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This study investigates the toxic effects of the insecticide spinetoram on the model organism Bombyx mori (Linnaeus) and explores the potential ameliorative properties of O-Vanillin. Sub-lethal concentrations of spinetoram were given to silkworm larvae via oral feed, resulting in reduced body weight, larval length, and impaired cocoon characteristics. A study of the enzymatic and non-enzymatic antioxidants revealed oxidative stress in the gut, fat body, and silk gland tissues, characterized by decreased antioxidants and increased lipid peroxidation. However, post-treatment with O-Vanillin effectively mitigated these toxic effects, preserving antioxidant capacities and preventing lipid peroxidation. Additionally, O-Vanillin prevented the loss of body weight and improved cocoon characteristics. At the histological level, spinetoram exposure caused mild histological damage in the gut, fat body, and silk gland. However, O-Vanillin post-treatment had ameliorative effects and mitigated the histological damages. To delve deeper into the mechanism of amelioration of O-Vanillin, in silico studies were used to study the interaction between an important xenobiotic metabolism protein of the Bombyx mori, i.e., Cytochrome p450, specifically CYP9A19, and O-Vanillin. We performed blind molecular docking followed by molecular dynamic simulation, and the results demonstrated stable binding interactions between O-Vanillin and CYP9A19, a cytochrome P450 protein in silkworm, belonging to the subfamily CYP9A, suggesting a potential role for O-vanillin in modulating xenobiotic metabolism.
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Benzaldeídos , Bombyx , Inseticidas , Larva , Estresse Oxidativo , Animais , Bombyx/efeitos dos fármacos , Estresse Oxidativo/efeitos dos fármacos , Benzaldeídos/farmacologia , Larva/efeitos dos fármacos , Simulação de Acoplamento Molecular , Antioxidantes , Peroxidação de Lipídeos/efeitos dos fármacosRESUMO
Alcohol acyltransferases (AATs) play a crucial role in catalyzing the transfer of acyl groups, contributing to the diverse aroma of fruits, including strawberries. In this research we identified nine AAT genes in strawberries through a comprehensive analysis involving phylogenetics, gene structure, conserved motifs, and structural protein model examinations. The study used the 'Camarosa' strawberry genome database, and experiments were conducted with fruits harvested at different developmental and ripening stages. The transcriptional analysis revealed differential expression patterns among the AAT genes during fruit ripening, with only four genes (SAAT, FaAAT2, FaAAT7, and FaAAT9) showing increased transcript accumulation correlated with total AAT enzyme activity. Additionally, the study employed in silico methods, including sequence alignment, phylogenetic analysis, and structural modeling, to gain insights into the AAT protein model structures with increase expression pattern during fruit ripening. The four modeled AAT proteins exhibited structural similarities, including conserved catalytic sites and solvent channels. Furthermore, the research investigated the interaction of AAT proteins with different substrates, highlighting the enzymes' promiscuity in substrate preferences. The study contributes with valuable information to unveil AAT gene family members in strawberries, providing scientific background for further exploration of their biological characteristics and their role in aroma biosynthesis during fruit ripening.
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Fragaria , Frutas , Filogenia , Proteínas de Plantas , Fragaria/genética , Fragaria/enzimologia , Fragaria/metabolismo , Fragaria/crescimento & desenvolvimento , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Frutas/genética , Frutas/crescimento & desenvolvimento , Frutas/enzimologia , Frutas/metabolismo , Aciltransferases/genética , Aciltransferases/metabolismo , Regulação da Expressão Gênica de Plantas , Sequência de AminoácidosRESUMO
Multiple drug-resistant fungal species are associated with the development of diseases. Thus, more efcient drugs for the treatment of these aetiological agents are needed. Rondonin is a peptide isolated from the haemolymph of the spider Acanthoscurria rondoniae. Previous studies have shown that this peptide has antifungal activity against Candida sp. and Trichosporon sp. strains, acting on their genetic material. However, the molecular targets involved in its biological activity have not yet been described. Bioinformatics tools were used to determine the possible targets involved in the biological activity of Rondonin. The PharmMapper server was used to search for microorganismal targets of Rondonin. The PatchDock server was used to perform the molecular docking. UCSF Chimera software was used to evaluate these intermolecular interactions. In addition, the I-TASSER server was used to predict the target ligand sites. Then, these predictions were contrasted with the sites previously described in the literature. Molecular dynamics simulations were conducted for two promising complexes identifed from the docking analysis. Rondonin demonstrated consistency with the ligand sites of the following targets: outer membrane proteins F (id: 1MPF) and A (id: 1QJP), which are responsible for facilitating the passage of small molecules through the plasma membrane; the subunit of the favoprotein fumarate reductase (id: 1D4E), which is involved in the metabolism of nitrogenous bases; and the ATP-dependent Holliday DNA helicase junction (id: 1IN4), which is associated with histone proteins that package genetic material. Additionally, the molecular dynamics results indicated the stability of the interaction of Rondonin with 1MPF and 1IN4 during a 10 ns simulation. These interactions corroborate with previous in vitro studies on Rondonin, which acts on fungal genetic material without causing plasma membrane rupture. Therefore, the bioprospecting methods used in this research were considered satisfactory since they were consistent with previous results obtained via in vitro experimentation.
