High-throughput protein crystallography and drug discovery

Single crystal X-ray diffraction is the technique of choice for studying the interactions of small organic molecules with proteins by determining their three-dimensional structures; however the requirement for highly purified protein and lack of process automation have traditionally limited its use in this field. Despite these shortcomings, the use of crystal structures of therapeutically relevant drug targets in pharmaceutical research has increased significantly over the last decade. The application of structure-based drug design has resulted in several marketed drugs and is now an established discipline in most pharmaceutical companies. Furthermore, the recently published full genome sequences of Homo sapiens and a number of micro-organisms have provided a plethora of new potential drug targets that could be utilised in structure-based drug design programs. In order to take maximum advantage of this explosion of information, techniques have been developed to automate and speed up the various procedures required to obtain protein crystals of suitable quality, to collect and process the raw X-ray diffraction data into usable structural information, and to use three-dimensional protein structure as a basis for drug discovery and lead optimisation.This tutorial review covers the various technologies involved in the process pipeline for high-throughput protein crystallography as it is currently being applied to drug discovery. It is aimed at synthetic and computational chemists, as well as structural biologists, in both academia and industry, who are interested in structure-based drug design.     

Quantum chemical study of solvent and substituent effects on the 1,5-hydride shift in 2,6-dimethyl-2-heptyl cations

The mechanism of the degenerate 1,5-hydride shift in 2,6-dimethyl-2-heptyl cations has been investigated using ab initio MP2 and density functional theory (DFT) hybrid (B3LYP) calculations. The potential-energy profile for the 1,5-hydride shift consists of three minima corresponding to two equivalent acyclic carbocations and one symmetrically mu-hydrido-bridged carbocation, while two equivalent unsymmetrically hydrido-bridged carbocations were located as transition-state structures. The calculated relative energy differences between acyclic carbocations and symmetrically mu-hydrido-bridged structure are significantly affected by introduction of alkyl and (CH2)n-substituents at the C4 position of the 2,6-dimethyl-2-heptyl cation structure. DFT self-consistent isodensity polarizable continuum method (SCI-PCM) and MP2 PCM continuum methods have been used to calculate the effect of solvation on geometries and relative energies of the species involved in the 1,5-hydride shift. It is found that relative energies of acyclic and mu-hydrido-bridged carbocation structures as well as the energy barriers for 1,5-hydride shifts are in accord with experimental data if solvation effects are taken into account.     

Micro-HPLC–UV analysis of cocaine and its adulterants in illicit cocaine samples seized by Austrian police from 2012 to 2017

The worldwide consumption of illicit drugs presents a big problem in terms of health care and prosecution. In the recent years, hundreds of novel psychoactive substances came up and were traded through the Internet, but there is still a big demand for classic illicit drugs such as cocaine, heroin, cannabis, and ecstasy. Among these, cocaine particularly is frequently altered not only with excipients but also with other physiologically active substances. The purpose of this work was to estimate the trend of cocaine purity and abundance of its adulterants in samples seized by Austrian police from 2012 to 2017. A micro-HPLC method for quantification of cocaine and its most common adulterants was developed and validated using gradient elution and UV detection at four wavelengths. A total of 110 cocaine samples were analyzed. In all the samples, cocaine was present as hydrochloric salt. Caffeine, procaine, levamisole, phenacetin, lidocaine, and benzocaine were the most abundant adulterants.     

Couplage d'un modèle stochastique lagrangien sous-maille avec une simulation grandes échelles

A large eddy simulation (LES) is used to compute passive scalar dispersion in a turbulent flow. Instead of resolving the passive scalar transport equation, fluid particles are tracked in a Lagrangian way and a Langevin stochastic modelling is used for the small scale component of the velocity of fluid particles at a subgrid-scale level. The stochastic model is written in terms of subgrid-scale statistics. The specificity of this study resides in the coupling of a LES with a stochastic model using the filtered subgrid-scale statistics in inhomogeneous turbulence. The results are compared with the wind tunnel experiments of Fackrell and Robins [J. Fluid Mech. 117 (1982) 1–26]. To cite this article: I. Vinkovic et al., C. R. Mecanique 333 (2005).     

