Analytical biochemistry最新文献

{"title":"A biocompatible fluorescent probe for endogenous hydrogen sulfide detection and imaging","authors":"Xitian Zhu ,&nbsp;Huijia Chen ,&nbsp;Fang Ke","doi":"10.1016/j.ab.2024.115718","DOIUrl":"10.1016/j.ab.2024.115718","url":null,"abstract":"<div><div>Hydrogen sulfide (H₂S) acts as a messenger molecule and can mediate a variety of physiological functions. Conventional methods are seldom used to detect endogenous H₂S and present some difficulties in selective and accurate detection. Reaction-based recognition of endogenous H₂S by organic small molecule probes with good specificity and biocompatibility. To address this challenge, we developed a novel H₂S fluorescent probe 4-(2-(6-hydroxy-2-naphthyl) ethyl)-1-methylpyridinium (<strong>DSNP</strong>) that triggers a thiolysis reaction through a strong electron withdrawing group, releasing a fluorescent molecule. The simple probe <strong>DSNP</strong> not only have good selectivity, large Stokes shifts and biocompatibility, but also demonstrated a detection limit as low as 28.4 nM and reaction times as quick as 30 min. Moreover, it has been successfully applied to imaging intracellular H₂S in myeloma cells and zebrafish. This study opens new insights to help push this probe forward for its applicability for detailed H₂S localization studies in osteosarcoma.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115718"},"PeriodicalIF":2.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel colorimetric assay for the detection of urinary N1, N12-diacetylspermine, a known biomarker for colorectal cancer","authors":"Dipanjan Bhattacharyya ,&nbsp;Marcia A. LeVatte ,&nbsp;Upasana Singh ,&nbsp;Fleur Issac ,&nbsp;Mahmoud Karim ,&nbsp;Saira Ali ,&nbsp;August Sieben ,&nbsp;Suyenna Huang ,&nbsp;David S. Wishart","doi":"10.1016/j.ab.2024.115717","DOIUrl":"10.1016/j.ab.2024.115717","url":null,"abstract":"<div><div>Urinary N¹, N¹²-diacetylspermine (DAS) is a known biomarker for colorectal cancer (CRC). However, DAS levels in both healthy and CRC patients’ urine samples are extremely low and often challenging to quantify. Complex and expensive methods do exist to detect DAS in urine, but simpler, less expensive methods to detect DAS are needed, especially in low resource settings. Here we describe a highly efficient, fast, precise, and inexpensive colorimetric assay to detect low levels of DAS in human urine samples. We used recombinant diacetylspermine oxidase (rDAS Ox), expressed and extracted from <em>E. coli</em>, to oxidize DAS, producing three products including hydrogen peroxide (H₂O₂). The level of DAS present, which correlates with H₂O₂ levels, was measured using horseradish peroxidase (HRP), which together with H₂O₂, oxidized Amplex™ Red to produce the pink-colored resorufin. The concentration of resorufin is directly proportional to H₂O₂ (and DAS) levels. As urine contains metabolites which interfere with these oxidation reactions, we developed a simple two column-based protocol using ion exchange resins to remove these compounds and concentrate the DAS. With this novel cleaning and concentrating method, DAS was concentrated 15 times (confirmed by nuclear magnetic resonance (NMR) spectroscopy) and &lt;1 μM DAS could be detected. Correlation graphs of urine samples spiked with known DAS concentrations versus assay-determined DAS concentrations had high coefficients of determination (R²) for 0–10 μM DAS (0.94) and for 0–1 μM DAS (0.91), clearly demonstrating the excellent performance of the two-column protocol with the rDAS Ox reaction mixture. To the best of our knowledge, this is first reported colorimetric enzymatic assay that quantitates DAS in urine.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115717"},"PeriodicalIF":2.6,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assays to measure small molecule Hsp70 agonist activity in vitro and in vivo","authors":"Olivia Shapiro ,&nbsp;Clara Woods ,&nbsp;Amanda M. Gleixner ,&nbsp;Sara Sannino ,&nbsp;Marilyn Ngo ,&nbsp;Michael D. McDaniels ,&nbsp;Peter Wipf ,&nbsp;Neil A. Hukriede ,&nbsp;Christopher J. Donnelly ,&nbsp;Jeffrey L. Brodsky","doi":"10.1016/j.ab.2024.115712","DOIUrl":"10.1016/j.ab.2024.115712","url":null,"abstract":"<div><div>Hsp70 prevents protein aggregation and is cytoprotective, but sustained Hsp70 overexpression is problematic. Therefore, we characterized small molecule agonists that augment Hsp70 activity. Because cumbersome assays were required to assay agonists, we developed cell-based and <em>in vivo</em> assays in which disease-associated consequences of Hsp70 activation can be quantified. One assay uses an optogenetic system in which the formation of TDP-43 inclusions can be controlled, and the second assay employs a zebrafish model for acute kidney injury (AKI). These complementary assays will facilitate future work to identify new Hsp70 agonists as well as optimized agonist derivatives.