Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: Renaissance of the Free-Wilson methodology

Drug design is a multi-parameter task present in the analysis of experimental data for synthesized compounds and in the prediction of new compounds with desired properties. This article describes the implementation of a binned scoring and composite ranking scheme for 11 experimental parameters that were identified as key drivers in the MC4R project. The composite ranking scheme was implemented in an AstraZeneca tool for analysis of project data, thereby providing an immediate re-ranking as new experimental data was added. The automated ranking also highlighted compounds overlooked by the project team. The successful implementation of a composite ranking on experimental data led to the development of an equivalent virtual score, which was based on Free-Wilson models of the parameters from the experimental ranking. The individual Free-Wilson models showed good to high predictive power with a correlation coefficient between 0.45 and 0.97 based on the external test set. The virtual ranking adds value to the selection of compounds for synthesis but error propagation must be controlled. The experimental ranking approach adds significant value, is parameter independent and can be tuned and applied to any drug discovery project.     

Crystal Structure of BaNb6.3(1)Ti3.6(1)O16 containing Nb6O12, fused Ti3O13 Clusters and Ti3O10 Units

A new phase, BaNb_6.3(1)Ti_3.6(1)O₁₆, has been synthesised. Electron diffraction studies indicate an hexagonal substructure with unit cell parameters a ≈ 8.9 Å and c ≈ 9.5 Å. In some of the ED patterns superstructure reflections are present, indicating a supercell with a = √3 · a_sub and c = c_sub. However, X‐ray single‐crystal diffraction studies of a crystallite yielding reflections corresponding to the supercell revealed it to be monoclinic, with the unit cell parameters a = 26.811(2) Å, b = 15.4798(2) Å, c = 9.414(2) Å, β = γ = 90° and α = 90.0(3)°. The average crystal structure was refined, using the subcell with a = 8.937(2) Å, b = 15.479(2) Å, c = 9.414(2) Å, β = γ = 90° and α = 90.0(3)°, space group Cm11, and Z = 4, to R_I = 3.24% and R_wI = 3.44%. The structure can be described as an hexagonal close packing layers of Nb₆ octahedra, Ba, and O atoms (A1, A2) and layers of O atoms (B1, B2), appearing in the packing sequence: A1B1A2B2. The Nb₆ octahedra are found in isolated Nb₆O₁₂O₆ clusters, and the Ti atoms in Ti₃O₁₃ and Ti₃O₁₀ units in octahedral and tetrahedral voids formed by O atoms, respectively. The Ti positions were found to be only partly occupied. Microanalysis indicates that some Nb atoms are located in the Ti₃ triangles. A model is presented that interprets these not fully occupied Ti₃ triangles as a result of a superimposing of three different structures. Two of these consist of two fused Ti₃O₁₃ units, forming an Ti₆O₁₉ unit, and a Ti₃O₁₀ unit, while the third consists of alternating Ti₃O₁₃ units.     

Molecular dynamics simulations of biotin carboxylase

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg2+ ions and contained altered conformations of key active-site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactions of the two catalytically critical Mg2+ ions bound in the active site are presented along with a reevaluation of the conformations of active-site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.     

Regular and irregular deswelling of polyacrylate and hyaluronate gels induced by oppositely charged surfactants

New multiresponsive core-shell microgels have been synthesized, with a thermoresponsive core and a glucose-responsive shell, made respectively of poly(N-isopropylacrylamide) (pNIPAM) and pNIPAM-co-acrylamidophenylboronic acid (pNIPAM-co-APBA). The structure of the particles was elucidated by means of dynamic light scattering. Their thermal properties were investigated and compared to those of the core alone. Without glucose, the hydrophobic shell prevented the core from swelling in a certain temperature range where the shell was shown to be collapsed. This core compression vanished upon glucose addition, when the shell became hydrophilic and swelled. Therefore, the extent of core swelling was regulated by two processes: its own internal stimulus, i.e. temperature, and shell compression, which is proportional to glucose concentration, even at physiological salinity. The concept was applied to a selected chemical composition. Core-shell microgels with a response to glucose at physiological pH were obtained and used to encapsulate insulin. Insulin release was shown to be regulated by the presence of glucose.     

Mechanisms of air oxidation of ethoxylated surfactants--computational estimations of energies and reaction behaviors

Pathways for formation of previously observed autoxidation products of ethoxylated surfactants have been studied by DFT (B3LYP). In addition to the established radical-chain reaction, several mechanistic possibilities for intramolecular fragmentation of the intermediate radicals have been characterized concerning reaction barriers and energies of transition states. The results can rationalize the formation of previously observed autoxidation products, including several, which have been implicated as strongly allergenic.     

The effect of polymers on the phase behavior of balanced microemulsions: diblock-copolymer and comb-polymers

The effect of some amphipilic diblock-copolymers and comb-polymers on a balanced Winsor III microemulsion system is investigated with the quaternary system n-octyl-β-d-glucoside/1-octanol/n-octane/D₂O as basis system. The diblock-copolymers are polyethyleneoxide-co-polydodecenoxide (PEO _x PEDODO _y ) and polyethyleneoxide-co-polybutyleneoxide (PEO _x PEBU _y ), constituted of a straight chain hydrophilic part and a bulky hydrophobic part. Addition of the diblock-copolymer leads to an enhancement of the swelling of the middle phase by uptake of water and oil; a maximum boosting factor of 6 was obtained for PEO₁₁₁PEDODO₂₅. Nuclear magnetic resonance diffusometry yields the self-diffusion coefficients of all the components in the system. The diffusion experiments provide information on how the microstructure of the bicontinuous microemulsion changes upon addition of the polymers. The reduced self-diffusion coefficients of water and oil are sensitive to the type of polymer that is incorporated in the film. For the diblock-copolymers, as mainly used here, the reduced self-diffusion coefficient of oil and water will respond to how the polymer bends the film. When the film bends away from water, the reduced self-diffusion of the water will increase, whereas the oil diffusion will decrease due to the film acting as a barrier, hindering free diffusion. The self-diffusion coefficient of the polymer and surfactant are similar in magnitude and both decrease slightly with increasing polymer concentration.     

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.     

Conductivity percolation in loosely compacted microcrystalline cellulose: An in situ study by dielectric spectroscopy during densification

The present study aims at contributing to a complete understanding of the water-induced ionic charge transport in cellulose. The behavior of this transport in loosely compacted microcrystalline cellulose (MCC) powder was investigated as a function of density utilizing a new type of measurement setup, allowing for dielectric spectroscopy measurement in situ during compaction. The ionic conductivity in MCC was found to increase with increasing density until a leveling-out was observed for densities above approximately 0.7 g/cm3. Further, it was shown that the ionic conductivity vs density followed a percolation type behavior signifying the percolation of conductive paths in a 3D conducting network. The density percolation threshold was found to be between approximately 0.2 and 0.4 g/cm3, depending strongly on the cellulose moisture content. The observed percolation behavior was attributed to the forming of interparticulate bonds in the MCC and the percolation threshold dependence on moisture was linked to the moisture dependence of particle rearrangement and plastic deformation in MCC during compaction. The obtained results add to the understanding of the density-dependent water-induced ionic transport in cellulose showing that, at given moisture content, the two major parameters determining the magnitude of the conductivity are the connectedness of the interparticluate bonds and the connectedness of pores with a diameter in the 5-20 nm size range. At densities between approximately 0.7 and 1.2 g/cm3 both the bond and the pore networks have percolated, facilitating charge transport through the MCC compact.