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1.
Biochemistry (Mosc) ; 85(1): 99-107, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32079521

RESUMO

Poly(ADP-ribose) polymerase 1 (PARP-1) is a key DNA repair enzyme and an important target in cancer treatment. Conventional methods of studying the reaction mechanism of PARP-1 have limitations because of the complex structure of PARP-1 substrates; however, the necessary data can be obtained by molecular modeling. In this work, a molecular dynamics model for the PARP-1 enzyme-substrate complex containing NAD+ molecule and the end of the poly(ADP-ribose) chain in the form of ADP molecule was obtained for the first time. Interactions with the active site residues have been characterized where Gly863, Lys903, Glu988 play a crucial role, and the SN1-like mechanism for the enzymatic ADP-ribosylation reaction has been proposed. Models of PARP-1 complexes with more sophisticated two-unit fragments of the growing polymer chain as well as competitive inhibitors 3-aminobenzamide and 7-methylguanine have been obtained by molecular docking.


Assuntos
Poli(ADP-Ribose) Polimerase-1/química , Poli Adenosina Difosfato Ribose/química , Sítios de Ligação , Humanos , Simulação de Acoplamento Molecular/métodos , Inibidores de Poli(ADP-Ribose) Polimerases/química , Especificidade por Substrato
2.
Parasit Vectors ; 13(1): 20, 2020 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-31931867

RESUMO

BACKGROUND: MF6p/host defense molecules (HDMs) are a broad family of small proteins secreted by helminth parasites. Although the physiological role of MF6p/HDMs in trematode parasites is not fully understood, their potential biological function in maintaining heme homeostasis and modulating host immune response has been proposed. METHODS: A gene encoding the MF6p/HDM of Clonorchis sinensis (CsMF6p/HDM) was cloned. Recombinant CsMF6p/HDM (rCsMF6p/HDM) was expressed in Escherichia coli. The biochemical and immunological properties of rCsMF6/HDM were analyzed. CsMF6p/HDM induced pro-inflammatory response in RAW 264.7 cells was analyzed by cytokine array assay, reverse transcription polymerase chain reaction, and enzyme-linked immunosorbent assay. The structural feature of CsMF6p/HDM was analyzed by three-dimensional modeling and molecular docking simulations. RESULTS: The CsMF6p/HDM shares a high level of amino acid sequence similarity with orthologs from other trematodes and is expressed in diverse developmental stages of the parasite. The rCsMF6p/HDM bound to bacteria-derived lipopolysaccharide (LPS), without effectively neutralizing LPS-induced inflammatory response in RAW 264.7 macrophage cells. Rather, the rCsMF6p/HDM induced pro-inflammatory immune response, which is characterized by the expression of TNF-α and IL-6, in RAW 264.7 cells. The rCsMF6p/HDM-induced pro-inflammatory immune response was regulated by JNK and p38 MAPKs, and was effectively down-regulated via inhibition of NF-κB. The structural analysis of CsMF6p/HDM and the docking simulation with LPS suggested insufficient capture of LPS by CsMF6p/HDM, which suggested that rCsMF6p/HDM could not effectively neutralize LPS-induced inflammatory response in RAW 264.7 cells. CONCLUSIONS: Although rCsMF6p/HDM binds to LPS, the binding affinity may not be sufficient to maintain a stable complex of rCsMF6p/HDM and LPS. Moreover, the rCsMF6p/HDM-induced pro-inflammatory response is characterized by the release of IL-6 and TNF-α in RAW 264.7 macrophage cells. The pro-inflammatory response induced by rCsMF6p/HDM is mediated via NF-κB-dependent MAPK signaling pathway. These results collectively suggest that CsMF6p/HDM mediates C. sinensis-induced inflammation cascades that eventually lead to hepatobiliary diseases.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/genética , Clonorchis sinensis/metabolismo , Macrófagos/imunologia , Animais , Peptídeos Catiônicos Antimicrobianos/imunologia , Peptídeos Catiônicos Antimicrobianos/metabolismo , Clonagem Molecular , Clonorquíase/etiologia , Citocinas/metabolismo , Doenças do Sistema Digestório/etiologia , Doenças do Sistema Digestório/parasitologia , Escherichia coli , Imunidade Celular , Inflamação/metabolismo , Sistema de Sinalização das MAP Quinases , Macrófagos/parasitologia , Camundongos , Simulação de Acoplamento Molecular/métodos , NF-kappa B/metabolismo , Células RAW 264.7 , Trematódeos , Proteínas Quinases p38 Ativadas por Mitógeno/metabolismo
3.
Phys Chem Chem Phys ; 22(6): 3149-3159, 2020 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-31995074

