Bioinformatics and Biology Insights最新文献

{"title":"Effectiveness of Narciclasine in Suppressing the Inflammatory Response in Sepsis: Molecular Docking and In Silico Studies.","authors":"Manoj Kumar Kingsley, Gurugubelli Krishna Rao, Ballambattu Vishnu Bhat","doi":"10.1177/11779322241233436","DOIUrl":"10.1177/11779322241233436","url":null,"abstract":"<p><p>Narciclasine is an alkaloid belonging to the Amaryllidaceae family which has been reported to have many beneficial properties. Especially its anticancer properties have been widely reported. Here, we have focused on its potential use in suppressing the inflammatory response in sepsis using in silico methods. Lipopolysaccharide (LPS) is an endotoxin which is present in the outer membrane of gram-negative bacteria and is a crucial player in the pathogenesis of gram-negative sepsis. Activation of toll-like receptor 4 (TLR4) signaling by LPS is an important event in the pathogenesis of gram-negative sepsis. This initiates a downstream signaling pathway comprising of several adaptor proteins such as toll/interleukin-1 receptor domain-containing adapter protein (TIRAP), myeloid differentiation primary response protein 88 (MyD88), interleukin-1 receptor-associated kinase (IRAK)-1, IRAK-4, interferon regulatory factor 3 (IRF-3), tumor necrosis factor receptor-associated factor 6 (TRAF-6) leading to nuclear factor kappa B (NF-κβ) activation resulting in elevated production of inflammatory cytokines such as tumor necrosis factor alpha (TNF-α) and interleukin (IL)-6. S100 calcium binding proteins A8/A9 (S100A8/A9) have been found to be an agonist of TLR4, and it amplifies the inflammatory response in sepsis. Molecular docking studies of narciclasine with target proteins associated with the LPS-TLR4 pathway showed that it has good binding affinity and stable interactions with the targets studied. Molecular dynamics (MD) simulation studies over 100 ns showed that most of the ligand-target complexes were stable. The structures of all the targets except TRAF-6 were retrieved from the Protein Data Bank (PDB) database. Homology modeling was done to predict the 3-dimensional structure of TRAF-6. MD simulation of narciclasine-TRAF-6 complex showed that the structure is stable. Metapocket was used for active site prediction in the target proteins. Toxicity analysis by admetSAR revealed that narciclasine was readily biodegradable and exhibited minimum toxicity. These results indicate that narciclasine has effective anti-inflammatory properties which could be useful in suppressing the inflammatory response in sepsis.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241233436"},"PeriodicalIF":5.8,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating D-Amino Acid Oxidase Expression and Interaction Network Analyses in Pathways Associated With Cellular Stress: Implications in the Biology of Aging.","authors":"V Kalidasan, Darshinie Suresh, Nurulisa Zulkifle, Yap Siew Hwei, Leong Kok Hoong, Reena Rajasuriar, Kumitaa Theva Das","doi":"10.1177/11779322241234772","DOIUrl":"10.1177/11779322241234772","url":null,"abstract":"<p><p>D-amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids by oxidative deamination, producing hydrogen peroxide (H₂O₂) as a by-product. The generation of intracellular H₂O₂ may alter the redox-homeostasis mechanism of cells and increase the oxidative stress levels in tissues, associated with the pathogenesis of age-related diseases and organ decline. This study investigates the effect of DAO knockdown using clustered regularly interspaced short palindromic repeats (CRISPR) through an <i>in silico</i> approach on its protein-protein interactions (PPIs) and their potential roles in the process of aging. The target sequence and guide RNA of DAO were designed using the CCTop database, PPI analysis using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Reactome biological pathway, protein docking using GalaxyTongDock database, and structure analysis. The translated target sequence of DAO lies between amino acids 43 to 50. The 10 proteins that were predicted to interact with DAO are involved in peroxisome pathways such as acyl-coenzyme A oxidase 1 (ACOX1), alanine-glyoxylate and serine-pyruvate aminotransferase (AGXT), catalase (CAT), carnitine O-acetyltransferase (CRAT), glyceronephosphate O-acyltransferase (GNPAT), hydroxyacid oxidase 1 (HAO1), hydroxyacid oxidase 2 (HAO2), trans-L-3-hydroxyproline dehydratase (L3HYPDH), polyamine oxidase (PAOX), and pipecolic acid and sarcosine oxidase (PIPOX). In summary, DAO mutation would most likely reduce activity with its interacting proteins that generate H₂O₂. However, DAO mutation may result in peroxisomal disorders, and thus, alternative techniques should be considered for an <i>in vivo</i> approach.