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CONTEXT: 2,2,2-Trifluoroethanol has been widely used to study the structure and dynamic properties of intrinsically disordered proteins. Experimentally, it is known that TFE-water mixtures stabilize secondary structures of IDPs, and therefore, it allows the studying of conformational ensembles of these proteins. In the last decades, molecular dynamic simulations have helped study the IDPs' conformational ensemble. Unfortunately, conventional MD requires very long simulation times to describe the properties of IDPs. Therefore, a variety of accelerated sampling techniques have been developed and employed. The TFE-water mixture arrangement description through MD has faced substantial difficulties since emulating the TFE nanocrowding at certain TFE:H[Formula: see text]O ratios (around 15-40% of TFE). In this work, we determine the most suitable conditions that reproduce experimentally reported properties of TFE-water mixtures. We compared the employment of conventional MD and GaMD simulations and various water parameters. Our results show that the combination of parameters that better reproduce the experimental information is the combination of the TIP4PD water model and GaMD simulations. Therefore, these conditions help accurately describe the structural ensemble of IDPs in TFE-water mixtures. METHODS: Conventional MD and GaMD simulations were performed under AMBER 18 software. The TFE and water molecules were described using GAFF2 and a variety of water models, such as TIP3P, TIP4P2005, TIP4PD, and TIP5P, respectively. The systems were simulated a 100 ns at 298 K.
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Suppressor of gamma response 1 (SOG1) is a member of the NAC domain family transcription factors of the DNA damage response (DDR) signaling in the plant's genome. SOG1 is directly involved in transcriptional response to DNA damage, cell cycle checkpoints and ATR or ATM-mediated activation of the DNA damage responses and repair functioning in programmed cell death and regulation of end reduplication. Different mutations in the SOG1 protein lead to severe diseases and, ultimately, cell death. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that cause different diseases or programmed cell death. The current study applied different computational approaches to Arabidopsis thaliana L. SOG1 protein to identify the potential deleterious nsSNPs and monitor their impact on the structure, function and protein stability. Various bioinformatics tools were applied to analyze the retrieved 34 nsSNPs and interestingly extracted four deleterious nsSNPs, that is, ensvath13968004 (Q166L), tmp18998388 (P159L), ensvath01103049 (K199N) and tmp18998295 (Y190F). For example, homology modeling, conservation and conformational analysis of the mutant's models were considered to scrutinize the deviations of these variants from the native SOG1 structure. All atoms molecular dynamic simulation confirmed the significance of these mutations on the protein stability, residual and structural conformation, compactness, surface conformation, dominant motion, Gibbs free energy distribution and dynamic effects. Similarly, protein-protein interaction revealed that SOG1 operates as a hub-linking cluster of various proteins, and any changes in the SOG1 might result in the disassociation of several signal transduction cascades.Communicated by Ramaswamy H. Sarma.