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115712"},"PeriodicalIF":2.6,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an assay to quantify tranexamic acid levels in plasma","authors":"Paul Y. Kim ,&nbsp;Michelle Vong ,&nbsp;Dani Lee ,&nbsp;Chengliang Wu","doi":"10.1016/j.ab.2024.115714","DOIUrl":"10.1016/j.ab.2024.115714","url":null,"abstract":"<div><div>Dysregulations of blood clot breakdown (fibrinolysis) during vascular trauma can lead to excessive blood loss. Tranexamic acid (TXA) is an inhibitor of fibrinolysis that works by blocking the interaction between plasminogen and fibrin degradation products (FDPs) – a key step in fibrinolysis. Despite the widespread usage, there are no tests available in a clinical setting to monitor TXA levels. We developed a fluorescence resonance energy transfer (FRET)-based assay to quantify TXA concentrations in plasma by using 1) fluorescently labeled plasminogen, and 2) FDPs labeled with a fluorescence quencher. Once plasminogen binds the FDPs, the fluorescent signal is quenched. TXA causes plasminogen to dissociate from the FDPs, thus increasing fluorescence signal in a dose-dependent manner. The dose response was sensitive between 1 and 100 μM (0.16 and 15.7 mg/L). The intraassay and interassay variabilities were determined to be 5.7 % and 3.0 %, respectively. Limit of detection was estimated to be 0.28 μM (0.044 mg/L). When tested for measuring known levels of TXA added to plasma samples, the ratio between measured and expected TXA concentration was 1.0151. Our study demonstrates a novel assay that can rapidly quantify TXA concentrations in plasma samples, thus demonstrating its potential as an in-hospital tool.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115714"},"PeriodicalIF":2.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Specialized greenness sustainability tools for evaluation of the spectrophotometric methodologies greenness: Spectral signal manipulation for resolving the interfering telmisartan and metoprolol succinate spectra in their bulk and pharmaceutical formulation","authors":"Michael Gamal Fawzy ,&nbsp;Soad S. Abd El-Hay ,&nbsp;Alaa Ahmed Mostafa ,&nbsp;Youstina Mekhail Metias","doi":"10.1016/j.ab.2024.115711","DOIUrl":"10.1016/j.ab.2024.115711","url":null,"abstract":"<div><div>Hypertension is a leading cause of cardiovascular mortality, often accompanied by complications such as arrhythmia and stroke. This silent killer requires a multifaceted pharmacological approach for effective management. This article presents new, environmentally friendly spectrophotometric methods for simultaneous quantification of telmisartan (TER) and metoprolol succinate (MTR) in laboratory prepared mixtures and pharmaceutical formulations. The suggested methodologies include the following: area under the curve method (AUC) utilizing area at specific wavelength ranges 228–233 nm (<em>λ</em>₁ – <em>λ</em>₂) and 240–245 nm (<em>λ</em>₃ – <em>λ</em>₄) for each analyte and Fourier self-deconvolution method (FD) depending on built-in function to address spectral interferences. In addition, the induced dual wavelength method (IDWL) employing equality factors to obtain absorbance differences at designated wavelengths, ratio difference method (RD) utilizing divisor-based ratio spectra where the utilized divisors were TER 40 μg/mL and MTR 90 μg/mL, and ratio derivative method (RDV) generating spectra through first derivative application that was measured at 266 nm and 246 nm for TER and MTR, respectively. These methods offer green alternatives for the accurate and precise determination of TER and MTR with exceptional linearity of 3–45, and 15–200 μg/mL for TER and MTR, respectively. Furthermore, the methods showed a coefficient of determination exceeding 0.9995 and good detection and quantification levels. A comprehensive greenness assessment, employing five distinct evaluation tools, confirmed the reduced environmental impact of the proposed methods in terms of waste generation, chemical consumption, and instrument safety. Successful analysis of pharmaceutical formulations and laboratory prepared mixtures containing different TER and MTR ratios confirmed the validity of the proposed methods. Standard addition studies further supported these findings, and the statistical results were comparable to those obtained using a reference method.