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241234772"},"PeriodicalIF":2.3,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10903195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Transcriptomics Data Profiling Reveals E2F Targets as an Important Biological Pathway Overexpressed in Intellectual Disability Disorder.","authors":"Prekshi Garg, Farrukh Jamal, Prachi Srivastava","doi":"10.1177/11779322231224665","DOIUrl":"10.1177/11779322231224665","url":null,"abstract":"<p><p>Intellectual disability (ID) is an early childhood neurodevelopmental disorder that is characterized by impaired intellectual functioning and adaptive behavior. It is one of the major concerns in the field of neurodevelopmental disorders across the globe. Diversified approaches have been put forward to overcome this problem. Among all these approaches, high throughput transcriptomic analysis has taken an important dimension. The identification of genes causing ID rapidly increased over the past 3 to 5 years owing to the use of sophisticated high throughput sequencing platforms. Early monitoring and preventions are much important for such disorder as their progression occurs during fetal development. This study is an attempt to identify differentially expressed genes (DEGs) and upregulated biological processes involved in development of ID patients through comparative analysis of available transcriptomics data. A total of 7 transcriptomic studies were retrieved from National Center for Biotechnology Information (NCBI) and were subjected to quality check and trimming prior to alignment. The normalization and differential expression analysis were carried out using DESeq2 and EdgeR packages of Rstudio to identify DEGs in ID. In progression of the study, functional enrichment analysis of the results obtained from both DESeq2 and EdgeR was done using gene set enrichment analysis (GSEA) tool to identify major upregulated biological processes involved in ID. Our findings concluded that monitoring the level of E2F targets, estrogen, and genes related to oxidative phosphorylation, DNA repair, and glycolysis during the developmental stage of an individual can help in the early detection of ID disorder.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322231224665"},"PeriodicalIF":5.8,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10865946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Studies on 6-Pyruvoyl Tetrahydropterin Synthase (6-PTPS) of <i>Plasmodium falciparum</i>.","authors":"Shalom N Chinedu, Mercy Bella-Omunagbe, Esther Okafor, Rufus Afolabi, Ezekiel Adebiyi","doi":"10.1177/11779322241230214","DOIUrl":"10.1177/11779322241230214","url":null,"abstract":"<p><p>6-Pyruvoyl tetrahydropterin synthase (6-PTPS) is a lyase involved in the synthesis of tetrahydrobiopterin. In <i>Plasmodium</i> species where dihydroneopterin aldolase (DHNA) is absent, it acts in the folate biosynthetic pathway necessary for the growth and survival of the parasite. The 6-pyruvoyl tetrahydropterin synthase of <i>Plasmodium falciparum</i> (<i>Pf</i>PTPS) has been identified as a potential antimalarial drug target. This study identified potential inhibitors of <i>Pf</i>PTPS using molecular docking techniques. Molecular docking and virtual screening of 62 compounds including the control to the deposited Protein Data Bank (PDB) structure was carried out using AutoDock Vina in PyRx. Five of the compounds, <i>N,N</i>-dimethyl-<i>N</i>'-[4-oxo-6-(2,2,5-trimethyl-1,3-dioxolan-4-yl)-3H-pteridin-2-yl]methanimidamide (140296439), 2-amino-6-[(1R)-3-cyclohexyl-1-hydroxypropyl]-3H-pteridin-4-one (140296495), 2-(2,3-dihydroxypropyl)-8,9-dihydro-6H-pyrimido[2,1-b]pteridine-7,11-dione (144380406), 2-(dimethylamino)-6-[(2,2-dimethyl-1,3-dioxolan-4-yl)-hydroxymethyl]-3H-pteridin-4-one (135573878), and [1-acetyloxy-1-(2-methyl-4-oxo-3H-pteridin-6-yl)propan-2-yl] acetate (136075207), showed better binding affinity than the control ligand, biopterin (135449517), and were selected and screened. Three conformers of 140296439 with the binding energy of -7.2, -7.1, and -7.0 kcal/mol along with 140296495 were better than the control at -5.7 kcal/mol. In silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies predicted good pharmacokinetic properties of all the compounds while reporting a high risk of irritant toxicity in 140296439 and 144380406. The study highlights the five compounds, 140296439, 140296495, 144380406, 135573878 and 136075207, as potential inhibitors of PfPTPS and possible compounds for antimalarial drug development.