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Using molecular docking to investigate the anti-breast cancer activity of low molecular weight compounds present on wild mushrooms.

Froufe, Hugo J.C.; Abreu, Rui M.V.; Ferreira, Isabel C.F.R.
Fonte: Taylor & Francis Publicador: Taylor & Francis
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
66.2%
Mushrooms represent an unlimited source of compounds with antitumor and immunostimulating properties and mushroom intake as been shown to reduce the risk of breast cancer. A large number of LMW (low molecular weight) compounds present in mushrooms have been identified including: phenolic acids, flavonoids, tocopherols, carotenoids, sugars and fatty acids. In order to evaluate which wild mushroom LMW compounds may be involved in anti-breast cancer activity we selected a representative dataset of 43 LMW compounds and performed molecular docking against 3 known protein targets involved in breast cancer (Aromatase, Estrone Sulfatase and 17β-HSD-1) using AutoDock4 as docking software. The estimated inhibition constants for all LMW compounds were determined and the potential structure-activity relationships for the compounds with the best estimated inhibition constants are discussed for each compound family. 4-O-caffeoylquinic, naringin and lycopene stand out as the top ranked potential inhibitors for Aromatase, Estrone Sulfatase and 17β-HSD1, respectively, and the 3-D docked conformation for these compounds are discussed in detail. This information provides several interesting starting points for further development of Aromatase, Estrone Sulfatase and 17β-HSD1 inhibitors.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Barros, Rodrigo Coelho; Winck, Ana T.; Machado, Karina S.; Basgalupp, Marcio P.; Carvalho, André C. P. L. F. de; Ruiz, Duncan D.; Souza, Osmar Norberto de
Fonte: BIOMED CENTRAL LTD; LONDON Publicador: BIOMED CENTRAL LTD; LONDON
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
56.16%
Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition...

Investigação da interação de ligantes fluorescentes derivados de benzazóis com B-DNA por docking e dinâmica molecular

Grasel, Fábio dos Santos
Fonte: Universidade Federal do Rio Grande do Sul Publicador: Universidade Federal do Rio Grande do Sul
Tipo: Tese de Doutorado Formato: application/pdf
POR
Relevância na Pesquisa
56.28%
Neste trabalho foi realizado o estudo por docagem e simulação de dinâmica molecular de doze derivados benzazólicos fluorescentes por ESIPT, interagindo com o dodecâmero de Dickerson-Drew na forma B-DNA. Estes doze ligantes foram divididos em dois grupos (A e B), sendo o primeiro grupo composto por derivados do 2-(2’-hidroxifenil)-benzoxazol e o segundo grupo composto por três derivados do 2-(4’-amino-2’-hidroxifenil)-benzazóis, alternando entre N, S e O no anel azólico, mais três bases de Tröger derivadas dos mesmos. Na análise da docagem molecular do grupo A, os derivados com grupamento –NH2 no anel fenólico apresentaram energias de interação mais favoráveis com o DNA, verificando um favorecimento ainda maior, para os ligantes que continham –NO2 como substituinte no anel benzoxazólico. Na análise da docagem molecular para grupo B, as bases de Tröger (4ac) apresentaram interações significativamente mais favoráveis, quando comparados com seus respectivos precursores (3ac). Na análise da DM, tanto o grupo A, quanto o B, apresentaram a formação de complexos estáveis. O grupo A apresentou uma indução a alterações estruturais mínimas no DNA, sendo as maiores alterações a abertura do Rise quando os ligantes estavam intercalados...

