Search

We recently described glutathione peroxidase 4 (GPX4) as a promising target for killing therapy-resistant cancer cells via ferroptosis. The onset of therapy resistance by multiple types of treatment results in a stable cell state marked by high levels of polyunsaturated lipids and an acquired dependency on GPX4. Unfortunately, all existing inhibitors of GPX4 act covalently via a reactive alkyl chloride moiety that confers poor selectivity and pharmacokinetic properties. Here, we report our discovery that masked nitrile-oxide electrophiles, which have not been explored previously as covalent cellular probes, undergo remarkable chemical transformations in cells and provide an effective strategy for selective targeting of GPX4. The new GPX4-inhibiting compounds we describe exhibit unexpected proteome-wide selectivity and, in some instances, vastly improved physiochemical and pharmacokinetic properties compared to existing chloroacetamide-based GPX4 inhibitors. These features make them superior tool compounds for biological interrogation of ferroptosis and constitute starting points for development of improved inhibitors of GPX4.

Transient receptor potential canonical (TRPC) channels constitute a group of receptor-operated calcium-permeable nonselective cation channels of the TRP superfamily. The seven mammalian TRPC members, which can be further divided into four subgroups (TRPC1, TRPC2, TRPC4/5, and TRPC3/6/7) based on their amino acid sequences and functional similarities, contribute to a broad spectrum of cellular functions and physiological roles. Studies have revealed complexity of their regulation involving several components of the phospholipase C pathway, G i and G o proteins, and internal Ca 2+ stores. Recent advances in cryogenic electron microscopy have provided several high-resolution structures of TRPC channels. Growing evidence demonstrates the involvement of TRPC channels in diseases, particularly the link between genetic mutations of TRPC6 and familial focal segmental glomerulosclerosis. Because TRPCs were discovered by the molecular identity first, their pharmacology had lagged behind. This is rapidly changing in recent years owning to great efforts from both academia and industry. A number of potent tool compounds from both synthetic and natural products that selective target different subtypes of TRPC channels have been discovered, including some preclinical drug candidates. This review will cover recent advancements in the understanding of TRPC channel regulation, structure, and discovery of novel TRPC small molecular probes over the past few years, with the goal of facilitating drug discovery for the study of TRPCs and therapeutic development., Competing Interests: Declaration of Competing Interest The authors claim no conflict of interest., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Programmed biosensors with tunable quantification range and sensitivity would greatly broaden their application in medical diagnosis, food safety and environmental analysis. Herein, we proposed a graphene-nucleic acid biointerface-engineered biosensor, allowing target molecules to be detected with adjustable dynamic ranges and sensitivities. The biosensors were programmed by simply tuning the poly A tail of aptamer probes. The tuning of the poly A tail would allow the interaction between aptamer probes and graphene oxide (GO) to be modulated, in turn programing the competitive binding processes of aptamer probes to target molecules and GO. The biosensors, termed affinity-tunable aptasensors (atAptasensors) could be easily tuned with different dynamic ranges by using aptamer probes with different tail lengths, and the dynamic range could be extended to be over 3 orders by a combined use of multiple aptamer probes. Remarkably, the specificity of aptamer probes could be increased by increasing the interaction between aptamer probes and GO. Reliability of atAptasensor for ATP detection was tested in serum and milk samples, and we also applied atAptasensor for culture-independent analysis of microorganism pollution.

19 F NMR spectroscopy provides the ability to quantitatively analyze single species in complex solutions but is often limited by the modest sensitivity inherent to NMR. 4 R - and 4 S -Perfluoro- tert -buyl hydroxyproline contain 9 equivalent fluorines, in amino acids with strong conformational preferences. In order to test the ability to use these amino acids as sensitive probes of protein modifications, the perfluoro- tert -buyl hydroxyprolines were incorporated into substrate peptides of the protein kinases PKA and Akt. Peptides containing each diastereomeric proline were rapidly phosphorylated by each protein kinase and exhibited 19 F chemical shift changes as a result of phosphorylation. The sensitivity of the perfluoro- tert -butyl group allowed quantitative analysis of the kinetics of phosphorylation over three half-lives at single-digit micromolar concentrations of each species. The distinct conformational preferences of these amino acids allowed the optimization of the substrate with a conformationally matched amino acid, in order to maximize the rate of phosphorylation. PKA preferred the 4 R -amino acid at the -1 position, whereas the closely related AGC kinase Akt preferred the 4 S -amino acid. These data, combined with analysis of structures of the Michaelis complexes of these kinases in the PDB, suggest that PKA recognizes the PPII conformation at the P-1 position relative to the phosphorylation site, while Akt/PKB recognizes an extended conformation at this position. These results suggest that conformational targeting may be employed to increase specificity in recognition by protein kinases. Perfluoro- tert- butyl hydroxyprolines were applied to the real-time detection and quantification of PKA activity and inhibition of PKA activity in HeLa cell extracts via 19 F NMR spectroscopy. The coupling of proline ring pucker with main chain conformation suggests broad application of perfluoro- tert -butyl hydroxyprolines in molecular sensing and imaging.

Unprecedented progress made in the treatment of cancer using the body's own immune system has encouraged the development of synthetic molecule based immunotherapeutics. An emerging class of these compounds, called Antibody Recruiting Molecules (ARMs) or Antibody Engagers (AEs), functions by reversibly binding antibodies naturally present in human serum and recruiting these to cancer cells. The recruited antibodies then engage immune cells to form quaternary complexes that drive cancer erradication. Despite their promise, the requirement to form quaternary complexes governed by multiple equilibria complicates an understanding of their in vivo efficacy. Particularly problematic are low endogenous serum antibody concentrations and rapid clearance of AEs from circulation. Here we describe a new class of trifunctional chemical tools we call covalent immune recruiters (CIRs). CIRs covalently label specific serum antibodies in a selective manner with a target protein binding ligand. CIRs thereby exert well-defined control over antibody recruitment and simplify quaternary complex equilibium, enabling probing of the resultant effects on immune recognition. We demonstrate CIRs can selectively covalently label anti-DNP IgG, a natural human antibody, directly in human serum to drive efficient immune cell recognition of targets. We expect CIRs will be useful tools to probe how quaternary complex stability impacts the immune recognition of cancer in vivo , revealing new design principles to guide the development of future AEs.

