Virtual screening methods that complement HTS

In this review, we discuss a number of computational methods that have been developed or adapted for molecule classification and virtual screening (VS) of compound databases. In particular, we focus on approaches that are complementary to high-throughput screening (HTS). The discussion is limited to VS methods that operate at the small molecular level, which is often called ligand-based VS (LBVS), and does not take into account docking algorithms or other structure-based screening tools. We describe areas that greatly benefit from combining virtual and biological screening and discuss computational methods that are most suitable to contribute to the integration of screening technologies. Relevant approaches range from established methods such as clustering or similarity searching to techniques that have only recently been introduced for LBVS applications such as statistical methods or support vector machines. Finally, we discuss a number of representative applications at the interface between VS and HTS.     

Hexacyanometalate molecular chemistry: di-, tri-, tetra-, hexa- and heptanuclear heterobimetallic complexes; control of nuclearity and structural anisotropy

Following a bottom-up approach to nanomaterials, we present a rational synthetic route to high-spin and anisotropic molecules based on hexacyanometalate [M(CN)(6)](3-) cores. Part 1 of this series was devoted to isotropic heptanuclear clusters; herein, we discuss the nuclearity and the structural anisotropy of nickel(II) derivatives. By changing either the stoichiometry, the nature of the terminal ligand, or the counterion, it is possible to tune the nuclearity of the polynuclear compounds and therefore to control the structural anisotropy. We present the synthesis and the characterisation by mass spectrometry, X-ray crystallography and magnetic susceptibility of bi-, tri-, tetra-, hexa- and heptanuclear species [M(CN)(n)(CN-M'L)(6-n)](m+) (with n=0-5; M=Cr(III), Co(III), M'=Ni(II); L=pentadentate ligand). Thus, with M=Cr(III), d(3), S=3/2, a dinuclear complex [Cr(III)(CN)(5)(CN-NiL(n))](9+), (L(n)=polydentate ligand) was built and characterised, showing a spin ground state, S(G)=5/2, with a ferromagnetic interaction J(Cr,Cu)=+18.5 cm(-1). With M=Co(III) (d(6), S=0) were built di-, tri-, tetra-, hexa and hepanuclear CoNi species: CoNi, CoNi(2), CoNi(3), CoNi(5) and CoNi(6). By a first approximation, they behave as one, two, three, five and six isolated nickel(II) complexes, respectively, but more accurate studies allow us to evaluate the weak antiferromagnetic coupling constant between two next-nearest neighbours M'-Co-M'.     

Similarity search profiling reveals effects of fingerprint scaling in virtual screening

Fingerprint scaling is a method to increase the performance of similarity search calculations. It is based on the detection of bit patterns in keyed fingerprints that are signatures of specific compound classes. Application of scaling factors to consensus bits that are mostly set on emphasizes signature bit patterns during similarity searching and has been shown to improve search results for different fingerprints. Similarity search profiling has recently been introduced as a method to analyze similarity search calculations. Profiles separately monitor correctly identified hits and other detected database compounds as a function of similarity threshold values and make it possible to estimate whether virtual screening calculations can be successful or to evaluate why they fail. This similarity search profile technique has been applied here to study fingerprint scaling in detail and better understand effects that are responsible for its performance. In particular, we have focused on the qualitative and quantitative analysis of similarity search profiles under scaling conditions. Therefore, we have carried out systematic similarity search calculations for 23 biological activity classes under scaling conditions over a wide range of scaling factors in a compound database containing approximately 1.3 million molecules and monitored these calculations in similarity search profiles. Analysis of these profiles confirmed increases in hit rates as a consequence of scaling and revealed that scaling influences similarity search calculations in different ways. Based on scaled similarity search profiles, compound sets could be divided into different categories. In a number of cases, increases in search performance under scaling conditions were due to a more significant relative increase in correctly identified hits than detected false-positives. This was also consistent with the finding that preferred similarity threshold values increased due to fingerprint scaling, which was well illustrated by similarity search profiling.     