Molecular Docking and Molecular Dynamic Studies of Semi-Synthetic Piperidine Alkaloids as Acetylcholinesterase Inhibitors

Danuello, Amanda; Romeiro, Nelilma C.; Giesel, Guilherme M.; Pivatto, Marcos; Viegas, Claudio; Verli, Hugo; Barreiro, Eliezer J.; Fraga, Carlos A. M.; Castro, Newton G.; Bolzani, Vanderlan da Silva
Fonte: Soc Brasileira Quimica Publicador: Soc Brasileira Quimica
Tipo: Artigo de Revista Científica Formato: 163-U505
ENG
Relevância na Pesquisa
56.16%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Processo FAPESP: 03/02176-7; The mixture of semi-synthetic derivatives (-)-3-O-acetyl-cassine hydrochloride and (-)-3-O-acetyl-spectaline hydrochloride, prepared from the mixture of natural alkaloids (-)-cassine and (-)-spectaline (4:1) isolated from Senna spectabilis, has been shown to be a potent acetylcholinesterase (AChE) inhibitor, thereby prompting further molecular studies. In this sense, docking and dynamic molecular studies were carried out in this work, aiming to acquire a deeper understanding about all the structural aspects of molecules (-)-3-O-acetyl-cassine and (-)-3-O-acetyl-spectaline hydrochlorides, which differ with respect to their AChE inhibitory potentials. Both molecules establish important interactions with the peripheral anionic site within the catalytic gorge of Torpedo californica AChE. However, only the major compound (-)-3-O-acetyl-cassine hydrochloride significantly interacts with the catalytic triad. Explicit-solvent molecular dynamic simulations were conducted in order to gain better understanding about the hypothetical interactions taking place between the semi-synthetic alkaloid molecules (-)-3-O-acetyl-cassine and (-)-3-O-acetyl-spectaline hydrochlorides and AChE. The data obtained in this study indicated that (-)-3-O-acetyl-cassine hydrochloride is the most potent inhibitor of AChE possibly due to the favorable interactions of this molecule with the target protein...

Scalar algorithms for molecular docking in heterogeneous platforms

Costa, Rui Sérgio Magalhães da
Fonte: Universidade do Minho Publicador: Universidade do Minho
Tipo: Dissertação de Mestrado
Publicado em 15/12/2011 ENG
Relevância na Pesquisa
66.36%
Dissertação de mestrado em Engenharia de Informática; The high throughput screening of new candidate drugs uses computational intensive molecular docking simulations. State-of-the art implementations for multicore-CPU systems still have performance, precision and accuracy limitations, which require an increase in the efficiency and scalability of both molecular docking algorithms and their coding. Current heterogenous platforms that merge multicore CPU with CUDA enabled GPU devices are an affordable accelerating technology that may overcome the performance limitations. The dissertation work aims to efficiently port to an heterogeneous platform a popular open source software package for molecular docking, Autodock Vina, keeping the functionality of the original algorithms whenever feasible. The new version, ScalaVina, predicts the noncovalent chemical interaction of a small molecule (ligand) against the binding site of a receptor macromolecule (receptor), evaluating the fitness of the ligand inside the binding pocket using a scoring function, and searching the best structural fit between ligand and receptor with the lowest local minima binding energy. The original Vina supports multithreaded parallelism at a high level...

Novel benzopsoralen analogues : synthesis, biological activity and molecular docking studies

Francisco, Carla Santana; Rodrigues, L. R.; Cerqueira, N. M. F. S. A.; Campos, Ana M. F. Oliveira; Esteves, Ana Paula
Fonte: Elsevier BV Publicador: Elsevier BV
Tipo: Artigo de Revista Científica
Publicado em //2014 ENG
Relevância na Pesquisa
66.1%
New benzopsoralen analogues were synthesized and their inhibitory effect on the growth of tumourtumour cell lines (MDA MB231 and TCC-SUP) was evaluated. The in vitro antitumour activity of the new benzopsoralen analogues was discussed in terms of structure–activity relationship. Molecular docking studies with human-CYP2A6 enzymes were also carried out with the synthesized compounds to evaluate the potential of these molecules to interact with the haem group of the enzymes. The results demonstrated that the compounds that are able to interact with the iron ion of the haem cofactor and at the same time with active site Asn297 are those that have better anti-proliferative activity.

