Analytical biochemistry最新文献

{"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":"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":"Design of a microneedle-based enzyme biosensor using a simple and cost-effective electrochemical strategy to monitor superoxide anion released from cancer cells","authors":"Razieh Seyfi Zouleh ,&nbsp;Mostafa Rahimnejad ,&nbsp;Ghasem Najafpour-Darzi ,&nbsp;Davood Sabour","doi":"10.1016/j.ab.2024.115710","DOIUrl":"10.1016/j.ab.2024.115710","url":null,"abstract":"<div><div>Early detection of Reactive oxygen species (ROS) concentration is very important in cancer diagnosis, pathological examinations, and health screening. Studies show that changes in ROS concentration occurs in a short time, causing irreparable damage to living cells and organs. Miniaturized sensors and microelectrodes are capable of online monitoring of electrochemical reactions both <em>in vitro</em> and <em>in vivo</em>. In this study, an enzymatic biosensor based on an electrochemically roughened gold microneedle electrode (RAuME) has been developed to measure superoxide anion released from prostate cancer cells. A uniform layer of reduced graphene oxide (rGO) was deposited onto the gold microelectrode through electrochemical reduction, followed by electrodeposition of yttrium hexacyanoferrate (YHCF) nanoparticles. The deposited layers improved the current response of the microneedle electrode in CV, Impedance, and Amperometric analysis. Furthermore, chitosan was utilized to superoxide dismutase (SOD) immobilization. The presence of chitosan maintained the catalytic properties of the SOD enzyme. The developed microsensor monitored the superoxide anion in a wide linear range from 0.304 to 314 μM with detection limit of 17 nm. According to the physiological concentration of the superoxide anion (10–100 nm), we hypothesized that the developed micro-biosensor can mediate a fast monitoring of ROS that facilitates early-stage cancer diagnosis and treatment.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115710"},"PeriodicalIF":2.6,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581904","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":"An ATP detection system based on the enzyme reaction with biotin protein ligase","authors":"Shinji Sueda,&nbsp;Satoshi Fujii","doi":"10.1016/j.ab.2024.115698","DOIUrl":"10.1016/j.ab.2024.115698","url":null,"abstract":"<div><div>Adenosine triphosphate (ATP) is the energy currency of all living organisms and can be used as an indicator for cell proliferation and cytotoxicity. In the present work, we have developed a novel ATP detection system by combining the biotinylation reaction from archaeon <em>Sulfolobus tokodaii</em> with fluorescence resonance energy transfer (FRET). In biotinylation from <em>S. tokodaii</em>, an enzyme known as biotin protein ligase (BPL) forms a very stable complex with its product, biotinylated substrate protein (BCCP). Here, BPL and BCCP were fused to the fluorescent proteins Cerulean and Clover, respectively, and ATP detection was accomplished by monitoring the FRET signal between the two fluorescent proteins, since ATP is an essential component for biotinylation and the tight BPL-BCCP complex is formed only after biotinylation. Using this system, we have succeeded in detecting 5 nM of ATP by biotinylation reaction with 50 nM of each fusion protein. Our method has a characteristic that the signal does not decay for at least 2 h after the start of the reaction, unlike in the case of the luminescence-based assay with luciferase commonly used for the ATP detection. Thus, our system allows for ATP detection which is not significantly constrained by measurement timing.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"696 ","pages":"Article 115698"},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493132","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":"Analytical and drug delivery strategies for short peptides: From manufacturing to market","authors":"Ashwini Chawathe ,&nbsp;Vishal Ahire ,&nbsp;Kshitiz Luthra ,&nbsp;Bhumika Patil ,&nbsp;Kalpna Garkhal ,&nbsp;Nitish Sharma","doi":"10.1016/j.ab.2024.115699","DOIUrl":"10.1016/j.ab.2024.115699","url":null,"abstract":"<div><div>In recent times, biopharmaceuticals have gained attention because of their tremendous potential to benefit millions of patients globally by treating widespread diseases such as cancer, diabetes and many rare diseases. Short peptides (SP), also termed as oligopeptides, are one such class of biopharmaceuticals, that are majorly involved in efficient functioning of biological systems. Peptide chains that are 2–20 amino acids long are considered as oligopeptides by researchers and are some of the functionally vital compounds with widespread applications including self-assembly material for drug delivery, targeting ligands for precise/specific targeting and other biological uses. Using functionalised biomacromolecules such as short chained peptides, helps in improving pharmacokinetic properties and biodistribution profile of the drug. Apart from this, functionalised SP are being employed as cell penetrating peptides and prodrug to specifically and selectively target tumor sites. In order to minimize any unwanted interaction and adverse effects, the stability and safety of SP should be ensured throughout its development from manufacturing to market. Formulation development and characterization strategies of these potential molecules are described in the following review along with various applications and details of marketed formulations.