RESUMO
Antimicrobial resistance (AMR) is one of the biggest threats in modern times. It was estimated that in 2019, 1.27 million deaths occurred around the globe due to AMR. Methicillin-resistant Staphylococcus aureus (MRSA) strains, a pathogen considered of high priority by the World Health Organization, have proven to be resistant to most of the actual antimicrobial treatments. Therefore, new treatments are required to be able to manage this increasing threat. Under this perspective, an important metabolic pathway for MRSA survival, and absent in mammals, is the shikimate pathway, which is involved in the biosynthesis of chorismate, an intermediate for the synthesis of aromatic amino acids, folates, and ubiquinone. Therefore, the enzymes of this route have been considered good targets to design novel antibiotics. The fifth step of the route is performed by shikimate kinase (SK). In this study, an in-house chemical library of 170 benzimidazole derivatives was screened against MRSA shikimate kinase (SaSK). This effort led to the identification of the first SaSK inhibitors, and the two inhibitors with the greatest inhibition activity (C1 and C2) were characterized. Kinetic studies showed that both compounds were competitive inhibitors with respect to ATP and non-competitive for shikimate. Structural analysis through molecular docking and molecular dynamics simulations indicated that both inhibitors interacted with ARG113, an important residue involved in ATP binding, and formed stable complexes during the simulation period. Biological activity evaluation showed that both compounds were able to inhibit the growth of a MRSA strain. Mitochondrial assays showed that both compounds modify the activity of electron transport chain complexes. Finally, ADMETox predictions suggested that, in general, C1 and C2 can be considered as potential drug candidates. Therefore, the benzimidazole derivatives reported here are the first SaSK inhibitors, representing a promising scaffold and a guide to design new drugs against MRSA.
Assuntos
Benzimidazóis , Staphylococcus aureus Resistente à Meticilina , Simulação de Acoplamento Molecular , Fosfotransferases (Aceptor do Grupo Álcool) , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/enzimologia , Fosfotransferases (Aceptor do Grupo Álcool)/antagonistas & inibidores , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Fosfotransferases (Aceptor do Grupo Álcool)/química , Benzimidazóis/farmacologia , Benzimidazóis/química , Cinética , Antibacterianos/farmacologia , Antibacterianos/química , Simulação de Dinâmica Molecular , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/química , Humanos , Testes de Sensibilidade Microbiana , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/químicaRESUMO
Clusia is one of the most important genera of the Clusiaceae family, comprising up to 400 species. This review describes the identification of twenty-two flavonoids from Clusia species, which includes five flavonols (1-4 and 11), six flavones (5-10), one catechin (12), one flavanone (13), and nine biflavonoids (14-22). O- and C-glycosylation are frequently observed amongst these flavonoids. Furthermore, seven biphenyls (23-29) and nine xanthones (30-38) have been isolated from Clusia species. Biphenyls and xanthones show limited occurrence within the genus, but together with biosynthetic insights, they might offer important chemophenetics leads for the consolidation of the genus Clusia within the Clusiaceae family. Altogether, this work provides an overview of the chemistry of the genus Clusia in terms of flavonoids, biphenyls and xanthones, as well as it discusses biological activities and chemophenetics of the isolated compounds, when appropriate.
RESUMO
Bacteria resistance to antibiotics is a concerning global health problem; in this context, methicillin-resistant Staphylococcus aureus (MRSA) is considered as a high priority by the World Health Organization. Furthermore, patients with a positive result for COVID-19 received early antibiotic treatment, a fact that potentially encourages the increase in antibiotic resistance. Therefore, there is an urgency to develop new drugs with molecular mechanisms different from those of the actual treatments. In this context, enzymes from the shikimate pathway, a route absent in humans, such as dehydroquinate dehydratase (DHQD), are considered good targets. In this work, a computer-aided drug design strategy, which involved exhaustive virtual screening and molecular dynamics simulations with MM-PBSA analysis, as well as an in silico ADMETox characterization, was performed to find potential noncovalent inhibitors of DHQD from MRSA (SaDHQD). After filtering the 997 million compounds from the ZINC database, 6700 compounds were submitted to an exhaustive virtual screening protocol. From these data, four molecules were selected and characterized (ZINC000005753647 (1), ZINC000001720488 (2), ZINC000082049768 (3), and ZINC000644149506 (4)). The results indicate that the four potential inhibitors interacted with residues important for substrate binding and catalysis, with an estimated binding free energy like that of the enzyme's substrate. Their ADMETox-predicted properties suggest that all of them support the structural characteristics to be considered good candidates. Therefore, the four compounds reported here are excellent option to be considered for future in vitro studies to design new SaDHQD noncovalent inhibitors and contribute to the search for new drugs against MRSA.
