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1.
Braz. j. biol ; 84: e256732, 2024. tab, graf
Article in English | LILACS-Express | MEDLINE, LILACSEXPRESS, LILACS, VETINDEX | ID: biblio-1364524

ABSTRACT

Abstract Germin-like proteins (GLPs) play an important role against various stresses. Vitis vinifera L. genome contains 7 GLPs; many of them are functionally unexplored. However, the computational analysis may provide important new insight into their function. Currently, physicochemical properties, subcellular localization, domain architectures, 3D structures, N-glycosylation & phosphorylation sites, and phylogeney of the VvGLPs were investigated using the latest computational tools. Their functions were predicted using the Search tool for the retrieval of interacting genes/proteins (STRING) and Blast2Go servers. Most of the VvGLPs were extracellular (43%) in nature but also showed periplasmic (29%), plasma membrane (14%), and mitochondrial- or chloroplast-specific (14%) expression. The functional analysis predicted unique enzymatic activities for these proteins including terpene synthase, isoprenoid synthase, lipoxygenase, phosphate permease, receptor kinase, and hydrolases generally mediated by Mn+ cation. VvGLPs showed similarity in the overall structure, shape, and position of the cupin domain. Functionally, VvGLPs control and regulate the production of secondary metabolites to cope with various stresses. Phylogenetically VvGLP1, -3, -4, -5, and VvGLP7 showed greater similarity due to duplication while VvGLP2 and VvGLP6 revealed a distant relationship. Promoter analysis revealed the presence of diverse cis-regulatory elements among which CAAT box, MYB, MYC, unnamed-4 were common to all of them. The analysis will help to utilize VvGLPs and their promoters in future food programs by developing resistant cultivars against various biotic (Erysiphe necator and in Powdery Mildew etc.) and abiotic (Salt, drought, heat, dehydration, etc.) stresses.


Resumo As proteínas do tipo germin (GLPs) desempenham um papel importante contra vários estresses. O genoma de Vitis vinifera L. contém 7 GLPs; muitos deles são funcionalmente inexplorados. No entanto, a análise computacional pode fornecer informações importantes sobre sua função. Atualmente, as propriedades físico-químicas, localização subcelular, arquitetura de domínio, estruturas 3D, sítios de N-glicosilação e fosforilação e estudos filogenéticos dos VvGLPs foram conduzidos usando as ferramentas computacionais mais recentes. Suas funções foram previstas usando a ferramenta Search para recuperação de genes/proteínas em interação (STRING) e servidores Blast2Go. A maioria dos VvGLPs são extracelulares (43%) na natureza, mas também mostraram expressão periplasmática (29%), na membrana plasmática (14%) e específica para mitocôndrias ou cloroplastos (14%). A análise funcional previu atividades enzimáticas únicas para essas proteínas, incluindo terpeno sintase, isoprenoide sintase, lipoxigenase, fosfato permease, receptor quinase e hidrolases geralmente mediadas por cátion Mn +. VvGLPs mostraram similaridade na estrutura geral, forma e posição do domínio cupin. Funcionalmente, os VvGLPs controlam e regulam a produção de metabólitos secundários para lidar com vários estresses. Filogeneticamente, VvGLP1, -3, -4, -5 e VvGLP7 mostraram maior similaridade devido à duplicação, enquanto VvGLP2 e VvGLP6 revelaram uma relação distante. A análise do promotor revelou a presença de diversos elementos cis-reguladores, entre os quais CAAT box, MYB, MYC, sem nome-4, sendo comum a todos eles. A análise ajudará a utilizar VvGLPs e seus promotores em programas alimentares futuros, desenvolvendo cultivares resistentes contra vários estresses bióticos (Erysiphe necator e no oídio, etc.) e abióticos (sal, seca, calor, estresse hídrico, etc.).

2.
Braz. j. biol ; 82: e244735, 2022. tab, graf
Article in English | LILACS | ID: biblio-1249280

ABSTRACT

Abstract L-Asparaginase catalysing the breakdown of L-Asparagine to L-Aspartate and ammonia is an enzyme of therapeutic importance in the treatment of cancer, especially the lymphomas and leukaemia. The present study describes the recombinant production, properties and anticancer potential of enzyme from a hyperthermophilic archaeon Pyrococcus abyssi. There are two genes coding for asparaginase in the genome of this organism. A 918 bp gene encoding 305 amino acids was PCR amplified and cloned in BL21 (DE3) strain of E. coli using pET28a (+) plasmid. The production of recombinant enzyme was induced under 0.5mM IPTG, purified by selective heat denaturation and ion exchange chromatography. Purified enzyme was analyzed for kinetics, in silico structure and anticancer properties. The recombinant enzyme has shown a molecular weight of 33 kDa, specific activity of 1175 U/mg, KM value 2.05mM, optimum temperature and pH 80°C and 8 respectively. No detectable enzyme activity found when L-Glutamine was used as the substrate. In silico studies have shown that the enzyme exists as a homodimer having Arg11, Ala87, Thr110, His112, Gln142, Leu172, and Lys232 being the putative active site residues. The free energy change calculated by molecular docking studies of enzyme and substrate was found as ∆G - 4.5 kJ/mole indicating the affinity of enzyme with the substrate. IC50 values of 5U/mL to 7.5U/mL were determined for FB, caco2 cells and HepG2 cells. A calculated amount of enzyme (5U/mL) exhibited 78% to 55% growth inhibition of caco2 and HepG2 cells. In conclusion, the recombinant enzyme produced and characterized in the present study offers a good candidate for the treatment of cancer. The procedures adopted in the present study can be prolonged for in vivo studies.


