Diffusion in macromolecular crowded media: Monte Carlo simulation of obstructed diffusion vs. FRAP experiments

The diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. First, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed through a Monte Carlo (MC) simulation procedure. Secondly, fluorescence recovery after photobleaching (FRAP) experiments have been carried out to study the diffusion of a model protein (alpha-chymotrypsin) in in vitro crowded solution where two type of Dextran molecules are used as crowder agents. To facilitate the comparison, the relative size between the tracer and the crowder is the same in both studies. The results indicate a qualitative agreement between the diffusional behaviors observed in the two studies. The dependence of the anomalous diffusion exponent and the limiting diffusion coefficient on the obstacle size and excluded volume shows, in both cases, a similar tendency. The introduction of a reduced mobility parameter in the simulation model accounting for the short-range tracer?Cobstacle interactions allows obtaining a quantitative agreement between the limiting diffusion coefficient values yielded by both procedures. The simulation?Cexperiment quantitative agreement for the anomalous diffusion exponent requires further improvements. As far as we know, this is the first reported work where both techniques are used in parallel to study the diffusion in macromolecular crowded media.     

Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids

We present a method to study hydrodynamic phenomena from atomistic simulations. In statistical mechanics, these fields are computed as the ensemble average over the time dependent probability density function corresponding to the time evolution of an initial conditional probability density function consistent with some initial conditions. These initial conditions typically consist in constraints on some macroscopic fields, e.g. the density field. We show how these processes can be studied by combining the dynamical approach to non-equilibrium molecular dynamics with the restrained simulation approach. As an illustration of our method, we study the relaxation to the equilibrium of an interface between two immiscible liquids. We show that, at a variance with the local time average method, the standard atomistic approach used in this field, our method is able to produce (macroscopic) fields satisfying the symmetry conditions of the problem.     

New insights into diffusion in 3D crowded media by Monte Carlo simulations: effect of size, mobility and spatial distribution of obstacles

Particle diffusion in crowded media was studied through Monte Carlo simulations in 3D obstructed lattices. Three particular aspects affecting the diffusion, not extensively treated in a three-dimensional geometry, were analysed: the relative particle-obstacle size, the relative particle-obstacle mobility and the way of having the obstacles distributed in the simulation space (randomly or uniformly). The results are interpreted in terms of the parameters that characterize the time dependence of the diffusion coefficient: the anomalous diffusion exponent (α), the crossover time from anomalous to normal diffusion regimes (τ) and the long time diffusion coefficient (D*). Simulation results indicate that there are a more anomalous diffusion (smaller α) and a lower long time diffusion coefficient (D*) when obstacle concentration increases, and that, for a given total excluded volume and immobile obstacles, the anomalous diffusion effect is less important for bigger size obstacles. However, for the case of mobile obstacles, this size effect is inverted yielding values that are in qualitatively good agreement with in vitro experiments of protein diffusion in crowded media. These results underline that the pattern of the spatial partitioning of the obstacle excluded volume is a factor to be considered together with the value of the excluded volume itself.     

Microwave assisted organic synthesis (MAOS) of small molecules as potential HIV-1 integrase inhibitors

Integrase (IN) represents a clinically validated target for the development of antivirals against human immunodeficiency virus (HIV). In recent years our research group has been engaged in the stucture-function study of this enzyme and in the development of some three-dimensional pharmacophore models which have led to the identification of a large series of potent HIV-1 integrase strand-transfer inhibitors (INSTIs) bearing an indole core. To gain a better understanding of the structure-activity relationships (SARs), herein we report the design and microwave-assisted synthesis of a novel series of 1-H-benzylindole derivatives.     

Water-soluble IrIII N-heterocyclic carbene based catalysts for the reduction of CO2 to formate by transfer hydrogenation and the deuteration of aryl amines in water

Two new water-soluble [IrI(2)(AcO)(bis-NHC)] complexes (NHC=N-heterocyclic carbene) incorporating a sulfonate functionality have been synthesized. The two complexes have been tested in the reduction of CO(2) with H(2) and iPrOH, and their activity has been compared with similar species without the sulfonate moiety. In both reactions, the complex with the two abnormally bound NHCs shows the best catalytic efficiencies, due to the higher σ-electron-donor character of the ligand. Remarkably, the activities obtained for the reduction of CO(2) under the transfer hydrogenation conditions are the best reported to date in terms of TON value (max. TON=2700). The two new complexes have also shown very good activity in the selective deuteration of arylamines, a process that is known to proceed through a chelate assisted N-directed process.     

Complete stereocontrol in organocatalytic additions of β-ketosulfoxides to conjugated aldehydes

The use of β-ketosulfoxides as nucleophiles in reactions with α,β-unsaturated aldehydes catalyzed by proline derivatives allows complete control of configuration at the two chiral centers that are created during 1,4-addition reactions. The sulfinyl group can be used to create additional chiral centers in the resulting compounds and then removed while preserving the chirality of the carbon joined to the sulfur. The catalyst and the sulfinyl group are mainly responsible for the configurational control of the carbon atoms acting as electrophile and nucleophile, respectively, which allows the preparation of the four possible diastereoisomers in optically pure form. Theoretical calculations of the possible chiral nucleophilic species bearing diastereotopic faces allow us to postulate, for the first time, that enolates, instead of enols, are the active reagents in these reactions.     

NMR studies of inclusion complexation of the pyrrolizidine alkaloid retronecine and p-sulfonic acid calix[6]arene

Accidental or intentional drug toxicity in humans and animals is a major concern and the search for detoxificant agents is a challenge. Pyrrolizidine-producing forages are a threat not only to livestock, but also to humans as a consequence of food contamination. Supramolecular systems are promising as detoxificant agents by decreasing the bioavailability of toxic compounds in biological environment. Cyclodextrin and calix[n]arenes are well known hosts for a variety of molecules and/or ions. Surprisingly, only few studies describe the potential of calix[n]arenes as host for toxic molecules. This study focused on the use of NMR techniques as tools for the investigation of the interactions between p-sulfonic acid calix[6]arene and retronecine, a toxic pyrrolizidine alkaloid.