RESUMO
Tuberculosis (TB) is one of the main causes of death from a single pathological agent, Mycobacterium tuberculosis (Mtb). In addition, the emergence of drug-resistant TB strains has exacerbated even further the treatment outcome of TB patients. It is thus needed the search for new therapeutic strategies to improve the current treatment and to circumvent the resistance mechanisms of Mtb. The shikimate kinase (SK) is the fifth enzyme of the shikimate pathway, which is essential for the survival of Mtb. The shikimate pathway is absent in humans, thereby indicating SK as an attractive target for the development of anti-TB drugs. In this work, a combination of in silico and in vitro techniques was used to identify potential inhibitors for SK from Mtb (MtSK). All compounds of our in-house database (Centro de Pesquisas em Biologia Molecular e Funcional, CPBMF) were submitted to in silico toxicity analysis to evaluate the risk of hepatotoxicity. Docking experiments were performed to identify the potential inhibitors of MtSK according to the predicted binding energy. In vitro inhibitory activity of MtSK-catalyzed chemical reaction at a single compound concentration was assessed. Minimum inhibitory concentration values for in vitro growth of pan-sensitive Mtb H37Rv strain were also determined. The mixed approach implemented in this work was able to identify five compounds that inhibit both MtSK and the in vitro growth of Mtb.
Assuntos
Mycobacterium tuberculosis , Tuberculose , Humanos , Simulação de Acoplamento Molecular , Antituberculosos/farmacologia , Antituberculosos/química , Tuberculose/tratamento farmacológicoRESUMO
BACKGROUND: Glyphosate-resistant Salsola tragus accessions have been identified in the USA and Argentina; however, the mechanisms of glyphosate resistance have not been elucidated. The goal of this study was to determine the mechanism/s of glyphosate resistance involved in two S. tragus populations (R1 and R2) from Argentina. RESULTS: Both glyphosate-resistant populations had a six-fold lower sensitivity to glyphosate than the S population (i.e. resistance index). No evidence of differential absorption, translocation or metabolism of glyphosate was found in the R1 and R2 populations compared to a susceptible population (S). No 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) mutations were detected, but S. tragus R1 and R2 plants had ≈14-fold higher EPSPS gene relative copy number compared to the S counterpart. In R1 and R2, EPSPS duplication entailed a greater constitutive EPSPS transcript abundance by approximately seven-fold and a basal EPSPS activity approximately three-fold higher than the S population. CONCLUSION: The current study reports EPSPS gene duplication for the first time as a mechanism of glyphosate resistance in S. tragus populations. The increase of glyphosate dose needed to kill R1 and R2 plants was linked to the EPSPS transcript abundance and level of EPSPS activity. This evidence supports the convergent evolution of the overexpression of the EPSPS gene in several Chenopodiaceae/Amaranthaceae species adapted to drought environments and the role of gene duplication as an adaptive advantage for plants to withstand stress. © 2022 Society of Chemical Industry.