Nonapoptotic cell death is important for human health and disease. Here, we show how various tools and techniques drawn from the chemical biology field have played a central role in the discovery and characterization of nonapoptotic cell death pathways. Focusing on the example of ferroptosis, we describe how phenotypic screening, chemoproteomics, chemical genetic analysis, and other methods enabled the elucidation of this pathway. Synthetic small-molecule inducers and inhibitors of ferroptosis identified in early studies have now been leveraged to identify an even broader set of compounds that affect ferroptosis and to validate new chemical methods and probes for various ferroptosis-associated processes. A number of limitations associated with specific chemical biology tools or techniques have also emerged and must be carefully considered. Nevertheless, the study of ferroptosis provides a roadmap for how chemical biology methods may be used to discover and characterize nonapoptotic cell death mechanisms., Competing Interests: Declaration of Interests S.J.D. is on the scientific advisory board of Ferro Therapeutics, has consulted for Toray Industries and AbbVie Inc., and is an inventor on patents related to ferroptosis., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Ferroptosis is a recently described form of cell death driven by iron-dependent lipid peroxidation. This type of cell death was first observed in response to treatment of tumor cells with a small-molecule chemical probe named erastin. Most subsequent advances in understanding the mechanisms governing ferroptosis involved the use of genetic screens and small-molecule probes. We describe herein the utility and limitations of chemical probes that have been used to analyze and perturb ferroptosis, as well as mechanistic studies of ferroptosis that benefitted from the use of these probes and genetic screens. We also suggest probes for ferroptosis and highlight mechanistic questions surrounding this form of cell death that will be a high priority for exploration in the future., Competing Interests: Declaration of Interests B.R.S. holds equity in and serves as a consultant to Inzen Therapeutics and is an inventor on patents and patent applications related to ferroptosis. X.J. is an inventor on patents related to cell death and autophagy., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Ferroptosis is an iron-dependent cell-death modality driven by oxidative phospholipid damage. In contrast to apoptosis, which enables organisms to eliminate targeted cells purposefully at specific times, ferroptosis appears to be a vulnerability of cells that otherwise use high levels of polyunsaturated lipids to their advantage. Cells in this high polyunsaturated lipid state generally have safeguards that mitigate ferroptotic risk. Since its recognition, ferroptosis has been implicated in degenerative diseases in tissues including kidney and brain, and is a targetable vulnerability in multiple cancers-each likely characterized by the high polyunsaturated lipid state with insufficient or overwhelmed ferroptotic safeguards. In this Perspective, we present progress toward defining the essential roles and key mediators of lipid peroxidation and ferroptosis in disease contexts. Moreover, we discuss gaps in our understanding of ferroptosis and list key challenges that have thus far limited the full potential of targeting ferroptosis for improving human health., Competing Interests: Declaration of Interests S.L.S. serves on the Board of Directors of the Genomics Institute of the Novartis Research Foundation (“GNF”); is a shareholder and serves on the Board of Directors of Jnana Therapeutics; is a shareholder of Forma Therapeutics; is a shareholder and advises Kojin Therapeutics, Kisbee Therapeutics, Decibel Therapeutics, and Eikonizo Therapeutics; serves on the Scientific Advisory Boards of Eisai Co., Ltd., Ono Pharma Foundation, Exo Therapeutics, and F-Prime Capital Partners; and is a Novartis Faculty Scholar. Kojin Therapeutics in particular explores the medical potential of cell plasticity related to ferroptosis. Y.Z. declares no conflict of interest related to this work., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Glutathione (GSH) is often upregulated in cancer, where it serves to mitigate oxidative stress. γ-glutamyl-transferase (GGT) is a key enzyme in GSH homeostasis, and compared to normal brain its expression is elevated in tumors, including in primary glioblastoma. GGT is therefore an attractive imaging target for detection of glioblastoma. The goal of our study was to assess the value of hyperpolarized (HP) γ-glutamyl-[1- 13 C]glycine for non-invasive imaging of glioblastoma. Nude rats bearing orthotopic U87 glioblastoma and healthy controls were investigated. Imaging was performed by injecting HP γ-glutamyl-[1- 13 C]glycine and acquiring dynamic 13 C data on a preclinical 3T MR scanner. The signal-to-noise (SNR) ratios of γ-glutamyl-[1- 13 C]glycine and its product [1- 13 C]glycine were evaluated. Comparison of control and tumor-bearing rats showed no difference in γ-glutamyl-[1- 13 C]glycine SNR, pointing to similar delivery to tumor and normal brain. In contrast, [1- 13 C]glycine SNR was significantly higher in tumor-bearing rats compared to controls, and in tumor regions compared to normal-appearing brain. Importantly, higher [1- 13 C]glycine was associated with higher GGT expression and higher GSH levels in tumor tissue compared to normal brain. Collectively, this study demonstrates, to our knowledge for the first time, the feasibility of using HP γ-glutamyl-[1- 13 C]glycine to monitor GGT expression in the brain and thus to detect glioblastoma.

Herein we report a pair of redox-responsive manganese complexes Mn(iii)/(ii)-N,N'-bis(2-hydroxy-4-trifluoromethylbenzyl)ethylenediamine-N,N'-diacetate (HTFBED, L1), which are water soluble and biologically interconvertible, as reversible redox-responsive probes in 1H/19F MRI for detecting and imaging biological redox species, offering a means to access valuable redox information associated with various diseases.

A reliable tool for real-time tracking the neuroinflammatory progress is highly desired for interpretation and treatment of neurological disorders. Herein, a blood-brain barrier (BBB) permeable and HOCl-activatable upconversion (UC) nanoprobe with NIR emission was designed for visual study on neuroinflammation (NI) in vivo . This UC probe consists of three parts: upconversion nanoparticles (UCNPs) as signal reporter, the Cy-HOCl dye acting as energy acceptor of UCNPs as well as the recognition unit of HOCl, and amphiphilic polymers endowing the probe with biocompatibility and BBB permeability. Upon intravenous injection into mice, the probe crossed the BBB via low-density lipoprotein receptor related protein (LRP) mediated transcytosis and was then lightened up by overproduced HOCl in an NI process. This probe was able to differentiate inflammation and the normal state of the brain in LPS-induced NI and monitor the progress of NI occurring in mice with cerebral stroke, providing a practical tool for noninvasive and visual assessment of NI.

