EXCLI Journal最新文献

{"title":"Empirical comparison and analysis of machine learning-based approaches for druggable protein identification.","authors":"Watshara Shoombuatong,&nbsp;Nalini Schaduangrat,&nbsp;Jaru Nikom","doi":"10.17179/excli2023-6410","DOIUrl":"https://doi.org/10.17179/excli2023-6410","url":null,"abstract":"<p><p>Efficiently and precisely identifying drug targets is crucial for developing and discovering potential medications. While conventional experimental approaches can accurately pinpoint these targets, they suffer from time constraints and are not easily adaptable to high-throughput processes. On the other hand, computational approaches, particularly those utilizing machine learning (ML), offer an efficient means to accelerate the prediction of druggable proteins based solely on their primary sequences. Recently, several state-of-the-art computational methods have been developed for predicting and analyzing druggable proteins. These computational methods showed high diversity in terms of benchmark datasets, feature extraction schemes, ML algorithms, evaluation strategies and webserver/software usability. Thus, our objective is to reexamine these computational approaches and conduct a comprehensive assessment of their strengths and weaknesses across multiple aspects. In this study, we deliver the first comprehensive survey regarding the state-of-the-art computational approaches for <i>in silico</i> prediction of druggable proteins. First, we provided information regarding the existing benchmark datasets and the types of ML methods employed. Second, we investigated the effectiveness of these computational methods in druggable protein identification for each benchmark dataset. Third, we summarized the important features used in this field and the existing webserver/software. Finally, we addressed the present constraints of the existing methods and offer valuable guidance to the scientific community in designing and developing novel prediction models. We anticipate that this comprehensive review will provide crucial information for the development of more accurate and efficient druggable protein predictors.</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41117947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The underappreciated wrong of AIgiarism - bypass plagiarism that risks propagation of erroneous and bias content.","authors":"Bor Luen Tang","doi":"10.17179/excli2023-6435","DOIUrl":"https://doi.org/10.17179/excli2023-6435","url":null,"abstract":"We address here the use of ChatGPT in a specific aspect of research, namely academic writing, in particular its presumably common use to produce a primary or first draft of manuscripts for publication. We identify such acts as a form of plagiarism","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41121122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The prey's perspective on the rise of predatory publishing.","authors":"Leandro Machado Camargo,&nbsp;Mykyta Smirnov,&nbsp;Igor Lima Maldonado","doi":"10.17179/excli2023-6392","DOIUrl":"https://doi.org/10.17179/excli2023-6392","url":null,"abstract":"","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41096397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphatidylcholine (PCL) fortified nano-phytopharmaceuticals for improvement of therapeutic efficacy.","authors":"Devesh U Kapoor, Mansi Gaur, Akshay Parihar, Bhupendra G Prajapati, Sudarshan Singh, Ravish J Patel","doi":"10.17179/excli2023-6345","DOIUrl":"10.17179/excli2023-6345","url":null,"abstract":"<p><p>Phytopharmaceuticals, derived from plants, are increasingly recognized for their potential therapeutic benefits. However, their effectiveness is often hindered by challenges such as poor bioavailability, stability, and targeted delivery. In this study, we aimed to address these limitations by developing PCL (phosphatidylcholine) fortified nano-phytopharmaceuticals to enhance therapeutic efficacy. PCL, a biocompatible and biodegradable polymer, was employed to encapsulate the phytopharmaceuticals, thereby improving their stability and bioavailability. The encapsulation process utilized nanoprecipitation, resulting in the formation of nanoparticles with controlled size and morphology. Various analytical techniques were employed to characterize the physicochemical properties of PCL fortified nano-phytopharmaceuticals, including