Real-time detection of Cu(Ⅱ) with PEDOT:PSS based organic electrochemical transistors

Copper is an essential element in the environment and the human body,but at the same time,exposure to high concentrations of Cu~(2+) ions will potentially lead to acute toxicity and various neurodegenerative diseases.Thus,it is of great significance for the development of highly sensitive and selective strategies for the detection of Cu~(2+) ions.Here,we report a highly efficient poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid)(PEDOT:PSS) based organic electrochemical transistor(OECT)sensor,for real-time Cu~(2+) ions detection.The detection limit of the OECT device is as low as 100 nM,far beyond the sensitivity required for practical uses.The detection mechanism may base on the chemical reactivity of Cu~(2+) ions oxiding the PEDOT:PSS in solution both in absence and presence of the base potential.The OECT devices also exhibit excellent selective response to Cu~(2+)ions rather than other metal ions.Finally,we also demonstrate the determination of Cu~(2+) ions in tap water with the OECT Cu~(2+)sensor.Considering the high sensitivity and selectivity,as well as the real-time and low cost features of our Cu~(2+) OECT sensor,it is ideal for portable and disposable applications for environment monitoring and public health.     

Cell surface-anchored fluorescent aptamer sensor enables imaging of chemical transmitter dynamics

A fluorescent aptamer sensor was applied to the analysis of extracellular chemical transmitter dynamics. We utilized a tocopherol-labeled aptamer, which allowed the direct anchoring of the fluorescent aptamer on the cell surface while retaining its performance as a fluorescent sensor. The fast-responsive fluorescent DNA aptamer sensor, which targets adenine compounds, was anchored on the surface of brain astrocytes. Fluorescence imaging of the aptamer-anchored astrocytes enabled the real-time monitoring of release of adenine compounds as a gliotransmitter, which was synchronized with calcium wave propagation in neighboring cells.     

Functionalized graphene-based biomimetic microsensor interfacing with living cells to sensitively monitor nitric oxide release

It is a great challenge to develop electrochemical sensors with superior sensitivity that concurrently possess high biocompatibility for monitoring at the single cell level. Herein we report a novel and reusable biomimetic micro-electrochemical sensor array with nitric oxide (NO) sensing-interface based on metalloporphyrin and 3-aminophenylboronic acid (APBA) co-functionalized reduced graphene oxide (rGO). The assembling of high specificity catalytic but semi-conductive metalloporphyrin with high electric conductive rGO confers the sensor with sub-nanomolar sensitivity. Further coupling with the small cell-adhesive molecule APBA obviously enhances the cytocompatibility of the microsensor without diminishing the sensitivity, while the reversible reactivity between APBA and cell membrane carbohydrates allows practical reusability. The microsensor was successfully used to sensitively monitor, in real-time, the release of NO molecules from human endothelial cells being cultured directly on the sensor. This demonstrates its potential application in the detection of NO with very low bioactive concentrations for the better understanding of its physiological function and for medical tracking of patient states.     

Development of a volatile amine sensor for the monitoring of fish spoilage

A sensor with potential for the development of a “chemical barcode” for real-time monitoring of fish freshness is described. This on-package sensor contains a pH sensitive dye, bromocresol green, that responds through visible colour change to basic volatile spoilage compounds, such as trimethylamine (TMA), ammonia (NH₃) and dimethylamine (DMA) collectively known as Total Volatile Basic Nitrogen (TVB-N). The sensor characteristics were studied as well as its response with standard ammonia gas. Trials on cod and under-utilised species have verified that the sensor response correlates with bacterial growth patterns in fish samples thus enabling the “real-time” monitoring of spoilage in various fish species. The sensor response can be interrogated with a simple, inexpensive reflectance colorimeter that we have developed based on two light emitting diodes (LEDs) and a photodetector.     