RESUMO

The identification and optimization of lead compounds are inalienable components in drug design and discovery pipelines. As a powerful computational approach for the identification of hits with novel structural scaffolds, structure-based virtual screening (SBVS) has exhibited a remarkably increasing influence in the early stages of drug discovery. During the past decade, a variety of techniques and algorithms have been proposed and tested with different purposes in the scope of SBVS. Although SBVS has been a common and proven technology, it still shows some challenges and problems that are needed to be addressed, where the negative influence regardless of protein flexibility and the inaccurate prediction of binding affinity are the two major challenges. Here, focusing on these difficulties, we summarize a series of combined strategies or workflows developed by our group and others. Furthermore, several representative successful applications from recent publications are also discussed to demonstrate the effectiveness of the combined SBVS strategies in drug discovery campaigns.


Assuntos
Simulação de Acoplamento Molecular/métodos , Proteínas/química , Bibliotecas de Moléculas Pequenas/química , Algoritmos , Desenho de Fármacos , Ligantes , Estrutura Molecular , Ligação Proteica , Relação Estrutura-Atividade , Termodinâmica , Fluxo de Trabalho
4.
J Mass Spectrom ; 55(1): e4463, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31671229

RESUMO

Noncovalent interactions between drugs and proteins play significant roles for drug metabolisms and drug discoveries. Mass spectrometry has been a commonly used method for studying noncovalent interactions. However, the harsh ionization process in electrospray ionization mass spectrometry (ESI-MS) is not conducive to the preservation of noncovalent and unstable biomolecular complexes compared with the cold spray ionization mass spectrometry (CSI-MS). A cold spray ionization providing a stable solvation-ionization at low temperature is milder than ESI, which was more suitable for studying noncovalent drug-protein complexes with exact stoichiometries. In this paper, we apply CSI-MS to explore the interactions of ginsenosides toward amyloid-ß-peptide (Aß) and clarify the therapeutic effect of ginsenosides on Alzheimer's disease (AD) at the molecular level for the first time. The interactions of ginsenosides with Aß were performed by CSI-MS and ESI-MS, respectively. The ginsenosides Rg1 bounded to Aß at the stoichiometries of 1:1 to 5:1 could be characterized by CSI-MS, while dehydration products are more readily available by ESI-MS. The binding force depends on the number of glycosyls and the type of ginsenosides. The relative binding affinities were sorted in order as follows: Rg1 ≈ Re > Rd ≈ Rg2 > Rh2, protopanaxatriol by competition experiments, which were supported by molecular docking experiment. CSI-MS is expected to be a more appropriate approach to determine the weak but specific interactions of proteins with other natural products especially polyhydroxy compounds.


Assuntos
Peptídeos beta-Amiloides/química , Ginsenosídeos/química , Simulação de Acoplamento Molecular/métodos , Espectrometria de Massas por Ionização por Electrospray/métodos , Sítios de Ligação , Ligação Proteica , Sapogeninas/química , Relação Estrutura-Atividade
5.
Chem Biol Interact ; 315: 108873, 2020 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-31669219

RESUMO

Multiple-targeting compounds might reduce complex polypharmacy of multifactorial diseases, such as diabetes, and contribute to the greater therapeutic success. Targeting reactive oxygen species-producing enzymes, as xanthine oxidase (XO), might suppress progression of diabetes-associated vascular complications. In this study a small series of benzimidazole derivatives (1-9) was evaluated for inhibitory activity against dipeptidyl peptidase-4 (DPP-4) and XO. One 1,3-disubstituted-benzimidazole-2-imine (5) and 1,3-thiazolo[3,2-a]benzimidazolone derivative (8) were shown as effective dual DPP-4 and XO inhibitors, with IC50 values lower than 200 µM, and predicted binding modes with both target enzymes. Both selected dual inhibitors (compounds 5 and 8) did not show cytotoxicity to a greater extent on Caco-2 cells even at concentration of 250 µM. These structures represent new non-purine scaffolds bearing two therapeutic functionalities, being DPP-4 and XO inhibitors, more favorable in comparison to DPP-4 inhibitors with DPP-4 as a single target due to pleiotropic effects of XO inhibition.