dynamic light scattering, scanning electron microscopy, and Fourier-transform infrared spectroscopy. Furthermore, the release kinetics of encapsulated phytopharmaceuticals from PCL nanoparticles were evaluated, demonstrating sustained and controlled release profiles, essential for prolonged therapeutic effects. Cytotoxicity studies conducted on <i>in vitro</i> cell culture models confirmed the biocompatibility and non-toxic nature of the developed nano-phytopharmaceuticals. Additionally, <i>in vivo</i> studies were conducted to assess the therapeutic efficacy of PCL fortified nano-phytopharmaceuticals in animal models. The results showIased improved bioavailability, targeted tissue distribution, and enhanced therapeutic effects compared to free phytopharmaceuticals. Moreover, the developed nano-phytopharmaceuticals exhibited prolonged circulation time in the bloodstream, enabling improved drug delivery and reduced dosing frequency. This review highlights the promising potential of PCL fortified nano-phytopharmaceuticals as an effective approach for enhancing the therapeutic efficacy of phytopharmaceuticals. The improved stability, bioavailability, sustained release, and targeted delivery achieved through this formulation strategy offer promising opportunities for advancing plant-based therapies. See also the Graphical abstract(Fig. 1).</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Upper gastrointestinal bleeding due to Dieulafoy's lesion of the stomach: a rare case report.","authors":"Alsalt Al-Busaidi,&nbsp;Jaifar Alomairi,&nbsp;Omer Alabri,&nbsp;Eissa Alwheibi,&nbsp;Alazhar Almaghadari,&nbsp;Mhmod R Kadom,&nbsp;P Ronan O'Connell","doi":"10.17179/excli2023-6407","DOIUrl":"10.17179/excli2023-6407","url":null,"abstract":"<p><p>Dieulafoy's lesion is a life-threatening and rare vascular malformation of the submucosal vessel that protrudes to the mucosa of the gastrointestinal tract. The vessel is abnormally dilated, and if it ruptures, it can cause severe acute gastrointestinal bleeding. We report an upper GI bleeding case due to Dieulafoy's lesion in the gastric fundus of the stomach in a 76-year-old female. The patient presented with hematemesis and melena associated with anemia. An esophagogastroduodenoscopy (OGD) was performed which showed profuse pulsatile bleeding at the gastric fundus. Following that, gastrotomy confirmed the diagnosis of Dieulafoy's lesion. Endoscopy is the main diagnostic and therapeutic tool for Dieulafoy's lesion. Endoscopic treatment includes injective, ablative and mechanical therapies. The majority of cases are treated endoscopically, while in some cases, surgical intervention is deemed to be necessary as it is currently the only definitive treatment of Dieulafoy's lesion.</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>GLUL</i> gene knockdown and restricted glucose level show synergistic inhibitory effect on the luminal subtype breast cancer MCF7 cells' proliferation and metastasis.","authors":"Arezu Karimpur Zahmatkesh,&nbsp;Mohammad Khalaj-Kondori,&nbsp;Mohammad Ali Hosseinpour Feizi,&nbsp;Behzad Baradaran","doi":"10.17179/excli2023-6287","DOIUrl":"10.17179/excli2023-6287","url":null,"abstract":"<p><p>The glutamine synthetase path is one of the most important metabolic pathways in luminal breast cancer cells, which plays a critical role in supplying glutamine as an intermediate in the biosynthesis of amino acids and nucleotides. On the other hand, glycolysis and its dominant substrate, glucose, are the most critical players in cancer metabolism. Accordingly, targeting these two critical paths might be more efficient in luminal-type breast cancer treatment. MCF7 cells were cultivated in media containing 4.5, 2, and 1 g/L glucose to study its effects on GLUL (Glutamate Ammonia Ligase) expression. Followingly, high and low glucose cell cultures were transfected with 220 pM of siGLUL and incubated for 48 h at 37 ºC. The cell cycle progression and apoptosis were monitored and assessed by flow cytometry. Expression of GLUL, known as glutamine synthetase, was evaluated in mRNA and protein levels by qRT-PCR and western blotting, respectively. To examine the migration and invasion capacity of studied cells exploited from wound healing assay and subsequent expression studies of glutathione-S-transferase Mu3 (GSTM3) and alfa-enolase (ENO1). Expression of GLUL significantly