Assuntos
Herbicidas , Salsola , Duplicação Gênica , Fosfatos , Herbicidas/farmacologia , Resistência a Herbicidas/genética , Poaceae/metabolismo , 3-Fosfoshikimato 1-Carboxiviniltransferase/genética , 3-Fosfoshikimato 1-Carboxiviniltransferase/metabolismo , GlifosatoRESUMO
Tuberculosis (TB) remains one of the leading causes of death due to a single pathogen. The emergence and proliferation of multidrug-resistant (MDR-TB) and extensively drug-resistant strains (XDR-TB) represent compelling reasons to invest in the pursuit of new anti-TB agents. The shikimate pathway, responsible for chorismate biosynthesis, which is a precursor of important aromatic compounds, is required for Mycobacterium tuberculosis growth. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (MtbDAHPS) catalyzes the first step in the shikimate pathway and it is an attractive target for anti-tubercular agents. Here, we used a CRISPRi system to evaluate the DAHPS as a vulnerable target in M. tuberculosis. The silencing of aroG significantly reduces the M. tuberculosis growth in both rich medium and, especially, in infected murine macrophages. The supplementation with amino acids was only able to partially rescue the growth of bacilli, whereas the Aro supplement (aromix) was enough to sustain the bacterial growth at lower rates. This study shows that MtbDAHPS protein is vulnerable and, therefore, an attractive target to develop new anti-TB agents. In addition, the study contributes to a better understanding of the biosynthesis of aromatic compounds and the bacillus physiology. IMPORTANCE Determining the vulnerability of a potential target allows us to assess whether its partial inhibition will impact bacterial growth. Here, we evaluated the vulnerability of the enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) from M. tuberculosis by silencing the DAHPS-coding aroG gene in different contexts. These results could lead to the development of novel and potent anti-tubercular agents in the near future.
Assuntos
3-Desoxi-7-Fosfo-Heptulonato Sintase , Mycobacterium tuberculosis , 3-Desoxi-7-Fosfo-Heptulonato Sintase/química , 3-Desoxi-7-Fosfo-Heptulonato Sintase/genética , 3-Desoxi-7-Fosfo-Heptulonato Sintase/metabolismo , Animais , Antituberculosos/farmacologia , Camundongos , Mycobacterium tuberculosis/metabolismo , FosfatosRESUMO
Changes in photosynthetic machinery can induce physiological and biochemical damage in plants. Low doses of glyphosate have been shown to exert a positive effect in mitigating the deleterious effects of water deficit in plants. Here, the physiological and biochemical mechanisms of safflower plants (Carthamus tinctorius L.) were studied under conditions of water deficit mediated by the attenuating effect of low-dose glyphosate. The plants were divided into two groups of water regimes in soil, without water deficit (-10 kPa) and with water deficit (-70 kPa), and were exposed to different concentrations of glyphosate (0, 1.8, 3.6, 7.2, 18, 36, 72, 180, 360, and 720 g a.e. ha-1). Evident protective responses at the physiological and biochemical levels were obtained after applying low doses of glyphosate to plants under water deficit, with a limiting dose for the occurrence of hormesis (LDS) = 72 g a.e. ha-1. The water deficit in plants resulted in hydrogen peroxide (H2O2) accumulation and consequently lipid peroxidation (LPO) associated with the accumulation of shikimic acid and glyphosate in plants, which triggered an increase in the activity of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) that act by dismuting the levels of reactive oxygen species (ROS), maintaining, and/or increasing the maximum quantum efficiency of photosystem II (Fv/Fm), effective quantum yield of photosystem II (ΦPSII), electron transport rate (ETR), photochemical extinction coefficient (qP), and non-photochemical extinction coefficient (NPQ). APX appears to be the main enzyme involved in eliminating H2O2. Low doses of glyphosate act as water deficit ameliorators, allowing the plant to maintain/increase metabolism at physiological and biochemical levels by activating antioxidant enzymes in the dismutation of ROS in safflower plants.