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Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Simulação de Dinâmica Molecular , Fatores de Transcrição/genética , Dano ao DNA , Mutação , Polimorfismo de Nucleotídeo Único , Proteínas de Arabidopsis/genéticaRESUMO
When dental infections occur, various types of antibiotics are used to combat them. The most common antibiotics to be used are tetracycline and chloramphenicol; likewise, the most common bacteria in dental infections are Enterococcus faecalis and Streptococcus mutans. In the present work, we have studied by molecular mechanics methods the interactions of the ribosomal proteins L16 present in Enterococcus faecalis and Streptococcus mutans, identified with UNIPROT code Q839F7 and Q8DS20, respectively. We evaluated the interactions between Q839F7 and Q8DS20 with tetracycline and chloramphenicol antibiotics. We found that the interaction between Enterococcus faecalis (Q839F7) is much more favorable when treated with chloramphenicol. In contrast, the interaction with tetracycline is favored in the case of Q8DS20 present in Streptococcus mutans. This suggests that the treatment should be differentiated depending on the infection level and the presence of some of these bacteria.
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In the present work, a library of 239 frentizole derivatives formerly synthesized by our research group were virtually screened on the FRB domain of mTOR in a search of potential binders for further experimental evaluation. 39 compounds from this library were virtually selected and classified in 7 groups according to their structural features. 9 representative compounds of these 7 groups were further submitted to rounds of MD simulation and MM-PBSA calculations. Analysis of our results pointed to the most promising among these groups as binders to the FRB domain of mTOR. We believe that they structurally represent a priority portion of the original library for further experimental evaluation.
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Simulação de Dinâmica Molecular , Serina-Treonina Quinases TOR , Serina-Treonina Quinases TOR/metabolismoRESUMO
Deschampsia antarctica Desv. (Poaceae) is one of the two vascular plants that have colonized the Antarctic Peninsula, which is usually exposed to extreme environmental conditions. To support these conditions, the plant carries out modifications in its morphology and metabolism, such as modifications to the cell wall. Thus, we performed a comparative study of the changes in the physiological properties of the cell-wall-associated polysaccharide contents of aerial and root tissues of the D. antarctica via thermogravimetric analysis (TGA) combined with a computational approach. The result showed that the thermal stability was lower in aerial tissues with respect to the root samples, while the DTG curve describes four maximum peaks of degradation, which occurred between 282 and 358 °C. The carbohydrate polymers present in the cell wall have been depolymerized showing mainly cellulose and hemicellulose fragments. Additionally, a differentially expressed sequence encoding for an expansin-like (DaEXLA2), which is characterized by possessing cell wall remodeling function, was found in D. antarctica. To gain deep insight into a probable mechanism of action of the expansin protein identified, a comparative model of the structure was carried out. DaEXLA2 protein model displayed two domains with an open groove in the center. Finally, using a cell wall polymer component as a ligand, the protein-ligand interaction was evaluated by molecular dynamic (MD) simulation. The MD simulations showed that DaEXLA2 could interact with cellulose and XXXGXXXG polymers. Finally, the cell wall component description provides the basis for a model for understanding the changes in the cell wall polymers in response to extreme environmental conditions.
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Parede Celular , Poaceae , Celulose/química , Ligantes , Simulação de Dinâmica Molecular , Poaceae/fisiologiaRESUMO
DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock Vina, DOCK 6, and Consensus, implemented into Molecular Architect (MolAr), were evaluated for their ability to analyze those interactions, considering visual inspection, redocking, and ROC curve. Ligands were refined by Parametric Method 7 (PM7), and ligands and decoys were docked into the minor DNA groove (PDB code: 1VZK). As a result, the area under the ROC curve (AUC-ROC) was 0.98, 0.88, and 0.99 for AutoDock Vina, DOCK 6, and Consensus methodologies, respectively. In addition, we proposed a machine learning model to determine the experimental ∆Tm value, which found a 0.84 R2 score. Finally, the selected ligands mono imidazole lexitropsin (42), netropsin (45), and N,N'-(1H-pyrrole-2,5-diyldi-4,1-phenylene)dibenzenecarboximidamide (51) were submitted to Molecular Dynamic Simulations (MD) through NAMD software to evaluate their equilibrium binding pose into the groove. In conclusion, the use of MolAr improves the docking results obtained with other methodologies, is a suitable methodology to use in the DNA system and was proven to be a valuable tool to estimate the ∆Tm experimental values of DNA intercalating agents.
