-like multivalent epitope recognition patterns.We successfully integrated these or-thogonal protecting groups with acylation and made a mock second-generation DNA-encoded display combination.This work illustrates a strategy to produce larger encoded multiple display on a constant macrocyclic scaffold,which could facilitate potential binder discovery with enhanced affinity to clinically significant PPI targets.

Discovery and synthesis of N^2,N^4-substitued-cycloalkyl[d]pyrimidine-2,4-diamine analogs: The first examples of small-molecular FGFR-1 activator

A series of novel, cycloalkyl-modified pazopanib analogs 2 and 3 were designed and synthesized. Their kinase modulatory effects on FGFR-1, VEGFR-2, PDGFR-β and c-KIT were evaluated by the caliper mobility shift assay. Introduction of cycloalkyl into the pyrimidine linker of pazopanib almost abolished the four kinases inhibitory potency of compounds 2 and 3, but surprisingly, resulted in good activation effects on FGFR-1. Compounds 3d and 3g showed double-digit, nanomolar, selective activation effects on FGFR-1, and could be classified as first-generation small molecular activators of FGFR-1 kinase.