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1.
PLoS One ; 14(9): e0215793, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31483779

RESUMO

Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results suggest that the base-assisted mechanism is preferred over the substrate-assisted pathway when one Mg2+ is present in the active site, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity.


Assuntos
Quinase 2 Dependente de Ciclina/química , Quinase 2 Dependente de Ciclina/metabolismo , Modelos Químicos , Modelos Moleculares , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Fosforilação , Conformação Proteica , Teoria Quântica , Relação Estrutura-Atividade , Especificidade por Substrato
2.
ChemistryOpen ; 8(5): 627-636, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31139552

RESUMO

The imino-Diels-Alder reaction is one of the most common strategies in organic chemistry and is an important tool for providing a broad spectrum of biologically active heterocyclic systems. A combined theoretical and experimental study of the imino-Diels-Alder reaction is described. The new phenanthroline-tetrahydroquinolines were evaluated as cholinesterase inhibitors. Their cytotoxicity in human neuroblastoma SH-SY5Y cells was also evaluated. The theoretical results suggest that compounds formation in stages can be explained by endo cycloadducts under the established reaction conditions, thereby confirming experimental results obtained for percentage yield. These results allowed us to establish that pyridine substituent remarkably influences activation energy and reaction yield, as well as in acetylcholinesterase (AChE) activity. Among these derivatives, compounds with 4-pyridyl and 4-nitrophenyl showed favorable AChE activity and proved to be non-cytotoxic.

3.
Biochemistry ; 57(26): 3560-3563, 2018 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-29812917

RESUMO

Clavulanate is used as an effective drug in combination with ß-lactam antibiotics to treat infections of some antibiotic resistant bacteria. Here, we perform combined quantum mechanics/molecular mechanics simulations of several covalent complexes of clavulanate with class A ß-lactamases KPC-2 and TEM-1. Simulations of the deacylation reactions identify the decarboxylated trans-enamine complex as being responsible for inhibition. Further, the obtained free energy barriers discriminate clinically relevant inhibition (TEM-1) from less effective inhibition (KPC-2).


Assuntos
Ácido Clavulânico/farmacologia , Escherichia coli/enzimologia , Klebsiella pneumoniae/enzimologia , Inibidores de beta-Lactamases/farmacologia , beta-Lactamases/metabolismo , Ácido Clavulânico/química , Escherichia coli/química , Escherichia coli/efeitos dos fármacos , Escherichia coli/metabolismo , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/microbiologia , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/química , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Termodinâmica , Inibidores de beta-Lactamases/química , beta-Lactamases/química
4.
Comput Biol Chem ; 74: 218-229, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29655025

RESUMO

Given the wide spectrum of biological uses of pyrazolo[1,5-c]quinazoline and spiro-quinazoline derivatives as anticancer, anti-inflammatory analgesic agents, and their therapeutic applications in neurodegenerative disorders, it is compulsory to find easy, efficient, and simple methods to obtain and chemically diversify these families of compounds, thereby improving their biological applications. In this paper, we report the design and eco-friendly two-step synthesis of novel, fused spiro-pyrazolo[1,5-c]quinazoline derivatives as cholinesterase inhibitors. In addition, we studied their protein-ligand interactions via molecular docking and MM/GBSA calculations for a further rational design of more potent inhibitors. In first step, 2-(1H-pyrazol-5-yl)anilines were obtained through microwave (MW) assisted solvent-free/catalyst-free conditions and the second step involved the synthesis of the spiro-pyrazolo[1,5-c]quinazolines by a cyclocondensation reaction between 2-(1H-pyrazol-5-yl)anilines and cyclic ketones, or acetophenones, using stirring at room temperature. The compounds were obtained in high purity, good yields (50-97%), and at varying reaction times. The spiro-compounds were evaluated as acetylcholinesterase and butyrylcholinesterase inhibitors (AChEIs/BuChEIs) respectively, and the most potent compound exhibited a moderate AChE inhibitory activity (5f: IC50 = 84 µM). Molecular docking studies indicated that the binding mode of the compound 5f share common characteristics with the galantamine/donepezil-AChE complexes. Moreover, free binding energy (ΔG) calculations showed a good agreement with the experimental biological activity values. Our theoretical results indicated that halogen bond interactions could be involved with differential potency of these compounds and provide a new starting point to design novel pyrazolo[1,5-c]quinazolines as new anti-Alzheimer agents.


