No abstract

Background: Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS2B/NS3 protease complex is a target for designing specific antivirals due to its importance in viral replication and its high degree of conservation.Methods: NS2B/NS3 protease complex structural information was employed to find small molecules that are capable of inhibiting the activity of the enzyme complex. This inhibitory activity was probed with in vitro assays using a fluorescent substrate and the complex NS2B/NS3 obtained by recombinant DNA techniques, for testing the activity against dengue virus replication, HepG2 cells infected with dengue virus serotype 2 were used. Results: A total of 210,903 small molecules from PubChem were docked in silico to the NS2B/NS3 structure (PDB: 2FOM) to find molecules that were capable of inhibiting this protein complex. Five of the best 500 leading compounds, according to their affinity values (-11.6 and -13.5 kcal/mol), were purchased. The inhibitory protease activity on the recombinant protein and antiviral assays was tested. Conclusions: Chemicals CID54681617, CID54692801 and CID54715399 were strong inhibitors of NS2B/NS3, with IC 50 values (µM) and percentages of viral titer reductions of 19.9, 79.9%; 17.5, 69.8%; and 9.1, 73.9 %, respectively. Multivariate methods applied to the molecular descriptors showed two compounds that were structurally different from other DENV inhibitors. General significance: This discovery opens new possibilities for obtaining drug candidates against Dengue virus.

No abstract

No abstract

No abstract

Natural compounds commonly found in foods may contribute to protect cells against the deleterious effects of inflammation. These anti-inflammatory properties have been linked to the modulation of transcription factors that control expression of inflammation-related genes, including the inducible nitric oxide synthase (iNOS), rather than a direct inhibitory action on these proteins. In this study, forty two natural dietary compounds, known for their ability to exert an inhibitory effect on the expression of iNOS, have been studied in silico as docking ligands on two available 3D structures for this protein (PDB ID: 3E7G and PDB ID: 1NSI). Natural compounds such as silibinin and cyanidin-3-rutinoside and other flavonoids showed the highest theoretical affinities for iNOS. Docking affinity values calculated for several known iNOS inhibitors significatively correlated with their reported half maximal inhibitory concentrations (R = 0.842, P < 0.0001), suggesting the computational reliability of the predictions made by our docking simulations. Moreover, docking affinity values for potent iNOS inhibitors are of similar magnitude to those obtained for some studied natural products. Results presented here indicate that, in addition to gene expression modulation of proteins involved in inflammation, some chemicals present in food may be acting by direct binding and possible inhibiting actions on iNOS.

No abstract

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.