RESUMO
Understanding the interactions of petroleum asphaltenes with mineral surfaces is important for diluted bitumen spill response and modeling. In this study, molecular dynamics and umbrella sampling simulations are performed using interfacially active and non-interfacially active asphaltene model compounds individually positioned near each of the surfaces of kaolinite in the presence of explicit solvent environments containing water, toluene, and mixtures of toluene and water in varying proportions. The interfacially active asphaltene bonds the strongest to the silicon oxide surface of kaolinite in pure water and the bonding weakens to nearly zero in toluene-water mixtures. The non-interfacially active asphaltenes bond to kaolinites silicon oxide surface in water about half as strongly as the interfacially active one in water and the bonding weakens in the presence of toluene. The number of non-hydrogen bonded contacts between the interfacially active asphaltene and the aluminum hydroxide surface of kaolinite increases as the proportion of toluene is increased and the contacts with water are decreased. In these conditions, the non-interfacially active asphaltenes do not form non-hydrogen bonded contacts with kaolinite. On the silicon oxide surface, the number of non-hydrogen bonded contacts of all asphaltenes with kaolinite tends to decrease as the proportion of toluene is increased and the contacts with water are decreased. The number of hydrogen bonds of the interfacially active asphaltene with water decreases as the proportion of toluene is increased. The radii of gyration indicate that the interfacially active asphaltene is extended in water and when adsorbed on kaolinite, and becomes compact as the proportion of toluene is increased. The simulation results highlight the competitive interfacial interactions in the complex scenario of diluted bitumen spills in the presence of water and clay minerals.
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The carbazole moiety is a commonly identified structural motif in the high-molecular-weight components of petroleum, known as asphaltenes. Detailed characterization of carbazoles is important for understanding the structure of asphaltenes and addressing challenges in the areas of heavy oil recovery, transportation, upgrading, and oil spills, arising from asphaltene properties and composition. In this work we study carbazole and the four N-substituted carbazoles 9-methylcarbazole, 9-ethylcarbazole, 9-vinylcarbazole and 9-phenylcarbazole. Experimental far- and mid-infrared spectra of these five carbazoles are measured using transmission and photoacoustic techniques. The molecular structures of the monomers and the respective dimers, optimized at the ωB97X-D/6-311++G(d,p) level of the density functional theory (DFT), are subjected to harmonic vibrational frequency calculations. The effect of changing substituents on the N-H bond, π-π stacking distances, and angles between monomers within the dimers, in addition to intermolecular interactions, is investigated. Noncovalent interaction analysis is employed to highlight the areas of attractive and repulsive interactions in the dimers. Thermochemistry calculations show that the formation of dimers of all carbazoles is spontaneous at 298 K. Comparison of the calculated vibrational spectra of these compounds with experimental spectra indicates that the existence of both monomers and dimers must be invoked to account for the observed bands in the infrared spectra. Excellent correlations between the experimentally-determined and calculated harmonic vibrational energies are obtained, with an experimental-to-calculated scaling factor of 0.95-0.96. These findings highlight the coupled computational-experimental approach for the interpretation of vibrational spectra and are essential for improving the spectroscopic characterization of N-substituted carbazoles.
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PURPOSE: To explore possible ways in which yew tree tubulin is naturally resistant to paclitaxel. While the yew produces a potent cytotoxin, paclitaxel, it is immune to paclitaxel's cytotoxic action. METHODS: Tubulin sequence data for plant species were obtained from Alberta 1000 Plants Initiative. Sequences were assembled with Trinity de novo assembly program and tubulin identified. Homology modeling using MODELLER software was done to generate structures for yew tubulin. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann calculations were performed with the Amber package to determine binding affinity of paclitaxel to yew tubulin. ClustalW2 program and PHYLIP package were used to perform phylogenetic analysis on plant tubulin sequences. RESULTS: We specifically analyzed several important regions in tubulin structure: the high-affinity paclitaxel binding site, as well as the intermediate binding site and microtubule nanopores. Our analysis indicates that the high-affinity binding site contains several substitutions compared to human tubulin, all of which reduce the binding energy of paclitaxel. CONCLUSIONS: The yew has achieved a significant reduction of paclitaxel's affinity for its tubulin by utilizing several specific residue changes in the binding pocket for paclitaxel.