Assuntos
Inibidores da Colinesterase/farmacologia , Desenho de Fármacos , Simulação de Acoplamento Molecular , Pirazóis/farmacologia , Teoria Quântica , Quinazolinas/farmacologia , Compostos de Espiro/farmacologia , Acetilcolinesterase/metabolismo , Butirilcolinesterase/metabolismo , Inibidores da Colinesterase/síntese química , Inibidores da Colinesterase/química , Relação Dose-Resposta a Droga , Humanos , Micro-Ondas , Estrutura Molecular , Pirazóis/síntese química , Pirazóis/química , Quinazolinas/síntese química , Quinazolinas/química , Compostos de Espiro/síntese química , Compostos de Espiro/química , Relação Estrutura-Atividade
5.
Chem Biol Drug Des ; 91(1): 29-38, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28643389

RESUMO

A combination of three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular modelling methods were used to understand the potent inhibitory NAD(P)H:quinone oxidoreductase 1 (NQO1) activity of a set of 52 heterocyclic quinones. Molecular docking results indicated that some favourable interactions of key amino acid residues at the binding site of NQO1 with these quinones would be responsible for an improvement of the NQO1 activity of these compounds. The main interactions involved are hydrogen bond of the amino group of residue Tyr128, π-stacking interactions with Phe106 and Phe178, and electrostatic interactions with flavin adenine dinucleotide (FADH) cofactor. Three models were prepared by 3D-QSAR analysis. The models derived from Model I and Model III, shown leave-one-out cross-validation correlation coefficients (q2LOO ) of .75 and .73 as well as conventional correlation coefficients (R2 ) of .93 and .95, respectively. In addition, the external predictive abilities of these models were evaluated using a test set, producing the predicted correlation coefficients (r2pred ) of .76 and .74, respectively. The good concordance between the docking results and 3D-QSAR contour maps provides helpful information about a rational modification of new molecules based in quinone scaffold, in order to design more potent NQO1 inhibitors, which would exhibit highly potent antitumor activity.


Assuntos
Simulação de Acoplamento Molecular , NAD(P)H Desidrogenase (Quinona)/metabolismo , Relação Quantitativa Estrutura-Atividade , Quinonas/metabolismo , Sítios de Ligação , Desenho Assistido por Computador , Flavina-Adenina Dinucleotídeo/química , Flavina-Adenina Dinucleotídeo/metabolismo , Humanos , Análise dos Mínimos Quadrados , NAD(P)H Desidrogenase (Quinona)/antagonistas & inibidores , Estrutura Terciária de Proteína , Quinonas/química , Eletricidade Estática
6.
PLoS One ; 11(4): e0153057, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27078149

RESUMO

Aroma and flavor are important factors of fruit quality and consumer preference. The specific pattern of aroma is generated during ripening by the accumulation of volatiles compounds, which are mainly esters. Alcohol acyltransferase (AAT) (EC 2.3.1.84) catalyzes the esterification reaction of aliphatic and aromatic alcohols and acyl-CoA into esters in fruits and flowers. In Fragaria x ananassa, there are different volatiles compounds that are obtained from different alcohol precursors, where octanol and hexanol are the most abundant during fruit ripening. At present, there is not structural evidence about the mechanism used by the AAT to synthesize esters. Experimental data attribute the kinetic role of this enzyme to 2 amino acidic residues in a highly conserved motif (HXXXD) that is located in the middle of the protein. With the aim to understand the molecular and energetic aspects of volatiles compound production from F. x ananassa, we first studied the binding modes of a series of alcohols, and also different acyl-CoA substrates, in a molecular model of alcohol acyltransferase from Fragaria x ananassa (SAAT) using molecular docking. Afterwards, the dynamical behavior of both substrates, docked within the SAAT binding site, was studied using routine molecular dynamics (MD) simulations. In addition, in order to correlate the experimental and theoretical data obtained in our laboratories, binding free energy calculations were performed; which previous results suggested that octanol, followed by hexanol, presented the best affinity for SAAT. Finally, and concerning the SAAT molecular reaction mechanism, it is suggested from molecular dynamics simulations that the reaction mechanism may proceed through the formation of a ternary complex, in where the Histidine residue at the HXXXD motif deprotonates the alcohol substrates. Then, a nucleophilic attack occurs from alcohol charged oxygen atom to the carbon atom at carbonyl group of the acyl CoA. This mechanism is in agreement with previous results, obtained in our group, in alcohol acyltransferase from Vasconcellea pubescens (VpAAT1).


