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.     

Photophysics of ruthenium(II) complexes with 2-(2′-pyridyl) pyrimidine and 2,2′-bipyridine ligands in fluid solution

The photophysics of three complexes of the form Ru(bpy)₃₋(pypm)²⁺ (where bpy2,2′-bipyridine, pypm 2-(2′-pyridyl)pyrimidine and P=1, 2 or 3) was examined in H₂O, propylene carbonate, CH₃CN and 4:1 (v/v) C₂H₅OH---CH₃OH; comparison was made with the well-known photophysical behavior of Ru(bpy)₃²⁺. The lifetimes of the luminescent metal-to-ligand charge transfer (MLCT) excited states were determined as a function of temperature (between −103 and 90 °C, depending on the solvent), from which were extracted the rate constants for radiative and non-radiative decay and ΔE, the energy gap between the MLCT and metal-centered (MC) excited states. The results indicate that ^*Ru(bpy)₂(pypm)²⁺ decays via a higher lying MLCT state, whereas ^*Ru(pypm)₃²⁺ and ^*Ru(pypm)₂(bpy)²⁺ decay predominantly via the MC state.     

THE EFFECTS OF NEAR-UV RADIATION ON HUMAN LENS β-CRYSTALLINS: PROTEIN STRUCTURAL CHANGES and THE PRODUCTION OF O2_ and H2O2

beta-Crystallins (beta 1-, beta 2- and beta 3-crystallin) comprise nearly half the protein of the human lens. The effect of near-UV radiation, which is one of the possible risk factors in cataract formation, on the beta-crystallins is investigated in this study. Protein intersubunit crosslinking, change in charge of the protein subunits to more acidic species and changes in protein tertiary structure (conformation) by 300 nm irradiation are reported. The fluorescence yield of protein tryptophan residues decreases by 300 nm irradiation. There is an increase in nontryptophan fluorescence (lambda cx 340 nm, lambda cm 400-600 nm), and in protein absorption at 340 nm, due to the formation of tryptophan photooxidation products. Both tryptophan and its oxidation products can be photoexcited by 300 nm irradiation and the latter are known to be good photosensitizers. The results provide evidence for the generation of H2O2 in the irradiated human beta-crystallin solutions by the Type I photosensitizing action of the chromophores absorbing at 300 nm. The H2O2 is generated via the intermediate production of O2 anion; the latter spontaneously dismutates to H2O2, presumably via O2- protein interactions. The amount of H2O2 generated per absorbed photon is compared for various solutions of beta 1-, beta 2- and beta 3-crystallins from human lenses of different age.     

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.     

Biogenetically inspired approach to the Strychnos alkaloids. Concise syntheses of (+/-)-akuammicine and (+/-)-strychnine

A linear synthesis of the indole alkaloid (+/-)-akuammicine (2) was completed by a novel sequence of reactions requiring only 10 steps from commercially available starting materials. The approach features a tandem vinylogous Mannich addition and an intramolecular hetero Diels-Alder reaction to rapidly assemble the pentacyclic heteroyohimboid derivative 8 from the readily available hydrocarboline 6. Oxidation of the E ring of 8 gave the lactone 9 that was converted into deformylgeissoschizine (11). The subsequent elaboration of 11 into 2 was effected by a biomimetically patterned transformation that involved sequential oxidation and base-induced skeletal reorganization. A variation of these tactics was then applied to the synthesis of the C(18) hydroxylated akuammicine derivative 36. Because 36 had previously been converted into strychnine (1) in four steps, its preparation constitutes a concise, formal synthesis of this complex alkaloid.     

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.