Consensus Computational Ligand-Based Design for the Identification of Novel Modulators of Human Estrogen Receptor Alpha.

We describe the first targeted validation of fFLASH, a molecular similarity program from IBM that has been previously proposed as suitable for the virtual screening (VS) of compound libraries based on explicit 3D flexible superimpositions, as part of its deployment within a novel consensus ligand-based virtual screening cascade. A virtual screening protocol using fFLASH for the human estrogen receptor alpha (ERα) was advanced and benchmarked against screens completed using established commercial screening softwares - Catalyst and ROCS. The optimised protocol was applied to a ∼6000 member physical screening collection and virtual 'hits' sourced and biologically assayed. The approach identified a novel, potent and highly selective partial antagonist of the ERα. This study firstly validates the clique detection algorithm utilised by fFLASH and secondly, emphasises the benefits of the consensus approach of employing more than one program in a VS protocol.

Hydrodynamic and species transfer simulations in the USP 4 dissolution apparatus: considerations for dissolution in a low velocity pulsing flow.

PURPOSE: To simulate the hydrodynamics in the flow-through (USP 4) dissolution apparatus and investigate the effects of hydrodynamics on mass transfer in a low velocity pulsing flow. METHODS: Computational fluid dynamics (CFD) was used to simulate the hydrodynamics and mass transfer in pulsing flow. Experimental flow visualisation was used to qualitatively confirm simulated hydrodynamic and mass transfer features. The experimental dissolution rate at 8 ml min(-1) (22.6 mm flow-through cell) was compared to the experimental dissolution rate in a free convection system. RESULTS: Simulations revealed periods of low velocity at all flow rates, evidence of boundary layer separation, and, at higher flow rates, residual fluid motion during zero inlet velocity periods. The simulated diffusion boundary layer thickness varied in certain regions over the course of the pulse. The experimental dissolution rate in the free convection system was faster than that at 8 ml min(-1) in the flow-through apparatus. CONCLUSIONS: A low velocity pulsing flow running counter to gravity inhibited the experimental dissolution rate compared to that in a free convection system. From the CFD simulations generated, simulation of both hydrodynamics and species transfer is recommended to characterise the influence of hydrodynamics on dissolution in a low velocity pulsing flow.

Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble.

A recently defined charge set, to be used in conjunction with the all-atom CHARMM27r force field, has been validated for a series of phosphatidylcholine lipids. The work of Sonne et al. successfully replicated experimental bulk membrane behaviour for dipalmitoylphosphatidylcholine (DPPC) under the isothermal-isobaric (NPT) ensemble. Previous studies using the defined CHARMM27r charge set have resulted in lateral membrane contraction when used in the tensionless NPT ensemble, forcing the lipids to adopt a more ordered conformation than predicted experimentally. The current study has extended the newly defined charge set to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (PDPC). Molecular dynamics simulations were run for each of the lipids (including DPPC) using both the CHARMM27r charge set and the newly defined modified charge set. In all three cases a significant improvement was seen in both bulk membrane properties and individual atomistic effects. Membrane width, area per lipid and the depth of water penetration were all seen to converge to experimental values. Deuterium order parameters generated with the new charge set showed increased disorder across the width of the bilayer and reflected both results from experiment and similar simulations run with united atom models. These newly validated models can now find use in mixed biological simulations under the tensionless ensemble without concern for lateral contraction.

Computational fluid dynamics modeling of the paddle dissolution apparatus: agitation rate, mixing patterns, and fluid velocities.

The purpose of this research was to further investigate the hydrodynamics of the United States Pharmacopeia (USP) paddle dissolution apparatus using a previously generated computational fluid dynamics (CFD) model. The influence of paddle rotational speed on the hydrodynamics in the dissolution vessel was simulated. The maximum velocity magnitude for axial and tangential velocities at different locations in the vessel was found to increase linearly with the paddle rotational speed. Path-lines of fluid mixing, which were examined from a central region at the base of the vessel, did not reveal a region of poor mixing between the upper cylindrical and lower hemispherical volumes, as previously speculated. Considerable differences in the resulting flow patterns were observed for paddle rotational speeds between 25 and 150 rpm. The approximate time required to achieve complete mixing varied between 2 to 5 seconds at 150 rpm and 40 to 60 seconds at 25 rpm, although complete mixing was achievable for each speed examined. An analysis of CFD-generated velocities above the top surface of a cylindrical compact positioned at the base of the vessel, below the center of the rotating paddle, revealed that the fluid in this region was undergoing solid body rotation. An examination of the velocity boundary layers adjacent to the curved surface of the compact revealed large peaks in the shear rates for a region within ~3 mm from the base of the compact, consistent with a "grooving" effect, which had been previously seen on the surface of compacts following dissolution, associated with a higher dissolution rate in this region.

Simulating the hydrodynamic conditions in the United States Pharmacopeia paddle dissolution apparatus.

The objective of this work was to examine the feasibility of developing a high-performance computing software system to simulate the United States Pharmacopeia (USP) dissolution apparatus 2 (paddle apparatus) and thus aid in characterizing the fluid hydrodynamics in the method. The USP apparatus was modeled using the hydrodynamic package Fluent. The Gambit program was used to create a "wireframe" of the apparatus and generate the 3-dimensional grids for the computational fluid dynamics solver. The Fluent solver was run on an IBM RS/6000 SP distributed memory parallel processor system, using 8 processors. Configurations with and without a tablet present were developed and examined. Simulations for a liquid-filled vessel at a paddle speed of 50 rpm were generated. Large variations in fluid velocity magnitudes with position in the vessel were evident. Fluid velocity predictions were in good agreement with those previously published, using laser Doppler velocity measurements. A low-velocity domain was evident directly below the center of the rotating paddle. The model was extended to simulate the impact of the presence of a cylindrical tablet in the base of the dissolution vessel. The presence of the tablet complicated the local fluid flow, and large fluid shear rates were evident at the base of the compact. Fluid shear rates varied depending on the tablet surface and the location on the surface and were consistent with the reported asymmetrical dissolution of model tablets. The approach has the potential to explain the variable dissolution results reported and to aid in the design/prediction of optimal dissolution conditions for in vitro--in vivo correlations.