Resumo A L-asparaginase, que catalisa a degradação da L-asparagina em L-aspartato e amônia, é uma enzima de importância terapêutica no tratamento do câncer, especialmente dos linfomas e da leucemia. O presente estudo descreve a produção recombinante, propriedades e potencial anticancerígeno da enzima de Pyrococcus abyssi, um archaeon hipertermofílico. Existem dois genes que codificam para a asparaginase no genoma desse organismo. Um gene de 918 bp, que codifica 305 aminoácidos, foi amplificado por PCR e clonado na cepa BL21 (DE3) de E. coli usando o plasmídeo pET28a (+). A produção da enzima recombinante foi induzida sob 0,5mM de IPTG, purificada por desnaturação seletiva por calor e cromatografia de troca iônica. A enzima purificada foi analisada quanto à cinética, estrutura in silico e propriedades anticancerígenas. A enzima recombinante apresentou peso molecular de 33 kDa, atividade específica de 1.175 U / mg, valor de KM 2,05 mM, temperatura ótima de 80º C e pH 8. Nenhuma atividade enzimática detectável foi encontrada quando a L-glutamina foi usada como substrato. Estudos in silico mostraram que a enzima existe como um homodímero, com Arg11, Ala87, Thr110, His112, Gln142, Leu172 e Lys232 sendo os resíduos do local ativo putativo. A mudança de energia livre calculada por estudos de docking molecular da enzima e do substrato foi encontrada como ∆G - 4,5 kJ / mol, indicando a afinidade da enzima com o substrato. Valores de IC50 de 5U / mL a 7,5U / mL foram determinados para células FB, células caco2 e células HepG2. Uma quantidade de enzima (5U / mL) apresentou inibição de crescimento de 78% a 55% das células caco2 e HepG2, respectivamente. Em conclusão, a enzima recombinante produzida e caracterizada no presente estudo é uma boa possibilidade para o tratamento do câncer. Os procedimentos adotados na presente pesquisa podem ser aplicados para estudos in vivo.


Subject(s)
Humans , Asparaginase/biosynthesis , Asparaginase/pharmacology , Pyrococcus abyssi/enzymology , Antineoplastic Agents/pharmacology , Substrate Specificity , Enzyme Stability , Recombinant Proteins/biosynthesis , Recombinant Proteins/pharmacology , Caco-2 Cells , Escherichia coli/genetics , Molecular Docking Simulation , Hydrogen-Ion Concentration
3.
Braz. j. biol ; 82: e239449, 2022. tab, graf
Article in English | LILACS | ID: biblio-1249271

ABSTRACT

Abstract Alpha amylase, catalyzing the hydrolysis of starch is a ubiquitous enzyme with tremendous industrial applications. A 1698 bp gene coding for 565 amino acid amylase was PCR amplified from Geobacillus thermodenitrificans DSM-465, cloned in pET21a (+) plasmid, expressed in BL21 (DE3) strain of E. coli and characterized. The recombinant enzyme exhibited molecular weight of 63 kDa, optimum pH 8, optimum temperature 70°C, and KM value of 157.7µM. On pilot scale, the purified enzyme efficiently removed up to 95% starch from the cotton fabric indicating its desizing ability at high temperature. 3D model of enzyme built by Raptor-X and validated by Ramachandran plot appeared as a monomer having 31% α-helices, 15% β-sheets, and 52% loops. Docking studies have shown the best binding affinity of enzyme with amylopectin (∆G -10.59). According to our results, Asp 232, Glu274, Arg448, Glu385, Asp34, Asn276, and Arg175 constitute the potential active site of enzyme.