Molecular docking and molecular dynamic studies of semi-synthetic piperidine alkaloids as acetylcholinesterase inhibitors

Danuello,Amanda; Romeiro,Nelilma C.; Giesel,Guilherme M.; Pivatto,Marcos; Viegas Jr.,Claudio; Verli,Hugo; Barreiro,Eliezer J.; Fraga,Carlos A. M.; Castro,Newton G.; Bolzani,Vanderlan S.
Fonte: Sociedade Brasileira de Química Publicador: Sociedade Brasileira de Química
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2012 EN
Relevância na Pesquisa
56.16%
The mixture of semi-synthetic derivatives (-)-3-O-acetyl-cassine hydrochloride and (-)-3-O-acetyl-spectaline hydrochloride, prepared from the mixture of natural alkaloids (-)-cassine and (-)-spectaline (4:1) isolated from Senna spectabilis, has been shown to be a potent acetylcholinesterase (AChE) inhibitor, thereby prompting further molecular studies. In this sense, docking and dynamic molecular studies were carried out in this work, aiming to acquire a deeper understanding about all the structural aspects of molecules (-)-3-O-acetyl-cassine and (-)-3-O-acetyl-spectaline hydrochlorides, which differ with respect to their AChE inhibitory potentials. Both molecules establish important interactions with the peripheral anionic site within the catalytic gorge of Torpedo californica AChE. However, only the major compound (-)-3-O-acetyl-cassine hydrochloride significantly interacts with the catalytic triad. Explicit-solvent molecular dynamic simulations were conducted in order to gain better understanding about the hypothetical interactions taking place between the semi-synthetic alkaloid molecules (-)-3-O-acetyl-cassine and (-)-3-O-acetyl-spectaline hydrochlorides and AChE. The data obtained in this study indicated that (-)-3-O-acetyl-cassine hydrochloride is the most potent inhibitor of AChE possibly due to the favorable interactions of this molecule with the target protein...

3D-QSAR and Molecular Docking Studies on Fused Pyrazoles as p38α Mitogen-Activated Protein Kinase Inhibitors

Lan, Ping; Huang, Zhi-Jian; Sun, Jun-Rong; Chen, Wei-Min
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 17/09/2010 EN
Relevância na Pesquisa
56.15%
The p38α mitogen-activated protein kinase (MAPK) has become an attractive target for the treatment of many diseases such as rheumatoid arthritis, inflammatory bowel disease and Crohn’s disease. In this paper, 3D-QSAR and molecular docking studies were performed on 59 p38α MAPK inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to determine the structural requirements for potency in inhibiting p38α MAPK. The resulting model of CoMFA and CoMSIA exhibited good r2cv values of 0.725 and 0.609, and r2 values of 0.961 and 0.905, respectively. Molecular docking was used to explore the binding mode between the inhibitors and p38α MAPK. We have accordingly designed a series of novel p38α MAPK inhibitors by utilizing the structure-activity relationship (SAR) results revealed in the present study, which were predicted with excellent potencies in the developed models. The results provided a useful guide to design new compounds for p38α MAPK inhibitors.

In Silico Prediction of Estrogen Receptor Subtype Binding Affinity and Selectivity Using Statistical Methods and Molecular Docking with 2-Arylnaphthalenes and 2-Arylquinolines

Wang, Zhizhong; Li, Yan; Ai, Chunzhi; Wang, Yonghua
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 20/09/2010 EN
Relevância na Pesquisa
56.14%
Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ERα and ERβ inhibitory activities was built, and quantitative structure-activity relationship (QSAR) methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR) and a nonlinear statistical method (Bayesian regularized neural network, BRNN) were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ERα and ERβ, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ERα: for MLR, Rtr2 = 0.72, Qte2 = 0.63; for PLSR, Rtr2 = 0.92, Qte2 = 0.84. ERβ: for MLR, Rtr2 = 0.75, Qte2 = 0.75; for PLSR, Rtr2 = 0.98, Qte2 = 0.80). The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in Rtr2 = 0.74 and Qte2 = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ERα and ERβ is more correlated with the atom fragment type...