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"696 ","pages":"Article 115699"},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493133","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":"Voltammetric-based immunosensing of Newcastle disease virus on polyethylene glycol-containing self-assembled monolayer modified gold electrode","authors":"Mohamad Farid Abd Muain ,&nbsp;Amir Syahir Amir Hamzah ,&nbsp;Suet Lin Chia ,&nbsp;Khatijah Yusoff ,&nbsp;Hong Ngee Lim ,&nbsp;Ikeno Shinya ,&nbsp;Asilah Ahmad Tajudin","doi":"10.1016/j.ab.2024.115700","DOIUrl":"10.1016/j.ab.2024.115700","url":null,"abstract":"<div><div>A voltammetric immunosensor for the detection of Newcastle disease virus (NDV) has been developed by employing polyclonal antibody targeting NDV (anti-NDV) as a bioreceptor. Anti-NDV was immobilized on polyethylene glycol (PEG)-containing self-assembled monolayer (SAM) which was activated with N-(3-dimethylaminopropyl)-N′-ethylcarbodiimidehydrochloride (EDC) and N-hydroxy succinimide (NHS) coupling on screen-printed gold electrode (SPGE). The introduction of PEG-containing SAM on the SPGE allowed the bioreceptor to covalently bound to the electrode surface whilst still providing a hydrophilic layer on the electrode which is important to greatly reduce non-specific bindings. The bioreceptor functionalized electrode was then allowed to be incubated with NDV-spiked samples. The electrode surface modification with PEG-containing SAM, immobilization of anti-NDV as bioreceptor, up to the detection of NDV were characterized electrochemically through differential pulse voltammetry (DPV) analysis in [Fe(CN)₆]^3- as the redox probe. Decrement of anodic current peak (I_pa) of [Fe(CN)₆]^3- was seen as the concentration of NDV increased from 0.156 to 20 HA μL⁻¹ with the limit of detection (LoD) of 1.50 HA μL⁻¹ at 3σ m⁻¹. The detection of NDV in HA μL⁻¹ unit in this study would ease interlaboratory interpretation as it was the same unit used in hemagglutination (HA) assay of conventional NDV diagnosis. The specificity of anti-NDV used as bioreceptor towards NDV was confirmed through western blot analysis, whilst the selectivity of the bioreceptor-functionalized electrode has been tested with allantoic fluid as the negative control in which no apparent changes of anodic peak (I_pa) has been seen. This simple, fast, and less laborious electrochemical detection method could become an alternative to the conventional method for NDV detection.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115700"},"PeriodicalIF":2.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493138","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}

{"title":"Detection of Salmonella by competitive ELISA of lipopolysaccharide secreted into the culture medium","authors":"Elena Kiseleva,&nbsp;Konstantin Mikhailopulo,&nbsp;Oleg Sviridov","doi":"10.1016/j.ab.2024.115695","DOIUrl":"10.1016/j.ab.2024.115695","url":null,"abstract":"<div><div>Detection of <em>Salmonella</em> in food is topical due to known cases of salmonellosis epidemics. Immunochemical methods including ELISA are widely used for <em>Salmonella</em> detection. Traditionally, commercial ELISA kits are based on sandwich technique and detect lipopolysaccharide (LPS), which is considered to be the component of the outer membrane of Gram-negative bacteria. Our aim was elaboration of competitive ELISA test for <em>Salmonella</em> detection in food with improved parameters. It was shown that in the <em>Salmonella</em> culture after the standard sample preparation procedure LPS is present mainly outside cells as a component of outer membrane vesicles. Improved sample preparation procedure includes separation of bacteria from the medium and analysis of the medium, which increases analytical sensitivity. Immobilization of the bovine serum albumin (BSA)-LPS conjugate in microplate wells allows to obtain a more homogeneous coating than immobilization of LPS itself. Thus, we have developed test system for <em>Salmonella</em> detection in food by competitive ELISA of LPS secreted into the culture medium with the immobilized BSA-LPS conjugate and monoclonal antibodies (mAb) to LPS core in the liquid phase. New competitive ELISA test is high sensitive, give reproducible results, allows the detection of any <em>Salmonella</em> serotype and is important for the protection of human health.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115695"},"PeriodicalIF":2.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493134","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":"Micro scale chromatography of human plasma proteins for nano LC-ESI-MS/MS","authors":"Zhuo Zhen Chen,&nbsp;Jaimie Dufresne,&nbsp;Peter Bowden,&nbsp;Dominika Celej,&nbsp;Ming Miao,&nbsp;John G. Marshall","doi":"10.1016/j.ab.2024.115694","DOIUrl":"10.1016/j.ab.2024.115694","url":null,"abstract":"<div><div>Organic precipitation of proteins with acetonitrile demonstrated complete protein recovery and improved chromatography of human plasma proteins. The separation of 25 μL of human plasma into 22 fractions on a QA SAX resin facilitated more effective protein discovery despite the limited sample size. Micro chromatography of plasma proteins over quaternary amine (QA) strong anion exchange (SAX) resins performed best, followed by diethylaminoethyl (DEAE), heparin (HEP), carboxymethyl cellulose (CMC), and propyl sulfate (PS) resins. Two independent statistical methods, Monte Carlo comparison with random MS/MS spectra and the rigorous X!TANDEM goodness of fit algorithm protein p-values corrected to false discovery rate <em>q</em>-values (<em>q</em> ≤ 0.01) agreed on at least 12,000 plasma proteins, each represented by at least three fully tryptic corrected peptide observations. There was qualitative agreement on 9393 protein/gene symbols between the linear quadrupole versus orbital ion trap but also quantitative agreement with a highly significant linear regression relationship between log observation frequency (F value 4,173, p-value 2.2e-16)<strong>.</strong> The use of a QA resin showed nearly perfect replication of all the proteins that were also found using DEAE-, HEP-, CMC-, and <em>P</em>S-based chromatographic methods combined and together estimated the size of the size of the plasma proteome as ≥12,000 gene symbols.</div></div>","PeriodicalId":7830,"journal":{"name":"Analytical biochemistry","volume":"697 ","pages":"Article 115694"},"PeriodicalIF":2.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493136","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}