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In silico prospective analysis of the medicinal plants activity on the caga oncoprotein from Helicobacter pylori

World Journal of Clinical Oncology 2024年第5期15卷 653-663页

作者： Rafaela Viana Vieira ga.rielle ca.olin. peiter Fabrício Freire de Melo Ana carla Zarpelon-Schutz Kádima Nayara Teixeira Universidade Federal do Paraná Campus ToledoToledo 85919-899Brazil Universidade Tecnológica Federal do Paraná Campus ToledoParaná85902-490Brazil Universidade Federal da Bahia Instituto Multidisciplinar em Saúde-Campus Anísio TeixeiraVitória da Conquista 45029-094Brazil Universidade Federal do Paraná-Setor Palotina Programa de Pós-graduação em BiotecnologiaPalotina 85950-000Brazil

BACKGROUND Colonization with Helicobacter pylori(***)has a strong correlation with gastric cancer,and the virulence factor caga is implicated in *** have been conducted using medicinal plants with the aim of eliminating the pathogen;however,the possibility of blocking ***-induced cell differentiation to prevent the onset and/or progression of tumors has not been *** type of study is expensive and time-consuming,requiring in vitro and/or in vivo tests,which can be solved using ***,prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the caga *** To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the caga oncoprotein of *** In this in silico study,the structures of the phenolic compounds(ligands)kaempferol,myricetin,quercetin,ponciretin(flavonoids),and chlorogenic acid(phenolic acid)were selected from the PubChem *** phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate *** *** three-dimensional structure model of the caga oncoprotein of ***(receptor)was obtained through molecular modeling using computational tools from the I-Tasser platform,employing the threading *** primary sequence of caga was sourced from GenBank(BAK52797.1).A screening was conducted to identify binding sites in the structure of the caga oncoprotein that could potentially interact with the ligands,utilizing the GRaSP online *** the ligands and receptor were prepared for molecular docking using AutoDock Tools 4(ADT)software,and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 *** sets of simulations were performed:One involving the central region of caga with phenolic compounds,and another involvi

关键词： caga oncoprotein Phenolic compounds Helicobacter pylori In silico analyses Medicinal plants Prospective analysis

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Lafoensia pacari alleviates intestinal damage by modulating cyclooxygenase-2:In silico and in vivo evaluation in a colitis model

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World Journal of gastroenterology 2023年第17期29卷 2628-2641页

作者： ga.rielle ca.olin. peiter Thayene Kamyli Moesch Queiroz Edson Luiz Michalkiewicz Jr Raphael Henrique Chappuis Jennefer Sousa Luz Luiz Henrique casagrande Piovezani Cleison Ferreira Silva Matheus Nozomi Tsutumi Augusto Fernandes Chaves Rafael Messias Luiz Cinthia Façanha Wendel Ana carla Zarpelon-Schutz Kádima Nayara Teixeira Programa Multicêntrico de Pós-graduação em Biquímica e Biologia Molecular-Setor Palotina Universidade Federal do ParanáPalotina 85.950-000ParanáBrazil Programa de Pós-graduação em Biotecnologia-Setor Palotina Universidade Federal do ParanáPalotina 85.950-000ParanáBrazil campus Toledo Universidade Federal do ParanáToledo 85.919-899ParanáBrazil

BACKGROUND Inflammatory bowel diseases(IBD)are a worldwide health problem and mainly affect young people,consequently affecting the *** treatments are often associated with side effects,and new therapeutic options are *** centuries,plants have represented important substrates in the field of drug *** pacari(***)is a plant whose pharmaceutical potential has been described,and may have biological activity relevant to the treatment of IBD *** To investigate the activity of keto-alcoholic extracts of *** with respect to ameliorating the inflammatory and nociceptive symptoms of acute experimental colitis in *** Keto-alcoholic extracts of *** leaves and bark were administered to male andfemale Swiss mice weighing 25 g to 30 g(n=8 male mice and n=8 female mice).The effect of these extracts was observed in an acetic acid-induced acute experimental model of colitis with regard to antinociception/analgesia and inflammatory tissue *** macroscopic indices included the Wallace score and the colon weight obtained using a precision *** hyperalgesia was determined using an electronic *** related to overt pain was determined by quantifying the number of writhing instances within 20 min of administration of acetic *** docking was performed using human and murine cyclooxygenase-2(COX-2)with 3 flavonoids(ellagic acid,kaempferol,and quercetin)on the AutoDock Vina *** of variance followed by Tukey’s posttest was used with Pcating *** In this murine model of colitis,administration of extracts from *** ameliorated acetic acidinduced writhing and colitis-associated inflammatory *** improvements may be attributable to the reduction in edema,inflammation(e.g.,ulcers,hyperemia,and bowel wall damage),and the intensity of abdominal *** keto-alcoholic extracts of *** leaves and bark administered at a

关键词： Antinociceptive activity Anti-inflammatory activity Cyclooxygenase-2 Flavonoids Inflammatory bowel disease Lafoensia pacari