Resumo A alfa-amilase, que catalisa a hidrólise do amido, é uma enzima ubíqua com imensas aplicações industriais. Um gene de 1698 pb que codifica a amilase de 565 aminoácidos foi amplificado por PCR, a partir de Geobacillus thermodenitrificans DSM-465, clonado no plasmídeo pET21a (+), expresso na cepa BL21 (DE3) de E. coli e caracterizado. A enzima recombinante exibiu peso molecular de 63 kDa, pH ótimo igual a 8, temperatura ótima de 70° C e valor KM de 157,7 µM. Em escala piloto, a enzima purificada removeu com eficiência até 95% de amido do tecido de algodão, indicando sua capacidade de desengomagem em alta temperatura. O modelo 3D da enzima construída por Raptor-X e validada por Ramachandran plot apareceu como um monômero com 31% de hélices alfa, 15% de folhas beta e 52% de loops. Os estudos de docking mostraram melhor afinidade de ligação da enzima com amilopectina (∆G: - 10,59). De acordo com nossos resultados, Asp 232, Glu274, Arg448, Glu385, Asp34, Asn276 e Arg175 constituem o sítio ativo potencial da enzima.


Subject(s)
Escherichia coli/genetics , alpha-Amylases/genetics , alpha-Amylases/metabolism , Temperature , Enzyme Stability , Cloning, Molecular , Geobacillus , Hydrogen-Ion Concentration
4.
Tropical Biomedicine ; : 214-221, 2021.
Article in English | WPRIM | ID: wpr-904744

ABSTRACT

@# Corona virus SARS-CoV-2-induced viral disease (COVID-19) is a zoonotic disease that was initially transmitted from animals to humans. The virus surfaced towards the end of December 2019 in Wuhan, China where earlier SARS (Severe Acute Respiratory Syndrome) had also surfaced in 2003. Unlike SARS, SARS-CoV-2 (a close relative of the SARS virus) created a pandemic, and as of February 24 2021, caused 112,778,672 infections and 2,499,252 deaths world-wide. Despite the best efforts of scientists, no drugs against COVID-19 are yet in sight; five vaccines have received emergency approval in various countries, but it would be a difficult task to vaccinate twice the world population of 8 billion. The objective of the present study was to evaluate through in silico screening a number of phytochemicals in Allium cepa (onion) regarding their ability to bind to the main protease of COVID-19 known as the 3C-like protease or 3CLpro, (PDB ID: 6LU7), 3CLpro of SARS (PDB ID: 3M3V), and human angiotensin converting enzyme-2 (ACE-2), [PDB ID: 1R42], which functions as a receptor for entry of the virus into humans. Molecular docking (blind docking, that is docking not only against any target pocket) were done with the help of AutoDockVina. It was observed that of the twenty-two phytochemicals screened, twelve showed good binding affinities to the main protease of SARS-CoV-2. Surprisingly, the compounds also demonstrated good binding affinities to ACE-2. It is therefore very likely that the binding affinities shown by these compounds against both 3CLpro and ACE-2 merit further study for their potential use as therapeutic agents.

5.
Acta Pharmaceutica Sinica B ; (6): 3417-3432, 2021.
Article in English | WPRIM | ID: wpr-922805

ABSTRACT

Compounds that selectively modulate multiple targets can provide clinical benefits and are an alternative to traditional highly selective agents for unique targets. High-throughput screening (HTS) for multitarget-directed ligands (MTDLs) using approved drugs, and fragment-based drug design has become a regular strategy to achieve an ideal multitarget combination. However, the unexpected presence of pan-assay interference compounds (PAINS) suspects in the development of MTDLs frequently results in nonspecific interactions or other undesirable effects leading to artefacts or false-positive data of biological assays. Publicly available filters can help to identify PAINS suspects; however, these filters cannot comprehensively conclude whether these suspects are "bad" or innocent. Additionally, these

6.
Chinese Journal of Biotechnology ; (12): 2836-2844, 2021.
Article in Chinese | WPRIM | ID: wpr-887846

ABSTRACT

It has been reported that ODB genes play an important role in homologous recombination-directed DNA repair, suggesting their potential applications in plant breeding. To analyze the expression characteristics of tobacco NtODB gene, the cDNA sequence of NtODB was obtained using in silico cloning technique. The physicochemical properties, signal peptide, and advanced structures of the predicted protein were analyzed using bioinformatics tools. The results showed that the NtODB gene has a 579-bp open reading frame which encodes a protein with 192 amino acid residues. The protein NtODB is predicted to be alkaline and hydrophilic. Real-time quantitative PCR showed that NtODB was constitutively expressed in different tissues. Subcellular localization showed that NtODB was mainly expressed in cell membrane and chloroplast. These results may help us to better understand and elucidate the roles of ODB genes in the homologous recombination-directed DNA repair.