Assuntos
Benzimidazóis/farmacologia , Dipeptidil Peptidase 4/metabolismo , Inibidores da Dipeptidil Peptidase IV/farmacologia , Xantina Oxidase/antagonistas & inibidores , Sítios de Ligação , Células CACO-2 , Linhagem Celular Tumoral , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/metabolismo , Humanos , Hipoglicemiantes/farmacologia , Simulação de Acoplamento Molecular/métodos , Espécies Reativas de Oxigênio/metabolismo , Relação Estrutura-Atividade
6.
Mol Immunol ; 116: 106-116, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31634814

RESUMO

Shigellosis is a severe diarrheal disease with high mortality and morbidity rate. Until now, there is no approved vaccine against the disease. Therefore, the present study was planned to design a novel multi-epitope vaccine against Shigella spp., the causative agents of the disease based on the immunoinformatic tools. For this end, firstly seven conserved antigens of the bacteria, including IpaA, IpaB, IpaC, IpaD, OmpC, OmpF and VirG were selected. Then, linear B-cell epitope mapping of these proteins was carried out and top-ranked and shared epitopes were selected based on antigenicity, allergenicity, stability, toxicity and physicochemical properties for further analysis. In next step, B-cell derived T-cell epitopes were determined and appropriate epitopes were selected for incorporation into the final construct. Moreover, the selected epitopes and two mucosal adjuvants including ctxB and LT-IIc were joined using appropriate linkers. The three dimensional structure of the final construct was modeled and evaluated in term of structural quality and presence of conformational B-cell epitopes. Furthermore, binding affinity of the proposed vaccine to MHC I and II molecules were evaluated through molecular docking method using Hex 8.0. as well as the stability of the vaccine-MHC complexes was monitored by molecular dynamics method using the NAMD graphical user interface embedded in visual molecular dynamics. Finally, to evaluate the immunogenicity of the designed protein, the protein was administered to BALB/c mice and the serum IgG was determined by ELISA. The results indicated that the proposed vaccine has high structural quality and binding affinity to both MHC I and II molecules. Moreover, molecular dynamics studies confirmed that the vaccine-MHC docked complexes were stable during simulation time. Animal study showed that the proposed protein is able to evoke mice's humoral immune response. In sum, the results suggested that the proposed candidate vaccine could be considered as a promising anti-shigellosis vaccine.


Assuntos
Vacinas Bacterianas/imunologia , Proteção Cruzada/imunologia , Shigella/imunologia , Adjuvantes Imunológicos , Animais , Linfócitos B/imunologia , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/imunologia , Feminino , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Humanos , Imunidade Humoral/imunologia , Imunoglobulina G/imunologia , Camundongos , Camundongos Endogâmicos BALB C , Simulação de Acoplamento Molecular/métodos , Vacinologia/métodos
7.
Chemosphere ; 235: 976-984, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31561314

RESUMO

Triclosan (TCS) is chemically designated as 5-chloro-2-(2,4-dichlorophenoxy) phenol and is considered as endocrine-disrupting chemical (EDC). The various diseases found due to exposure of TCS, have been linked with modulation of the human enoyl-acyl carrier protein-reductase (hER). However, the new protein targets for TCS other than hER, which are responsible for various diseases, are still unknown. In the present study, a bioinformatics approach was used to identify new possible targets for TCS. A text mining study was initially performed to understand the association of TCS in various biochemical processes. Discovery studio software 4.1 was used to carry out inverse virtual screening for 226 numbers of pathway proteins by docking study using CHARMm based docking tool, and twenty proteins were screened. CDOCKER energy values lower than -12.65 kcal/mol was considered for the screening of selected proteins. Three new proteins; Receptor-interacting protein 1 (RIP1), Apoptosis signal-regulating kinase 1 (ASK1) and B-cell lymphoma 2 (Bcl-2) from Apoptosis Signaling Pathway revealed best CDOCKER energy with triclosan which was -26.88, -23.34 and -22.96 kcal/mol respectively. The interaction of TCS with RIP1 and ASK1 were mostly hydrophobic; however, hydrogen bond type interaction was found in TCS/Bcl2 complex. Therefore, docking-based inverse virtual screening study suggests that TCS has other targets rather than hER, which can modulate various biochemical processes. The docking protocol was validated through evaluation of root-mean-square deviation (RMSD), key interaction score system (KISS) and the relationship between the docking energy and toxicity data available in ToxCast database. Low RMSD value (0.55 ˚A) and high KISS score (0.66) along with higher correlation (R2 = 0.9798) between docking affinity and toxicity indicated that docking protocol can be used to optimize the binding energetics.