Large eddy simulation of droplet dispersion for inhomogeneous turbulent wall flow

A large eddy simulation (LES) coupled with a Lagrangian stochastic model has been applied to the study of droplet dispersion in a turbulent boundary layer. Droplets are tracked in a Lagrangian way. The velocity of the fluid particle along the droplet trajectory is considered to have a large-scale part and a small-scale part given by a modified three-dimensional Langevin model using the filtered subgrid scale (SGS) statistics. An appropriate Lagrangian correlation timescale is considered in order to include the influences of gravity and inertia. Two-way coupling is also taken into account. The inter-droplet collision has been introduced as the main mechanism of secondary breakup. A stochastic model for breakup has been generalized for coalescence simulation, thereby two phenomena, coalescence and breakup are simulated in the framework of a single stochastic model. The parameters of this model, selectively for coalescence and for breakup, are computed dynamically by relating them to the local resolved properties of the dispersed phase compared to the main fluid. The model is validated by comparison with an agglomeration model and with experimental results on secondary breakup. The LES coupled with Lagrangian particle tracking and the model for droplet coalescence and breakup is applied to the study of the atmospheric dispersion of wet cooling tower plumes. The simulations are done for different droplet size distributions and volume fractions. We focused on the influence of these parameters on mean concentration, concentration variance and mass flux profiles.     

Corrélations de vitesse lagrangienne et échelle intégrale temporelle en simulation des grandes échellesLagrangian velocity correlations and timescales by a large-eddy simulation

Velocity correlations and Lagrangian timescales are studied numerically by means of a direct numerical simulation (DNS) and a large-eddy simulation (LES) coupled with a subgrid Lagrangian stochastic model, in the case of a homogeneous and isotropic turbulence. A Langevin model is used to determine the subgrid component of the velocity of fluid particles. Numerical results of Lagrangian velocity correlations and timescales are presented. These quantities play an important role in turbulent mixing and scalar dispersion. To cite this article: G. Wei et al., C. R. Mecanique 334 (2006).     

Spontaneous CO Release from RuII(CO)2–Protein Complexes in Aqueous Solution,Cells, and Mice

We demonstrate that Ru^II(CO)₂–protein complexes, formed by the reaction of the hydrolytic decomposition products of [fac‐RuCl(κ²‐H₂NCH₂CO₂)(CO)₃] (CORM‐3) with histidine residues exposed on the surface of proteins, spontaneously release CO in aqueous solution, cells, and mice. CO release was detected by mass spectrometry (MS) and confocal microscopy using a CO‐responsive turn‐on fluorescent probe. These findings support our hypothesis that plasma proteins act as CO carriers after in vivo administration of CORM‐3. CO released from a synthetic bovine serum albumin (BSA)–Ru^II(CO)₂ complex leads to downregulation of the cytokines interleukin (IL)‐6, IL‐10, and tumor necrosis factor (TNF)‐α in cancer cells. Finally, administration of BSA–Ru^II(CO)₂ in mice bearing a colon carcinoma tumor results in enhanced CO accumulation at the tumor. Our data suggest the use of Ru^II(CO)₂–protein complexes as viable alternatives for the safe and spatially controlled delivery of therapeutic CO in vivo.     

Two-population dynamics in a growing network model

We introduce a growing network evolution model with nodal attributes. The model describes the interactions between potentially violent V and non-violent N agents who have different affinities in establishing connections within their own population versus between the populations. The model is able to generate all stable triads observed in real social systems. In the framework of rate equations theory, we employ the mean-field approximation to derive analytical expressions of the degree distribution and the local clustering coefficient for each type of nodes. Analytical derivations agree well with numerical simulation results. The assortativity of the potentially violent network qualitatively resembles the connectivity pattern in terrorist networks that was recently reported. The assortativity of the network driven by aggression shows clearly different behavior than the assortativity of the networks with connections of non-aggressive nature in agreement with recent empirical results of an online social system.     

Direct numerical simulation of particle interaction with ejections in turbulent channel flows

Direct numerical simulations (DNS) of incompressible turbulent channel flows coupled with Lagrangian particle tracking are performed to study the characteristics of ejections that surround solid particles. The behavior of particles in dilute turbulent channel flows, without particle collisions and without feedback of particles on the carrier fluid, is studied using high Reynolds number DNS (Re = 12,500). The results show that particles moving away from the wall are surrounded by ejections, confirming previous studies on this issue. A threshold value separating ejections with only upward moving particles is established. When normalized by the square root of the Stokes number and the square of the friction velocity, the threshold profiles follow the same qualitative trends, for all the parameters tested in this study, in the range of the experiments. When compared to suspension thresholds proposed by other studies in the Shields diagram, our simulations predict a much larger value because of the measure used to characterize the fluid and the criterion chosen to decide whether particles are influenced by the surrounding fluid. However, for intermediate particle Reynolds numbers, the threshold proposed here is in fair agreement with the theoretical criterion proposed by Bagnold (1966) [Bagnold, R., 1966. Geological Survey Professional Paper, vol. 422-1]. Nevertheless, further studies will be conducted to understand the normalization of the threshold.