3D-QSAR and Molecular Docking Studies on Derivatives of MK-0457, GSK1070916 and SNS-314 as Inhibitors against Aurora B Kinase

Zhang, Baidong; Li, Yan; Zhang, Huixiao; Ai, Chunzhi
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 02/11/2010 EN
Relevância na Pesquisa
56.14%
Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q2 = 0.605, r2pred = 0.826), (q2 = 0.52, r2pred = 0.798) and (q2 = 0.582, r2pred = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover...

Structural Determination of Three Different Series of Compounds as Hsp90 Inhibitors Using 3D-QSAR Modeling, Molecular Docking and Molecular Dynamics Methods

Liu, Jianling; Wang, Fangfang; Ma, Zhi; Wang, Xia; Wang, Yonghua
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 30/01/2011 EN
Relevância na Pesquisa
56.23%
Hsp90 is involved in correcting, folding, maturation and activation of a diverse array of client proteins; it has also been implicated in the treatment of cancer in recent years. In this work, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), molecular docking and molecular dynamics were performed on three different series of Hsp90 inhibitors to build 3D-QSAR models, which were based on the ligand-based or receptor-based methods. The optimum 3D-QSAR models exhibited reasonable statistical characteristics with averaging internal q2 > 0.60 and external r2pred > 0.66 for Benzamide tetrahydro-4H-carbazol-4-one analogs (BT), AT13387 derivatives (AT) and Dihydroxylphenyl amides (DA). The results revealed that steric effects contributed the most to the BT model, whereas H-bonding was more important to AT, and electrostatic, hydrophobic, H-bond donor almost contributed equally to the DA model. The docking analysis showed that Asp93, Tyr139 and Thr184 in Hsp90 are important for the three series of inhibitors. Molecular dynamics simulation (MD) further indicated that the conformation derived from docking is basically consistent with the average structure extracted from MD simulation. These results not only lead to a better understanding of interactions between these inhibitors and Hsp90 receptor but also provide useful information for the design of new inhibitors with a specific activity.

Combined 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Derivatives of Peptide Epoxyketone and Tyropeptin-Boronic Acid as Inhibitors Against the β5 Subunit of Human 20S Proteasome

Liu, Jianling; Zhang, Hong; Xiao, Zhengtao; Wang, Fangfang; Wang, Xia; Wang, Yonghua
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 09/03/2011 EN
Relevância na Pesquisa
56.21%
An abnormal ubiquitin-proteasome is found in many human diseases, especially in cancer, and has received extensive attention as a promising therapeutic target in recent years. In this work, several in silico models have been built with two classes of proteasome inhibitors (PIs) by using 3D-QSAR, homology modeling, molecular docking and molecular dynamics (MD) simulations. The study resulted in two types of satisfactory 3D-QSAR models, i.e., the CoMFA model (Q2 = 0.462, R2pred = 0.820) for epoxyketone inhibitors (EPK) and the CoMSIA model (Q2 = 0.622, R2pred = 0.821) for tyropeptin-boronic acid derivatives (TBA). From the contour maps, some key structural factors responsible for the activity of these two series of PIs are revealed. For EPK inhibitors, the N-cap part should have higher electropositivity; a large substituent such as a benzene ring is favored at the C6-position. In terms of TBA inhibitors, hydrophobic substituents with a larger size anisole group are preferential at the C8-position; higher electropositive substituents like a naphthalene group at the C3-position can enhance the activity of the drug by providing hydrogen bond interaction with the protein target. Molecular docking disclosed that residues Thr60, Thr80, Gly106 and Ser189 play a pivotal role in maintaining the drug-target interactions...

Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus

Lu, Shih-Jen; Chong, Fok-Ching
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 10/04/2012 EN
Relevância na Pesquisa
56.15%
Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R2 = 0.75.