Assuntos
Aciltransferases/metabolismo , Álcoois/metabolismo , Fragaria/enzimologia , Proteínas de Plantas/metabolismo , Acil Coenzima A/química , Acil Coenzima A/metabolismo , Aciltransferases/química , Aciltransferases/genética , Álcoois/química , Motivos de Aminoácidos/genética , Sequência de Aminoácidos , Sítios de Ligação/genética , Ésteres/química , Ésteres/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Proteínas de Plantas/química , Proteínas de Plantas/genética , Ligação Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Termodinâmica , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/metabolismo
7.
Phys Chem Chem Phys ; 16(27): 14047-58, 2014 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-24901037

RESUMO

A conformational selection method, based on hydrogen bond (Hbond) network analysis, has been designed in order to rationalize the configurations sampled using molecular dynamics (MD), which are commonly used in the estimation of the relative binding free energy of ligands to macromolecules through the MM/GBSA or MM/PBSA method. This approach makes use of protein-ligand complexes obtained from X-ray crystallographic data, as well as from molecular docking calculations. The combination of several computational approaches, like long MD simulations on protein-ligand complexes, Hbond network-based selection by scripting techniques and finally MM/GBSA, provides better statistical correlations against experimental binding data than previous similar reported studies. This approach has been successfully applied in the ranking of several protein kinase inhibitors (CDK2, Aurora A and p38), which present both diverse and related chemical structures.


Assuntos
Algoritmos , Hidrogênio/química , Modelos Químicos , Simulação de Acoplamento Molecular/métodos , Inibidores de Proteínas Quinases/química , Proteínas Quinases/química , Sítios de Ligação , Simulação por Computador , Ligação de Hidrogênio , Ligação Proteica
8.
Ultrason Sonochem ; 21(5): 1666-74, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24650611

RESUMO

Given the broad spectrum of uses of acrylonitrile derivatives as fluorescent probes, AChE inhibitors, and others, it is necessary to find easy, efficient and simple methods to synthesize and diversify these compounds. We report the results of a comparative study of the effects of three techniques on the reactions between heterocyclic aldehydes and 2-(benzo[d]thiazol-2-yl)acetonitrile: stirring; ultrasound coupled to PTC conditions (US-PTC); and MW irradiation (MWI) under solvent and catalyst-free conditions. The effects of conditions on reaction parameters were evaluated and compared in terms of reaction time, yield, purity and outcomes. The US-PTC method is more efficient than the MWI and conventional methods. The reaction times were considerably shorter, with high yields (>90%) and good levels of purity. In addition, X-ray diffraction analysis and quantum mechanical calculations, at the level of density functional theory (DFT), ratify obtaining acrylonitrile isomers with E configurations. The crystal structure of 3c is stabilized by weak C-Ho⋯N intermolecular interactions (Ho⋯NC=2.45 Å, Co⋯NC=3.348(3) Å, Ho⋯NC=162°), forming centrosymmetric ring R2(2) (20) along the crystallographic a axis.


Assuntos
Nitrilas/química , Nitrilas/efeitos da radiação , Ultrassom/métodos , Aldeídos/química , Aldeídos/efeitos da radiação , Catálise , Corantes Fluorescentes , Indicadores e Reagentes , Micro-Ondas , Solventes , Difração de Raios X
9.
J Mol Graph Model ; 39: 71-8, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23220284

RESUMO

The interaction of poly(amidoamine)-G3 (PAMAM-G3) dendrimer with nicotinic acid (NA) was investigated by using molecular dynamics (MD) simulations. First, sample free energy profiles of NA crossing PAMAM-G3 at pH 6 and 3 were computed using the adaptive biasing force (ABF) method. We found that PAMAM-G3 provides a more appropriate environment for NA inclusion when internal tertiary amine groups are unprotonated (at pH 6). However, when internal tertiary amine groups are protonated (at pH 3), the PAMAM cavities are less hydrophobic; therefore the drug-dendrimer interactions become similar to drug-solvent interactions. Traditional MD simulations were also performed to investigate the structural stability of the PAMAM-NA complexes near the free energy minima at pH 6. We found that association of NA and PAMAM adopts a preferred binding mode around the surface of PAMAM, where hydrogen bond (HB) interactions with the amino and amide NH groups of the nearby monomers are established. These interactions are very stable whether additional van der Waals interactions between pyridine ring of NA and methylene groups of the more external monomers of PAMAM are established.