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241230214"},"PeriodicalIF":5.8,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10851736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139705932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Enrichment Analysis of Tumor Microenvironment-Driven Molecular Alterations That Facilitate Epithelial-to-Mesenchymal Transition and Distant Metastasis.","authors":"Mahnaz Abdolahi, Parnian Ghaedi Talkhounche, Mohammad Hossein Derakhshan Nazari, Haniyeh Sadat Hosseininia, Niloofar Khoshdel-Rad, Amin Ebrahimi Sadrabadi","doi":"10.1177/11779322241227722","DOIUrl":"10.1177/11779322241227722","url":null,"abstract":"<p><p>Nowadays, hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths, and identifying the effective factors in causing this disease can play an important role in its prevention and treatment. Tumors provide effective agents for invasion and metastasis to other organs by establishing appropriate communication between cancer cells and the microenvironment. Epithelial-to-mesenchymal transition (EMT) can be mentioned as one of the effective phenomena in tumor invasion and metastasis. Several factors are involved in inducing this phenomenon in the tumor microenvironment, which helps the tumor survive and migrate to other places. It can be effective to identify these factors in the use of appropriate treatment strategies and greater patient survival. This study investigated the molecular differences between tumor border cells and tumor core cells or internal tumor cells in HCC for specific EMT genes. Expression of NOTCH1, ID1, and LST1 genes showed a significant increase at the HCC tumor border. Targeting these genes can be considered as a useful therapeutic strategy to prevent distant metastasis in HCC patients.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241227722"},"PeriodicalIF":5.8,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10840405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the Antidiabetic Activities of the Fruit of <i>Parquetina nigrescens</i> (Afzel.) Bullock and <i>In Silico</i> Identification of Its Antidiabetic Agent.","authors":"Marcus D Ayoola, Yetunde B Ogundeko, Temiloluwa D Obanleowo, Deborah O Omole, Blessing N Chukwu, Kolade O Faloye","doi":"10.1177/11779322231223857","DOIUrl":"10.1177/11779322231223857","url":null,"abstract":"<p><p>The study investigated the antidiabetic potentials of the fruit extract of <i>Parquetina nigrescens</i> with the aim of justifying its folkloric antidiabetic usage in some part of Nigeria. Acute toxicity test of the plant extract was assessed using Lorke's method. Its antidiabetic activities were assayed in α-amylase, α-glucosidase, glucose, and streptozotocin-induced diabetic rats' models at various doses with acarbose and glibenclamide (5 mg/kg) as positive controls. Molecular docking studies were performed to identify the antidiabetic constituent of the extract and elucidate its possible mechanism of action. The estimated median lethal dose <b>(LD₅₀)</b> of the extract was above 5000 mg/kg. In the α-amylase, α-glucosidase study, the extract elicited concentration-dependent activity similar to acarbose. In the glucose-induced hyperglycaemic model, 200 mg/kg of the extract was the most effective dose with comparable (<i>P</i> > .05) antihyperglycaemic activity to glibenclamide (5 mg kg) at 1 to 4 h. Also in the streptozotocin-induced diabetic rats model, 100 and 200 mg/kg of the extract gave comparable (<i>P</i> > 0.05) activity on days 4 to 14 that were significantly better than that of glibenclamide on days 4 to 7. The n-hexane and ethylacetate fractions of the extract, both at 200 mg/kg were the most active with comparable activity to glibenclamide at all time points. The molecular docking studies identified isorhoifolin as the best binder against alpha amylase with binding energy (-9.1 kcal/mol), alpha glucosidase (-9.4 kcal/mol), sodium-glucose cotransporter-2 (-9.5 kcal/mol), peroxisome proliferator activated receptor gamma (-10.3 kcal/mol), <i>11β</i>-<i>Hydroxysteroid dehydrogenase</i> (-10.8 kcal/mol), and dipeptidyl peptidase IV (-9.4 kcal/mol). The results of the antidiabetic study of <i>P nigrescence</i> fruit extract justified its usage in ethnomedicne in diabetes management.