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N-(2-Hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) is a valproic acid (VPA) derivative that has shown promising antiproliferative effects in different cancer cell lines, such as A204, HeLa, and MDA-MB-231. However, its low water solubility could reduce its therapeutic effectiveness. To solve this problem, in this work, we incorporated HO-AAVPA into dimyristoyl-phosphatidylcholine (DMPC) liposomes in the presence or absence of cholesterol (CHOL). Using differential scanning calorimetry (DSC), we found that the transition enthalpy (ΔHtr) of DMPC liposomes is reduced in the presence of CHOL and/or HO-AAVPA, indicating the favorable interactions between CHOL and/or HO-AAVPA and DMPC. Further, by molecular dynamics simulations it was possible to observed that HO-AAVPA migrates from the center of the bilayer toward the water and lipid interface of the DPMC bilayer systems exposing the amine group to water and the aliphatic chain toward the interior of the bilayer. As a consequence, we observed an ordering of the lipid bilayer. Moreover, CHOL harbors into the inner bilayer membrane, increasing the order parameter of the system. The liposomal solutions loaded with HO-AAVPA were tested in the NIH3T3 cell line, showing a reduction in cell proliferation compared to those cells presented without liposomes.Communicated by Ramaswamy H. Sarma.
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Dimiristoilfosfatidilcolina , Lipossomos , Camundongos , Animais , Dimiristoilfosfatidilcolina/química , Dimiristoilfosfatidilcolina/metabolismo , Lipossomos/química , Células NIH 3T3 , Bicamadas Lipídicas/química , Colesterol/química , ÁguaRESUMO
Anaerobic sewage treatment is a proven technology in warm climate regions, and sponge-bed trickling filters (SBTFs) are an important post-treatment technology to remove residual organic carbon and nitrogen. Even though SBTFs can achieve a reasonably good effluent quality, further process optimization is hampered by a lack of mechanistic understanding of the factors influencing nitrogen removal, notably when it comes to mainstream anaerobically treated sewage. In this study, the factors that control the performance of SBTFs following anaerobic (i.e., UASB) reactors for sewage treatment were investigated. A demo-scale SBTF fed with anaerobically pre-treated sewage was monitored for 300 days, showing a median nitrification efficiency of 79% and a median total nitrogen removal efficiency of 26%. Heterotrophic denitrification was limited by the low organic carbon content of the anaerobic effluent. It was demonstrated that nitrification was impaired by a lack of inorganic carbon rather than by alkalinity limitation. To properly describe inorganic carbon limitation in models, bicarbonate was added as a state variable and sigmoidal kinetics were applied. The resulting model was able to capture the overall long-term experimental behaviour. There was no nitrite accumulation, which indicated that nitrite oxidizing bacteria were little or less affected by the inorganic carbon limitation. Overall, this study indicated the vital role of influent characteristics and operating conditions concerning nitrogen conversions in SBTFs treating anaerobic effluent, thus facilitating further process optimization.
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Desnitrificação , Nitrogênio , Anaerobiose , Reatores Biológicos , Carbono , Nitrificação , Nitrogênio/análise , Esgotos , Eliminação de Resíduos LíquidosRESUMO
Having rigorous mathematical models is essential for the design and scaling of adsorption columns. In this study, the dynamic behavior of the sulfamethoxazole adsorption on sugarcane bagasse was studied and compared using analytical models and a theoretical mechanistic model. Initially, fixed-bed column tests were carried out at different flow rates and bed heights. Then, the experimental data were fitted with the most widely used analytical kinetic models, and their fit and fixed-bed parameters were compared with the mechanistic model. Of all analytical models analyzed, the Log-Gompertz model was the one that had the best agreed with experimental data. Although some analytical models fitted the experimental data accurately, their usefulness was questionable. Their parameters did not show a clear relationship with the change in operating conditions, and in certain cases had different behavior from that observed in experimentation. Conversely, the mechanistic model not only predicted the breakthrough curves with great accuracy in the initial and transition stage (R2 > 0.92; SSE < 0.06), but it also estimated relevant parameters. Additionally, the effects of the global mass transfer coefficient (Ki) and the axial dispersion coefficient (Dz) on breakthrough curves were studied using the mechanistic model. Increasing Ki increased the slope of the breakthrough curves with a faster adsorption rate. Similarly, high values of Dz produced lower adsorption capacities of the adsorbent; and it was established that the axial dispersion is relevant in SMX adsorption on SB. The theoretical model presented can be used for the design, scaling, and optimization of adsorption columns.
