Molecular Docking of Aromatase Inhibitors

Suvannang, Naravut; Nantasenamat, Chanin; Isarankura‐Na‐Ayudhya, Chartchalerm; Prachayasittikul, Virapong

doi:10.3390/molecules16053597

Cited by 87 publications

(67 citation statements)

References 66 publications

(81 reference statements)

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“…The force eld was assigned as AMBER14. 23 The AM1-BCC model was used to operate the partial atomic charges of the ligand. The complex was placed in a water box with a size of 100.04 A Â 100.04 A Â 100.04 A along the x, y, and z axes, and then a periodic boundary condition was applied.…”

Section: Fluorescence Lifetimementioning

confidence: 99%

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

et al. 2018

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Trametinib is a novel anticancer drug for treating metastatic cutaneous melanoma. The present study probed into the binding of trametinib to human serum albumin (HSA) through spectroscopy methods and molecular simulations. Trametinib could quench the fluorescence of HSA through static quenching which could be probed via fluorescence spectroscopy and time-resolved fluorescence. Thermodynamic parameters and docking results indicated that hydrogen bonds and van der Waals forces play crucial roles in this binding process, which exerts almost no effect on the HSA conformation under synchronous fluorescence, three-dimensional fluorescence, circular dichroism spectra, and molecular dynamics simulations. Site marker displacement experiments and molecular docking reveal that trametinib primarily binds to Sudlow site I of HSA. In addition, the trametinib-HSA interaction was hardly influenced by varying amino acid (glutamine, alanine, glycine, and valine) concentrations. This study can provide useful information for the pharmacokinetic properties of trametinib.

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Section: Fluorescence Lifetimementioning

confidence: 99%

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

et al. 2018

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“…First 1000 steps employed steepest descents minimizer and remaining steps used Conjugate-gradients minimizer. [28] The first cycle of minimization placed 25 kcal/mol/Angstrom^2 force constant. This force was reduced to 5 kcal/mol/angstrom^2 and the last cycle of minimization was performed without any restraining potentials for final energy minimization.…”

Section: Selection Of Calcineurin Protein and Optimizationmentioning

confidence: 99%

Virtual Screening and Docking Analysis of Novel lavonoidanalogues as Antipsoriaticagents

2018

IJCRR

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Introduction: Psoriasis is an immune-mediated chronic, inflammatory skin disease characterized by hyper proliferative keratinocytes and their infiltration into the dermis of T cells, dendritic cells, macrophages and neutrophils. There is ample evidence suggesting the key role of dysregulation of immune cells in the skin, particularly T cells, in the pathogenesis of psoriasis. Calcineurin, a calcium and calmodulin dependent serine/threonine protein phosphatase plays a major role in increasing the production of T cells and thus in the development of psoriasis. Flavonoids such as quercetin and kaempferol are known to inhibit development of psoriasis.

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“…39 The protocol included (i) a 5000 fs period, beginning at 0 to 300 K, as a heating protocol, (ii) a 10000 fs period at 300 K was employed for equilibration and (iii) 20000 fs at 300 K were used in the simulations with a time step of 1 fs. 40 After these simulations were concluded, the affinities of R-ALA for the protein in each one of the final complexes obtained under MM and MD protocols were calculated, 41 and the geometry and affinities of the these complexes were compared to that given by the structure directly obtained from TarFisDock server.…”

Section: Counterpoise-corrected Interaction Energy (Cp-cie) Calculationsmentioning

confidence: 99%

Searching of protein targets for alpha lipoic acid

Maldonado-Rojas¹,

Olívero-Verbel²,

Ortega-Zúñiga³

2011

J. Braz. Chem. Soc.

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Ácido alfa lipóico (ALA) é um dos oxidantes mais poderosos e um cofactor em complexos enzimáticos, apesar de seus mecanismos ainda não serem conhecidos. A pesquisa por alvos proteicos de ALA é fundamental para compreender seus processos de sinalização. Uma abordagem bioinformática foi usada a fim de se encontrar alvos hipotéticos para ALA usando o servidor Target Fishing Dock (TarFisDock). Contagens de afinidade para os melhores resultados foram calculadas pelo AutoDock Vina. Alvos relevantes incluíram leucotrieno A4 hidrolase, canal de potássio voltagem-dependente, alfa-hidroxiesteróide desidrogenase, epóxido hidrolase, proteínas estas envolvidas no câncer, diabetes, desordens neurológica e cardiovascular. As energias de interação corrigidas segundo padrão conterpoise foram calculadas para proteínas que ligam R-ALA, e mostraram interações R-ALA-resíduos favoráveis. A sobreposição de R-ALA com inibidores conhecidos daquelas proteínas, permitu concluir que R-ALA adota diferentes conformações espaciais em seus sítios de ligação, podendo ser um inibidor fraco plausível destes alvos e, portanto, este efeito deveria ser considerado quando da realização de estudos sobre seus efeitos bioquímicos.Alpha lipoic acid (ALA) is one of the most powerful antioxidants and a cofactor in enzyme complexes, although its mechanisms are still unknown. The search for protein targets of ALA is fundamental to understand its signaling pathways. A bioinformatics approach was used to find hypothetical targets for ALA using the Target Fishing Dock Server (TarFisDock). Affinity scores for the best hits were calculated by AutoDock Vina. Relevant targets included leukotriene A4 hydrolase, voltage gated potassium channel, alpha hydroxysteroid dehydrogenase and epoxide hydrolase, proteins involved in cancer, diabetes, and neurological and cardiovascular disorders. The counterpoise-corrected interaction energies calculated for proteins that bind R-ALA showed favorable interactions R-ALA-residues. Superpositioning of R-ALA with known inhibitors of those proteins, together with the finding that R-ALA adopts different spatial conformations in their binding sites, suggests R-ALA could be a plausible weak inhibitor of these targets, and this effect should be considered when studying its biochemical effects.

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Molecular Docking of Aromatase Inhibitors

Cited by 87 publications

References 66 publications

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

Virtual Screening and Docking Analysis of Novel lavonoidanalogues as Antipsoriaticagents

Searching of protein targets for alpha lipoic acid

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