Assuntos
Anti-Infecciosos Locais/farmacologia , Disruptores Endócrinos/farmacologia , Simulação de Acoplamento Molecular/métodos , Proteínas/metabolismo , Software , Triclosan/farmacologia , Anti-Infecciosos Locais/metabolismo , Disruptores Endócrinos/metabolismo , Humanos , Interações Hidrofóbicas e Hidrofílicas , Ligantes , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Proteínas/química , Proteínas/efeitos dos fármacos , Triclosan/metabolismo
8.
J Chromatogr Sci ; 57(9): 838-846, 2019 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-31504273

RESUMO

There is an increasing interest in screening and developing natural tyrosinase inhibitors widely applied in medicinal and cosmetic products, as well as in the food industry. In this study, an approach by ultrafiltration LC-MS and molecular docking was used to screen and identify tyrosinase inhibitors from Semen Oroxyli extract. The samples were first incubated with the tyrosinase to select the optimal binding conditions including tyrosinase concentration, incubation time and the molecular weight of ultrafiltration membrane. By comparison of the chromatographic profiles of the extracts after ultrafiltration with activated and inactivated tyrosinase, the potential inhibitors were obtained and then identified by LC-MS. The relative binding affinities of the potential inhibitors were also calculated based on the decrease of peak areas of those. As a result, seven compounds were fished out as tyrosinase inhibitors by this assay. Among them, oroxin A and baicalein showed higher tyrosinase inhibitory than resveratrol as positive drug, and their binding mode with enzyme was further verified via the molecular docking analysis. The test results showed that the proposed method was a simple, rapid, effective, and reliable method for the discovery of natural bioactive compounds, and it can be extended to screen other bioactive compounds from traditional Chinese medicines.


Assuntos
Bignoniaceae , Descoberta de Drogas/métodos , Inibidores Enzimáticos , Monofenol Mono-Oxigenase/antagonistas & inibidores , Extratos Vegetais , Cromatografia Líquida de Alta Pressão/métodos , Inibidores Enzimáticos/análise , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Flavonas/análise , Flavonas/química , Flavonas/metabolismo , Glucosídeos/análise , Glucosídeos/química , Glucosídeos/metabolismo , Espectrometria de Massas/métodos , Simulação de Acoplamento Molecular/métodos , Monofenol Mono-Oxigenase/química , Monofenol Mono-Oxigenase/metabolismo , Extratos Vegetais/análise , Extratos Vegetais/química , Extratos Vegetais/metabolismo , Ultrafiltração/métodos
9.
Int J Mol Sci ; 20(18)2019 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-31487867

RESUMO

Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineating structure-activity relationships (SAR), without knowing a priori the chemical structure of other target modulators. Although it was originally developed to help understanding the mechanisms of molecular recognition between small and large molecules, uses and applications of docking in drug discovery have heavily changed over the last years. In this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. Then, we illustrate newer and emergent uses and applications of docking, including prediction of adverse effects, polypharmacology, drug repurposing, and target fishing and profiling, discussing also future applications and further potential of this technique when combined with emergent techniques, such as artificial intelligence.


Assuntos
Descoberta de Drogas/métodos , Simulação de Acoplamento Molecular/métodos , Animais , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/etiologia , Humanos , Polifarmacologia , Relação Quantitativa Estrutura-Atividade
10.
Life Sci ; 239: 116872, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31525427

RESUMO

AIMS: G protein-coupled receptor (GPCR) kinases (GRKs) are mainly involved in the desensitization of GPCRs. Among them, GRK2 has been described to be upregulated in many pathological conditions and its crucial role in cardiac hypertrophy, hypertension, and heart failure promoted the search for pharmacological inhibitors of its activity. There have been several reports of potent and selective inhibitors of GRK2, most of them directed to the kinase domain of the protein. However, the homologous to the regulator of G protein signaling (RH) domain of GRK2 has also been shown to regulate GPCRs signaling. Herein, we searched for potential inhibitors of receptor desensitization mediated by RH domain of GRK2. MATERIALS AND METHODS: We performed a docking-based virtual screening utilizing the crystal structure of GRK2 to search for potential inhibitors of the interaction between GRK2 and Gαq protein. To evaluate the biological activity of compounds we measured, calcium response of histamine H1 receptor (H1R) using Fura-2AM dye and H1R internalization by saturation binding experiments in A549 cells. GRK2(45-178)GFP translocation was determined in HeLa cells through confocal fluorescence imaging. KEY FINDINGS: We identified inhibitors of GRK2 able to reduce the RH mediated desensitization of the histamine H1 receptor and GRK2 translocation to plasma membrane. Also candidates presented adequate lipophilia and cytotoxicity profile. SIGNIFICANCE: We obtained compounds with the ability of reducing RH mediated actions of GRK2 that can be useful as a starting point in the development of novel drug candidates aimed to treat pathologies were GRK2 plays a key role.