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COVID-19 liver and gastroenterology findings:An in silico analysis of SARS-CoV-2 interactions with liver molecules

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World Journal of Hepatology 2022年第6期14卷 1131-1141页

作者： ga.rielle ca.olin. peiter Cristiano de Bem Torquato de Souza Lucca Miketen de Oliveira Luis Gustavo Pagliarin Valentina Nunes Fontoura dos Anjos Filipe Antônio França da Silva Fabrício Freire de Melo Kádima Nayara Teixeira Universidade Federal do Paraná Campus ToledoToledo 85919-899ParanáBrazil Universidade Federal da Bahia Campus Anísio TeixeiraVitória da Conquista 45029-094BahiaBrazil

BACKGROUND Coronavirus disease 19(COVID-19)has not only been shown to affect the respiratory system,but has also demonstrated variable clinical presentations including gastrointestinal tract *** addition,abnormalities in liver enzymes have been reported indicating hepatic *** is known that severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)might infect cells via the viral receptor angiotensin-converting enzyme 2(ACE2)which is expressed in several organs including the *** viral Spike glycoprotein binds to ACE2 and must be cleaved by Furin and Type 2 Serine Protease to enter the *** that,the Akt/mTOR signaling pathway is activated and several COVID-19 changes are *** To analyze liver and gastrointestinal symptoms and cell signaling pathways triggered by SARS-CoV-2 infection due to virus-liver interactions in *** In this in silico study,the three-dimensional structures of the Akt,mTORC1 and Furin(receptors)were selected from the Protein Data Bank(PDB)and the structures of inhibitors(ligands)MK-2206,CC-223 and Naphthofluorescein were selected from PubChem and ZINC *** files were downloaded as 2D structures and converted to optimized 3D structures using ViewerLite 4.2 *** Sketch®software was used to calculate prediction of the protonated form of inhibitors in a physiological environment(pH 7.4).AutoDock Tools(ADT)software was used to calculate and delimit the Grid box used in the molecular docking of each structure selected in the *** addition,protonated ligands were prepared for molecular docking using ADT *** docking was performed using ADT software tools connected to Vina *** of the amino acid residues involved in ligand interactions,as well as ligand twists,the atoms involved in interactions,bond type and strength of interactions were performed using PyMol^(■)and Discovery Studio^(■)(BIOVIA)*** Molecular docking analysis showed that the mTOR

关键词： Bioinformatics Cell signaling pathway COVID-19 Liver injury SARS-CoV-2

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Temporal pattern of humoral immune response in mild cases of COVID-19

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World Journal of Biological Chemistry 2023年第2期14卷 40-51页

作者： Isadora Maria Pilati campos Milena Marques ga.rielle ca.olin. peiter Ana Paula carneiro Brandalize Mauricio Bedim dos Santos Fabrício Freire de Melo Kádima Nayara Teixeira campus Toledo Universidade Federal do ParanáToledo 85.919-899ParanáBrazil Setor Palotina Universidade Federal do ParanáPalotina 85.950-000ParanáBrazil campus Anísio Teixeira Universidade Federal da BahiaVitória da Conquista 45029-094BahiaBrazil

BACKGROUND Understanding the humoral response pattern of coronavirus disease 2019(COVID-19)is one of the essential factors to better characterize the immune memory of patients,which allows understanding the temporality of reinfection,provides answers about the efficacy and durability of protection against severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),and consequently helps in global public health and vaccination *** the patients who became infected with SARS-CoV-2,the majority who did not progress to death were those who developed the mild COVID-19,so understanding the pattern and temporality of the antibody response of these patients is certainly *** To investigate the temporal pattern of humoral response of specific immunoglobulin G(IgG)in mild cases of *** Blood samples from 191 COVID-19 real-time reverse transcriptase-polymerase chain reaction(RT-qPCR)-positive volunteers from the municipality of Toledo/Paraná/Brazil,underwent two distinct serological tests,enzyme-linked immunosorbent assay,and detection of anti-nucleocapsid *** samples and clinicoepidemiological data of the volunteers were collected between November 2020 and February *** assays were performed in duplicate and the manufacturers'recommendations were strictly *** data were statistically analyzed using multiple logistic regression;the variables were selected by applying the Pcal tests to detect specific IgG were performed on serum samples from volunteers who were diagnosed as being positive by RT-qPCR for COVID-19 or had disease onset in the time interval from less than 1 mo to 7 *** time periods when the highest number of participants with detectable IgG was observed were 1,2 and 3 *** was observed that 9.42%of participants no longer had detectable IgG antibodies 1 mo only after being infected with SARS-CoV-2 and 1.57%were also IgG negative at less than 1 *** 5 mo,3.14%of volunteers were IgG n

关键词： Humoral response Immunoglobulin G antibody Immune memory Mild cases COVID-19 SARS-CoV-2 infection Serological test

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Three-dimensional models of antigens with serodiagnostic potential for leprosy:An in silico study

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World Journal of Clinical Infectious Diseases 2023年第1期13卷 1-10页

