X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Effect of aluminum on the morphological and textural properties of CuO-ZnO/H-Ferrierite

Hybrid catalysts containing CuO-ZnO or CuO-ZnO-Al₂O₃ as the metallic component and the zeolite H-ferrierite as support were prepared by both the coprecipitation-impregnation and coprecipitation-sedimentation methods. They were characterized by XRD, BET, and TEM. Aluminum was added to the metallic component, and the effects on the hybrid catalyst properties were studied. The metallic component blocked the zeolite micropore volume, and spaces were created between agglomerate particles of the first component, increasing mesopore volume. Aluminum introduction at a Cu/Zn/Al ratio of 55/30/15 favored the formation of hydrotalcite as a precursor to CuO/ZnO/Al₂O₃. In this case, small, highly dispersed particles of these oxides were obtained. In the coprecipitation-impregnation method, greater contact between the H-ferrierite zeolite and the metallic component was observed.     

eNelator: A simulation system for large-scale vulnerability analysis of species-, disease- and process-specific protein networks

The identification of vulnerabilities in protein networks is a promising approach to predicting potential therapeutic targets. Different methods have been applied to domain-specific applications, with an emphasis on single-node deletions. There is a need to further assess significant associations between vulnerability, functional essentiality and topological features across species, processes and diseases. This requires the development of open, user-friendly systems to generate and test existing hypotheses about the vulnerability of networks in the face of dysfunctional components. We implemented methodologies to estimate the vulnerability of different networks to the dysfunction of different combinations of components, under random and directed attack scenarios. To demonstrate the relevance of our approaches and software, published protein–protein interaction (PPI) networks from Saccharomyces cerevisiae, Escherichia coli and Homo sapiens were analyzed. A PPI network implicated in the development of human heart failure, and signaling networks relevant to Caspase3 and P53 regulation were also investigated. Known essential proteins (individually or in groups) have no detectable effects on network stability. Some of the most vulnerable proteins are neither essential nor hubs. Known diagnostic biomarkers have little effect on the communication efficiency of the disease network. Predictions made on the signaling networks are consistent with recent experimental evidence. Our system, which integrates other quantitative measures, can assist in the identification of potential drug targets and systems-level properties. The system for large-scale analysis of random and directed attacks is freely available, as a Cytoscape plugin, on request from the authors.     

X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

Synergistic interaction in emulsions stabilized by a mixture of silica nanoparticles and cationic surfactant

Using a range of complementary experiments, a detailed investigation into the behavior of dodecane-water emulsions stabilized by a mixture of silica nanoparticles and pure cationic surfactant has been made. Both emulsifiers prefer to stabilize o/w emulsions. At high pH, particles are ineffective emulsifiers, whereas surfactant-stabilized emulsions become increasingly stable to coalescence with concentration. In mixtures, no emulsion phase inversion occurs although synergism between the emulsifiers leads to enhanced stability at either fixed surfactant concentration or fixed particle concentration. Emulsions are most stable under conditions where particles have negligible charge and are most flocculated. Freeze fracture scanning electron microscopy confirms the presence of particle flocs at drop interfaces. At low pH, particles and surfactant are good emulsifiers alone. Synergism is also displayed in these mixtures, with the extent of creaming being minimum when particles are most flocculated. Experiments have been undertaken in order to offer an explanation for the latter synergy. By determining the adsorption isotherm of surfactant on particles in water, we show that surfactant addition initially leads to particle flocculation followed by re-dispersion. Using suitable contact angle measurements at oil-water-solid interfaces, we show that silica surfaces initially become increasingly hydrophobic upon surfactant addition, as well as surfactant adsorption lowering the oil-water interfacial tension. A competition exists between the influence of surfactant on the contact angle and the tension in the attachment energy of a particle to the interface.     

Novel stabilization of emulsions via the heteroaggregation of nanoparticles

The stabilization of emulsions by a mixture of oppositely charged nanoparticles is investigated in relation to their behavior in water before emulsification. No emulsion can be prepared using either negatively or positively charged silica particles alone because the particles are too hydrophilic. Certain mixtures of the two particle types lead to heteroaggregation and a lowering of the net charge. Such mixtures, of increased hydrophobicity as verified by contact angle measurements, are capable of forming stable oil-in-water emulsions of excellent coalescence stability. The increased viscosity of the continuous phase also contributes to such stability.     

Discovery and preliminary SAR of 5-arylidene-2,2-dimethyl-1,3-dioxane- 4,6-diones as platelet aggregation inhibitors

We herein document the discovery of 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones as a novel family of platelet aggregation inhibitors. The preliminary optimization study enabled us to establish the most salient features of the structure-activity relationships in this series as well as to identify novel derivatives that are upto 60 times more potent than the hit structure 1 and slightly superior to the reference drug Milrinone.