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322231223857"},"PeriodicalIF":2.3,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139569643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches.","authors":"Masriana Vivi Simanjuntak, Muhammad Miftah Jauhar, Putri Hawa Syaifie, Adzani Gaisani Arda, Etik Mardliyati, Wervyan Shalannanda, Beni Rio Hermanto, Isa Anshori","doi":"10.1177/11779322231224187","DOIUrl":"10.1177/11779322231224187","url":null,"abstract":"<p><p>Breast cancer is the most commonly diagnosed cancer globally, with the highest incidence of breast cancer occurring in Asian countries including Indonesia. Among the types of breast cancer, the estrogen receptor (ER)-positive subtype which is prominent with estrogen receptor alpha (<i>ERα</i>) and heat shock protein 90 (<i>HSP90</i>) overexpression genes becomes the most prevalent than the others, approximately 75% of all breast cancer cases. ERα and HSP90 play a role in breast cancer activities including breast tumor growth, invasion, and metastasis mechanism. Propolis, a natural bee product, has been explored for its anticancer activity. However, there is lack of studies that evaluated the potential inhibitor from propolis compounds to the ERα and HSP90 proteins. Therefore, this article focuses on examining the correlation between ERα and HSP90's role in breast cancer and investigating the potential of 93 unique propolis compositions in inhibiting these genes in breast cancer using in silico approaches. This study revealed the positive correlation between <i>ERα</i> and <i>HSP90</i> genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-β-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322231224187"},"PeriodicalIF":2.3,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10809879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139563486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neomangiferin, a Naturally Occurring Mangiferin Congener, Inhibits Sodium-Glucose Co-transporter-2: An <i>In silico</i> Approach.","authors":"Ayobami J Olusola, Samson O Famuyiwa, Kolade O Faloye, Oluwaseun E Olatunji, Uduak I Olayemi, Abiodun A Adeyemi, John O Balogun, Seun B Ogundele, Blessing O Babamuyiwa, Rajesh B Patil","doi":"10.1177/11779322231223851","DOIUrl":"10.1177/11779322231223851","url":null,"abstract":"<p><p>Type 2 diabetes is a major health concern contributing to most of diabetic cases worldwide. Mangiferin and its congeners are known for their diverse pharmacological properties. This study sought to investigate the inhibitory property of naturally occurring mangiferin congeners on sodium-glucose co-transporter 2 protein (SGLT-2) using comprehensive computational methods. The naturally occurring mangiferin congeners were subjected to molecular docking, molecular dynamics (MDs) simulation (100 ns), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy, density functional theory calculations (B3LYP 6-31G basis set), and ADMET approaches to identify potential SGLT-2 inhibitor. The molecular docking studies revealed neomangiferin (-9.0 kcal/mol) as the hit molecule compared with dapagliflozin (-8.3 kcal/mol). Root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) plots from the MD simulations established that neomangiferin stabilizes SGLT-2 better than the dapagliflozin, a standard drug. The MM-PBSA binding free energy calculations showed that neomangiferin (-26.05 kcal/mol) elicited better binding affinity than dapagliflozin (-17.42 kcal/mol). The electronic studies showed that neomangiferin (3.48 eV) elicited high electrophilicity index compared with mangiferin (3.31 eV) and dapagliflozin (2.11 eV). Also, the ADMET properties showed that the hit molecule is safe when administered to diabetic subjects. The current <i>in silico</i> studies suggest that neomangiferin could emerge as a promising lead molecule as a SGLT-2 inhibitor.