Assuntos
Quinase 2 de Receptor Acoplado a Proteína G/antagonistas & inibidores , Quinase 2 de Receptor Acoplado a Proteína G/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Células A549 , Simulação por Computador , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Quinase 2 de Receptor Acoplado a Proteína G/química , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/metabolismo , Células HeLa , Humanos , Programas de Rastreamento , Simulação de Acoplamento Molecular/métodos , Fosforilação , Ligação Proteica , Domínios Proteicos , Inibidores de Proteínas Quinases/química , Receptores Histamínicos H1/metabolismo , Transdução de Sinais
11.
Med Sci Monit ; 25: 4923-4932, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31268042

RESUMO

Thyroid-associated ophthalmopathy is the commonest orbital disease in adults. However, shortcomings still exist in treatments. The aim of this study was to identify the efficacy and potential mechanism of gypenosides in the treatment of thyroid-associated ophthalmopathy. The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was screened for active compounds of gypenosides, and targets were predicted using Swiss Target Prediction. The targets of thyroid-associated ophthalmopathy were obtained from Online Mendelian Inheritance in Man, Comparative Toxicogenomic Database and GeneCards Human gene database. Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome Pathways were determined based on the common targets. Protein-protein interaction (PPI) network was constructed to further understand of relationship among target genes, compounds and proteins. Molecular docking was performed to investigate the binding ability between gypenosides and hub genes. A total of 70 targets for gypenosides and 804 targets for thyroid-associated ophthalmopathy were obtained with 8 common targets identified. GO analysis and KEGG pathway analysis revealed that the hub genes were enriched in JAK-STAT, while Reactome pathways analysis indicated genes enriched in interleukin pathways. PPI network showed STAT1, STAT3, and STAT4 were at the center. Additionally, molecular docking indicated that STAT1 and STAT3 display good binding forces with gypenosides. This study indicates that target genes mainly enriched in JAK-STAT signaling pathway, particularly in STATs, which can be combined with gypenosides. This may suggest that gypenosides have curative effect on thyroid-associated ophthalmopathy via the JAK-STAT pathway.


Assuntos
Biologia Computacional/métodos , Oftalmopatia de Graves/tratamento farmacológico , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica/genética , Ontologia Genética , Redes Reguladoras de Genes/genética , Oftalmopatia de Graves/genética , Oftalmopatia de Graves/metabolismo , Gynostemma/metabolismo , Humanos , Medicina Tradicional Chinesa , Simulação de Acoplamento Molecular/métodos , Extratos Vegetais/metabolismo , Extratos Vegetais/uso terapêutico , Mapas de Interação de Proteínas/genética , Fatores de Transcrição STAT/genética , Fatores de Transcrição STAT/metabolismo , Transdução de Sinais/genética
12.
Biochimie ; 165: 32-39, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31278967

RESUMO

Matrix metalloproteinases are a class of enzymes, which degrade extracellular matrix components such as collagens, elastin, laminin or fibronectin. So far, four matrix metalloproteinases have been shown to degrade elastin and its precursor tropoelastin, namely matrix metalloproteinase-2, -7, -9 and -12. This study focuses on investigating the elastinolytic capability of membrane-type 1 matrix metalloproteinase, also known as matrix metalloproteinase-14. We digested recombinant human tropoelastin and human skin elastin with matrix metalloproteinase-14 and analyzed the peptide mixtures using complementary mass spectrometric techniques and bioinformatics tools. The results and additional molecular docking studies show that matrix metalloproteinase-14 cleaves tropoelastin as well as elastin. While tropoelastin was well degraded, fewer cleavages occurred in the highly cross-linked mature elastin. The study also provides insights into the cleavage preferences of the enzyme. Similar to cleavage preferences of matrix metalloproteinases-2, -7, -9 and -12, matrix metalloproteinase-14 prefers small and medium-sized hydrophobic residues including Gly, Ala, Leu and Val at cleavage site P1'. Pro, Gly and Ala were preferably found at P1-P4 and P2'-P4' in both tropoelastin and elastin. Cleavage of mature skin elastin by matrix metalloproteinase-14 released a variety of bioactive elastin peptides, which indicates that the enzyme may play a role in the development and progression of cardiovascular diseases that go along with elastin breakdown.