A chemically consistent graph architecture for massive reaction networks applied to solid-electrolyte interphase formation

Modeling reactivity with chemical reaction networks could yield fundamental mechanistic understanding that would expedite the development of processes and technologies for energy storage, medicine, catalysis, and more. Thus far, reaction networks have been limited in size by chemically inconsistent graph representations of multi-reactant reactions (e.g. A + B → C) that cannot enforce stoichiometric constraints, precluding the use of optimized shortest-path algorithms. Here, we report a chemically consistent graph architecture that overcomes these limitations using a novel multi-reactant representation and iterative cost-solving procedure. Our approach enables the identification of all low-cost pathways to desired products in massive reaction networks containing reactions of any stoichiometry, allowing for the investigation of vastly more complex systems than previously possible. Leveraging our architecture, we construct the first ever electrochemical reaction network from first-principles thermodynamic calculations to describe the formation of the Li-ion solid electrolyte interphase (SEI), which is critical for passivation of the negative electrode. Using this network comprised of nearly 6000 species and 4.5 million reactions, we interrogate the formation of a key SEI component, lithium ethylene dicarbonate. We automatically identify previously proposed mechanisms as well as multiple novel pathways containing counter-intuitive reactions that have not, to our knowledge, been reported in the literature. We envision that our framework and data-driven methodology will facilitate efforts to engineer the composition-related properties of the SEI – or of any complex chemical process – through selective control of reactivity.

A chemically consistent graph architecture enables autonomous identification of novel solid-electrolyte interphase formation pathways from a massive reaction network.     

Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups

Non-specific chemical modification of protein thiol groups continues to be a significant source of false positive hits from high-throughput screening campaigns and can even plague certain protein targets and chemical series well into lead optimization. While experimental tools exist to assess the risk and promiscuity associated with the chemical reactivity of existing compounds, computational tools are desired that can reliably identify substructures that are associated with chemical reactivity to aid in triage of HTS hit lists, external compound purchases, and library design. Here we describe a Bayesian classification model derived from more than 8,800 compounds that have been experimentally assessed for their potential to covalently modify protein targets. The resulting model can be implemented in the large-scale assessment of compound libraries for purchase or design. In addition, the individual substructures identified as highly reactive in the model can be used as look-up tables to guide chemists during hit-to-lead and lead optimization campaigns.     

Effects of solute-matrix interaction on monitoring the conformational changes of immobilized proteins by surface plasmon resonance sensor

A real-time and labeling-free surface plasmon resonance (SPR) sensor was used to monitor the conformational changes of immobilized globule proteins (RNase A and lysozyme) in chemical unfolding and refolding. The effects of chemical denaturants on the protein structures were investigated. The methodology in protein conformational study on the solid surface is refined through the theoretic calculations and the conformational information of native/denatured proteins in solution. Additionally, our observation illustrates that the ambient buffer solution is merit to influence the refractive index of immobilized protein films and directly be observed from the SPR resonance angle shifts.     

可视交叉传感阵列对蛋白质及其热变性过程的快速识别

以卟啉及其衍生物和特异性染料为敏感化学元件, 基于交叉响应原理构建了识别蛋白质的可视6×6阵列. 该阵列以颜色差谱图显示其与蛋白质作用呈现的特异性光谱反应, 采用聚类分析、 主成分分析和欧氏距离对图谱进行了分析. 结果表明, 该阵列可以鉴别模式蛋白牛血清白蛋白(BSA)、 牛血红蛋白(BHb)和卵清白蛋白(Ova)及其混合物, 且有望实现定量分析. 此外, 阵列的高敏感性使其不仅能识别天然蛋白质和不同变性程度的蛋白质, 还能对其热变性过程进行可视化实时监控. 该阵列产生的特殊颜色变化与蛋白质的空间构型、 微环境pH值的差异及溶解度有关. 因此, 该方法不仅能实现对蛋白质的快速识别, 为蛋白质热变性机理的研究提供新途径, 而且在临床医学和食品安全等的实时快速检测方面有潜在的应用价值.     

Ligand field effect at oxide-metal interface on the chemical reactivity of ultrathin oxide film surface

Ultrathin oxide film is currently one of the paramount candidates for a heterogeneous catalyst because it provides an additional dimension, i.e., film thickness, to control chemical reactivity. Here, we demonstrate that the chemical reactivity of ultrathin MgO film grown on Ag(100) substrate for the dissociation of individual water molecules can be systematically controlled by interface dopants over the film thickness. Density functional theory calculations revealed that adhesion at the oxide-metal interface can be addressed by the ligand field effect and is linearly correlated with the chemical reactivity of the oxide film. In addition, our results indicate that the concentration of dopant at the interface can be controlled by tuning the drawing effect of oxide film. Our study provides not only profound insight into chemical reactivity control of ultrathin oxide film supported by a metal substrate but also an impetus for investigating ultrathin oxide films for a wider range of applications.     