Subject(s)
Amino Acid Sequence , Base Sequence , Cloning, Molecular , Computational Biology , Computer Simulation , DNA, Complementary , Phylogeny , Plant Breeding , Tobacco/genetics
7.
Article in Chinese | WPRIM | ID: wpr-883516

ABSTRACT

Taxifolin has a plethora of therapeutic activities and is currently isolated from the stem bark of the tree Larix gmelinni(Dahurian larch).It is a flavonoid of high commercial interest for its use in supplements or in antioxidant-rich functional foods.However,its poor stability and low bioavailability hinder the use of flavonoid in nutritional or pharmaceutical formulations.In this work,taxifolin isolated from the seeds of Mimusops balata,was evaluated by in silico stability prediction studies and in vitro forced degradation studies(acid and alkaline hydrolysis,oxidation,visible/UV radiation,dry/humid heating)monitored by high performance liquid chromatography with ultraviolet detection(HPLC-UV)and ultrahigh perfor-mance liquid chromatography-electrospray ionization-mass spectrometry(UPLC-ESI-MS).The in silico stability prediction studies indicated the most susceptible regions in the molecule to nucleophilic and electrophilic attacks,as well as the sites susceptible to oxidation.The in vitro forced degradation tests were in agreement with the in silico stability prediction,indicating that taxifolin is extremely unstable(class 1)under alkaline hydrolysis.In addition,taxifolin thermal degradation was increased by humidity.On the other hand,with respect to photosensitivity,taxifolin can be classified as class 4(stable).Moreover,the alkaline degradation products were characterized by UPLC-ESI-MS/MS as dimers of taxifolin.These results enabled an understanding of the intrinsic lability of taxifolin,contributing to the development of stability-indicating methods,and of appropriate drug release systems,with the aims of preserving its stability and improving its bioavailability.

8.
Rev. cuba. invest. bioméd ; 40(supl.1): e678, 2021. tab, graf
Article in Spanish | LILACS, CUMED | ID: biblio-1289466

ABSTRACT

Introducción: Los hongos comestibles, en particular Pleurotus ostreatus, representan una importante fuente de metabolitos bioactivos con propiedades inmunomoduladoras, antioxidantes y antiinflamatorias. Trabajos recientes han demostrado que extractos y compuestos purificados a partir de esta seta, entre ellos, la fracción rica en fenoles, inhiben el factor nuclear kappa B(NF-κB), la cicloxigenasa (COX) y modulan cascadas de señalización relacionadas con el balance redox. De acuerdo con estos antecedentes, dichos compuestos podrían actuar, además, como inhibidores de la enzima 5- lipoxigenasa (5-LOX). Objetivo: Evaluar el efecto in silico de trece compuestos fenólicos presentes en la especie Pleurotus ostreatus sobre la enzima 5-LOX, al utilizar como compuesto de referencia la mangiferina. Métodos: El acoplamiento se llevó a cabo a través del programa AutoDock 4.2 (http://autodock.scripps.edu) y la estructura de 5 LOX se obtuvo con la base de datos de proteínas, PDB (www.wwpdb.org). Se estimaron la energía libre (ΔG), la constante de disociación (Ki) y la eficiencia de ligando (LE). Se obtuvieron los parámetros de similitud a un fármaco y los relacionados con la absorción, distribución, metabolismo, excreción y toxicidad (ADME/T) de los mejores modelos de acoplamiento. Resultados: Los mejores indicadores de ΔG y Ki, correspondieron a los ácidos homogentísico, clorogénico y gentísico, con valores de ΔG (-11,81; -12,28 y -11,67 kcal/moL) y Ki (2,19 10-9; 9,99 10-10, 2,79 10-9 M), respectivamente. La eficiencia de ligando alcanzó valores adecuados para estos tres compuestos fenólicos. El modelo de acoplamiento del ácido homogentísico mostró los mejores resultados en cuanto a la similitud a un fármaco y pruebas ADME/T. Conclusiones: El estudio in silico reveló las potencialidades de la fracción rica en fenoles de P. ostreatus, y en particular, del ácido homogentísico como inhibidor de la enzima 5 -LOX, y justifica el desarrollo de ensayos confirmativos in vitro/ in vivo que corroboren sus efectos antioxidantes y antinflamatorios(AU)