Multipose Binding in Molecular Docking

Atkovska, Kalina; Samsonov, Sergey A.; Paszkowski-Rogacz, Maciej; Pisabarro, M. Teresa
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 14/02/2014 EN
Relevância na Pesquisa
56.32%
Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

FReMI: a middleware to handle molecular docking simulations of fully-flexible receptor models in HPC environments

De Paris, Renata
Fonte: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Publicador: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre
Tipo: Dissertação de Mestrado
PORTUGUêS
Relevância na Pesquisa
56.27%
Simulações de docagem molecular de modelos de receptores totalmente flexíveis (Fully-Flexible Receptor - FFR) estão se tornando cada vez mais frequentes. Entretanto, tais simulações exigem alto nível de processamento e sua execução sequencial pode se tornar uma tarefa impraticável. Este trabalho apresenta um middleware, chamado Middleware de Receptores Flexível (Flexible Receptor Middleware – FReMI), que auxilia a reduzir o tempo total de execução nas simulações de docagem molecular de receptores totalmente flexíveis. FReMI manipula uma quantidade intensiva de dados e tarefas para executar a triagem virtual de modelos de receptores totalmente flexíveis, e provê interoperabilidade entre o web workflow de docagem de receptores flexíveis (Web Fully-flexible Docking Workflow - W-FReDoW) e dois diferentes ambientes de alto desempenho (High Performance Computing – HPC). FReMI utiliza protocolos de internet para comunicar com o W-FReDoW , o qual auxilia na redução da dimensão do modelo FFR por meio de um padrão de dados. Além disso, FReMI envia tarefas de simulações de docagem para serem executadas em um cluster dedicado e também em um alternativo modelo de cluster virtual construído por meio de nuvens de computadores elásticos da Amazon (Amazon’s Elastic Compute Cloud – EC2). Os resultados apresentam uma arquitetura conceitual do FReMI e dois conjuntos de experimentos a partir da execução do FReMI.O primeiro conjunto relatou os experimentos realizados com FReMI...

Smart execution of molecular docking simulations of a fully-flexible receptor model

Frantz, Fábio André
Fonte: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre Publicador: Pontifícia Universidade Católica do Rio Grande do Sul; Porto Alegre
Tipo: Dissertação de Mestrado
PORTUGUêS
Relevância na Pesquisa
56.23%
Simulações de docagem molecular com modelos de Receptores Totalmente Flexíveis (FFR) estão adquirindo maturidade. No entanto, isto demanda atividades computacionais de paralelização para geração e execução de grande volume de dados que precisam ser analizados. Computação multi-tarefa é um paradigma atrativo e que vem sendo aplicado frequentemente para executar tarefas intensivas. Neste trabalho propomos um ambiente para executar simulações de docagem molecular no modelo FFR com pequenas moléculas integradas a um componente MTC. Este ambiente é baseado no padrão Múltiplas Instâncias Autoadaptáveis (P-SaMI) que possui regras para redução do número de experimentos, provendo um modelo de Receptores Totalmente Flexíveis Reduzido (RFFR). A principal contribuição desta pesquisa está na comprovação de que as regras do P-SaMI podem ser usadas em Simulações de Docagem Molecular através de um ambiente web integrado com um componente MTC.; Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments...

Analysis of α4 β1integrin specific antagonists binding modes: structural insights by molecular docking, molecular dynamics and linear interaction energy method for free energy calculations