A conceptual framework for predicting the toxicity of reactive chemicals: modeling soft electrophilicity

Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point for modeling reactive toxicity is the applicability of the general rules of organic chemical reactions and the association of these reactions to cellular targets of importance in toxicology. The identification of plausible "molecular initiating events" based on covalent reactions with nucleophiles in proteins and DNA provides the unifying concept for a framework for reactive toxicity. This paper outlines the proposed framework for reactive toxicity. Empirical measures of the chemical reactivity of xenobiotics with a model nucleophile (thiol) are used to simulate the relative rates at which a reactive chemical is likely to bind irreversibly to cellular targets. These measures of intrinsic reactivity serve as correlates to a variety of toxic effects; what's more they appear to be more appropriate endpoints for QSAR modeling than the toxicity endpoints themselves.     

Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation

The chemical synthesis of the 184‐residue ferric heme‐binding protein nitrophorin 4 was accomplished by sequential couplings of five unprotected peptide segments using α‐ketoacid‐hydroxylamine (KAHA) ligation reactions. The fully assembled protein was folded to its native structure and coordinated to the ferric heme b cofactor. The synthetic holoprotein, despite four homoserine residues at the ligation sites, showed identical properties to the wild‐type protein in nitric oxide binding and nitrite dismutase reactivity. This work establishes the KAHA ligation as a valuable and viable approach for the chemical synthesis of proteins up to 20 kDa and demonstrates that it is well‐suited for the preparation of hydrophobic protein targets.     

An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids

Whereas spectroscopic and chromatographic techniques for the detection of small organic molecules have achieved impressive results, these methods are generally slow and cumbersome, and thus the development of a general means for the real-time, electronic detection of such targets remains a compelling goal. Here we demonstrate a potentially general, label-free electronic method for the detection of small-molecule targets by building a rapid, reagentless biosensor for the detection of cocaine. The sensor, based on the electrochemical interrogation of a structure-switching aptamer, specifically detects micromolar cocaine in seconds. Because signal generation is based on binding-induced folding, the sensor is highly selective and works directly in blood serum and in the presence of commonly employed interferents and cutting agents, and because all of the sensor components are covalently attached to the electrode surface, the sensor is also reusable: we achieve >99% signal regeneration upon a brief, room temperature aqueous wash. Given recent advances in the generation of highly specific aptamers, this detection platform may be readily adapted for the detection of other small molecules of a wide range of clinically and environmentally relevant small molecules.     

Designing Novel Compounds for the Treatment and Management of RET-Positive Non-Small Cell Lung Cancer—Fragment Based Drug Design Strategy

Rearranged during transfection (RET) is an oncogenic driver receptor that is overexpressed in several cancer types, including non-small cell lung cancer. To date, only multiple kinase inhibitors are widely used to treat RET-positive cancer patients. These inhibitors exhibit high toxicity, less efficacy, and specificity against RET. The development of drug-resistant mutations in RET protein further deteriorates this situation. Hence, in the present study, we aimed to design novel drug-like compounds using a fragment-based drug designing strategy to overcome these issues. About 18 known inhibitors from diverse chemical classes were fragmented and bred to form novel compounds against RET proteins. The inhibitory activity of the resultant 115 hybrid molecules was evaluated using molecular docking and RF-Score analysis. The binding free energy and chemical reactivity of the compounds were computed using MM-GBSA and density functional theory analysis, respectively. The results from our study revealed that the developed hybrid molecules except for LF21 and LF27 showed higher reactivity and stability than Pralsetinib. Ultimately, the process resulted in three hybrid molecules namely LF1, LF2, and LF88 having potent inhibitory activity against RET proteins. The scrutinized molecules were then subjected to molecular dynamics simulation for 200 ns and MM-PBSA analysis to eliminate a false positive design. The results from our analysis hypothesized that the designed compounds exhibited significant inhibitory activity against multiple RET variants. Thus, these could be considered as potential leads for further experimental studies.     

Pim Kinase Inhibitors Evaluated with a Single‐Molecule Engineered Nanopore Sensor

Protein kinases are critical therapeutic targets. Pim kinases are implicated in several leukaemias and cancers. Here, we exploit a protein nanopore sensor for Pim kinases that bears a pseudosubstrate peptide attached by an enhanced engineering approach. Analyte binding to the sensor peptide is measured through observation of the modulation of ionic current through a single nanopore. We observed synergistic binding of MgATP and kinase to the sensor, which was used to develop a superior method to evaluate Pim kinase inhibitors featuring label‐free determination of inhibition constants. The procedure circumvents many sources of bias or false‐positives inherent in current assays. For example, we identified a potent inhibitor missed by differential scanning fluorimetry. The approach is also amenable to implementation on high throughput chips.     