Assuntos
Elastina/metabolismo , Metaloproteinase 14 da Matriz/metabolismo , Proteólise , Tropoelastina/metabolismo , Humanos , Simulação de Acoplamento Molecular/métodos
13.
Mar Drugs ; 17(7)2019 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-31288374

RESUMO

Marine organisms are recognized as a source of compounds with interesting biological activities. Vibrio neocaledonicus has been reported on for its high effectiveness against corrosion in metals but it has been little studied for its chemical and biological activities. In this study, four compounds were isolated from V. neocaledonicus: indole (1); 1H-indole-3-carboxaldehyde (2); 4-hydroxybenzaldehyde (3) and Cyclo (-Pro-Tyr) (4); using a bioassay-guided method, since in a previous study it was found that the ethyl acetate extract was active on the enzymes acetylcholinesterase (AChE), alpha-glucosidase (AG) and xanthine oxidase (XO). The inhibitory activities of the three compounds against AChE, AG and XO was also evaluated. In addition, the enzymatic inhibitory activity of indole to the toxins from the venom of Bothrops asper was tested. Results showed that indole exhibited strong inhibitory activity to AG (IC50 = 18.65 ± 1.1 µM), to AChE, and XO (51.3% and 44.3% at 50 µg/mL, respectively). 1H-indole-3-carboxaldehyde displayed strong activity to XO (IC50 = 13.36 ± 0.39 µM). 4-hydroxybenzaldehyde showed moderate activity to XO (50.75% at 50 µg/mL) and weak activity to AChE (25.7% at 50 µg/mL). Furthermore, indole showed a significant in vitro inhibition to the coagulant effect induced by 1.0 µg of venom. The findings were supported by molecular docking. This is the first comprehensive report on the chemistry of V. neocaledonicus and the bioactivity of its metabolites.


Assuntos
Organismos Aquáticos/química , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Enzimas/química , Vibrio/química , Benzaldeídos/química , Benzaldeídos/farmacologia , Indóis/química , Indóis/farmacologia , Simulação de Acoplamento Molecular/métodos
14.
Int J Mol Sci ; 20(13)2019 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-31261636

RESUMO

Protein-ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein-ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant in binding affinity and ligand selectivity. In this paper, a novel piece of open-source software to approach this problem is presented, called GPathFinder. It is built as an extension of the modular GaudiMM platform and is able to simulate ligand diffusion pathways at atomistic level. The method has been benchmarked on a set of 20 systems whose ligand-binding routes were studied by other computational tools or suggested from experimental "snapshots". In all of this set, GPathFinder identifies those channels that were already reported in the literature. Interestingly, the low-energy pathways in some cases indicate novel possible binding routes. To show the usefulness of GPathFinder, the analysis of three case systems is reported. We believe that GPathFinder is a software solution with a good balance between accuracy and computational cost, and represents a step forward in extending protein-ligand docking capacities, with implications in several fields such as drug or enzyme design.


Assuntos
Simulação de Acoplamento Molecular/métodos , Software , Algoritmos , Aquaporinas/química , Aquaporinas/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Sítios de Ligação , Citocromo P-450 CYP2C19/química , Citocromo P-450 CYP2C19/metabolismo , Humanos , Indolamina-Pirrol 2,3,-Dioxigenase/química , Indolamina-Pirrol 2,3,-Dioxigenase/metabolismo , Ligantes , Ligação Proteica
15.
Int J Mol Sci ; 20(11)2019 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-31174295

RESUMO

Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein's ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers, as is done with a template compound in the ligand-based screening. This cavity-based rigid docking has been demonstrated to work with genuine drug targets in both benchmark testing and drug candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D conformer generation software for acquiring the best NIB screening results using cyclooxygenase-2 (COX-2) as the example system. Secondly, the entire NIB workflow from the protein structure preparation, model build-up, and ligand conformer generation to the similarity comparison is performed for COX-2. Accordingly, hands-on instructions are provided on how to employ the NIB methodology from start to finish, both with the rigid docking and docking rescoring using noncommercial software. The practical aspects of the NIB methodology, especially the effect of ligand conformers, are discussed thoroughly, thus, making the methodology accessible for new users.