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115711"},"PeriodicalIF":2.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of a high throughput screening platform to identify inhibitors of asymmetric diadenosine polyphosphatases","authors":"David N. Frick ,&nbsp;Mujidat Shittu ,&nbsp;Chase R. Bock ,&nbsp;Zoe P. Wardle ,&nbsp;Abdullah A. Rauf ,&nbsp;Julian N. Ramos ,&nbsp;Joshua G. Thomson ,&nbsp;Daniel J. Sheibley ,&nbsp;Suzanne F. O'Handley","doi":"10.1016/j.ab.2024.115713","DOIUrl":"10.1016/j.ab.2024.115713","url":null,"abstract":"<div><div>When stressed, cells synthesize di-adenosine polyphosphates (Ap_nA), and cellular organisms also express proteins that degrade these compounds to release ATP. Most of these proteins are members of the nudix hydrolase superfamily, and several are involved in bacterial pathogenesis, neurodevelopment, and cancer. The goal of this project is to assist in the discovery of inhibitors of these enzymes that could be used to study Ap_nA function and the cellular role of these nudix enzymes. Because these enzymes cleave Ap₄A and Ap₅A to produce ATP, two standard ATP detection techniques were optimized and compared here for their suitability for high throughput screening. In the first assay, cleavage is monitored by coupling to a reaction catalyzed by firefly luciferase. In the second assay, cleavage is detected by coupling to hexokinase, glucose 6-phosphate dehydrogenase, and diaphorase. Although the former assay was more sensitive, the latter was more reproducible, linear, and suitable for screening and kinetic analyses. The assays were used to characterize the kinetics of reactions catalyzed by various nudix enzymes isolated from <em>E. coli</em>, humans, and <em>Mycobacterium tuberculosis</em>, the bacterium that causes tuberculosis<em>.</em> Results reveal subtle differences between the proteins that might be exploited to identify specific small molecule inhibitors.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115713"},"PeriodicalIF":2.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simple and enzyme-free method for sensitive p53 analysis based on DNAzyme-mediated signal amplification.","authors":"Jia Deng, Ye Yuan, Min Zou, Xudong Liu, Xianxian Zhao, Hongli Liu","doi":"10.1016/j.ab.2024.115716","DOIUrl":"https://doi.org/10.1016/j.ab.2024.115716","url":null,"abstract":"<p><p>There is an urgent demand for a simple yet extremely accurate biosensor to analyze tumorigenesis. Herein, we present a novel fluorescent and enzyme-free approach for detecting p53 gene cascading proximity ligation-mediated catalytic hairpin assembly and DNAzyme-assisted signal reaction. When the target p53 gene is present, the interaction between p53 and L1 and L2 chains initiates catalytic hairpin assembly and subsequently exposes DNAzyme in the P3 probe. The exposed DNAzyme binds with the loop region of the P4 probe and generates a nicking site, resulting in the release of a significant amount of ATMND that is conjugated in the stem section of P4. This leads to an amplified fluorescence response, which serves as a fluorescence signal for the detection of the p53 gene. This method allows for the accurate and sensitive identification of the p53 gene, exhibiting a linear reaction range of 1 fM to 1 nM, with a limit of detection as low as 0.23 fM. Furthermore, this fluorescent method has been utilized for the examination of clinical samples with a favorable recovery rate. Crucially, this versatile platform may be expanded to analyze different targets by changing the corresponding recognition unit, showing great potential for point-of-care testing in tumorigenesis analysis.</p>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":" ","pages":"115716"},"PeriodicalIF":2.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iBhb-Lys: Identify lysine β-hydroxybutyrylation sites using autoencoder feature representation and fuzzy SVM algorithm","authors":"Zhe Ju,&nbsp;Qing-Bao Zhang","doi":"10.1016/j.ab.2024.115715","DOIUrl":"10.1016/j.ab.2024.115715","url":null,"abstract":"<div><div>Lysine β-hydroxybutyrylation (Kbhb) is newly discovered β-hydroxybutyrylate-derived histone modification which has been associated with the pathogenesis of many human diseases. To further elucidate the biological significance and molecular mechanism of Kbhb, it is necessary to accurately identify the Kbhb sites from protein sequences. In this study, a novel computational model named iBhb-Lys is developed for the identification of Kbhb sites. Four types of features are combined to encode each Kbhb