4-Arylation of 3-alkoxypyrazoles

Following the study of the alkoxypyrazoles nitrogen's reactivity toward arylation or alkylation reactions, we report here our results on the introduction of various aryl groups on carbon 4 position of 3-alkoxypyrazoles. This was achieved from the corresponding 4-halogeno derivatives via a Suzuki-Miyaura aryl-aryl coupling reaction. The unexpected difficulties (lack of reactivity or unwanted halogen reduction) encountered in the C-4 arylation of NH-free 4-halogenopyrazoles led us to design solutions to this recurrent problem. The cleavage of the 3-alkoxy group was also investigated using hydrogen bromide in acetic acid or boron tribromide in dichloromethane. This led, in one case, to the observation of a remarkable neighboring group-assisted electrophilic aryl boronylation. This second part of our work paves the way to the synthesis of many original chemical libraries featuring 3-alkoxy 1,4-diaryl pyrazoles as well as the corresponding 1,4-diaryl pyrazol-3-ones.     

The challenge of long-term stability for nucleic acid-based electrochemical sensors

Nucleic acid-based electrochemical sensors are a versatile technology enabling affinity-based detection of a great variety of molecular targets, regardless of inherent electrochemical activity or enzymatic reactivity. Additionally, their modular interface and ease of fabrication enable rapid prototyping and sensor development. However, the technology has inhibiting limitations in terms of long-term stability that have precluded translation into clinically valuable platforms like continuous molecular monitors. In this opinion, we discuss published methods to address various aspects of sensor stability, including thiol-based monolayers and anti-biofouling capabilities. We hope the highlighted works will motivate the field to develop innovative strategies for extending the long-term operational life of nucleic acid-based electrochemical sensors.     

Selenium and Selenocysteine in Protein Chemistry

Selenocysteine, the selenium‐containing analogue of cysteine, is the twenty‐first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.     

A conceptual framework for predicting the toxicity of reactive chemicals: modeling soft electrophilicity

Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point for modeling reactive toxicity is the applicability of the general rules of organic chemical reactions and the association of these reactions to cellular targets of importance in toxicology. The identification of plausible “molecular initiating events” based on covalent reactions with nucleophiles in proteins and DNA provides the unifying concept for a framework for reactive toxicity. This paper outlines the proposed framework for reactive toxicity. Empirical measures of the chemical reactivity of xenobiotics with a model nucleophile (thiol) are used to simulate the relative rates at which a reactive chemical is likely to bind irreversibly to cellular targets. These measures of intrinsic reactivity serve as correlates to a variety of toxic effects; what's more they appear to be more appropriate endpoints for QSAR modeling than the toxicity endpoints themselves.     

活性导向的化学探针在氨基酸反应活性表征中的应用进展

原创药物的研制得益于蛋白质新靶标的发现,而新靶标的发现依赖于高可信度、高通量的药物-蛋白质相互作用分析方法。蛋白质作为生命功能的执行者,其表达量、空间定位与结构差异直接影响药效的发挥。目前,超过85%的蛋白质尚被认为是无法成药的,主要原因是缺少药物分子靶向的空腔以及相应的反应活性位点。因此,基于蛋白质组学层次实现对氨基酸反应活性位点的表征成为原创共价靶向药物设计的关键,也是克服难以成药靶标蛋白问题的关键。近年来,质谱技术的飞速发展极大地推动了基于蛋白质组学技术的药物-靶蛋白相互作用研究。其中基于活性的蛋白质组分析(ABPP)策略是利用活性位点导向的化学探针分子在复杂样品中实现功能状态酶和药物靶标等蛋白质的检测。基于化学探针的开发和质谱定量技术的发展,ABPP技术在氨基酸反应活性表征研究中展现出重要的应用潜力,将助力于药物新靶标的发现和药物先导化合物的开发。ABPP策略主要基于蛋白质的活性特征进行富集,活性探针作为ABPP策略的核心,近年来取得了飞速进展。该文回顾了ABPP策略的发展历程,重点介绍基于广谱活性探针的ABPP技术在多种氨基酸反应活性筛选领域的研究进展,并对其在药物靶点发现中...