(±)-Dispirocochlearoids A-C ( 1 - 3 ), meroterpenoids with a 6/6/5/6/6/6 ring system, were isolated from Ganoderma cochlear . 1 - 3 are selective COX-2 inhibitors with an IC 50 value of (-)- 2 at 386 nM. Site-directed mutagenesis identified His351 as a COX-2 active site. In vivo anti-inflammatory activities of (-)- 2 were performed against acute lung injury in mice.

Inspired by the rapid progress and existing limitations in surface plasmon resonance (SPR) biosensing technology, we have summarized the recent trends in the fields of both chip-SPR and fiber optic (FO)-SPR biosensors during the past five years, primarily regarding smart layers design, multiplexing, continuous monitoring and in vivo sensing. Versatile surface chemistries, biomaterials and nanomaterials have been utilized thus far to generate smart layers on SPR platforms and as such achieve oriented immobilization of bioreceptors, improved fouling resistance and sensitivity enhancement, collectively aiming to improve the biosensing performance. Furthermore, often driven by the desires for time- and cost-effective quantification of multiple targets in a single measurement, efforts have been made to implement multiplex bioassays on SPR platforms. While this aspect largely remains difficult to attain, numerous alternative strategies arose for obtaining parallel analysis of multiple analytes in one single device. Additionally, one of the upcoming challenges in this field will be to succeed in using SPR platforms for continuous measurements and in vivo sensing, and as such match up other biosensing platforms where these goals have been already conquered. Overall, this review will give insight into multiple possibilities that have become available over the years for boosting the performance of SPR biosensors. However, because combining them all into one optimal sensor is practically not feasible, the final application needs to be considered while designing an SPR biosensor, as this will determine the requirements of the bioassay and will thus help in selecting the essential elements from the recent progress made in SPR sensing., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Professor Jeroen Lammertyn is a board member of FOx Biosystems, a spin-off company of KU Leuven commercializing FO-SPR platforms, next to the principal investigator of the Biosensors group., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry., Competing Interests: Declaration of competing interest The authors declare no competing interest., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

Targeted covalent inhibitors represent an increasingly popular approach to modulate challenging drug targets. Since covalent and non-covalent interactions are both contributing to the affinity of these compounds, evaluation of their reactivity is a key-step to find feasible warheads. There are well-established HPLC- and NMR-based kinetic assays to tackle this task, however, they use a variety of cysteine-surrogates including cysteamine, cysteine or acetyl-cysteine and GSH. The diverse nature of the thiol sources often makes the results incomparable that prevents compiling a comprehensive knowledge base for the design of covalent inhibitors. To evaluate kinetic measurements from different sources we performed a comparative analysis of the different thiol surrogates against a designed set of electrophilic fragments equipped with a range of warheads. Our study included seven different thiol models and 13 warheads resulting in a reactivity matrix analysed thoroughly. We found that the reactivity profile might be significantly different for various thiol models. Comparing the different warheads, we concluded that - in addition to its human relevance - glutathione (GSH) provided the best estimate of reactivity with highest number of true positives identified., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The prenyl-protein chaperone PDEδ modulates the localization of lipidated proteins in the cell, but current knowledge about its biological function is limited. Small-molecule inhibitors that target the PDEδ prenyl-binding site have proven invaluable in the analysis of biological processes mediated by PDEδ, like KRas cellular trafficking. However, allosteric inhibitor release from PDEδ by the Arl2/3 GTPases limits their application. We describe the development of new proteolysis-targeting chimeras (PROTACs) that efficiently and selectively reduce PDEδ levels in cells through induced proteasomal degradation. Application of the PDEδ PROTACs increased sterol regulatory element binding protein (SREBP)-mediated gene expression of enzymes involved in lipid metabolism, which was accompanied by elevated levels of cholesterol precursors. This finding for the first time demonstrates that PDEδ function plays a role in the regulation of enzymes of the mevalonate pathway., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Size selectivity is an important mechanism for molecular recognition based on the size difference between targets and non-targets. However, rational design of an artificial size-selective molecular recognition system for biological targets in living cells remains challenging. Herein, we construct a DNA molecular sieve for size-selective molecular recognition to improve the biosensing selectivity in living cells. The system consists of functional nucleic acid probes (e.g., DNAzymes, aptamers and molecular beacons) encapsulated into the inner cavity of framework nucleic acid. Thus, small target molecules are able to enter the cavity for efficient molecular recognition, while large molecules are prohibited. The system not only effectively protect probes from nuclease degradation and nonspecific proteins binding, but also successfully realize size-selective discrimination between mature microRNA and precursor microRNA in living cells. Therefore, the DNA molecular sieve provides a simple, general, efficient and controllable approach for size-selective molecular recognition in biomedical studies and clinical diagnoses.

Voltage-gated sodium (Nav) channels respond to changes in the membrane potential of excitable cells through the concerted action of four voltage-sensor domains (VSDs). Subtype Nav1.7 plays an important role in the propagation of signals in pain-sensing neurons and is a target for the clinical development of novel analgesics. Certain inhibitory cystine knot (ICK) peptides produced by venomous animals potently modulate Nav1.7; however, the molecular mechanisms underlying their selective binding and activity remain elusive. This study reports on the design of a library of photoprobes based on the potent spider toxin Huwentoxin-IV and the determination of the toxin binding interface on VSD2 of Nav1.7 through a photocrosslinking and tandem mass spectrometry approach. Our Huwentoxin-IV probes selectively crosslink to extracellular loop S1-S2 and helix S3 of VSD2 in a chimeric channel system. Our results provide a strategy that will enable mapping of sites of interaction of other ICK peptides on Nav channels., Competing Interests: Declaration of Interests F.T., H.X., T.L., N.G., C.K., J.P., and C.M.K. are/were Genentech employees. T.L., J.P., and C.M.K. hold shares in the Genentech/Roche group. E.W.T. is a Director and holds shares in Myricx Pharma Ltd., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Perfluorinated organic compounds (PFCs) are nontoxic, biocompatible, bioavailable, and bioorthogonal species which possess the unique ability to segregate away from both polar and nonpolar solvents producing a compact fluorophilic phase. Traditional techniques of fluorous chemical proteomics are generally applied to enrich biological samples in target protein(s) exploiting this property of PFCs to build fluorinated probes able to covalently bind to protein ensembles and being selectively extracted by fluorophilic solvents. Aiming at building a strategy able to avoid irreversible modification of the analyzed biosystem, a novel fully noncovalent probe is presented as an enabling tool for the recognition and isolation of biological protein(s). In our strategy, both the fluorophilic extraction and the biorecognition of a selected protein successfully occur via the establishment of reversible but selective interactions.