Introduction: Edible mushrooms, Pleurotus ostreatus in particular, are an important source of bioactive metabolites with immunomodulatory, antioxidant and anti-inflammatory properties. Recent studies have shown that extracts and compounds purified from this mushroom, among them the phenol-rich fraction, inhibit nuclear factor kappa B (NF-κB), cyclooxygenase (COX), and modulate signaling cascades related to redox balance. According to these antecedents, such compounds could also act as inhibitors of the enzyme 5-lipoxygenase (5-LOX). Objective: Evaluate the in silico effect of 13 phenolic compounds present in the species Pleurotus ostreatus on the enzyme 5-LOX using mangiferin as reference compound. Methods: Docking was carried out with the software AutoDock 4.2 (http://autodock.scripps.edu) and the 5-LOX structure was obtained with the protein database PDB (www.wwpdb.org). Estimation was performed of free energy (ΔG), dissociation constant (Kd) and ligand efficiency (LE). Drug-likeness parameters were obtained, as well as those related to absorption, distribution, metabolism, excretion and toxicity (ADMET) of the best docking models. Results: The best ΔG and Kd indicators were homogentisic, chlorogenic and gentisic acids, with ΔG and Kd values of -11.81, -12.28, -11.67 kcal/mol, and 2.19 10-9, 9.99 10-10, 2.79 10-9 M, respectively. Ligand efficiency achieved adequate values for these three phenolic compounds. The docking model for homogentisic acid showed the best results in terms of drug likeness and ADMET tests. Conclusions: The in silico study revealed the potential of the phenol-rich fraction of P. ostreatus, homogentisic acid in particular, as an enzyme 5-LOX inhibitor, and justifies the development of confirmatory in vitro / in vivo assays to corroborate its antioxidant and anti-inflammatory effects(AU)


Subject(s)
Humans , Male , Female , Arachidonate 5-Lipoxygenase , Pharmacokinetics , Reference Parameters
9.
Article | IMSEAR | ID: sea-212536

ABSTRACT

Background: Cancer is one of the major causes of death worldwide. Current cancer therapy is costly, it has poor therapeutic outcomes and many side effects. Therefore, new medications are needed. Plants have been used as sources of anticancer drugs. Vepris species have anticancer properties. The purpose of this study is to assess Vepris nobilis, a plant found in Kenya as a potential source of anticancer drugs.Methods: The dichloromethane/methanol (CH2Cl2/MeOH) 1:1 extract of the stem bark of Vepris nobilis led to the isolation of an alkaloid named, 4,6-dimethoxy-7-((3-methylbuta-1,3-dien-1-yl)oxy)furo[2,3-b]quinolone. SwissADME online tool was used to assess the compound’s pharmacokinetic parameters. Pass online tool identified potential targets while protox server described the toxicity of the compound. Chimera and Avogadro softwares were used for molecular docking studies.Results: In-silico pharmacokinetic studies, showed that the isolated compound complied with Lipinski rule of five, it showed high gastrointestinal activity, and it also inhibits cytochrome P450 (CYP) isoforms 1A2, 2C9 and 2C19. In toxicity studies the compound was relatively safe with a predicted median lethal dose (LD50) of 1600 mg/kg, apart from potential immunotoxicity and mutagenicity. Molecular docking studies demonstrated that, the compound has potential anticancer activity, it interacted with deoxyribonucleic acid (DNA) topoisomerase I in an almost similar manner to camptothecin though it had less binding potential.Conclusions: 4,6-dimethoxy-7-((3-methylbuta-1,3-dien-1-yl)oxy) furo[2,3-b]quinolone derived from Vepris nobilis is a potential drug for the management of cancer which can be administered orally.

10.
Article | IMSEAR | ID: sea-215884

ABSTRACT

Glycyrrhizin is a phytocompound which is derived from Glycyrrhiza glabra. It is used in treating the upper respiratory tract disease like cough, bronchitis, laryngitis, sore throat, etc. It has various medicinal uses in rheumatism, peptic ulcers, asthma, allergies, and inflammation. Glycyrrhizin has been reported to possess antibacterial, antiviral, antioxidant, anti inflammatory properties. In view of the above facts, the present in silicostudy was designed to demonstrate the molecular mechanism underlying the antimicrobial activity of glycyrrhizin against common dental pathogens such as Streptococcus mutans, Porphyromonas gingivalis, Treponema denticola, Enterococcus faecalisandTannerella forsythia.The STITCH tool was used to identify the drug-protein interaction. The functional class of the protein was deduced using VICMPred, followed by the identification of epitopes on the virulence factors using BepiPred. Further, the subcellular location of the virulence factors were also studied using PSORTb software. The computational analysis performed identified several virulence factors viz., short chain dehydrogenase/reductase family oxidoreductase of Treponema denticola and D-mannonate oxidoreductase of Tannerella forsythiawhich were found to interact with glycyrrhizin. Interestingly, phosphopyruvate hydratase was found to be the protein present in all the five genera was shown to interact with glycyrrhizin. Thus the present study reveals the target proteins on the dental pathogens which were shown to interact with glycyrrhizin. Furthermore,experimental validation of the resultsare warranted to provide substantial details on the anti-microbial activity of glycyrrhizin against common dental pathogens