site as a 3266-dimensional feature vector. And the autoencoder network is used to reduce the dimensionality of feature space, due to the high dimensionality of the combined features. In addition, to effectively reduce the influence of noise and outlier on classification, a new fuzzy support vector machine algorithm is proposed by incorporating the density around the sample into the fuzzy membership function. As illustrated by independent test, the AUC value of iBhb-Lys has increased by 2.22 % compared to the existing predictor KbhbXG. Feature analysis shows that some amino acid composition features, such as the occurrence frequency of leucine and histidine residues around Kbhb sites, contribute profoundly to the identification of Kbhb sites. The conclusions drawn in this study may provide useful reference for studying the molecular mechanism of Kbhb.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115715"},"PeriodicalIF":2.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alg-MFDL: A multi-feature deep learning framework for allergenic proteins prediction","authors":"Xiang Hu ,&nbsp;Jingyi Li ,&nbsp;Taigang Liu","doi":"10.1016/j.ab.2024.115701","DOIUrl":"10.1016/j.ab.2024.115701","url":null,"abstract":"<div><div>The escalating global incidence of allergy patients illustrates the growing impact of allergic issues on global health. Allergens are small molecule antigens that trigger allergic reactions. A widely recognized strategy for allergy prevention involves identifying allergens and avoiding re-exposure. However, the laboratory methods to identify allergenic proteins are often time-consuming and resource-intensive. There is a crucial need to establish efficient and reliable computational approaches for the identification of allergenic proteins. In this study, we developed a novel allergenic proteins predictor named Alg-MFDL, which integrates pre-trained protein language models (PLMs) and traditional handcrafted features to achieve a more complete protein representation. First, we compared the performance of eight pre-trained PLMs from ProtTrans and ESM-2 and selected the best-performing one from each of the two groups. In addition, we evaluated the performance of three handcrafted features and different combinations of them to select the optimal feature or feature combination. Then, these three protein representations were fused and used as inputs to train the convolutional neural network (CNN). Finally, the independent validation was performed on benchmark datasets to evaluate the performance of Alg-MFDL. As a result, Alg-MFDL achieved an accuracy of 0.973, a precision of 0.996, a sensitivity of 0.951, and an F1 value of 0.973, outperforming the most of current state-of-the-art (SOTA) methods across all key metrics. We anticipated that the proposed model could be considered a useful tool for predicting allergen proteins.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115701"},"PeriodicalIF":2.6,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research progress on Drug-Target Interactions in the last five years","authors":"Yun Zuo,&nbsp;Xubin Wu,&nbsp;Fei Ge,&nbsp;Hongjin Yan,&nbsp;Sirui Fei,&nbsp;Jingwen Liang,&nbsp;Zhaohong Deng","doi":"10.1016/j.ab.2024.115691","DOIUrl":"10.1016/j.ab.2024.115691","url":null,"abstract":"<div><div>The identification of Drug-Target Interaction (DTI) is an important step in drug discovery and drug repositioning, and has high application value in multiple fields such as drug discovery, drug repositioning, and repurposing. However, the high cost of experimental validation limits its identification. In contrast, computation-based approaches are both economical and efficient. This review first synthesizes existing chemical genomic approaches, provides a comprehensive summary of prevalent databases for predicting DTIs, and categorizes the feature encodings from recent years. This is followed by an overview and brief description of the methods currently in use for predicting DTIs. The strengths and weaknesses of newly proposed prediction methods in the last five years (2020–2024), including those based on network representation learning and graph neural networks, are then discussed in detail, evaluating the performance of the different methods on a wide range of datasets. Finally, this review explores potential directions for future DTI research, emphasizing how to improve prediction accuracy and efficiency by combining big data and emerging computing technologies.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115691"},"PeriodicalIF":2.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}