Scaffold mining of kinase hinge binders in crystal structure database

Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.     

Vibrational and electronic absorption spectra of 4-chloro 2-methyl, 4-chloro 3-methyl and 6-chloro 3-methyl phenols

The infrared spectra of 4-Cl 2-Me, 4-Cl 3-Me and 6-Cl 3-Me phenols have been recorded. The vibrational spectrum has been analysed assuming that the molecules belong toC _s point group and a tentative assignment of the observed frequencies to various modes of vibration has been proposed. The near ultraviolet absorption spectrum of these compounds has also been recorded. Assuming the transition to be electronically allowed the strongest band on the longer wavelength side has been assigned as the (0, 0) band in each case. The spectrum has been analysed in terms of several excited state frequencies which have been correlated with the ground state frequencies observed in the infrared spectrum.     

Studies on polymerization of vinyl acetate using ylide as an initiator and degradative transfer agent

Polymerization of vinyl acetate initiated by β-picolinium p-chlorophenacylide was carried out at 30, 35, and 40°C, using conventional dilatometric technique. The initiator and the monomer exponent values were 0.80 ± 0.15 and unity, respectively. The polymerization was inhibited in the presence of hydroquinone, but was favored by nonpolar solvent and polymerization temperature. The energy of activation was 90.3 KJ mol^?1. An average value of k/k_t for the present system was found to be 0.37 × 10^?2. The results are explained in terms of a radical mode of polymerization with degradative initiator transfer; the principal mode of termination, however, was bimolecular.     

Determination of aqueous plutonium oxidation states by solvent extraction

The reliability of two solvent extraction techniques for the determination of Pu oxidation states in solution was tested with low-ionic-strength solutions and with high-Na and high-Mg brines that contained Pu concentrations sufficient for spectrophotometric analysis. One procedure only differentiates between reduced Pu [Pu(III) and Pu(IV)] and oxidized Pu [Pu(V) and Pu(VI)], whereas the second procedure was designed to differentiate between Pu(IV), Pu(V), and Pu(VI) in solution. Both procedures successfully differentiated between oxidized and reduced Pu in both dilute solutions and brines when tested with samples that contained only the Pu(IV), Pu(V), or Pu(VI) oxidation states. However, when the second solvent extraction procedure, which differentiates between Pu(V) and Pu(VI), was employed for solutions that did not contain a strong oxidant to maintain the Pu(VI) oxidation state, significant quantities of Pu(VI) were reduced to Pu(V) during extraction, indicating that accurate quantification of Pu(V) and Pu(VI) is not possible with this procedure.Work supported by the U. S. Department of Energy under Contract DE-ACO6-76RLO 1830.     

The first ionic liquid-promoted one-pot diastereoselective synthesis of 2,5-diamino-/2-amino-5-mercapto-1,3-thiazin-4-ones using masked amino/mercapto acids

The first expeditious synthesis of 2,5-diamino-/2-amino-5-mercapto-1,3-thiazin-4-ones from masked and activated amino/mercapto acids, viz. 2-phenyl-1,3-oxazol-5-one or 2-methyl-2-phenyl-1,3-oxathiolan-5-one, aromatic aldehydes and thioureas using the ionic liquid [Bmim]Br as an environmentally benign reaction promoter is reported. The synthesis is highly diastereoselective and involves tandem Knoevenagel, Michael and ring transformation reactions in a one-pot procedure. The sequential reaction pathway is supported by the isolation of arylidene derivatives and their Michael adducts with thiourea, and quantitative conversion of the latter into the final products under the same reaction conditions.     

The first ionic liquid-promoted three-component coupling strategy for an expeditious synthesis of β-nitrocarbonitriles/thiocyanates

A novel and convenient three-component coupling reaction of nitromethane, aromatic aldehydes and trimethylsilyl cyanide (TMSCN) or ammonium thiocyanate has been developed for an expeditious synthesis of β-nitrocarbonitriles or β-nitrothiocyanates, respectively, via C-C and C-S bond-forming reactions. The synthetic protocol strategically involves a one-pot sequential Henry reaction and a Michael addition efficiently promoted by the same ionic liquid [bmim]OH. The main advantages of the present approach include the use of inexpensive simple substrates and an ionic liquid as an efficient reaction promoter for the mild synthesis in a one-pot procedure.