Assuntos
Carthamus tinctorius , Antioxidantes/metabolismo , Carthamus tinctorius/metabolismo , Glicina/análogos & derivados , Hormese , Peróxido de Hidrogênio , Fotossíntese , Estresse Fisiológico , Água , GlifosatoRESUMO
Methicillin-resistant Staphylococcus aureus (MRSA) is an important threat as it causes serious hospital and community acquired infections with deathly outcomes oftentimes, therefore, development of new treatments against this bacterium is a priority. Shikimate kinase, an enzyme in the shikimate pathway, is considered a good target for developing antimicrobial drugs; this is given because of its pathway, which is essential in bacteria whereas it is absent in mammals. In this work, a computer-assisted drug design strategy was used to report the first potentials inhibitors for Shikimate kinase from methicillin-resistant Staphylococcus aureus (SaSK), employing approximately 5 million compounds from ZINC15 database. Diverse filtering criteria, related to druglike characteristics and virtual docking screening in the shikimate binding site, were performed to select structurally diverse potential inhibitors from SaSK. Molecular dynamics simulations were performed to elucidate the dynamic behavior of each SaSK-ligand complex. The potential inhibitors formed important interactions with residues that are crucial for enzyme catalysis, such as Asp37, Arg61, Gly82, and Arg138. Therefore, the compounds reported provide valuable information and can be seen as the first step toward developing SaSK inhibitors in the search of new drugs against MRSA.
Assuntos
Antibacterianos/farmacologia , Desenho Assistido por Computador , Inibidores Enzimáticos/farmacologia , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Fosfotransferases (Aceptor do Grupo Álcool)/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/farmacologia , Antibacterianos/química , Desenho de Fármacos , Inibidores Enzimáticos/química , Staphylococcus aureus Resistente à Meticilina/enzimologia , Modelos Moleculares , Estrutura Molecular , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Bibliotecas de Moléculas Pequenas/químicaRESUMO
Bromus catharticus Vahl. has been used as a valuable forage crop, but it has also been noted as a weed of winter crops and an invader in several countries. In Argentina, a putative glyphosate-resistant population of B. catharticus was identified as a consequence of the lack of effective control with glyphosate in the pre-sowing of wheat. Plant survival and shikimate accumulation analysis demonstrated a lower glyphosate-sensitivity of this population in comparison to a susceptible B. catharticus population. The resistant population was 4-fold more resistant to glyphosate than its susceptible counterpart. There was no evidence of target-site mechanisms of glyphosate resistance or an enhanced capacity to metabolize glyphosate in the resistant population. However, the resistant plants showed a lower foliar retention of glyphosate (138.34 µl solution g-1 dry weight vs. 390.79 µl solution g-1 dry weight), a reduced absorption of 14C-glyphosate (54.18 vs. 73.56%) and lower translocation of 14C-glyphosate from the labeled leaf (27.70 vs. 62.36%). As a result, susceptible plants accumulated a 4.1-fold higher concentration of 14C-glyphosate in the roots compared to resistant plants. The current work describes the first worldwide case of glyphosate resistance in B. catharticus. A reduced foliar retention of herbicide, a differential rate of glyphosate entry into leaves and an altered glyphosate translocation pattern would be the most likely mechanisms of glyphosate exclusion.
RESUMO
Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is still responsible for a large number of fatal cases, especially in developing countries with alarming rates of incidence and prevalence worldwide. Mycobacterium tuberculosis has a remarkable ability to develop new resistance mechanisms to the conventional antimicrobials treatment. Because of this, there is an urgent need for novel bioactive compounds for its treatment. The dehydroquinate dehydratase II (DHQase II) is considered a key enzyme of shikimate pathway, and it can be used as a promising target for the design of new bioactive compounds with antibacterial action. The aim of this work was the construction of QSAR models to aid the design of new potential DHQase II inhibitors. For that purpose, various molecular modeling approaches, such as activity cliff, QSAR models and computer-aided ligand design were utilized. A predictive in silico 4D-QSAR model was built using a database comprising 86 inhibitors of DHQase II, and the model was used to predict the activity of the designed ligands. The obtained model proved to predict well the DHQase II inhibition for an external validation dataset ([Formula: see text] = 0.72). Also, the Activity Cliff analysis shed light on important structural features applied to the ligand design.