Assuntos
Paclitaxel/química , Taxus/química , Árvores/química , Tubulina (Proteína)/química , Tubulina (Proteína)/genética , Sequência de Aminoácidos , Sítios de Ligação , Humanos , Microtúbulos/genética , Microtúbulos/metabolismo , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Paclitaxel/farmacologia , Filogenia , Homologia de Sequência de Aminoácidos , Taxus/genética , Termodinâmica , Árvores/genética , Tubulina (Proteína)/metabolismoRESUMO
A series of fluorobenzoylated di- and tripeptides as potential leads for the development of molecular probes for imaging of COX-2 expression was prepared according to standard Fmoc-based solid-phase peptide synthesis. All peptides were assessed for their COX-2 inhibitory potency and selectivity profile in a fluorescence-based COX binding assay. Within the series of 15 peptides tested, cysteine-containing peptides numbered 7, 8, 11 and 12, respectively, were the most potent COX-2 inhibitors possessing IC(50) values ranging from 5 to 85 µM. Fluorobenzoylated tripeptides 7 and 8 displayed some COX-2 selectivity (COX-2 selectivity index 2.1 and 1.6), whereas fluorobenzoylated dipeptides 11 and 12 were shown not to be COX-2 selective. Fluorbenzoylated tripeptide FB-Phe-Cys-Ser-OH was further used in molecular modeling docking studies to determine the binding mode within the active site of the COX-2 enzyme.
Assuntos
Ácido Benzoico/química , Inibidores de Ciclo-Oxigenase 2/síntese química , Ciclo-Oxigenase 2/química , Dipeptídeos/química , Oligopeptídeos/química , Sequência de Aminoácidos , Animais , Sítios de Ligação , Domínio Catalítico , Ciclo-Oxigenase 2/metabolismo , Inibidores de Ciclo-Oxigenase 2/química , Dipeptídeos/síntese química , Flúor/química , Ligação de Hidrogênio , Camundongos , Simulação de Dinâmica Molecular , Oligopeptídeos/síntese química , Técnicas de Síntese em Fase SólidaRESUMO
A series of 1,5-diaryl-substituted tetrazole derivatives was synthesized via conversion of readily available diaryl amides into corresponding imidoylchlorides followed by reaction with sodium azide. All compounds were evaluated by cyclooxygenase (COX) assays in vitro to determine COX-1 and COX-2 inhibitory potency and selectivity. Tetrazoles 3a-e showed IC(50) values ranging from 0.42 to 8.1 mM for COX-1 and 2.0 to 200 µM for COX-2. Most potent compound 3c (IC(50) (COX-2)=2.0 µM) was further used in molecular modeling docking studies.
Assuntos
Inibidores de Ciclo-Oxigenase 2/síntese química , Inibidores de Ciclo-Oxigenase 2/farmacologia , Tetrazóis/síntese química , Tetrazóis/farmacologia , Inibidores de Ciclo-Oxigenase 2/química , Avaliação Pré-Clínica de Medicamentos , Ligação de Hidrogênio , Modelos Moleculares , Tetrazóis/químicaRESUMO
BACKGROUND: A maximum entropy approach is proposed to predict the cytotoxic effects of a panel of colchicine derivatives in several human cancer cell lines. Data was obtained from cytotoxicity assays performed with 21 drug molecules from the same family of colchicine compounds and correlate these results with independent tubulin isoform expression measurements for several cancer cell lines. The maximum entropy method is then used in conjunction with computed relative binding energy values for each of the drug molecules against tubulin isotypes to which these compounds bind with different affinities. RESULTS: We have found by using our analysis that alphabetaI and alphabetaIII tubulin isoforms are the most important isoforms in establishing predictive response of cancer cell sensitivity to colchicine derivatives. However, since alphabetaI tubulin is widely distributed in the human body, targeting it would lead to severe adverse side effects. Consequently, we have identified tubulin isotype alphabetaIII as the most important molecular target for inhibition of microtubule polymerization and hence cancer cell cytotoxicity. Tubulin isotypes alphabetaI and alphabetaII are concluded to be secondary targets. CONCLUSIONS: The benefit of being able to correlate expression levels of specific tubulin isotypes and the resultant cell death effect is that it will enable us to better understand the origin of drug resistance and hence design optimal structures for the elimination of cancer cells. The conclusion of the study described herein identifies tubulin isotype alphabetaIII as a target for optimized chemotherapy drug design.