Assuntos
Dendrímeros/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Niacina/química , Poliaminas/química , Concentração de Íons de Hidrogênio , Conformação Molecular
10.
Eur J Med Chem ; 58: 272-80, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23131541

RESUMO

Sunitinib (SU11248) is a highly potent tyrosine kinase inhibitor targeting vascular endothelial growth factor receptor (VEGFR). Radiolabeled inhibitors of receptor tyrosine kinases (RTKs) might be useful tools for monitoring RTKs levels in tumor tissue giving valuable information for anti-angiogenic therapy. Herein we report the synthesis of 5-methoxy-sunitinib 5 and its (11)C-radiolabeled analog [(11)C]-5. The non-radioactive reference compound 5 was prepared by Knoevenagel condensation of 5-methoxy-2-oxindole with the corresponding substituted 5-formyl-1H-pyrrole. A binding constant (K(d)) of 20 nM for 5 was determined by competition binding assay against VEGFR-2. In addition, the binding mode of sunitinib and its 5-methoxy substituted derivative was studied by flexible docking simulations. These studies revealed that the substitution of the fluorine at position 5 of the oxindole scaffold by a methoxy group did not affect the inhibitor orientation, but affected the electrostatic and van der Waals interactions of the ligand with residues near the DFG motif of VEGFR-2. 5-[(11)C]methoxy-sunitinib ([(11)C]-5) was synthesized by reaction of the desmethyl precursor with [(11)C]CH(3)I in the presence of DMF and NaOH in 17 ± 3% decay-corrected radiochemical yield at a specific activity of 162-205 GBq/µmol (EOS). In vivo stability studies of [(11)C]-5 in rat blood showed that more than 70% of the injected compound was in blood stream, 60 min after administration.


Assuntos
Indóis/farmacologia , Inibidores de Proteínas Quinases/farmacologia , Pirróis/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Isótopos de Carbono , Linhagem Celular , Relação Dose-Resposta a Droga , Humanos , Indóis/síntese química , Indóis/química , Estrutura Molecular , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Pirróis/síntese química , Pirróis/química , Relação Estrutura-Atividade , Sunitinibe , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
11.
Molecules ; 17(10): 12072-85, 2012 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-23085657

RESUMO

(E)-2-(benzo[d]thiazol-2-yl)-3-heteroarylacrylonitriles are described as a new class of selective inhibitors of acetylcholinesterase (AChE). The most potent compound in the series exhibited good AChE inhibitory activity (IC50 = 64 µM). Compound 7f was found to be more selective than galanthamine in inhibiting AChE and it showed a moderate selectivity index. Kinetic studies on AChE indicated that a competitive type of inhibition pattern exist for these acrylonitrile derivates. Molecular docking models of the ligand-AChE complexes suggest that compound 7 g is located on the periphery of the AChE active site.


Assuntos
Acrilonitrila/síntese química , Inibidores da Colinesterase/síntese química , Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Acrilonitrila/análogos & derivados , Acrilonitrila/química , Inibidores da Colinesterase/química , Concentração Inibidora 50 , Cinética , Simulação de Acoplamento Molecular , Ligação Proteica
12.
Curr Pharm Des ; 18(20): 2946-63, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22571663

RESUMO

Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have been identified as being implicated in many diseases. High-resolution X-ray crystallographic data exist for many PKs and, in many cases, these structures are co-complexed with inhibitors. Although this valuable information confirms the precise structure of PKs and their complexes, it ignores the dynamic movements of the structures which are relevant to explain the affinities and selectivity of the ligands, to characterize the thermodynamics of the solvated complexes, and to derive predictive models. Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. MD is a very useful computational method and a great counterpart for experimentalists, which helps them to derive important additional molecular information. That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. MD can be used to sample dynamic molecular processes, and can be complemented with more advanced computational methods (e.g., free energy calculations, structure-activity relationship analysis). This review focuses on the most commonly applications to study PK-inhibitor complexes using MD simulations. Our aim is that researchers working in the design of PK inhibitors be aware of the benefits of this powerful tool in the design of potent and selective PK inhibitors.