Assuntos
Antituberculosos/farmacologia , Inibidores Enzimáticos/farmacologia , Hidroliases/antagonistas & inibidores , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/metabolismo , Sítios de Ligação/efeitos dos fármacos , Desenho de Fármacos , Ligantes , Modelos Moleculares , Mycobacterium tuberculosis/enzimologia , Relação Quantitativa Estrutura-AtividadeRESUMO
In this study, we have investigated the enzyme shikimate 5-dehydrogenase from the causative agent of tuberculosis, Mycobacterium tuberculosis. We have employed a mixture of computational techniques, including molecular dynamics, hybrid quantum chemical/molecular mechanical potentials, relaxed surface scans, quantum chemical descriptors and free-energy simulations, to elucidate the enzyme's reaction pathway. Overall, we find a two-step mechanism, with a single transition state, that proceeds by an energetically uphill hydride transfer, followed by an energetically downhill proton transfer. Our mechanism and calculated free energy barrier for the reaction, 64.9 kJ mol- 1, are in good agreement with those predicted from experiment. An analysis of quantum chemical descriptors along the reaction pathway indicated a possibly important, yet currently unreported, role of the active site threonine residue, Thr65.
Assuntos
Oxirredutases do Álcool/metabolismo , Simulação de Dinâmica Molecular , Mycobacterium tuberculosis/enzimologia , Teoria Quântica , Oxirredutases do Álcool/química , Biocatálise , Especificidade por SubstratoRESUMO
The shikimate pathway consists of seven enzymatic steps involved in the conversion of erythrose-4-phosphate and phosphoenolpyruvate to chorismate and also responsible to the production of aromatic amino acids, such as phenylalanine, tyrosine, and tryptophan which are essential to the bacterial metabolism. The 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) catalyze important steps in the shikimate pathway using as substrate the phosphoenolpyruvate (PEP). Due to the importance of PEP in shikimate pathway, its structure has been investigated to develop new bioinspired competitive inhibitors against DAHPS and EPSPS. In the present study, we perform a literature survey of 28 PEP derivatives, then we analyzed the selectivity and affinity of these compounds against the EPSPS and DAHPS structures using consensual molecular docking, pharmacophore prediction, molecular dynamics (MD) simulations, and binding free energy calculations. Here, we propose consistent binding modes of the selected ligands and indicate that their structures show interesting pharmacophoric properties related to multi-targets inhibitors for both enzymes. Our computational results are supported by previous experimental findings related to the interactions of PEP derivatives with DAHPS and EPSPS structures.
Assuntos
3-Desoxi-7-Fosfo-Heptulonato Sintase , 3-Fosfoshikimato 1-Carboxiviniltransferase , Simulação de Acoplamento Molecular , Fosfoenolpiruvato , Ácido ChiquímicoRESUMO
Shikimic acid (SA) has witnessed a strong increase in recent years due to the increasing demand of the pharmaceutical and cosmetic industry. The SA is used as a precursor for the synthesis of oseltamivir phosphate (Tamiflu®), a potent viral inhibitor and is extracted from the plant Illicium verum Hook which has a limited availability. This article proposed the use of Urochloa plantaginea (Link.) webster and glyphosate, as an alternative source of SA. U. plantaginea plants with 3 - 4 tillers and 4 - 6 leaves were harvest at 3, 6, 9 and 12 days after application (DAT) of low rates of glyphosate. Samples were dried, extracted, analyzed by HPLC and LC-MS/MS. The maximum SA concentrations were observed at 6 days after glyphosate at 36 g.a.e.ha-1 was applied in plants of U. plantaginea with 4 to 6 leaves. The capability of this annual gramineae to produce elevated SA levels throughout the entire biomass affords its potential for a greater yield on a per hectare basis.(AU)
O interesse pelo ácido chiquímico (SA) tem apresentado um forte incremento nos últimos anos devido à crescente demanda da indústria farmacêutica e cosmética. O SA é utilizado como um precursor para a síntese do fosfato de oseltamivir (Tamiflu®), um potente inibidor viral. Este ácido é extraído principalmente da planta Illicium verum Hook. A disponibilidade desta planta é um fator limitante para o crescimento do mercado no futuro próximo. Este artigo propõe Urochloa plantaginea (Link.) webster tratada com sub doses de glifosato, como uma fonte alternativa de SA. Plantas de U. plantaginea com 3 - 4 perfilhos e 4 a 6 folhas foram tratadas com subdoses de glifosato e coletadas aos 0, 3, 6, 9 e 12 dias após sua aplicação (DAT). As amostras foram secas, extraídas e analisadas por HPLC e confirmadas por LC-MS/MS. As concentrações máximas de SA foram observadas aos seis dias após aplicação do glifosato a 36 g.e.a.ha-1 em plantas de U. plantaginea com 4 - 6 folhas. A capacidade anual dessa gramínea para produzir níveis elevados de SA em toda a biomassa, pode ser uma fonte economicamente viável de SA.(AU)