decreased in cells cultured at lower glucose levels compared to those at higher glucose levels. siRNA-mediated knockdown of GLUL expression in low glucose cultures significantly reduced growth, proliferation, migration, and invasion of the MCF7 cells and enhanced their apoptosis compared to the controls. Based on the results, GLUL suppression down-regulated GSTM3, a main detoxifying enzyme, and up-regulated Bax. According to the role of glycolysis as a ROS suppressor, decreased amounts of glucose could be associated with increased ROS; it can be considered an efficient involved mechanism in this study. Also, increased expression of Bax could be attributable to mTOR/AKT inhibition following GLUL repression. In conclusion, utilizing GLUL and glycolysis inhibitors might be a more effective strategy in luminal-type breast cancer therapy. See also Figure 1(Fig. 1).</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41115516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multifunctional role of zinc in human health: an update.","authors":"Despoina P Kiouri,&nbsp;Evi Tsoupra,&nbsp;Massimiliano Peana,&nbsp;Spyros P Perlepes,&nbsp;Maria E Stefanidou,&nbsp;Christos T Chasapis","doi":"10.17179/excli2023-6335","DOIUrl":"https://doi.org/10.17179/excli2023-6335","url":null,"abstract":"<p><p>Zinc is a multipurpose trace element for the human body, as it plays a crucial part in various physiological processes, such as cell growth and development, metabolism, cognitive, reproductive, and immune system function. Its significance in human health is widely acknowledged, and this has led the scientific community towards more research that aims to uncover all of its beneficial properties, especially when compared to other essential metal ions. One notable area where zinc has shown beneficial effects is in the prevention and treatment of various diseases, including cancer. This review aims to explain the involvement of zinc in specific health conditions such as cancer, coronavirus disease 2019 (COVID-19) and neurological disorders like Alzheimer's disease, as well as its impact on the gut microbiome.</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10539547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41109224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Innovative therapeutic strategies for cardiovascular disease.","authors":"Kenneth Maiese","doi":"10.17179/excli2023-6306","DOIUrl":"10.17179/excli2023-6306","url":null,"abstract":"<p><p>As a significant non-communicable disease, cardiovascular disease is the leading cause of death for both men and women, comprises almost twenty percent of deaths in most racial and ethnic groups, can affect greater than twenty-five million individuals worldwide over the age of twenty, and impacts global economies with far-reaching financial challenges. Multiple factors can affect the onset of cardiovascular disease that include high serum cholesterol levels, elevated blood pressure, tobacco consumption and secondhand smoke exposure, poor nutrition, physical inactivity, obesity, and concurrent diabetes mellitus. Yet, addressing any of these factors cannot completely eliminate the onset or progression of cardiovascular disorders. Novel strategies are necessary to target underlying cardiovascular disease mechanisms. The silent mating type information regulation 2 homolog 1 <i>(Saccharomyces cerevisiae</i>) (SIRT1), a histone deacetylase, can limit cardiovascular injury, assist with stem cell development, oversee metabolic homeostasis through nicotinamide adenine dinucleotide (NAD⁺) pathways, foster trophic factor protection, and control cell senescence through the modulation of telomere function. Intimately tied to SIRT1 pathways are mammalian forkhead transcription factors (FoxOs) which can modulate cardiac disease to reduce oxidative stress, repair microcirculation disturbances, and reduce atherogenesis through pathways of autophagy, apoptosis, and ferroptosis. AMP activated protein kinase (AMPK) also is critical among these pathways for the oversight of cardiac cellular metabolism, insulin sensitivity, mitochondrial function, inflammation, and the susceptibility to viral infections such as severe acute respiratory syndrome coronavirus that can impact cardiovascular disease. Yet, the relationship among these pathways is both intricate and complex and requires detailed insight to successfully translate these pathways into clinical care for cardiovascular disorders.