Assuntos
Simulação de Dinâmica Molecular , Inibidores de Proteínas Quinases/farmacologia , Proteínas Quinases/efeitos dos fármacos , Cristalografia por Raios X/métodos , Desenho de Fármacos , Humanos , Fosforilação , Inibidores de Proteínas Quinases/química , Proteínas Quinases/metabolismo , Relação Quantitativa Estrutura-Atividade , Transdução de Sinais
13.
Biochem J ; 442(1): 57-63, 2012 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-22070190

RESUMO

The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K(in)) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K(in) channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K(in) channel KAT1, mutations in the unique histidine exposed to the solvent (His267) do not affect the pH dependency. We demonstrate in the present study that His267 of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe266 shifts its pKa to undetectable values through a cation-π interaction. Instead, we show that Glu240 placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu240, several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel.


Assuntos
Proteínas de Arabidopsis/metabolismo , Concentração de Íons de Hidrogênio , Estômatos de Plantas/fisiologia , Canais de Potássio Corretores do Fluxo de Internalização/metabolismo , Sequência de Aminoácidos , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Ácido Glutâmico/química , Histidina/química , Canais de Potássio Corretores do Fluxo de Internalização/genética , Termodinâmica
14.
J Mol Graph Model ; 32: 39-48, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22070999

RESUMO

Semaxanib (SU5416) and 3-[4'-fluorobenzylidene]indolin-2-one (SU5205) are structurally similar drugs that are able to inhibit vascular endothelial growth factor receptor-2 (VEGFR2), but the former is 87 times more effective than the latter. Previously, SU5205 was used as a radiolabelled inhibitor (as surrogate for SU5416) and a radiotracer for positron emission tomography (PET) imaging, but the compound exhibited poor stability and only a moderate IC(50) toward VEGFR2. In the current work, the relationship between the structure and activity of these drugs as VEGFR2 inhibitors was studied using 3D-QSAR, docking and molecular dynamics (MD) simulations. First, comparative molecular field analysis (CoMFA) was performed using 48 2-indolinone derivatives and their VEGFR2 inhibitory activities. The best CoMFA model was carried out over a training set including 40 compounds, and it included steric and electrostatic fields. In addition, this model gave satisfactory cross-validation results and adequately predicted 8 compounds contained in the test set. The plots of the CoMFA fields could explain the structural differences between semaxanib and SU5205. Docking and molecular dynamics simulations showed that both molecules have the same orientation and dynamics inside the VEGFR2 active site. However, the hydrophobic pocket of VEGFR2 was more exposed to the solvent media when it was complexed with SU5205. An energetic analysis, including Embrace and MM-GBSA calculations, revealed that the potency of ligand binding is governed by van der Waals contacts.


Assuntos
Indóis/química , Simulação de Dinâmica Molecular , Pirróis/química , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Sítios de Ligação , Domínio Catalítico , Simulação por Computador , Humanos , Indóis/farmacologia , Modelos Moleculares , Pirróis/farmacologia , Relação Quantitativa Estrutura-Atividade , Relação Estrutura-Atividade
15.
J Chem Inf Model ; 51(11): 2920-31, 2011 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-22011048

RESUMO

N1 substituted pyrazole derivatives show diverse B-Raf kinase inhibitory activities when different hydroxy-substituted cycloalkyl groups are placed at this position. Docking, molecular dynamics (MD) simulations, and hybrid calculation methods (Quantum Mechanics/Molecular Mechanics (QM/MM)) were performed on the complexes, in order to explain these differences. Docking of the inhibitors showed the same orientation that X-ray crystal structure of the analogous (1E)-5-[1-(4-piperidinyl)-3-(4-pyridinyl)-1H-pyrazol-4-yl]-2,3-dihydro-1H-inden-1-one oxime. MD simulations of the most active diastereomer compounds containing cis- and trans-3-hydroxycyclohexyl substituents showed stable interactions with residue Ile463 at the entrance of the B-Raf active site. On the other hand, the less active diastereomer compounds containing cis- and trans-2-hydroxycyclopentyl substituents showed interactions with inner residues Asn580 and Ser465. We found that the differences in activity can be explained by considering the dynamic interactions between the inhibitors and their surrounding residues within the B-Raf binding site. We also explained the activity trend by using a testing scoring function derived from more reliable QM/MM calculations. In addition, we search for new inhibitors from a virtual screening carried out by fragment-based de novo design. We generated a set of approximately 200 virtual compounds, which interact with Ile463 and fulfill druglikeness properties according to Lipinski, Veber, and Ghose rules.