Silva,João Hermínio Martins da; Dardenne,Laurent Emmanuel; Savino,Wilson; Caffarena,Ernesto Raul
Fonte: Sociedade Brasileira de Química Publicador: Sociedade Brasileira de Química
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2010 EN
Relevância na Pesquisa
56.2%
The VLA-4 antigen (α4β1 integrin) is involved in the pathophysiology of a variety of diseases including asthma, multiple sclerosis, rheumatoid arthritis and diabetes. The ligand selectivity toward this integrin remains a difficult problem, mainly due to the fact that 3D structures of most integrins are still unknown. We initially built a 3D computational model of the α4β1 ligand binding site, taking the crystal structure of the integrin αVβ3 as template. Then, we performed a computational study on a set of seven α4β1 antagonists, evaluating the binding modes of 4-[N'-(2-methylphenyl)ureido]phenylacetyl and derivatives by molecular docking. Molecular dynamics simulations were used to improve the receptor-ligand energy landscape exploration by the docking algorithm. The compounds were systematically arranged in two main binding modes, and in all cases, pointed out that these antagonists preferably bind to the α4β1 integrin active site in an extended conformation that resembles the one in solution. LIE (linear interaction energy) calculations also confirmed this statement given that the most prevailing binding mode is also the energetically most favored one. This study benefits the comprehension of the mechanism of this family of antagonists and may provide useful information for rational drug design.

Investigation of the Interaction of 2-(2'-Hydroxyphenyl)-benzoxazoles and their Derivatives with B-DNA by Docking and Molecular Dynamics

Grasel,Fábio dos S.; Oliveira,Tiago E. de; Netz,Paulo A.
Fonte: Sociedade Brasileira de Química Publicador: Sociedade Brasileira de Química
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/03/2015 EN
Relevância na Pesquisa
56.2%
In this work we carried out a study covering conformational analysis, docking calculations and molecular dynamics (MD) simulations of six excited state intramolecular proton transfer (ESIPT)-fluorescent 2-(2'-hydroxyphenyl)-benzoxazoles, interacting with the Dickerson-Drew (d(CGCGAATTCGCG)2) dodecamer in B-DNA conformation. In the analysis of the molecular docking calculations, the derivatives with the -NH2 group in the phenolic ring presented the most favorable interaction energies with the DNA, and the scores were even more favorable for the ligands containing the -NO2 group as substituent in the benzoxazolic ring. In the analysis of the MD simulations, the complexes showed stable interactions, with minimal induced structural distortions in the DNA, being the largest increase of the Rise parameter when the ligands were intercalated, and also the unwinding of Twist. During all simulations, the ligands showed stable interactions with the oligonucleotide, without denaturation. Considering these interactions and the peculiar photophysical properties of this class of molecules, they could be used as biological probes.

Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

Mouradov, Dmitri; Craven, Ari; Forwood, Jade; Flanagan, Jack U; Garcia-Castellanos, Raquel; Gomis-Ruth, F. Xavier; Hume, D A; Martin, Jennifer Louise; Kobe, Bostjan; Huber, Thomas
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
66.2%
We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were

Molecular docking study of naturallyoccurring compounds as inhibitors of N-myristoyl transferase towards antifungal agents discovery

Guerrero-Perilla,Camilo; Bernal,Freddy A.; Coy-Barrera,Ericsson D.
Fonte: Revista Colombiana de Ciencias Químico - Farmacéuticas Publicador: Revista Colombiana de Ciencias Químico - Farmacéuticas
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/05/2015 EN
Relevância na Pesquisa
66.18%
Fungal infections currently remain as a common problem in public health. Actually, drug discovery programs are oriented to the searching for lead structures. Virtual screening and molecular docking constitute great alternatives in order to find hit compounds. Novel infection targets can also be defined and employed together with molecular docking tools in drug discovery programs. Thus, thirty-two natural compounds were docked within the active site of N-myristoyl transferase (NMT) as antifungal enzyme target. From tested compounds, alkaloids, flavonoids, xanthones, and quinones exhibited strongest mean interaction with NMT than terpenoids, coumarins and phenolics. Particularly, affinities for one aporphine alkaloid, a prenylated flavonoid and two xanthones resulted to be comparable with that of previously reported synthetic inhibitor. Several hydrophobic and polar contacts were demonstrated by comparing different computational tools. The present results let to establish three possible lead structures to develop antifungal drugs although subsequent SAR analyses are still required.