Assuntos
Ácido Chiquímico , Herbicidas/administração & dosagemRESUMO
Roughly a third of the world's population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
Assuntos
Antituberculosos/síntese química , Proteínas de Bactérias/antagonistas & inibidores , Inibidores Enzimáticos/síntese química , Regulação Bacteriana da Expressão Gênica , Mycobacterium tuberculosis/efeitos dos fármacos , Ácido Chiquímico/antagonistas & inibidores , Antituberculosos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Desenho de Fármacos , Inibidores Enzimáticos/farmacologia , Humanos , Tuberculose Latente/tratamento farmacológico , Tuberculose Latente/microbiologia , Redes e Vias Metabólicas/efeitos dos fármacos , Redes e Vias Metabólicas/genética , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/crescimento & desenvolvimento , Ácido Chiquímico/química , Ácido Chiquímico/metabolismo , Relação Estrutura-Atividade , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/microbiologiaRESUMO
ABSTRACT: Shikimic acid (SA) has witnessed a strong increase in recent years due to the increasing demand of the pharmaceutical and cosmetic industry. The SA is used as a precursor for the synthesis of oseltamivir phosphate (Tamiflu®), a potent viral inhibitor and is extracted from the plant Illicium verum Hook which has a limited availability. This article proposed the use of Urochloa plantaginea (Link.) webster and glyphosate, as an alternative source of SA. U. plantaginea plants with 3 - 4 tillers and 4 - 6 leaves were harvest at 3, 6, 9 and 12 days after application (DAT) of low rates of glyphosate. Samples were dried, extracted, analyzed by HPLC and LC-MS/MS. The maximum SA concentrations were observed at 6 days after glyphosate at 36 g.a.e.ha-1 was applied in plants of U. plantaginea with 4 to 6 leaves. The capability of this annual gramineae to produce elevated SA levels throughout the entire biomass affords its potential for a greater yield on a per hectare basis.
RESUMO: O interesse pelo ácido chiquímico (SA) tem apresentado um forte incremento nos últimos anos devido à crescente demanda da indústria farmacêutica e cosmética. O SA é utilizado como um precursor para a síntese do fosfato de oseltamivir (Tamiflu®), um potente inibidor viral. Este ácido é extraído principalmente da planta Illicium verum Hook. A disponibilidade desta planta é um fator limitante para o crescimento do mercado no futuro próximo. Este artigo propõe Urochloa plantaginea (Link.) webster tratada com sub doses de glifosato, como uma fonte alternativa de SA. Plantas de U. plantaginea com 3 - 4 perfilhos e 4 a 6 folhas foram tratadas com subdoses de glifosato e coletadas aos 0, 3, 6, 9 e 12 dias após sua aplicação (DAT). As amostras foram secas, extraídas e analisadas por HPLC e confirmadas por LC-MS/MS. As concentrações máximas de SA foram observadas aos seis dias após aplicação do glifosato a 36 g.e.a.ha-1 em plantas de U. plantaginea com 4 - 6 folhas. A capacidade anual dessa gramínea para produzir níveis elevados de SA em toda a biomassa, pode ser uma fonte economicamente viável de SA.
RESUMO
Computational analysis of protein-ligand interactions is of pivotal importance for drug design. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule as a ligand to the binding site of a protein target. Considering scoring functions available in docking programs such as AutoDock4, AutoDock Vina, and Molegro Virtual Docker, we could say that they all rely on equations that sum each type of protein-ligand interactions to model the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. In this chapter, we present the main physics concepts necessary to understand electrostatics interactions relevant to molecular recognition of a ligand by the binding pocket of a protein target. Moreover, we analyze the electrostatic potential energy for an ensemble of structures to highlight the main features related to the importance of this interaction for binding affinity.