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322231223851"},"PeriodicalIF":5.8,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10798119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139511512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic Characterization of Resistant <i>Salmonella</i> Strains in Typhoid Fever Patients in Nigeria.","authors":"Olukayode Olugbenga Orole, Jebes Ngolo Lamini, Aleruchi Chuku","doi":"10.1177/11779322231220194","DOIUrl":"10.1177/11779322231220194","url":null,"abstract":"<p><p><i>Salmonella</i> species are Enterobacteriaceae associated with typhoid fever. In this study, the distribution of broad-spectrum β-lactamase regulatory genes and genetic relatedness of isolates was determined. Stool samples (400) were collected from patients with fever in Dalhatu Araf Specialist Hospital (DASH), Lafia, Nigeria, between March 2020 and April 2021. <i>Salmonella</i> species were isolated and extended-spectrum β-lactamase distribution was determined among resistant isolates using polymerase chain reaction (PCR). Genetic relatedness of <i>Salmonella</i> species resistant to the 10 first-line antibiotics administered was determined among <i>S typhi</i> isolated. Of the 60 isolates that were confirmed to belong to the genus <i>Salmonella</i>, 12 (20.0%) isolates with <i>bla SHV</i> genes were the most prevalent, <i>blaOXA-1</i> and <i>blaCTX-M-9</i> were present in 5 isolates each, while <i>blaCTX-M-4</i> and <i>blaTEM</i> genes with a prevalence of 1.7% each were the least obtained in the isolates. Two isolates had a multidrug-resistant index (MDRI) of 1, and 2 others were positive with the <i>S typhi staG</i> gene. Sequencing to determine their diversity showed that isolates ST36 and ST138, respectively, had MDRI = 1 and are clustered in a group with a similarity coefficient of 0.00634. The 2 isolates had the highest genetic similarity, which indicates that the genetic diversity between the isolates is low, while <i>Salmonella</i> strain ST313L2 had a high level of genetic distance from the other isolates. The most resistant isolates are closely related which calls for concern.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322231220194"},"PeriodicalIF":5.8,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10777790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139428314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Analysis of the Dextransucrase Obtained From <i>Leuconostoc mesenteroides</i> Strain IBUN 91.2.98.","authors":"Luisa Alejandra García Galindo, Martha Margarita González, Jairo Alonso Cerón Salamanca, Sonia Amparo Ospina Sánchez","doi":"10.1177/11779322231212751","DOIUrl":"10.1177/11779322231212751","url":null,"abstract":"<p><p>The DSR-IBUN dextransucrase produced by <i>Leuconostoc mesenteroides</i> strain IBUN 91.2.98 has a short production time (4.5 hours), an enzymatic activity of 24.8 U/mL, and a specific activity of purified enzyme 2 times higher (331.6 U/mg) than that reported for similar enzymes. The aim of this study was to generate a structural model that, from an in silico approach, allows a better understanding, from the structural point of view, of the activity obtained by the enzyme of interest, which is key to continue with its study and industry application. For this, we translated the nucleotide sequence of the <i>dsr_IBUN</i> gene. With the primary structure of DSR-IBUN, the in silico prediction of physicochemical parameters, the possible subcellular localization, the presence of signal peptide, and the location of domains and functional and structural motifs of the protein were established. Subsequently, its secondary and tertiary structure were predicted and a homology model of the dextransucrase under study was constructed using Swiss-Model, performing careful template selection. The values obtained for the model, Global Model Quality Estimation (0.63), Quality Mean (-1.49), and root-mean-square deviation (0.09), allow us to affirm that the model for the enzyme dextransucrase DSR-IBUN is of adequate quality and can be used as a source of information for this protein.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231212751"},"PeriodicalIF":5.8,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138457725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}