In silico carborane docking to proteins and potential drug targets

The presence of boron atoms has made carboranes, C(2)B(10)H(12), attractive candidates for boron neutron capture therapy. Because of their chemistry and possible conjugation with proteins, they can also be used to enhance interactions between pharmaceuticals and their targets and to increase the in vivo stability and bioavailability of compounds that are normally metabolized rapidly. Carboranes are isosteric to a rotating phenyl group, which they can substitute successfully in biologically active systems. A reverse ligand-protein docking approach was used in this work to identify binding proteins for carboranes. The screening was carried out on the drug target database PDTD that contains 1207 entries covering 841 known potential drug targets with structures taken from the Protein Data Bank. First, for validation, the protocol was applied to three crystal structures of proteins in which carborane derivatives are present. Then, the model was applied to systems for which the protein structure is available, but the binding site of carborane has not been reported. These systems were used for further validation of the protocol, while simultaneously providing new insight into the interactions between cage and protein. Finally, the screening was carried out on the database to reveal potential carborane binding targets of interest for biological and pharmacological activity. Carboranes are predicted to bind well to protease and metalloprotease enzymes. Other carborane pharmaceutical targets are also discussed, together with possible protein carriers.     

Fullerenol entrapment in calcite microspheres

Hybrid microspheres of calcium carbonate/fullerenol were synthesized and characterized. Their morphology depends on the concentration of the fullerenol solutions. XRD and FT-IR measurements proved that the mineral phase is consistently calcite, while fluorescence confocal microscopy indicated that fullerenol is homogenously included in the crystalline matrix.     

Rolling up a Graphene Sheet

Carbon Nanotubes, CNTs, have been described as rolled‐up graphene layers. Matching this concept to experiments has been a great experimental challenge for it requires a method to exfoliate graphite, generate ordered and stable dangling carbon bonds, and roll up the layer without affecting the unpaired electrons of the dangling bonds that finally have to zip up in an orderly fashion: A tall order for any synthetic strategy. The combined use of ultrasonication of graphite in dimethylformamide and addition of ferrocene aldehyde just does it!     

Role of the intracellular cavity in potassium channel conductivity

The role of several fragments of the potassium channel KcsA has been examined by the Poisson-Nernst-Planck (PNP) theory. The efficiency of the computational method allowed comparing a large number of channel models, with different intracellular gate openings, partial atomic charges, and amino acid sequences. Perhaps counter-intuitively, the calculated ion current decreases when the mean radius of the entrance cavity increases. Widening of the vestibule, in fact, increases the volume accessible to water, which is the volume with a high dielectric constant. In turn, water screens the attractive charges of the P-loop backbone. The backbone charges of the M2 helixes instead oppose the entrance of potassium ions through a complicated mechanism that can be separated in the activity of two interfering dipoles. The conductance of the KcsA models increased when two neutral residues in M2 were mutated to glutamic acid, in agreement with experimental results (Brelidze, T. I.; Niu, X.; Magleby, K. L. PNAS 2003, 100, 9017-9022). As a general conclusion, a relation between channel conductance and potassium concentration in the intracellular cavity emerged. Although the ion transport is the result of the fine balance of a number of different effects, the experimental results can be reproduced quantitatively only on the basis of electrostatic forces, which are the only driving forces modeled by the PNP theory.     

Operations and Thermodynamics of an Artificial Rotary Molecular Motor in Solution

A general framework is provided that makes possible the estimation of time‐dependent properties of a stochastic system moving far from equilibrium. The process is investigated and discussed in general terms of nonequilibrium thermodynamics. The approach is simple and can be exploited to gain insight into the dynamics of any molecular‐level machine. As a case study, the dynamics of an artificial molecular rotary motor, similar to the inversion of a helix, which drives the motor from a metastable state to equilibrium, are examined. The energy path that the motor walks was obtained from the results of atomistic calculations. The motor undergoes unidirectional rotation and its entropy, internal energy, free energy, and net exerted force are given as a function of time, starting from the solution of Smoluchowski’s equation. The rather low value of the organization index, that is, the ratio of the work done by the particle against friction during the unidirectional motion per available free energy, reveals that the motion is mainly subject to randomness, and the amount of energy converted to heat due to the directional motion is very small.     

Conformation Diversity of a Fused‐Ring Pyrazine Derivative on Au(111) and Highly Ordered Pyrolytic Graphite

Heterocyclic aromatic compounds have attracted considerable attention because of their high carrier mobility that can be exploited in organic field‐effect transistors. This contribution presents a comparative study of the packing structure of 3,6‐didodecyl‐12‐(3,6‐didodecylphenanthro[9,10‐b]phenazin‐13‐yl)phenanthro[9,10‐b]phenazine (DP), an N‐heterocyclic aromatic compound, on Au(111) and highly ordered pyrolytic graphite (HOPG). High‐resolution scanning tunneling microscopy (STM) combined with atomistic simulations provide a picture of the interface of this organic semiconductor on an electrode that can have an impact on the field‐effect transistor (FET) performance. DP molecules adsorb with different conformational isomers (R/S: trans isomers; C: cis isomer) on HOPG and Au(111) substrates. All three isomers are found in the long‐range disordered lamella domains on Au(111). In contrast, only the R/S trans isomers self‐assemble into stable chiral domains on the HOPG surface. The substrate‐dependent adsorption configuration selectivity is supported by theoretical calculations. The van der Waals interaction between the molecules and the substrate dominates the adsorption binding energy of the DP molecules on the solid surface. The results provide molecular evidence of the interface structures of organic semiconductors on electrode surfaces.     

Interactions of Aromatic Heterocycles with Water: The Driving Force from Free‐Jet Rotational Spectroscopy and Model Electrostatic Calculations

The interaction of isolated aromatic nitrogen atoms with water is explored within free jets by using rotational spectroscopy. To the existing data on diazines, we add the case of the 1:1 complex of 1,3,5‐triazine and water (where water donates a proton to one of the nitrogen heterocyclic atoms to form a planar adduct). An electrostatic model based on distributed multipoles accurately reproduces the structures of the four azine–water complexes and allows us to understand the forces that stabilize these structures. The applied intermolecular potential allows us to estimate the changes in the thermodynamic functions of the complexes—compared to the separated constituents—and evaluate the temperature at which the complexes are stable under standard conditions.