11.
Article | IMSEAR | ID: sea-215877

ABSTRACT

The cell suicide pathway of apoptosis is a necessary event in the life of multicellular organisms. It is involved in many biological processes ranging from development to the immune response. Over expression of interleukin-1β-converting enzyme (later renamed caspase-1) was shown to be sufficient to induce apoptosis in mammalian cells. The present study aims to assess the gene alterations in the Caspase family of cytochromes so as to derive an association with HNSCC. Earlier eleven genes were found in the human genome to encode 11 human caspases, caspase-1 to caspase-10 and caspase-14, which is now populated to 13, whereas 10 genes were found in the mouse genome to encode 10 murine caspases including caspase-1, 2, 3, 6, 7, 8, 9, 11, 12 and 14 Caspases share a number of features distinguishable from other proteases. The analysis follows an observational study design, employing several computational tools to identify and predict the possible outcomes of gene alterations identified in HNSCC patients. cBioportal server was used to identify the gene alterations which was further analyzed using tools such as PROVEAN, I-Mutant and gnomAD. Several reported polymorphic variants were also identified. The pathogenicity and protein stability of gene alterations documented in the present study were identified at standard biological conditions. Further experimental studies would provide concrete evidence on the association of the observed genetic abnormalities with HNSCC especially in individuals exposed to habitual carcinogens

12.
Article | IMSEAR | ID: sea-210637

ABSTRACT

The studies have suggested that advanced glycation end products (AGEs) induce stress oxidative and inflammatorypathway, which results in chronic complication. Centella asiatica (CA) has been shown as a promising candidate forAGE inhibitor due to its ability of reducing AGE production. This study aims to explore the molecular docking ofCA active compound as an inhibitor of AGEs and receptor AGEs (RAGEs). The top three docking structures werepicked for molecular dynamic (MD) simulations. Based on MD simulation in this study, we found that CA activecompound had been proven to interact with AGEs and RAGE. AGEs bound to asiaticoside, madasiatic acid, andmadecassic acid with a binding energy of −11.8253, −10.6724, and −10.1462 kcal/mol, respectively. Nonetheless,Asn106, Asp324, Asp376, Tyr420, and Tyr500 of AGEs made a significant contribution to the complex of asiaticosideAGE, as well as those for the madasiatic acid AGE, which were Asn118 and Tyr500. RAGE bound to asiaticoside,asiatic acid, and isothankunik acid with a binding energy of −10.6125, −9.4469, and −9.1015 kcal/mol, respectively.CA active compounds, specifically asiatic acid, madasiatic acid, and madecassic acid, interacted with AGEs, whereasasiaticoside and isothankunik acid interacted with RAGE based on docking and model studies.

13.
Article | IMSEAR | ID: sea-210610

ABSTRACT

The aim of this research is to design the new mono-carbonyl analogs of curcumin, synthesize the molecules, anddetermine its activity in cyclooxygenase inhibition in vitro and in silico. New design MACs were performed bythe Quantitative Structure–Activity Relationship (QSAR) study using the BuildQSAR program. 2,6-bis-(3ʹ-ethoxy,4ʹ-hydroxybenzylidene)-cyclohexanone, 2,6-bis-(3ʹ-Bromo, 4ʹ-methoxybenzylidene)-cyclohexanone, and 2,6-bis-(3ʹ,4ʹ-dimethoxybenzylidene)-cyclohexanone had been synthesized using aldol condensation reaction. The anti-inflammatoryassay was performed to measure the level of malondialdehyde. In silico studies were carried out to evaluate the activityof cyclooxygenase inhibition in cyclooxygenase-1 and cyclooxygenase-2 specific proteins. Molecular operatingenvironment program was used for protocol docking. The results of the QSAR study reveal the good relationshipof anti-inflammatory activities. The in vitro anti-inflammatory activities of 6-bis-(3ʹ-ethoxy, 4ʹ-hydroxybenzylidene)-cyclohexanone, 2,6-bis-(3ʹ-Bromo, 4ʹ-methoxybenzylidene)-cyclohexanone, and 2,6-bis-(3ʹ,4ʹ-dimethoxybenzylidene)-cyclohexanone indicate the promising potential to inhibit cyclooxygenase enzyme with IC50 13.53 μM, 11.56 μM,and 20.52 μM, respectively. The in silico evaluation showing that O atoms (47, from ketones) of 2,6-bis-(3ʹ-Bromo,4ʹ-methoxybenzylidene)-cyclohexanone interact with ARG120 and TYR355 through H acceptor.