Assuntos
Inibidores de Ciclo-Oxigenase 2/química , Descoberta de Drogas/métodos , Simulação de Acoplamento Molecular/métodos , Sítios de Ligação , Ciclo-Oxigenase 2/química , Ciclo-Oxigenase 2/metabolismo , Inibidores de Ciclo-Oxigenase 2/farmacologia , Humanos , Ligação Proteica
16.
Int J Mol Sci ; 20(11)2019 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-31174387

RESUMO

Structure-based drug design is becoming an essential tool for faster and more cost-efficient lead discovery relative to the traditional method. Genomic, proteomic, and structural studies have provided hundreds of new targets and opportunities for future drug discovery. This situation poses a major problem: the necessity to handle the "big data" generated by combinatorial chemistry. Artificial intelligence (AI) and deep learning play a pivotal role in the analysis and systemization of larger data sets by statistical machine learning methods. Advanced AI-based sophisticated machine learning tools have a significant impact on the drug discovery process including medicinal chemistry. In this review, we focus on the currently available methods and algorithms for structure-based drug design including virtual screening and de novo drug design, with a special emphasis on AI- and deep-learning-based methods used for drug discovery.


Assuntos
Aprendizado Profundo , Descoberta de Drogas/métodos , Relação Quantitativa Estrutura-Atividade , Simulação de Acoplamento Molecular/métodos
17.
Mar Drugs ; 17(6)2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31238535

RESUMO

Modulation of multiple protein targets with a single compound is essential for the effective treatment of central nervous system disorders. In our previous G protein-coupled receptor (GPCR) cell-based study, a selective human monoamine oxidase (hMAO)-A inhibitor, eckol, stimulated activity of dopamine D3 and D4 receptors. This result led to our interest in marine phlorotannin-mediated modulation of hMAO enzymes and related GPCRs in neuronal disorders. Here, we evaluate the multi-target effects of phloroglucinol, phlorofucofuroeckol-A (PFF-A), and dieckol by screening their modulatory activity against hMAO-A and -B and various neuronal GPCRs. Among the tested phlorotannins, PFF-A showed the strongest inhibitory activity against both hMAO isoforms, with higher selectivity toward hMAO-B than hMAO-A. Enzyme kinetics and docking data revealed that PFF-A noncompetitively acts on hMAOs into the alternative binding pocket of enzymes with allosteric functions. In a functional assay for GPCR screening, dieckol and PFF-A exhibited a multi-target combination of D3R/D4R agonism and D1/5HT1A/NK1 antagonism. In particular, they effectively stimulated D3R and D4R, compared to other GPCRs. Docking analysis confirmed that dieckol and PFF-A successfully docked into the conserved active sites of D3R and D4R and interacted with aspartyl and serine residues in the orthosteric binding pockets of the respective receptors. Based on our experimental and computational data, we established the structure-activity relationship between tested phlorotannins and target proteins, including hMAOs and GPCRs. Our current findings suggest that hMAO inhibitors dieckol and PFF-A, major phlorotannins of edible brown algae with multi-action on GPCRs, are potential agents for treatment of psychological disorders and Parkinson's disease.


Assuntos
Antagonistas de Dopamina/farmacologia , Inibidores da Monoaminoxidase/farmacologia , Monoaminoxidase/metabolismo , Doenças do Sistema Nervoso/tratamento farmacológico , Receptores Dopaminérgicos/metabolismo , Taninos/farmacologia , Benzofuranos/farmacologia , Dioxinas/farmacologia , Dopamina/metabolismo , Humanos , Simulação de Acoplamento Molecular/métodos , Doenças do Sistema Nervoso/metabolismo , Feófitas/química , Receptores Acoplados a Proteínas-G/metabolismo , Relação Estrutura-Atividade
18.
Mar Drugs ; 17(6)2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31226863