作者： Bianca Luiza Melo de Assis Rafaela Viana Vieira Ian Theodoro Rudenco Gomes Palma Matheus Bertolini Coutinho Juliana de Moura ga.rielle ca.olin. peiter Kádima Nayara Teixeira campus Toledo Universidade Federal do ParanáToledo 85.919-899ParanáBrazil Departamento de Patologia Básica Universidade Federal do Paraná-Setor de Ciências BiológicasCuritiba 81.531-980ParanáBrazil Programa Multicêntrico de Pós-graduação em Bioquímica e Biologia Molecular-Setor Palotina Universidade Federal do ParanáPalotina 85.950-000ParanáBrazil

BACKGROUND Leprosy is a disease caused by Mycobacterium leprae(***),an intracellular pathogen that has tropism and affects skin and nervous system *** disease has two forms of presentation:Paucibacillary and multibacillary,with different clinical and immunological *** what occurs in the multibacillary form,the diagnostic tests for the paucibacillary form are nonspecific and not very sensitive,allowing the existence of infected individuals without treatment,which contributes to the spread of the pathogen in the *** mitigate this contamination,more sensitive diagnostic tests capable of detecting paucibacillary patients are *** To predict the three-dimensional structure models of *** antigens with serodiagnostic potential for *** In this in silico study,satisfactory templates were selected in the Protein Data Bank(PDB)using Basic Local Alignment Search Tool to predict the structural templates of ML2038,ML0286,ML0050,and 85B antigens by comparative *** templates were selected according to general criteria such as sequence identity,coverage,X-ray resolution,Global Model Quality Estimate value and phylogenetic relationship;Clustal X 2.1 software was used in this *** modeling was completed using the software Modeller *** of the models was made using ViewerLite 4.2 and PyMol software,and analysis of the quality of the predicted models was performed using the QMEAN score and ***,the three-dimensional moels were validated using the MolProbity and Verify 3D *** The three-dimensional structure models of ML2038,ML0286,ML0050,and 85B antigens of *** were predicted using the templates PDB:3UOI(90.51%identity),PDB:3EKL(87.46%identity),PDB:3FAV(40.00%identity),and PDB:1F0N(85.21%identity),*** QMEAN and Z-score values indicated the good quality of the structure *** data refer to the monomeric units of antigens,since some of these a

关键词： Antigens Leprosy diagnosis Mycobacterium leprae Molecular modelling Serological test In silico study

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In silico evidence of Remdesivir action in blood coagulation cascade modulation in COVID-19 treatment

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World Journal of Biological Chemistry 2023年第4期14卷 72-83页

作者： Luis Gustavo Pagliarin Lucca Miketen de Oliveira Valentina Nunes Fontoura dos Anjos Cristiano de Bem Torquato de Souza ga.rielle ca.olin. peiter Cinthia Façanha Wendel Anderson Dillmann Groto Fabrício Freire de Melo Kádima Nayara Teixeira campus Toledo Universidade Federal do ParanáToledo 85.919-899ParanáBrazil Programa Multicêntrico de Pós-graduação em Bioquímica e Biologia Molecular-Setor Palotina Universidade Federal do ParanáPalotina 85.950-000ParanáBrazil Instituto Multidisciplinar em Saúde-campus Anísio Teixeira Universidade Federal da BahiaVitória da Conquista 45.029-094BahiaBrazil

BACKGROUND Coronavirus disease 2019(COVID-19)has demonstrated several clinical manifestations which include not only respiratory system issues but also liver,kidney,and other organ *** of these abnormalities is coagulopathies,including thrombosis and disseminated intravascular *** of this,the administration of low molecular weight heparin is required for patients that need to be *** addition,Remdesivir is an antiviral that was used against Middle East Acute Respiratory Syndrome,Ebola,Acute Respiratory Syndrome,and other diseases,showing satisfactory results on ***,there is evidence suggesting that this medication can provide a better prognosis for patients with *** To investigate in silico the interaction between Remdesivir and clotting factors,pursuing a possibility of using it as *** In this in silico study,the 3D structures of angiotensin-converting enzyme 2(ACE2),Factor I(fibrinogen),Factor II(prothrombin),Factor III(thromboplastin),Factor V(proaccelerin),Factor VII(proconvertin),Factor VIII(antihemophilic factor A),Factor IX(antihemophilic factor B),Factor X(Stuart-Prower factor),and Factor XI(precursor of thromboplastin(these structures are technically called receptors)were selected from the Protein Data *** structures of the antivirals Remdesivir and Osetalmivir(these structures are called ligands)were selected from the PubChem database,while the structure of Atazanavir was selected from the ZINC *** software AutoDock Tools(ADT)was used to prepare the receptors for molecular ***,peptides,water molecules,and other ones were removed from each ligand,and then,hydrogen atoms were added to the *** grid box was delimited and calculated using the same software ADT.A physiological environment with pH 7.4 is needed to make the ligands interact with the receptors,and still the software Marvin sketch®(ChemAxon®)was used to forecast the protonation *** perform m

关键词： Clotting factors Coagulating blood cascade COVID-19 treatment Remdesivir SARS-CoV-2

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