Post-translational modification of proteins can form electrophilic cofactors that serve as a catalytic center. The derived electrophilic cofactors greatly expand protein activities and functions. However, there are few studies concerning how to profile the electrophiles in bacteria. Herein, we utilized a clickable probe called propargyl hydrazine to profile the protein-derived electrophilic cofactors in Escherichia coli ( E. coli ) cells. Since the cofactors are mostly carbonyl groups, the hydrazine-based probe can specifically react with the cofactors to form a Schiff base. The labeled proteins were then pulled down for mass spectrometry (MS) analysis. Fourteen proteins were shown to undergo enrichment by the probe and competitive binding by its analogue, propyl hydrazine. The identified proteins were further analyzed with targeted proteomics based on parallel reaction monitoring (PRM). Using this strategy, we obtained a global portrait of protein electrophiles in bacterial cells, among which the proteins of speD and panD were previously reported to derive pyruvoyl group as an electrophilic center while lpp can retain N-terminal formyl methionine. This quantitative chemical proteomics strategy can be used to find out protein electrophiles in bacteria and holds great potential to further characterize the protein functions.

With the development of social society, sleep deprivation has become a serious and common issue. Previous studies documented that there is a correlation between sleep deprivation and oxidative stress. However, the information of sleep deprivation related ROS has rarely been obtained. Also, it has been demonstrated that sleep deprivation can induce endoplasmic reticulum (ER) stress. As such, for a better understanding of sleep deprivation as well as its related diseases, it is important to develop probes with ER-targeting ability for detecting ROS generated in this process. Herein, a novel two-photon fluorescent molecular probe, JX-1, was designed for sensing HClO in live cells and zebrafish. The investigation data showed that in addition to real-time response (about 150 s), the probe also exhibited high sensitivity and selectivity. Moreover, the probe JX-1 demonstrated two-photon fluorescence, low cytotoxicity and ER targeting ability. These prominent properties enabled the utilization of the probe for monitoring exogenous and endogenous HClO in both live cells and zebrafish. Using this useful tool, it was found that sleep deprivation can induce the generation of HClO in zebrafish., (Copyright © 2019. Published by Elsevier B.V.)

In this work, we fabricated a dual-wavelength electrochemiluminescence ratiometric biosensor based on electrochemiluminescent resonance energy transfer (ECL-RET). In this biosensor, Au nanoparticle-loaded graphitic phase carbon nitride (Au-g-C 3 N 4 ) as a donor and Au-modified dimethylthiodiaminoterephthalate (TAT) analogue (Au@TAT) as an acceptor were investigated for the first time. Besides, tetrahedron DNA probe was immobilized onto Au-g-C 3 N 4 to improve the binding efficiency of the transcription factor and ECL ratiometric changes on the basis of the ratio of ECL intensities at 595 and 460 nm, which were obtained through the formation of a sandwich structure of DNA probe-antigen-antibody. Our biosensor achieved the assay of NF-κB p50 with a detection limit of 5.8 pM as well as high stability and specificity.

Fluorinated RNA molecules, particularly 2'-F RNA, have found a wide range of applications in RNA therapeutics, RNA aptamers, and ribozymes and as 19 F NMR probes for elucidating RNA structure. Owing to the instability of 4'-F ribonucleosides, synthesis of 4'-F-modified RNA has long been a challenge. In this study, we developed a strategy for synthesizing a 4'-F-uridine ( 4'F U) phosphoramidite, and we used it to prepare 4'-F RNA successfully. In the context of an RNA strand, 4'F U, which existed in a North conformation, was reasonably stable and resembled unmodified uridine well. The 19 F NMR signal of 4'F U was sensitive to RNA secondary structure, with a chemical shift dispersion as large as 4 ppm (compared with <1 ppm for 2'F U), which makes it a valuable probe for discriminating single-stranded RNA and A-type, B-type, and mismatched duplexes. In addition, we demonstrated that because RNA-processing enzymes treated 4'F U the same as unmodified uridine, 4'F U could be used to monitor RNA structural dynamics and enzyme-mediated RNA processing. Taken together, our results indicate that 4'-F RNA represents a probe with wide utility for elucidation of RNA structure and function by means of 19 F NMR spectroscopy.

A new portable molecular imprinting polymer (MIP)-SERS nanoprobe is fabricated by a convenient electrochemical method. Single-layered MoS 2 is electrochemically reduced on a screen-printed electrode as the scaffold. Functional monomers o-phenylenediamine (oPD), template theophylline (THP), and SERS-active Au nanoparticles (AuNPs) are then one-step electropolymerized on the scaffold. The morphology of the nanoprobe is found to be a three-dimensional and porous structure. The abundant AuNPs with the size of 45~50 nm are trapped within the growing MIP instead of being confined to the surface. The thickness of MIP film is calculated to 25.1 nm. The nanoprobe displays a strong SERS effect for THP using 532 nm as excitation wavelength with a detection limit (LOD) of 0.01 nM. The SERS peak intensity at 1487 cm -1 increases linearly with the concentration of THP in the range 0.1 nM to 0.1 mM. After the template is removed, the imprint-removed nanoprobe is generated for selective binding of THP. The re-binding kinetics study implies the portable MIP-SERS nanoprobe can reach the adsorption equilibrium within 8 min. This nanoprobe exhibits low SERS interference for structural analogues theobromine (THB) and caffeine (CAF). The nanoprobe was employed to THP determination in tea drink samples, with recoveries ranging from 99.0 to 102.0% and relative standard deviations of < 5.0%. Graphical abstractSchematic representation of a portable molecular imprinting SERS nanoprobe used for selective and sensitive theophylline recognition. The nanoprobe is fabricated by one-step electropolymerized o-phenylenediamine (oPD), theophylline, and electroreduced Au nanoparticles (AuNPs) on reduced MoS 2 (rMoS 2 ) modified screen-printed electrode (SPE).