Assuntos
Aminoácidos/química , Biologia Computacional/métodos , Descoberta de Drogas/métodos , Inibidores de Proteínas Quinases/metabolismo , Proteínas Proto-Oncogênicas B-raf/química , Pirazóis/metabolismo , Software , Aminoácidos/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Desenho de Fármacos , Humanos , Ligantes , Simulação de Dinâmica Molecular , Neoplasias/tratamento farmacológico , Neoplasias/enzimologia , Ligação Proteica , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacologia , Proteínas Proto-Oncogênicas B-raf/antagonistas & inibidores , Proteínas Proto-Oncogênicas B-raf/metabolismo , Pirazóis/química , Pirazóis/farmacologia , Relação Quantitativa Estrutura-Atividade , Teoria Quântica , Estereoisomerismo , Relação Estrutura-Atividade
16.
J Comput Aided Mol Des ; 25(4): 349-69, 2011 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21487786

RESUMO

We have performed docking of 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline (FPTA), 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline (FPPA), and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine (AFPP) derivatives complexed with c-Met kinase to study the orientations and preferred active conformations of these inhibitors. The study was conducted on a selected set of 103 compounds with variations both in structure and activity. Docking helped to analyze the molecular features which contribute to a high inhibitory activity for the studied compounds. In addition, the predicted biological activities of the c-Met kinase inhibitors, measured as IC(50) values were obtained by using quantitative structure-activity relationship (QSAR) methods: Comparative molecular similarity analysis (CoMSIA) and multiple linear regression (MLR) with topological vectors. The best CoMSIA model included steric, electrostatic, hydrophobic, and hydrogen bond-donor fields; furthermore, we found a predictive model containing 2D-autocorrelation descriptors, GETAWAY descriptors (GETAWAY: Geometry, Topology and Atom-Weight AssemblY), fragment-based polar surface area (PSA), and MlogP. The statistical parameters: cross-validate correlation coefficient and the fitted correlation coefficient, validated the quality of the obtained predictive models for 76 compounds. Additionally, these models predicted adequately 25 compounds that were not included in the training set.


Assuntos
Aminopiridinas/química , Compostos de Anilina/química , Inibidores de Proteínas Quinases/química , Proteínas Proto-Oncogênicas c-met/antagonistas & inibidores , Pirróis/química , Receptores de Fatores de Crescimento/antagonistas & inibidores , Sítios de Ligação , Ligação de Hidrogênio , Modelos Moleculares , Conformação Molecular , Estrutura Molecular , Relação Quantitativa Estrutura-Atividade
17.
J Chem Inf Model ; 50(6): 1101-12, 2010 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-20524689

RESUMO

Docking and molecular dynamics (MD) simulations of N1 substituted pyrazole derivatives complexed with B-Raf kinase were performed to gain insight into the structural and energetic preferences of these inhibitors. First, a comparative study of fully automated docking programs AutoDock, ICM, GLIDE, and Surflex-Dock in closely approximating the X-ray crystal structure of the inhibitor (1E)-5-[1-(4-piperidinyl)-3-(4-pyridinyl)-1H-pyrazol-4-yl]-2,3-dihydro-1H-inden-1-one oxime was performed. Afterward, the dynamics of the above-mentioned compound and the less active analogous compounds with 1-methyl-4-piperidinyl and tetrahydro-2H-pyran-4-yl groups at position N1 of pyrazole ring inside the B-Raf active site were analyzed by MD simulations. We found that the most active compound has stable interactions with residues Ile463 and His539 at the entrance of the B-Raf active site. Those interactions were in very good agreement with more reliable quantum mechanics/molecular mechanics calculations performed on the torsional angle phi between the pyrazole ring and the substituents at position N1. In addition, we identified a water wire connecting N2 of the pyrazole ring, Cys532, and Ser536, which is composed of three water molecules for the most active compound. We found some differences in the water wire hydrogen-bond network formed by less active compounds. We suggest that the differences between these structural features are responsible for the differences in activity among the studied compounds.