14.
Article | IMSEAR | ID: sea-215736

ABSTRACT

Aim:To systematically design, synthesize and evaluate the biological activities of new threonine-based sulfonamide derivatives in order to achieve improved drug potency.Methodology: Sulfamoyl carboxylic acidswere prepared by the reaction of threonine with the appropriate sulfonyl chloride while their acetylated, carboxamide and aniline derivatives were synthesized via Lumiere-Barbier acetylation, Schotten-Baumann ammonolysis and Buchwald-Hartwig cross-coupling methods respectively. The FTIR, 1H-NMR, 13C-NMR and elemental analytical data were employed in the structural characterization. In vitro andin silico antioxidant and antimicrobial studies were carried out.Results:Compounds 1b and 1d displayed thebest in vitro antibacterial activities againstEscherichia coli, Salmonella typhi, Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and antifungal activities against Candida albicansandAspergillus niger. Compound 1f (IC50= 1.150±0.003μg/ml) exhibited the best in vitro antioxidant activity. Compound 1a had a higherin silicoantibacterial (-11.51 kcal/mol) binding energies than antibacterial reference drug, penicillin (-10.89 kcal/mol). Compound 1c had the highest in silicoantifungal binding energy (-10.48kcal/mol)comparable to ketoconazole(-10.85 kcal/mol). Conclusion: All the compounds were found to be potential antioxidant and antimicrobial drug candidates having complied with Lipinski’s rule of five.

15.
Article | IMSEAR | ID: sea-210713

ABSTRACT

The study aimed to investigate the phytochemical profiles, in vitro antioxidant activity, and in silico molecular dockingantidiabetic activity of the aqueous root extracts of Ruellia tuberosa L. The phytochemical qualitative tests revealedthe positive detections of tannins, flavonoids, ascorbic acid, and phenolic compounds. Using Liquid chromatographyhigh-resolution mass spectrometry (LC-HRMS) analysis, 12 compounds were tentatively identified in the extracts.The major compounds were tentatively identified as betaine, daidzein, hispidulin, α-linoleic acid, and 4-coumaric acid.The aqueous root extracts have high antioxidant activity with the IC50 value of 15.2 mg/ml against DPPH free radicals.The major putatively identified compounds were docked to human pancreatic α-amylase protein, to investigate theirinhibitory activities to this enzyme. The interaction between betaine, daidzein, and hispidulin in docking with humanpancreatic a-amylase showed different binding sites to the protein. In addition, the types of bonds involved weremostly hydrogen and hydrophobic bonds which show the interactions between three ligands and α-amylase. Energygenerated from docking between betaine, daidzein, and hispidulin with α-amylase was −137.6, −245.8, and −236.7cal/mol, respectively. This study concludes that the aqueous root extracts of R. tuberosa L. have prospective as aninhibitor for a-amylase protein and to be used as antidiabetic agent. Further, in vitro and in vivo studies are needed toconfirm this work.

16.
Braz. j. biol ; 80(1): 39-46, Feb. 2020. graf
Article in English | LILACS | ID: biblio-1089293

ABSTRACT

Abstract The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics' tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.


Resumo O presente estudo objetivou avaliar se o polimorfismo causal A122V promove alterações nas propriedades funcionais e estruturais da proteína receptora de quimiocina CXC do tipo 1 (CXCR1) de bovino Bos taurus por análises in silico. Duas sequências de aminoácidos da CXCR1 bovina foram selecionadas a partir do banco de dados UniProtKB/Swiss-Prot: a) sequência não-polimórfica (A7KWG0) contendo alanina (A) na posição 122, e b) sequência polimórfica carreando o polimorfismo A122V, causando a substituição de alanina por valina (V) na mesma posição. As sequências CXCR1 foram analisadas por diferentes ferramentas de Bioinformática para examinar o efeito desse polimorfismo sobre sua estabilidade, função e estrutura, predizer eventuais alterações na sua modelagem estrutural 3-D, bem como estimar a qualidade dos modelos preditos. O polimorfismo A122V exerceu efeitos toleráveis e não-deletérios sobre a CXCR1 polimórfica, apresentando um modelo estrutural de alfa-hélice típico de uma proteína receptora transmembranar para ambas as proteínas. Embora maiores variações nas distâncias entre os pares de aminoácidos nas posições-alvo tenham sido detectadas na proteína polimórfica, mais do que 97% dos aminoácidos em ambos os modelos foram situados em regiões ditas favoráveis e permitidas nos diagramas de Ramachandran. Evidências sustentam que o polimorfismo de nucleotídeo único A122V na proteína receptora CXCR1 está associado à aumentada incidência de mastite clínica em vacas leiteiras. Assim, as descobertas descritas aqui comprovam que a substituição do aminoácido alanina por valina provoca mudanças conformacionais locais na proteína CXCR1 polimórfica, que podem estar diretamente afetando seus mecanismos de enovelamento pós-traducionais e sua função biológica.