Currently, there are no non-invasive tools to accurately diagnose wound and surgical site infections before they become systemic or cause significant anatomical damage. Fluorescence and photoacoustic imaging are cost-effective imaging modalities that can be used to noninvasively diagnose bacterial infections when paired with a molecularly targeted infection imaging agent. Here, we develop a fluorescent derivative of maltotriose (Cy7-1-maltotriose), which is shown to be taken up in a variety of gram-positive and gram-negative bacterial strains in vitro. In vivo fluorescence and photoacoustic imaging studies highlight the ability of this probe to detect infection, assess infection burden, and visualize the effectiveness of antibiotic treatment in E. coli-induced myositis and a clinically relevant S. aureus wound infection murine model. In addition, we show that maltotriose is an ideal scaffold for infection imaging agents encompassing better pharmacokinetic properties and in vivo stability than other maltodextrins (e.g. maltohexose).

For most immunoblots developed with chemiluminescence or with fluorochrome-based detection systems, it is possible to remove the primary and secondary antibodies from the membrane without affecting the bound antigen. This allows you to reuse the membrane for detection of another protein antigen. The blots developed with chromogenic substrates can also be stripped of antibodies and reprobed, but the bands detected in the first round of immunoblotting will remain unaffected. Stripping and reprobing of the membrane are particularly useful when the amount of sample is limited or when it is important to accurately compare the signal between two different protein antigens in the same sample. Examples of such experiments include determining the levels of a protein antigen in a series of samples relative to the loading control and comparison of the phosphorylated form to the total levels of the protein in the sample., (© 2020 Cold Spring Harbor Laboratory Press.)

Target engagement assays are crucial for establishing the mechanism-of-action of small molecules in living systems. Integral membrane transporters can present a challenging protein class for assessing cellular engagement by small molecules. The chemical proteomic discovery of alpha-chloroacetamide (αCA) compounds that covalently modify cysteine-54 (C54) of the MPC2 subunit of the mitochondrial pyruvate carrier (MPC) is presented. This finding is used to create an alkyne-modified αCA, YY4-yne, that serves as a cellular engagement probe for MPC2 in click chemistry-enabled western blotting or global mass spectrometry-based proteomic experiments. Studies with YY4-yne revealed that UK-5099, an alpha-cyanocinnamate inhibitor of the MPC complex, engages MPC2 with remarkable selectivity in human cells. These findings support a model where UK-5099 inhibits the MPC complex by binding to C54 of MPC2 in a covalent reversible manner that can be quantified in cells using the YY4-yne probe., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In this study, a novel label- and immobilization-free RNA aptamer-modified riboswitch-based biosensor was developed by using RNA aptamer modified secondary-structural scaffolds to control the identity of the ribosomal binding sequence (RBS). In the developed sensor, the duplex RNA aptamers-modified cis-repressor sequence is introduced upstream to the RBS of the indicating gene (gfp gene), leading to formatting an RNA bubble due to the none-complementary state of the RNA aptamers in the hairpin structure of the cis-repressor sequence. Without the presence of the target molecule, the ribosome cannot identify the RBS of the indicating gene as the RBS is hidden by the introduced cis-repressor, consequently, the indicating gene in the sensor would not be expressed, demonstrating the absence of the target. On the contrary, with the presence of the target molecule, the binding of aptamer with the target would induce the enlargement of the RNA bubble, leading to the separation of the cis-repressor sequence and RBS. Hence, the indicating gene would be expressed, manifesting the existence of the target. In addition, the developed sensor can quantitatively report the target concentrations by measuring the gfp gene-encoded GFP (green fluorescent protein) concentration. The approach proposed in this study can be used to construct sensors for detecting various chemicals by introducing the corresponding aptamers, therefore, this strategy can potentially provide a new set of analytical tools in the field of analytical chemistry., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface. Bioaffinity offers a unique mechanism to bind specific target and receptor molecules from a range of non-targets. The binding efficacy depends on the specificity of the affinity ligand toward the target molecule even at low concentrations. Aptamers are fragments of genetic materials, peptides, or oligonucleotides which possess enhanced specificity in targeting desired cell surface receptor molecules. Aptamer-target binding results from several inter-molecular interactions including hydrogen bond formation, aromatic stacking of flat moieties, hydrophobic interaction, electrostatic, and van der Waals interactions. Advancements in Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has created the opportunity to artificially generate aptamers that specifically bind to desired cancer and tumor surface receptors with high affinities. This article discusses the potential application of molecular dynamics (MD) simulation to advance aptamer-mediated receptor targeting in targeted cancer therapy. MD simulation offers real-time analysis of the molecular drivers of the aptamer-receptor binding and generate optimal receptor binding conditions for theranostic applications. The article also provides an overview of different cancer types with focus on receptor biomarking and targeted treatment approaches, conventional molecular probes, and aptamers that have been explored for cancer cells targeting., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