Assuntos
Domínio Catalítico , Simulação de Dinâmica Molecular , Nitrogênio/química , Proteínas Proto-Oncogênicas B-raf/metabolismo , Pirazóis/química , Pirazóis/metabolismo , Água/química , Humanos , Ligação de Hidrogênio , Ligação Proteica , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Proteínas Proto-Oncogênicas B-raf/antagonistas & inibidores , Proteínas Proto-Oncogênicas B-raf/química , Pirazóis/farmacologia , Relação Estrutura-Atividade , Especificidade por Substrato , Termodinâmica
18.
J Chem Inf Model ; 49(4): 886-99, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19323453

RESUMO

N2 and O6 substituted guanine derivatives are well-known as potent and selective CDK2 inhibitors. The ability of molecular docking using the program AutoDock3 and the hybrid method ONIOM, to obtain some quantum chemical descriptors with the aim to successfully rank these inhibitors, was assessed. The quantum chemical descriptors were used to explain the affinity, of the series studied, by a model of the CDK2 binding site. The initial structures were obtained from docking studies and the ONIOM method was applied with only a single point energy calculation on the protein-ligand structure. We obtained a good correlation model between the ONIOM derived quantum chemical descriptor "H-bond interaction energy" and the experimental biological activity, with a correlation coefficient value of R = 0.80 for 75 compounds. To the best of our knowledge, this is the first time that both methodologies are used in conjunction in order to obtain a correlation model. The model suggests that electrostatic interactions are the principal driving force in this protein-ligand interaction. Overall, the approach was successful for the cases considered, and it suggests that could be useful for the design of inhibitors in the lead optimization phase of drug discovery.


Assuntos
Algoritmos , Quinase 2 Dependente de Ciclina/antagonistas & inibidores , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/farmacologia , Guanina/análogos & derivados , Guanina/farmacologia , Cristalização , Bases de Dados Factuais , Transferência de Energia , Previsões , Guanina/síntese química , Ligação de Hidrogênio , Modelos Moleculares , Ligação Proteica , Relação Estrutura-Atividade
19.
J Phys Chem B ; 111(12): 3293-7, 2007 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-17388447

RESUMO

We report a theoretical study on a series of CDK2 inhibitors using a set of global reactivity indices defined in terms of the density of states. The statistical analysis was performed on the basis of two groups of 11 and 6 compounds, respectively, reported by Hardcastle et al. (J. Med. Chem. 2004, 47, 3710-3722). Both series were classified on the basis of the correlations obtained for the complete set of compounds and the sites targeted within the active site of CDK2. The comparison between the biological activity and the electronic chemical potential approached as the Fermi level yields poor results, thereby suggesting that the interaction between the hinge region (HR) of CDK2 and the ligands may have a marginal contribution from the charge transfer (CT) component. Comparison between the biological activity and global softness shows a better correlation, thereby suggesting that polarization effects outweigh the CT contribution in the HR-ligand interaction. We stress the importance to include in the evaluation of the reactivity indices all of the occupied energy states in order to assess the effects coming from the internal electronic structure involved in the HR-ligand interaction.


Assuntos
Quinase 2 Dependente de Ciclina/antagonistas & inibidores , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Algoritmos , Fenômenos Químicos , Físico-Química , Quinase 2 Dependente de Ciclina/química , Ligação de Hidrogênio , Modelos Químicos
20.
Biophys J ; 92(2): 430-9, 2007 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-17085505

RESUMO

We report a combined quantum mechanics/molecular mechanics (QM/MM) study to determine the protein-ligand interaction energy between CDK2 (cyclin-dependent kinase 2) and five inhibitors with the N(2)-substituted 6-cyclohexyl-methoxy-purine scaffold. The computational results in this work show that the QM/MM interaction energy is strongly correlated to the biological activity and can be used as a predictor, at least within a family of substrates. A detailed analysis of the protein-ligand structures obtained from molecular dynamics simulations shows specific interactions within the active site that, in some cases, have not been reported before to our knowledge. The computed interaction energy gauges the strength of protein-ligand interactions. Finally, energy decomposition and multiple regression analyses were performed to check the contribution of the electrostatic and van der Waals energies to the total interaction energy and to show the capabilities of the computational model to identify new potent inhibitors.


Assuntos
Quinase 2 Dependente de Ciclina/antagonistas & inibidores , Quinase 2 Dependente de Ciclina/química , Modelos Químicos , Modelos Moleculares , Inibidores de Proteínas Quinases/química , Purinas/química , Sítios de Ligação , Simulação por Computador , Quinase 2 Dependente de Ciclina/ultraestrutura , Desenho de Fármacos , Mecânica , Ligação Proteica , Conformação Proteica , Teoria Quântica
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