RESUMO

Enantiopure epoxides are versatile synthetic intermediates for producing optically active pharmaceuticals. In an effort to provide more options for the preparation of enantiopure epoxides, a variant of the epoxide hydrolase (vEH-Am) gene from a marine microorganism Agromyces mediolanus was synthesized and expressed in Escherichia coli. Recombiant vEH-Am displayed a molecular weight of 43 kDa and showed high stability with a half-life of 51.1 h at 30 °C. The purified vEH-Am exhibited high enantioselectivity towards styrene oxide (SO) and benzyl glycidyl ether (BGE). The vEH-Am preferentially converted (S)-SO, leaving (R)-SO with the enantiomeric excess (ee) >99%. However, (R)-BGE was preferentially hydrolyzed by vEH-Am, resulting in (S)-BGE with >99% ee. To investigate the origin of regioselectivity, the interactions between vEH-Am and enantiomers of SO and BGE were analyzed by molecular docking simulation. In addition, it was observed that the yields of (R)-SO and (S)-BGE decreased with the increase of substrate concentrations. The yield of (R)-SO was significantly increased by adding 2% (v/v) Tween-20 or intermittent supplementation of the substrate. To our knowledge, vEH-Am displayed the highest enantioselectivity for the kinetic resolution of racemic BGE among the known EHs, suggesting promising applications of vEH-Am in the preparation of optically active BGE.


Assuntos
Organismos Aquáticos/metabolismo , Epóxido Hidrolases/metabolismo , Compostos de Epóxi/metabolismo , Escherichia coli/metabolismo , Hidrólise , Cinética , Simulação de Acoplamento Molecular/métodos , Estereoisomerismo
19.
World Neurosurg ; 130: e294-e306, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31203065

RESUMO

OBJECTIVE: To screen ideal lead compounds from a drug library (ZINC15 database) with potential inhibition effect against O6-methylguanine-DNA methyltransferase (MGMT) to contribute to medication design and refinement. METHODS: A series of computer-aided virtual screening techniques were used to identify potential inhibitors of MGMT. Structure-based virtual screening by LibDock was carried out to calculate LibDock scores, followed by absorption, distribution, metabolism, and excretion and toxicity predictions. Molecule docking was employed to demonstrate binding affinity and mechanism between the selected ligands and MGMT protein. Molecular dynamics simulation was performed to evaluate stability of the ligand-MGMT complex under natural circumstances. RESULTS: Two novel natural compounds, ZINC000008220033 and ZINC000001529323, from the ZINC15 database were found to bind with MGMT with a higher binding affinity together with more favorable interaction energy. Also, they were predicted to have less rodent carcinogenicity, Ames mutagenicity, and developmental toxicity potential as well as noninhibition with cytochrome P-450 2D6. Molecular dynamics simulation analysis demonstrated that the 2 complexes ZINC000008220033-MGMT and ZINC000001529323-MGMT had more favorable potential energy compared with reference ligand O6-benzylguanine, and they could exist stably in the natural environment. CONCLUSIONS: This study elucidated that ZINC000008220033 and ZINC000001529323 were ideal lead compounds with potential inhibition targeting to MGMT protein. These compounds were selected as safe drug candidates and may contribute a solid basis for MGMT target medication design and improvement.


Assuntos
Sistemas de Liberação de Medicamentos/métodos , Descoberta de Drogas/métodos , Inibidores Enzimáticos/farmacologia , Simulação de Acoplamento Molecular/métodos , O(6)-Metilguanina-DNA Metiltransferase/antagonistas & inibidores , Bases de Dados Factuais , Avaliação Pré-Clínica de Medicamentos/métodos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Humanos , O(6)-Metilguanina-DNA Metiltransferase/química , O(6)-Metilguanina-DNA Metiltransferase/metabolismo , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína
20.
Artigo em Inglês | MEDLINE | ID: mdl-31172862

RESUMO

The interaction of the [Mn(mef)2(phen)H2O] complex in which mef is mefenamic acid drug and phen is 1,10 phenanthrolin ligand with calf thymus DNA (ct-DNA) was studied by using different spectroscopic methods, molecular docking and viscometery. The competitive fluorescence and UV-Vis absorption spectroscopy indicated that the complex interacted with ctDNA via intercalating binding mode with the binding constant of 1.16 × 104 Lmol-1. The thermodynamic studies showed that the reaction between the complex and ctDNA is exothermic. Furthermore, the complex induced changes in DNA viscosity. Circular dichroism spectroscopy (CD) was employed to measure the conformational changes of ctDNA in the presence of the complex and verified intercalation binding mode. The molecular modeling results illustrated that the complex interacted via intercalation by relative binding energy of -28.45 kJ mol-1.


Assuntos
Complexos de Coordenação/química , DNA/química , Substâncias Intercalantes/química , Manganês/química , Ácido Mefenâmico/química , Simulação de Acoplamento Molecular/métodos , Espectrometria de Fluorescência , Termodinâmica , Viscosidade
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