γ-Glutamyl transpeptidase (GGT) has attracted considerable attention for its regulatory effect on glutathione metabolism in living organisms; further, its close relationship with physiological dysfunctions such as hepatitis and liver cancers has enhanced its applicability. Therefore, the accurate detection of GGT levels is particularly important for the early diagnosis of diseases. Thus, we herein report the development of a surface-enhanced Raman spectroscopic (SERS) probe, namely bis-s,s'-((s)-4,4'-thiolphenylamide-Glu) (b-(s)-TPA-Glu), that comprises of a γ-glutamyl moiety for detection of the GGT activity. In this system, detection was achieved by observing differences in the SERS spectral profiles of the b-(s)-TPA-Glu probe and its corresponding hydrolysis product that resulted from the catalytic action of GGT. This SERS probe system exhibited a high selectivity toward GGT due to a combination of its specific catalytic action and the distinctive spectroscopic fingerprint of the SERS technique. The developed SERS approach was also found to be approximately linear in the range of 0.2-200 U/L, and a limit of detection of 0.09 U/L was determined. Furthermore, the proposed SERS method was suitable for detection of the GGT activity of clinical serum samples and also for evaluation of the inhibitors of GGT. Consequently, this approach is considered to be a promising diagnostic and drug screening tool for GGT-associated diseases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Gamma peptide nucleic acids (γPNAs), i.e., single-stranded PNA strands that are modified at the γ-position with (R)-diethylene glycol, and Invader probes, i.e., DNA duplexes with +1 interstrand zipper arrangements of 2'-O-(pyren-1-yl)methyl-RNA monomers, are two types of nucleic acid mimics that are showing promise for sequence-unrestricted recognition of double-stranded (ds) DNA targets. We recently demonstrated that recognition of dsDNA targets with self-complementary regions is challenging for single-stranded high-affinity probes like γPNAs due to their proclivity for secondary structure formation, but not so for Invader probes, which are engineered to form readily denaturing duplexes irrespective of the target sequence context. In the present study, we describe an approach that mitigates these limitations and improves the dsDNA-recognition properties of γPNAs in partially self-complementary target contexts. Chimeric probes between γPNAs and individual Invader strands are shown to form metastable duplexes that (i) are energetically activated for recognition of complementary mixed-sequence dsDNA target regions, (ii) reduce γPNA dimerization, and (iii) substantially improve the fidelity of the dsDNA-recognition process. Chimeric γPNA-Invader probes are characterized with respect to thermal denaturation properties, thermodynamic parameters associated with duplex formation, UV-Vis and fluorescence trends to establish pyrene binding modes, and dsDNA-recognition properties using DNA hairpin model targets.

When live imaging is not feasible, sample fixation allows preserving the ultrastructure of biological samples for subsequent microscopy analysis. This process could be performed with various methods, each one affecting differently the biological structure of the sample. While these alterations were well-characterized using traditional microscopy, little information is available about the effects of the fixatives on the spatial molecular orientation of the biological tissue. We tackled this issue by employing rotating-polarization coherent anti-Stokes Raman scattering (RP-CARS) microscopy to study the effects of different fixatives on the myelin sub-micrometric molecular order and micrometric morphology. RP-CARS is a novel technique derived from CARS microscopy that allows probing spatial orientation of molecular bonds while maintaining the intrinsic chemical selectivity of CARS microscopy. By characterizing the effects of the fixation procedures, the present work represents a useful guide for the choice of the best fixation technique(s), in particular for polarization-resolved CARS microscopy. Finally, we show that the combination of paraformaldehyde and glutaraldehyde can be effectively employed as a fixative for RP-CARS microscopy, as long as the effects on the molecular spatial distribution, here characterized, are taken into account.

Materials with short-wave infrared (SWIR) emission are promising contrast agents for in vivo animal imaging, providing high-contrast and high-resolution images of blood vessels in deep tissues. However, SWIR emitters have not been developed as molecular labels for microscopy applications in the life sciences, which require optimized probes that are bright, stable, and small. Here, we design and synthesize semiconductor quantum dots (QDs) with SWIR emission based on Hg x Cd 1- x Se alloy cores red shifted to the SWIR by epitaxial deposition of thin Hg x Cd 1- x S shells with a small band gap. By tuning alloy composition alone, the emission can be shifted across the visible-to-SWIR (VIR) spectra while maintaining a small and equal size, allowing direct comparisons of molecular labeling performance across a broad range of wavelength. After coating with click-functional multidentate polymers, the VIR-QD spectral series has high quantum yield in the SWIR (14-33%), compact size (13 nm hydrodynamic diameter), and long-term stability in aqueous media during continuous excitation. We show that these properties enable diverse applications of SWIR molecular probes for fluorescence microscopy using conjugates of antibodies, growth factors, and nucleic acids. A broadly useful outcome is a 10-55-fold enhancement of the signal-to-background ratio at both the single-molecule level and the ensemble level in the SWIR relative to visible wavelengths, primarily due to drastically reduced autofluorescence. We anticipate that VIR-QDs with SWIR emission will enable ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluorescence.

Stressed organelles are often challenging to image with canonical organelle probes owing to their propensity to dissipate from stressed organelles. We herein report the imaging of stressed lysosomes with color-switchable glyco-probes that contain an entity of mannose-6-carboxylate or sialic acid for targeting to and long-term retention in stressed lysosomes, and a diad of fluorescein/rhodamine-X-lactam exhibiting dramatic red-to-green fluorescence shift upon pH elevation. Relative to acidotropic dyes prone to dissipate from pH-elevated lysosomes, both glyco-probes are stably trapped in lysosomes without resorting to lysosomal acidity. Importantly, these probes are red emissive in acidic lysosomes (pH 4.5-5.8), but switched to green fluorescence in lysosomes of pH 6.0-7.4, allowing dual color discrimination of lysosomal pH alterations in cell starvation. These results support the use of sugar-armed sensors to investigate stressed lysosomes in biology and disease.

Tyrosinase is a key enzyme that has long been considered as a biomarker for melanoma as it catalyzes the oxidation of tyrosine and l-DOPA in melanogenesis. Recent studies also suggest a link between tyrosinase activity and Parkinson's disease; however, the mechanism of tyrosinase-mediated melanin formation in the brain is poorly understood. To better understand this connection, more advanced tools for the detection of tyrosinase in the brain are required. Herein, we successfully designed and synthesized a tyrosinase-targeting Gd(iii)-based MR contrast agent Tyr-GBCA 1. Tyr-GBCA 1 was synthesized by linking m-hydroxyphenyl to Gd-DOTA via a self-immolative linker. Tyr-GBCA 1 shows a 21% increase in the T1 relaxation rate (R1) in the presence of tyrosinase in artificial cerebral spinal fluid. Furthermore, Tyr-GBCA 1 is unreactive to hydrogen peroxide, which is a potential interferent in oxidation-based tyrosinase sensing systems. The reaction mechanism of the probe was studied by electrospray ionization (ESI) mass spectrometry and supports the cleavage of a reaction site.