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Saccharum , Poluentes Químicos da Água , Purificação da Água , Adsorção , Celulose , Modelos Teóricos , SulfametoxazolRESUMO
SARS-CoV and SARS-CoV-2 belong to the subfamily Coronaviridae and infect humans, they are constituted by four structural proteins: Spike glycoprotein (S), membrane (M), envelope (E) and nucleocapsid (N), and nonstructural proteins, such as Nsp15 protein which is exclusively present on nidoviruses and is absent in other RNA viruses, making it an ideal target in the field of drug design. A virtual screening strategy to search for potential drugs was proposed, using molecular docking to explore a library of approved drugs available in the DrugBank database in order to identify possible NSP15 inhibitors to treat Covid19 disease. We found from the docking analysis that the antiviral drugs: Paritaprevir and Elbasvir, currently both approved for hepatitis C treatment which showed some of the lowest free binding energy values were considered as repositioning drugs to combat SARS-CoV-2. Furthermore, molecular dynamics simulations of the Apo and Holo-Nsp15 systems were performed in order to get insights about the stability of these protein-ligand complexes.
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Antivirais/farmacologia , Benzofuranos/farmacologia , Tratamento Farmacológico da COVID-19 , Ciclopropanos/farmacologia , Endorribonucleases/antagonistas & inibidores , Imidazóis/farmacologia , Lactamas Macrocíclicas/farmacologia , Prolina/análogos & derivados , SARS-CoV-2/efeitos dos fármacos , Sulfonamidas/farmacologia , Proteínas não Estruturais Virais/antagonistas & inibidores , COVID-19/virologia , Reposicionamento de Medicamentos , Endorribonucleases/metabolismo , Humanos , Simulação de Acoplamento Molecular , Terapia de Alvo Molecular , Prolina/farmacologia , SARS-CoV-2/metabolismo , Proteínas não Estruturais Virais/metabolismoRESUMO
The aggregation of ß-amyloid peptides is associated to neurodegeneration in Alzheimer's disease (AD) patients. Consequently, the inhibition of both oligomerization and fibrillation of ß-amyloid peptides is considered a plausible therapeutic approach for AD. Herein, the synthesis of new naphthalene derivatives and their evaluation as anti-ß-amyloidogenic agents are presented. Molecular dynamic simulations predicted the formation of thermodynamically stable complexes between the compounds, the Aß1-42 peptide and fibrils. In human microglia cells, these compounds inhibited the aggregation of Aß1-42 peptide. The lead compound 8 showed a high affinity to amyloid plaques in mice brain ex vivo assays and an adequate log Poct/PBS value. Compound 8 also improved the cognitive function and decreased hippocampal ß-amyloid burden in the brain of 3xTg-AD female mice. Altogether, our results suggest that 8 could be a novel therapeutic agent for AD.
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Doença de Alzheimer/tratamento farmacológico , Peptídeos beta-Amiloides/antagonistas & inibidores , Naftalenos/farmacologia , Fármacos Neuroprotetores/farmacologia , Fragmentos de Peptídeos/antagonistas & inibidores , Agregados Proteicos/efeitos dos fármacos , Agregação Patológica de Proteínas/tratamento farmacológico , Doença de Alzheimer/metabolismo , Peptídeos beta-Amiloides/metabolismo , Animais , Astrócitos/efeitos dos fármacos , Astrócitos/metabolismo , Relação Dose-Resposta a Droga , Camundongos , Camundongos Endogâmicos C57BL , Simulação de Dinâmica Molecular , Estrutura Molecular , Naftalenos/síntese química , Naftalenos/química , Fármacos Neuroprotetores/síntese química , Fármacos Neuroprotetores/química , Fragmentos de Peptídeos/metabolismo , Agregação Patológica de Proteínas/metabolismo , Relação Estrutura-Atividade , TermodinâmicaRESUMO
Tissue softening accompanies the ripening of many fruits and initiates the processes of irreversible deterioration. Expansins are plant cell wall proteins that have been proposed to disrupt hydrogen bonds within the cell wall polymer matrix. Several authors have shown that FaEXPA2 is a key gene that shows an increased expression level during ripening and softening of the strawberry fruit. For this reason, FaEXPA2 is frequently used as a molecular marker of softening in strawberry fruit, and changes in its relative expression have been related to changes in fruit firmness. In this context, we previously reported that FaEXPA2 has a high accumulation rate during fruit ripening in four different strawberry cultivars; however, the molecular mechanism of FaEXPA2 or expansins in general is not yet clear. Herein, a 3D model of the FaEXPA2 protein was built by comparative modeling to understand how FaEXPA2 interacts with different cell wall components at the molecular level. First, the structure was shown to display two domains characteristic of the other expansins that were previously described. The protein-ligand interaction was evaluated by molecular dynamic (MD) simulation using four different long ligands (a cellulose fiber, two of the more important xyloglucan (XG) fibers found in strawberry (XXXG and XXFG type), and a pectin (homogalacturonic acid type)). The results showed that FaEXPA2 formed a more stable complex with cellulose than other ligands via the different residues present in the open groove surface of its two domains, while FaEXPA2 did not interact with the pectin ligand.