Subject(s)
Animals , Female , Polymorphism, Single Nucleotide , Receptors, Interleukin-8A , Cattle , Amino Acid Sequence
17.
Article | IMSEAR | ID: sea-206291

ABSTRACT

Delivering a potential drug is a predominant challenge in medicinal chemistry.in this study, bio organic compounds of Cymbopogon citratus was screened by analysing physiochemical properties like solubility, permeability, efficacy, toxicity, and metabolic stability. The optimization of drug potential against virulent protein was calculated by using docking algorithm Autodock 4.2.3. Structure based ligand docking reveals that the compounds having better inhibition potential against virulent enzymes with insoluble and impermeable activities. The organic compounds of Cymbopogon citratus were screened using Lipinski rule of five and ADME/T prediction for drug likeliness. The structure based ligand docking was done between bioactive compounds of plant and virulent protein that cause diseases. The interaction was visualized using Discovery studio and was studies. The molecular docking of bioactive compounds resulted in better inhibition potential with controlled lipophilicity level, without causing toxicity that harms the natural habitat of humans. The compounds, 1,3,4-trimethyl -3cyclohexene-1-carboxaldehyde exhibit binding energy -4.70 Kcal/mol followed by β-myrcene – 4.35 Kcal/mol and Geraniol -4.35 Kcal/mol. Hence, structure based ligand docking and in silico ADME/T studies revealed that the compounds have better inhibition potential against Apolipoprotein by improving the prediction of drug compounds.

18.
Mem. Inst. Oswaldo Cruz ; 115: e200179, 2020. graf
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1135266

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection depends on viral polyprotein processing, catalysed by the main proteinase (Mpro). The solution of the SARS-CoV-2 Mpro structure allowed the investigation of potential inhibitors. This work aims to provide first evidences of the applicability of commercially approved drugs to treat coronavirus disease-19 (COVID-19). We screened 4,334 compounds to found potential inhibitors of SARS-CoV-2 replication using an in silico approach. Our results evidenced the potential use of coagulation modifiers in COVID-19 treatment due to the structural similarity of SARS-CoV-2 Mpro and human coagulation factors thrombin and Factor Xa. Further in vitro and in vivo analysis are needed to corroborate these results.


Subject(s)
Humans , Protease Inhibitors/chemistry , Viral Nonstructural Proteins/antagonists & inhibitors , Betacoronavirus , Structure-Activity Relationship , Computer Simulation , Cysteine Endopeptidases , Coronavirus Infections/drug therapy , Coronavirus 3C Proteases , SARS-CoV-2 , COVID-19/drug therapy
19.
Article in Chinese | WPRIM | ID: wpr-865658

ABSTRACT

5-Dimethylaminopropylamino-8-hydroxytriazoloacridinone (C-1305) is a promising antitumor com-pound developed in our laboratory. A better understanding of its metabolic transformations is still needed to explain the multidirectional mechanism of pharmacological action of triazoloacridinone de-rivatives at all. Thus, the aim of the current work was to predict oxidative pathways of C-1305 that would reflect its phase Ⅰ metabolism. The multi-tool analysis of C-1305 metabolism included electrochemical conversion and in silico sites of metabolism predictions in relation to liver microsomal model. In the framework of the first approach, an electrochemical cell was coupled on-line to an electrospray ioni-zation mass spectrometer. The effluent of the electrochemical cell was also injected onto a liquid chromatography column for the separation of different products formed prior to mass spectrometry analysis. In silico studies were performed using MetaSite software. Standard microsomal incubation was employed as a reference procedure. We found that C-1305 underwent electrochemical oxidation pri-marily on the dialkylaminoalkylamino moiety. An unknown N-dealkylated and hydroxylated C-1305 products have been identified. The electrochemical system was also able to simulate oxygenation re-actions. Similar pattern of C-1305 metabolism has been predicted using in silico approach. Both proposed strategies showed high agreement in relation to the generated metabolic products of C-1305. Thus, we conclude that they can be considered as simple alternatives to enzymatic assays, affording time and cost efficiency.

20.
Article in English | WPRIM | ID: wpr-846744

ABSTRACT

Objective: To explore the efficacy of intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine and pyrimethamine (SP) against sensitive parasites. Methods: A pharmacological model was used to investigate the effectiveness of the previous recommended at least two-dose regimen, currently recommended three-dose regimen and 4, 6, 8-weekly regimens with specific focus on the impact of various non-adherence patterns in multiple transmission settings. Results: The effectiveness of the recommended three-dose regimen is high in all the transmission intensities, i.e. >99%, 98% and 92% in low, moderate and high transmission intensities respectively. The simulated 4 and 6 weekly IPTp-SP regimens were able to prevent new infections with sensitive parasites in almost all women (>99%) regardless of transmission intensity. However, 8 weekly interval dose schedules were found to have 71% and 86% protective efficacies in high and moderate transmission areas, respectively. It highlights that patients are particularly vulnerable to acquiring new infections if IPTp-SP doses are missed. Conclusions: The pharmacological model predicts that full adherence to the currently recommended three-dose regimen should provide almost complete protection from malaria infection in moderate and high transmission regions. However, it also highlights that patients are particularly vulnerable to acquiring new infections if IPTp doses are spaced too widely or if doses are missed. Adherence to the recommended IPTp-SP schedules is recommended.

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