Oxidative modifications of cysteine thiols in cellular proteins are pivotal to the way signal-stimulated reactive oxygen species are sensed and elicit appropriate or sometimes pathological responses, but the dynamic and often transitory nature of these modifications offer a challenge to the investigator trying to identify such sites and the responses they elicit. A number of reagents and workflows have been developed to identify proteins undergoing oxidation and to query the timing, extent and location of such modifications, as described in this minireview. While no approach is perfect to capture all the redox information in a functioning cell, best practices described herein can enable considerable insights into the "redox world" of cells and organisms., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

A near-infrared (NIR) ratiometric fluorescent probe, NIR-Ratio-CO, was developed for rapid detection of carbon monoxide (CO) in both solution and living cells through the strategy of Pd 0 -mediated Tsuji-Trost reaction. This probe shows a rapid, highly specific and sensitive detection process for CO, accompanied by colorimetric and distinct ratiometric fluorescence changes at 655 and 592 nm with a large Stokes shift up to 195 nm. The detection limit for CO was measured to be about 61 nM by the fluorescence method. In addition, this probe was successfully applied for ratiometric imaging of both exogenous and endogenous CO in living cells, indicating that it can be used as a novel tool for ratiometric fluorescent detection of CO in living systems., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ 37-42 and N 3 -Aβ 37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ 37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ 37-42 and N 3 -Aβ 37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides., (Copyright © 2019. Published by Elsevier B.V.)

In this work, 3-Phenyl-N-[4-(10,15,20-triphenyl-porphyrin-5-yl)-phenyl]- acrylamide (TPPCA) was synthesized for the determination of metronidazole (MTZ). It was found that the type of fluorescence quenching was static quenching determined by Stern-Volmer plot and UV absorption spectroscopy, and thermodynamic related parameters were also obtained. Furthermore, the corresponding measurement conditions: the acidity of the system, the type of surfactant, the concentration of TPPCA and the sequence of reagent addition were optimized. Under the optimal experimental conditions, the linear range of MTZ was determined to be 0.01-0.20 μg mL -1 , and the limit of detection (LOD) was 0.004 μg mL -1 . Importantly, this report provides a simple, fast, and sensitive probe for the determination of MTZ in pharmaceutical practice., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Lysosome as the typical acidic organelle involved in many biological processes, the dysfunction of its pH would alter many diseases. Small-molecule fluorescent probe has been considered as vital tool for monitoring pH fluctuation in living cells. Herein, a hemicyanine based ratiometric fluorescent probe was synthesized, namely, 2,3-trimethy-3-[2-(dimethyl-amino-4-yl) vinyl]-3H-benzo[e]indole (BiDL), for rapidly detection pH under acidic conditions. BiDL exhibited ratio fluorescence emission (F 534nm /F 622nm ) characteristic with pK a 4.25. BiDL showed good linearly response in pH 3.4-4.82, indicating that the probe can be used for quantitative detection pH. The probe also displayed large Stokes shift (112 nm/201 nm) under neutral and acidic conditions, respectively, which could effectively reduce the excitation interference. BiDL had excellent cell membrane permeability, good photo-stability and low toxicity in living cells. The dual-channel confocal fluorescent microscopic ratiometric imaging application of pH in HeLa cells and lysosome were achieved successfully, indicating that BiDL has good potential for investigating lysosome-relevant pathological and physiological processes., (Copyright © 2019 Elsevier B.V. All rights reserved.)

A long guanine-rich oliogonucleotide sequence can form multiple G-quadruplex (G4) tandem individuals in a single molecule with internal G4-G4 (inG4-G4) interfaces. The interface can exist at the stacked (s-inG4-G4) or unstacked (us-inG4-G4) state, dependent of the G4 conformation and environment. Because of the vital bioactivity of the G4 interface state, there is a great demand for developing a reliable multicolor fluorescence method to identify the interface state using a fluorophore that can emit at the individual wavelength for a specific interface. Herein, we found that a porphyrin with four dihydroxyphenyl substituents (OH 2 PP) can multicolorfully recognize the s-inG4-G4 dimer interface against the us-inG4-G4 dimer one. The s-inG4-G4 dimer cause significant red shifts in the excitation and emission bands of OH 2 PP in contrast to the us-inG4-G4 dimer and G4 monomers. OH 2 PP adopts a 1:1 binding mode with the s-inG4-G4 dimer, whereas a 2:1 binding mode occurs to the us-inG4-G4 dimer. The limit of detection (LOD) for the s-inG4-G4 structure is about tens of nM level. The observed binding dependence of OH 2 PP on the linker length between the G4 individuals suggests the interface binding with the s-inG4-G4 dimer. Deformation of the porphyrin macrocycle within the s-inG4-G4 interface confinement most likely contributes to the multicolorful response with the hyperporphyrin effect. Our work demonstrates that OH 2 PP is a promising fluorophore to fluorescently recognize the G4 multimer with an ideal interface-sensitive multicolor response., (Copyright © 2019 Elsevier B.V. All rights reserved.)