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A promising alternative to improve the ultra-gas-wet alteration process by the addition of nanoparticles was developed. This study is focused on studying the functionalization process of nanoparticles of γ-alumina (γ-Al2O3) and magnesia (MgO) using a commercial fluorocarbon surfactant (SYLNYL-FSJ), from an experimental and theoretical approach. Different fluorocarbon surfactant concentrations were used in the functionalization process of the nanoparticles, and the materials obtained were characterized by Fourier-transform infrared spectroscopy (FTIR) and dynamic light scattering (DLS). The experimental setup of the interaction between the surfactant and nanoparticles was reproduced by molecular simulations in order to obtain physical insights into the adsorption process. Experimental results show a suitable functionalization for both nanoparticles with the fluorocarbon surfactant. The γ-Al2O3 nanoparticles showed better behavior based on the obtained nonfrictional conditions, which lead the water and n-decane droplets to slide on the rock surface coated with the functionalized nanoparticles. The experimental contact angles on the functionalized γ-Al2O3 nanoparticles were reproduced by molecular dynamics simulations. From the interaction energies' evaluation, it was also determined that alumina nanoparticles could reduce the adhesive energy to 0.01 kcal mol-1, regarding magnesia nanoparticles. Also, a significant difference was obtained for the surfactant-liquid interactions between the two nanoparticles evaluated, with changes of 17% for surfactant-water interactions and 28% for the surfactant-n-decane. The obtained results explain the pronounced increase for the contact angles of n-decane on the functionalized γ-Al2O3 nanoparticles.
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Bovine viral diarrhea virus (BVDV) is a pestivirus whose infection in cattle is globally distributed. The use of antivirals could complement vaccination as a tool of control and reduce economic losses. The RNA-dependent RNA polymerase (RdRp) of the virus is essential for its genome replication and constitutes an attractive target for the identification of antivirals. With the aim of obtaining selective BVDV inhibitors, the crystal structure of BVDV RdRp was used to perform a virtual screening. Approximately 15,000 small molecules from commercial and in-house databases were evaluated and several structurally different compounds were tested in vitro for antiviral activity. Interestingly, of twelve evaluated compounds, five were active and displayed EC50 values in the sub and low-micromolar range. Time of drug addition experiment and measured intracellular BVDV RNA showed that compound 7 act during RNA synthesis. Molecular Dynamics and MM/PBSA calculation were done to characterize the interaction of the most active compounds with RdRp, which will allow future ligand optimization. These studies highlight the use of in silico screening to identify a new class of BVDV inhibitors.