</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10427777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10104033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel 2-substituted-5-(4-chloro-2-phenoxy)phenyl-1,3,4-oxadiazole derivatives, ligands of GABAA/benzodiazepine receptor complex: Design, synthesis, radioligand binding assay, and pharmacological evaluation","authors":"E. Rezaee, Fatemeh Ahmadi, M. Shabaninia, M. Khoramjouy, Zahra Azizi Farsani, S. Shahhosseini, S. Tabatabai, M. Faizi","doi":"10.2139/ssrn.4265851","DOIUrl":"https://doi.org/10.2139/ssrn.4265851","url":null,"abstract":"Agonists of Benzodiazepine (BZD) receptor are exhaustively used in the control of muscle spasms, seizure, anxiety, and insomnia. BZDs have some unwanted effects; therefore, the development of new BZD receptor agonists with better efficacy and fewer unwanted effects is one of the subjects of interest. In this study, based on the pharmacophore/receptor model of the BZD binding site of GABAA receptors, a series of new 2-substituted-5-(4-chloro-2-phenoxy)phenyl-1,3,4-oxadiazole derivatives (6a-f) were designed. Energy minima conformers of the designed compounds and diazepam were well matched in conformational analysis and showed proper interaction with the BZD-binding site of the GABAA receptor model (α1β2ϒ2) in docking studies. The designed compounds were synthesized in acceptable yield and evaluated for their in vitro affinity to the benzodiazepine receptor of rat brains by radioligand receptor binding assay. The results demonstrated that the affinities of most of the novel compounds were even higher than diazepam. The novel compound 6a with the best affinity in radioligand receptor binding assay (Ki=0.44 nM and IC50= 0.73±0.17 nM) had considerable hypnotic activity and weak anticonvulsant and anxiolytic effects with no negative effect on memory in animal models. Flumazenil as a selective benzodiazepine receptor antagonist was able to prevent hypnotic and anticonvulsant effects of 6a indicating the role of BZD receptors in these effects.","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87733751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antineoplastic multi-drug chemotherapy to sensitize tumors triggers multi-drug resistance and inhibits efficiency of maintenance treatment inglioblastoma cells.","authors":"Oguzhan Doganlar, Zeynep Banu Doganlar, Suat Erdogan, Emre Delen","doi":"10.17179/excli2022-5556","DOIUrl":"10.17179/excli2022-5556","url":null,"abstract":"<p><p>Combinations of the well-known antineoplastic agents 5-fluorouracil (5-Fu), cisplatin, and paclitaxel are employed to increase radiotherapy/immunotherapy efficacy against persistent and resistant tumors. However, data remains needed on the hormetic, chronic, and long-term side effects of these aggressive combination chemotherapies. Here we investigated cellular and molecular responses associated with these combined agents, and their potential to induce multi-drug resistance against the temozolomide (TMZ) and etoposide (EP) used in glioblastoma maintenance treatment. We analyzed resistance and survival signals in U87 MG cells using molecular probes, fluorescent staining, qRT-PCR, and immunoblot. Repeated treatment with combined 5-Fu, cisplatin, and paclitaxel induced cross-resistance against TMZ and EP. Resistant cells exhibited elevated gene/protein expression of MRP1/ABCC1, ABCC2, BRCP/ABCG2, and GST. Moreover, they managed oxidative stress, cell cycle, apoptosis, and autophagy signaling to ensure survival. In these groups TMZ and etoposide efficiency dramatically reduced. Our result suggests that combined high-dose treatments of classical antineoplastic agents to sensitize tumors may trigger multi-drug resistance and inhibit maintenance treatment. When deciding on antineoplastic combination therapy for persistent/resistant glioblastoma, we recommend analyzing the long-term hormetic and chronic effects on cross-resistance and multi-drug resistance in primary cell cultures from patients. See also the Graphical Abstract(Fig. 1).</p>","PeriodicalId":12247,"journal":{"name":"EXCLI Journal","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9837385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9117372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}