Assuntos
Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Proteínas/química , Eletricidade Estática , Algoritmos , Sítios de Ligação , Desenho de Fármacos , Modelos Moleculares , Ligação ProteicaRESUMO
Van der Waals forces are determinants of the formation of protein-ligand complexes. Physical models based on the Lennard-Jones potential can estimate van der Waals interactions with considerable accuracy and with a computational complexity that allows its application to molecular docking simulations and virtual screening of large databases of small organic molecules. Several empirical scoring functions used to evaluate protein-ligand interactions approximate van der Waals interactions with the Lennard-Jones potential. In this chapter, we present the main concepts necessary to understand van der Waals interactions relevant to molecular recognition of a ligand by the binding pocket of a protein target. We describe the Lennard-Jones potential and its application to calculate potential energy for an ensemble of structures to highlight the main features related to the importance of this interaction for binding affinity.
Assuntos
Desenho de Fármacos , Modelos Teóricos , Complexos Multiproteicos/química , Proteínas/química , Algoritmos , LigantesRESUMO
Fast and reliable evaluation of the hydrogen bond potential energy has a significant impact in the drug design and development since it allows the assessment of large databases of organic molecules in virtual screening projects focused on a protein of interest. Semi-empirical force fields implemented in molecular docking programs make it possible the evaluation of protein-ligand binding affinity where the hydrogen bond potential is a common term used in the calculation. In this chapter, we describe the concepts behind the programs used to predict hydrogen bond potential energy employing semi-empirical force fields as the ones available in the programs AMBER, AutoDock4, TreeDock, and ReplicOpter. We described here the 12-10 potential and applied it to evaluate the binding affinity for an ensemble of crystallographic structures for which experimental data about binding affinity are available.
Assuntos
Ligação de Hidrogênio , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Proteínas/química , Algoritmos , Desenho de Fármacos , Ligação ProteicaRESUMO
Chlorogenic acids (CGAs) and the biopolymer lignin are both products of the phenylpropanoid pathway. Whereas CGAs have been reported to play a role during stress responses, lignin is a major component of secondary cell walls, providing physical strength and hydrophobicity to supportive and water-conducting tissues. Because the chemical structure of CGAs largely resembles those of some lignin intermediates and because CGAs can be converted back to hydroxycinnamoyl-CoAs in vitro, CGAs have been considered authentic intermediates of the lignin biosynthetic pathway. However, it is still unclear whether and how the CGA pool can be channeled towards the production of lignin monomers in response to developmental or environmental signals. Comprehensive studies on the catalytic activity of recombinant enzymes together with functional characterizations in planta have been very useful in understanding the potential interdependence between these two metabolic routes. Here we present the current understanding on CGA metabolism and discuss the biochemical and molecular evidence of the metabolic re-routing of CGAs towards lignin.
Assuntos
Ácido Clorogênico/metabolismo , Lignina/biossíntese , Esterases/metabolismoRESUMO
One of the most widespread pathogens worldwide is methicillin-resistant Staphylococcus aureus, a bacterium that provokes severe life-threatening illnesses both in hospitals and in the community. The principal challenge lies in the resistance of MRSA to current treatments, which encourages the study of different molecular targets that could be used to develop new drugs against this infectious agent. With this goal, a detailed characterization of shikimate kinase from this microorganism (SaSK) is described. The results showed that SaSK has a Km of 0.153 and 224 µM for shikimate and ATP, respectively, and a global reaction rate of 13.4 µmol/min/mg; it is suggested that SaSK utilizes the Bi-Bi Ping Pong reaction mechanism. Furthermore, the physicochemical data indicated that SaSK is an unstable, hydrophilic, and acidic protein. Finally, structural information showed that SaSK presented folding that is typical of its homologous counterparts and contains the typical domains of this family of proteins. Amino acids that have been shown to be important for SaSK protein function are conserved. Therefore, this study provides fundamental information that may aid in the design of inhibitors that could be used to develop new antibacterial agents.