Cross-coupling reactions of phenylmagnesium halides with fluoroazines and fluorodiazines

The first nickel-catalyzed cross-coupling reactions between fluoroarenes and aryl organometallics using commercially available ligands are described. The nickel-catalyzed cross-coupling reactions between aryl Grignard reagents and fluoroazines and -diazines occurred in THF at room temperature using commercially available 1,2-bis(diphenylphosphino)ethane, 1,3-bis(diphenylphosphino)propane, or 1,1'-bis(diphenylphosphino)ferrocene as ligand. Various fluoro substrates such as pyridines, diazines (pyrazine, pyridazine), benzodiazines (quinoxaline), and quinolines were successfully involved in the reaction with phenylmagnesium halides (phenylmagnesium chloride, 2-methoxyphenylmagnesium bromide, and 4-methoxyphenylmagnesium bromide). The conditions used also allowed the cross-coupling of 4-fluorotoluene with arylmagnesium reagents.     

Solid State NMR and TG/MS Study on the Transformation of Methyl Groups During Pyrolysis of Preceramic Precursors to SiOC Glasses

The sol-gel method was used to prepare two different starting gels containing SiCH₃-groups for the preparation of SiOC ceramics. To understand the role of Si—H bonds in the incorporation of carbon into the SiOC network, gels prepared from a 1:2 mixture of triethoxysilane and methyldiethoxysilane (T^HD^H2) and solely methyltriethoxysilane (T^Me) were investigated. Thermogravimetric analysis coupled with mass spectroscopy (TG-MS) in inert atmosphere was performed to attain an insight into the decomposition reactions involved during gel-glass transformation. Samples calcined at different temperatures up to 1000°C were characterized by ²⁹Si and ¹³C magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy. The presence of SiH groups in the starting gel allows an efficient conversion of Si—CH₃ groups into CSi₄ sites at lower temperatures. As a result, despite a much lower amount of carbon in the starting T^HD^H2 gel (C/Si = 0.33) compared to the T^Me gel (C/Si = 1), the amount of carbon inserted into the SiOC network of both glasses is equivalent, but the T^Me sample contains the 10 fold amount of free carbon.     

Mechanism of Formation of Peroxocarbonates RhOOC(O)O(Cl)(P)(3) and Their Reactivity as Oxygen Transfer Agents Mimicking Monooxygenases. The First Evidence of CO(2) Insertion into the O-O Bond of Rh(eta(2)-O(2)) Complexes

Extended labeling experiments have shown that formation of rhodium peroxocarbonate from CO(2) and [RhCl(eta(2)-O(2))(P)(3)] (P is PEt(2)Ph or PEtPh(2)) proceeds through O-O bond cleavage and CO(2) insertion. O-transfer to ancillary phosphine ligand to give R(3)P=O selectively (>85%) involves the Rh-linked O atom of the peroxo group of RhCl(CO(4))(P)(3).     

Cationic lanthanide complexes of neutral tripodal N,O ligands: enthalpy versus entropy-driven podate formation in water

The cationic lanthanide complexes of two neutral tripodal N,O ligands, tpa (tris[(2-pyridyl)methyl]amine) and tpaam (tris[6-((2-N,N-diethylcarbamoyl)pyridyl)methyl]amine) are studied in water. The analysis of the proton lanthanide induced NMR shifts indicate that there is no abrupt structural change in the middle of the rare-earth series. Unexpectedly, the formation constant values of the lanthanide podates of tpaam and tpa in D2O at 298 K are similar, suggesting that the addition of the three amide groups to the ligand tpa does not lead to any increase in stability of the lanthanide complexes of tpaam in respect to tpa, even though the amide groups are coordinated to the metal in aqueous solution. The measurement of the enthalpy and entropy changes of the complexation reactions shows that the two similar ligands tpa and tpaam have different driving forces for lanthanide complexation. Indeed, the formation of tpa podates benefits from an exothermic enthalpy change associated with a small entropy change, whereas the complexation reaction with tpaam is clearly entropy-driven though opposed by a positive enthalpy change. The hydration states of the europium complexes were measured by luminescence and show the coordination of 4-5 water ligands in [Eu(tpa)]3+ whereas there are only 2 in [Eu(tpaam)]3+. Therefore the heptadentate ligand tpaam releases the translational entropy of more water molecules than does the tetradentate ligand tpa.