Assuntos
Antineoplásicos/farmacologia , Colchicina/farmacologia , Resistencia a Medicamentos Antineoplásicos/genética , Ensaios de Seleção de Medicamentos Antitumorais/métodos , Neoplasias/tratamento farmacológico , Tubulina (Proteína)/biossíntese , Linhagem Celular Tumoral , Desenho de Fármacos , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Isoformas de Proteínas/biossíntese , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Tubulina (Proteína)/química , Tubulina (Proteína)/genética , Moduladores de Tubulina/farmacologiaRESUMO
In this paper we provide an overview of the status of various colchicine derivatives in preclinical development with special focus on their anti-cancer activity. We discuss several groups of compounds that have been designed to differentially bind with specific affinities for tubulin ß isotypes, especially in regard to ßIII, which is commonly over-expressed in cancer. Computational prediction, protein-based and cell-based assays are summarized as well as some animal tests conducted on these compounds. It is concluded that an untapped potential exists for exploiting the colchicine scaffold as a pharmacophore with the possibility of increasing its affinity for tubulin isotypes overexpressed in cancer and decreasing it for normal cells thereby widening the therapeutic window.
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Antineoplásicos/farmacologia , Colchicina/farmacologia , Neoplasias/tratamento farmacológico , Animais , Antineoplásicos/síntese química , Antineoplásicos/química , Proliferação de Células/efeitos dos fármacos , Colchicina/síntese química , Colchicina/química , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Neoplasias/metabolismo , Neoplasias/patologia , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismoRESUMO
Human α-synuclein (αS) is an intrinsically disordered protein associated with Parkinson's disease. Molecular mechanisms of corruptive misfolding and aggregation of αS resulting in the disease, as well as the structure and other properties of the corresponding oligomers are not entirely understood yet, preventing the development of efficient therapies. In this study, we investigate the folding dynamics of initially unfolded hypothetical αS constructs in water using all-atom molecular dynamics simulations. We also employ the novel essential collective dynamics method to analyze the results obtained from the simulations. Our comparative analysis of monomeric, dimeric, and tetrameric αS models reveals pronounced differences in their structure and stability, emphasizing the importance of small oligomers, particularly dimers, in the process of misfolding.
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The binding free energies on human tubulin of selected colchicine and thiocolchicine compounds were determined. Two methods were used for the determination of binding free energies: one is based on theoretical prediction simulating the dissociation of the compound from tubulin using a series of molecular dynamics simulations, and the other method involves a series of experiments that measured the affinity of the compound on a synthetically expressed and purified tubulin protein using a spectrofluorometric technique.
Assuntos
Colchicina/química , Tubulina (Proteína)/química , Sítios de Ligação , Colchicina/metabolismo , Dimerização , Humanos , Cinética , Simulação de Acoplamento Molecular , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Espectrometria de Fluorescência , Termodinâmica , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismoRESUMO
Aptamers are short RNA/DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA/DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.
Assuntos
Aptâmeros de Nucleotídeos/química , Desenho de Fármacos , Entropia , Aptâmeros de Nucleotídeos/farmacologia , Simulação de Dinâmica Molecular , Fosfatidilserinas/química , Relação Estrutura-Atividade , Trombina/químicaRESUMO
Tubulin is the target for numerous small molecule ligands which alter microtubule dynamics leading to cell cycle arrest and apoptosis. Many of these ligands are currently used clinically for the treatment of several types of cancer, and they bind to one of three distinct binding sites within beta-tubulin (paclitaxel, vinca, and colchicine), all of which have been identified crystallographically. Unfortunately, serious side effects always accompany chemotherapy since these drugs bind to tubulin indiscriminately, leading to the death of both cancerous and healthy cells. However, the existence and distribution of divergent tubulin isoforms provide a platform upon which we may build novel chemotherapeutic drugs that can differentiate between different cell types and therefore reduce undesirable side effects. We report results of computational analysis that aims at predicting differences between the binding energies of a family of colchicine derivatives against 10 human alpha/beta-tubulin isoforms. Free energy perturbation method has been used in our calculations and the results provide a proof of principle by indicating significant differences both among the derivatives and between tubulin isoforms.