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Antivirais/farmacologia , Vírus da Diarreia Viral Bovina/efeitos dos fármacos , Animais , Antivirais/síntese química , Antivirais/química , Bovinos , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Testes de Sensibilidade Microbiana , Simulação de Dinâmica Molecular , Estrutura Molecular , Relação Estrutura-AtividadeRESUMO
HDAC6 is a protein involved in cancer, neurodegenerative disease and inflammatory disorders. To date, the full three-dimensional (3D) structure of human HDAC6 has not been elucidated; however, there are some experimental 3D structural homologs to HDAC6 that can be used as templates. In this work, we utilized molecular modeling procedures to model both of the catalytic domains of HDAC6 connected by the linker region where DMB region is placed. Once the 3D structure of human HDAC6 was obtained, it was structurally evaluated and submitted to docking and molecular dynamic (MD) simulations along with Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method to explore the stability and the binding free energy properties of the HDAC6-ligand complexes. In addition, its structural and energetic behavior was explored with each one of the catalytic domains in the molecular recognition of six selective HDAC6 inhibitors, HPOB, CAY10603, Nexturastat, Rocilinostat, Tubacin and Tubastatin A for DD2, and with the so-called 9-peptide which is DD1-HDAC6 selective substrate. The use of the whole system (DD1-DMB-DD2) showed a tendency toward the ligand affinity of DD2, CAY10603> Tubacin > Rocilinostat > Nexturastat > HPOB > Tubastatin > 9-peptide, which is in line with experimental reports. However, 9-peptide showed a higher affinity for DD1, which agrees with experimental reports elsewhere. Principal component analysis provided important information about the structural changes linked to the molecular recognition process, whereas per-residue decomposition analysis revealed the energetic contribution of the key residues in the molecular binding and structural characteristics that could assist in drug design.
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Desacetilase 6 de Histona/química , Inibidores de Histona Desacetilases/química , Anilidas/química , Carbamatos/química , Domínio Catalítico/genética , Análise por Conglomerados , Desacetilase 6 de Histona/antagonistas & inibidores , Desacetilase 6 de Histona/genética , Humanos , Ácidos Hidroxâmicos/química , Indóis/química , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Oxazóis/química , Compostos de Fenilureia/química , Análise de Componente Principal , Pirimidinas/química , Relação Estrutura-AtividadeRESUMO
Biofilm-based wastewater treatment systems have become attractive due to their numerous advantages when compared to other suspended growth processes. However, the mathematical modeling of these reactors is relatively complex, since it has to consider a wide range of phenomena to accurately describe the process behavior. This work deals with the modeling of a two-stage MBBR system run in pre-denitrification mode for the removal of organic matter and nitrogen from wastewater. The model development took into account diffusive phenomena and kinetics in a homogeneous biofilm composed of different bacterial functional groups (namely heterotrophs and nitrifiers). The thickness of the biofilm was treated as a variable, given that detachment of adhered biomass took place. The suspended biomass fraction was also considered to remove the pollutants by means of Monod-type kinetics associated with the activated sludge model. The dynamic behavior of the components involved in the system and their spatial distribution in the biofilm obtained from simulated data showed good agreement with those reported in the literature, demonstrating the reproducibility of the model and encouraging future applications in full-scale MBBR plants.
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Biofilmes , Reatores Biológicos , Eliminação de Resíduos Líquidos/instrumentação , Biomassa , Reatores Biológicos/microbiologia , Simulação por Computador , Desnitrificação , Difusão , Cinética , Modelos Teóricos , Reprodutibilidade dos Testes , Eliminação de Resíduos Líquidos/estatística & dados numéricos , Águas ResiduáriasRESUMO
Changes in the cellulose-hemicellulose fraction take place during ripening of strawberry fruit and are associated with the activity of a set of proteins and hydrolytic enzymes. Expansins are proteins located in the cell wall with no catalytic activity. In this context, FaEXPA1 was previously reported to have a high accumulation rate during fruit ripening in three different strawberry cultivars. In order to understand at the molecular level the expansin mechanism mode, a 3D model of FaEXPA1 protein was built by comparative modeling. FaEXPA1 protein model displayed two domains, a cellulose-binding domain with a ß-sandwich structure, and a second domain that included a HFD motif with a similar structure to the catalytic core of endoglucanase V from Humicola insolens. Additionally, in the center of the structure, an open groove was formed. Finally, using a cellulose polymer as a ligand, the protein-ligand interaction was evaluated by molecular dynamic (MD) simulation. Two MD simulations showed that FaEXPA1 can interact with cellulose via the flat aromatic surface of its binding domain D2, composed mainly of residues Trp99 and Trp225. In addition, FaEXPA1 formed a high number of hydrogen bonds with the glycan chain and the Asn81, Phe114 and Asn211 residues.