A streamlined analytical workflow was developed for the analysis of infant drink samples using a miniature mass spectrometry system preceded by solid-phase microextraction (SPME) and extraction nano-electrospray ionization. Potential chemical contaminants in infant drinks (milk, lactic acid bacteria beverage, and fruit juice) were extracted and enriched using a custom-made stainless-steel SPME probe, which was coated with a thin layer of polyaniline and multi-walled carbon nanotubes nanocomposites (PANI/MWCNTs) by electrochemical deposition. The resulting porous microstructure has a larger surface area and enhanced microextraction efficiency, with enrichment factors ranging from 3055 to 8695 for exemplary analytes of antibiotics, bisphenol A, and perfluorinated compounds. The enriched analytes on the electrochemically fabricated SPME probe were simultaneously desorbed and ionized within a pulled glass capillary by extraction nano-electrospray ionization. The ionized species were subjected to instrumental analysis on a miniature ion trap mass spectrometer with adequate tandem mass spectrometry capability. The developed method was optimized and validated in terms of sensitivity, linearity, repeatability, and recovery. The integrated experimental protocol combining SPME, ambient ionization, and miniature mass spectrometry is promising for rapid, on-site screening of hazardous substances in food to ensure consumer health., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Heat shock is a potentially fatal condition characterized by high body temperature (>40 °C), which may lead to physical discomfort and dysfunctions of organ systems. Acidic pH environment in lysosomes can activate enzymes, thus facilitating the degradation of proteins in cellular metabolism. Owing to the lack of a practical research tool, it remains difficult to exploit relationship between heat shock and lysosome. Herein, a NIR lysosomal pH chemosensor (NRLH) was developed. One typical lysosome-locating group, morpholine, was incorporated into NRLH. The fluorescence intensity showed pH-dependent characteristics and responded sensitively to pH fluctuations in the pH range of 3.0-5.5. NRLH with a pKa of 4.24 displayed rapid response and high selectivity for H + among common species. We also demonstrated NRLH was capable of targeting lysosomes. Importantly, NRLH was applied in cellular imaging and the data revealed that lysosomal pH increased but never decreased during the heat shock. Therefore, NRLH may act as an effective molecular tool for exploring the mechanisms of heat-related pathology in bio-systems., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Radical-pair reactions have been suggested to be sensitive to the direction of weak magnetic fields, thereby providing a mechanism for the magnetic compass in animals. Discovering the general principles that make radical pairs particularly sensitive to the direction of weak magnetic fields will be essential for designing bioinspired compass sensors and for advancing our understanding of the spin physics behind directional effects. The reference-probe model is a conceptual model introduced as a guide to identify radical-pair parameters for optimal directional effects. Radical pairs with probe character have been extensively shown to enhance directional sensitivity to weak magnetic fields, but investigations on the role of the reference radical are lacking. Here, we evaluate whether a radical has reference character and then study its relevance for optimal directional effects. We investigate a simple radical-pair model with one axially anisotropic hyperfine interaction using both analytical and numerical calculations. Analytical calculations result in a general expression of the radical-pair reaction yield, which in turn provides useful insights into directional effects. We further investigate the relevance of the reference character to robustness against variations of earth-strength magnetic fields and find that the reference character captures robust features as well. Extending this study to radical pairs with more hyperfine interactions, we discuss the interplay between reference character and optimal and robust directional effects in such more complex radical pairs.

Endosomal escape is a key step for intracellular drug delivery of nucleic acids, but reliable and sensitive methods for its quantitation remain an unmet need. In order to rationally optimize the mRNA transfection efficiency of a library of polymeric materials, we designed a deactivated Renilla luciferase-derived molecular probe whose activity can be restored only in the cytosol. This probe can be coencapsulated with mRNA in the same delivery vehicle, thereby accurately measuring its endosomal escape efficiency. We examined a library of poly(amine- co -ester) (PACE) polymers with different end groups using this probe and observed a strong correlation between endosomal escape and transfection efficiency ( R 2 = 0.9334). In addition, we found that mRNA encapsulation efficiency and endosomal escape, but not uptake, were determinant factors for transfection efficiency. The polymers with high endosomal escape/transfection efficiency in vitro also showed good transfection efficiency in vivo , and mRNA expression was primarily observed in spleens after intravenous delivery. Together, our study suggests that the luciferase probe can be used as an effective tool to quantitate endosomal escape, which is essential for rational optimization of intracellular drug delivery systems.

Intrinsically disordered proteins (IDPs) or regions of intrinsic disorder in otherwise folded proteins (IDRs) play important roles in many different biological processes, including formation of biological condensates via liquid-liquid phase separation. NMR spectroscopy is a powerful tool for obtaining site-specific structural and dynamical information on IDPs/IDRs, and recent efforts have focused on the development of experiments for atomic-resolution studies of these molecules. These include triple-resonance experiments that are based on 13 CO-direct detection of magnetization, exploiting increased sensitivity of cryogenically cooled probes. In order to evaluate the different classes of experiment for studies of IDRs or IDPs in both dilute and phase-separated environments, in particular at neutral and higher pHs where many of these proteins phase separate, we compared 13 CO-detect versus 1 H α -detect experiments, showing that significant sensitivity gains are achieved via proton detection under the conditions of our experiments. A suite of 1 H α -detect experiments was subsequently developed for studies of IDPs/IDRs and applied to the dilute phase of a 103-residue disordered region of CAPRIN1 that phase separates at neutral pH. Residue-specific chemical shifts derived from our study enable the accurate prediction of the importance of the N-terminal Arg-containing region of this construct for promoting phase separation relative to other Arg-rich stretches of sequence, subsequently confirmed by mutagenesis. Our study emphasizes that the sequence positions of key residues can be a critical factor in controlling phase separation and highlights the unique role of NMR in establishing the relations between amino acid sequence and phase-separation propensity.

This review discusses the advantages of using luminescent d 6 -transition-metal complexes as cell probes for optical microscopy. In particular it focusses on the Thomas group's use of specific complexes as "building blocks" toward the construction of biomolecular binding substrates, with DNA being a particular target. Using this approach, a range of new imaging probes for conventional optical microscopy, nanoscopy and transmission electron microscopy have been identified. Through selection of specific metal centres and by substitution of coordinated ligands we illustrate how new chemotherapeutics, photo-therapeutics, and theranostics have been identified and developed from the original architectures.

Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disease arising from mutations in the dystrophin gene. Upregulation of utrophin to compensate for the missing dystrophin offers a potential therapy independent of patient genotype. The first-in-class utrophin modulator ezutromid/SMT C1100 was developed from a phenotypic screen through to a Phase 2 clinical trial. Promising efficacy and evidence of target engagement was observed in DMD patients after 24 weeks of treatment, however trial endpoints were not met after 48 weeks. The objective of this study was to understand the mechanism of action of ezutromid which could explain the lack of sustained efficacy and help development of new generations of utrophin modulators. Using chemical proteomics and phenotypic profiling we show that the aryl hydrocarbon receptor (AhR) is a target of ezutromid. Several lines of evidence demonstrate that ezutromid binds AhR with an apparent K D of 50 nm and behaves as an AhR antagonist. Furthermore, other reported AhR antagonists also upregulate utrophin, showing that this pathway, which is currently being explored in other clinical applications including oncology and rheumatoid arthritis, could also be exploited in future DMD therapies., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

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., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)