A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies

Summary Previous structure-activity studies of captopril and related active angiotensin-converting enzyme (ACE) inhibitors have led to the conclusion that the basic structural requirements for inhibition of ACE involve (a) a terminal carboxyl group; (b) an amido carbonyl group; and (c) different types of effective zinc (Zn) ligand functional groups. Such structural requirements common to a set of compounds acting at the same receptor have been used to define a pharmacophoric pattern of atoms or groups of atoms mutually oriented in space that is necessary for ACE inhibition from a stereochemical point of view. A unique pharmacophore model (within the resolution of approximately 0.15 Å) was observed using a method for systematic search of the conformational hyperspace available to the 28 structurally different molecules under study. The method does not assume a common molecular framework, and, therefore, allows comparison of different compounds that is independent of their absolute orientation.Consequently, by placing the carboxyl binding group, the binding site for amido carbonyl, and the Zn atom site in positions determined by ideal binding geometry with the inhibitors' functional groups, it was possible to clearly specify a geometry for the active site of ACE.     

Why instantons are monopoles

It is shown that instantons are hyperbolic monopoles for the loop group with non-maximal symmetry breaking at infinity.Research supported in part by NSF grant DMS-8506130     

Synthesis of 5-trichloromethyl-Δ-1,2,4-oxadiazolines and their rearrangement into formamidine derivatives

A series of 5-trichloro-Δ⁴-1,2,4-oxadiazolines have been synthesised by 1,3-dipolar cycloaddition of nitrones to trichloroacetonitrile. These oxadiazolines rearrange into formamidine derivatives, via ring opening and a 1,2-aryl shift from carbon to the adjacent amino nitrogen. Both cycloaddition and rearrangement are facilitated when electron deficient nitriles and electron rich nitrones are used.     

Synthesis of the Phenylpyridal Scaffold as a Helical Peptide Mimetic

Phenylpyridal‐ and phenyldipyridal‐based scaffolds have been designed and synthesized as novel helical peptide mimetics. The synthesis required optimisation and selective alkylation in producing 2,6‐functionalized 3‐hydroxypyridine derivatives for a convergent scheme. The pyridine analogues were coupled by a series of Suzuki/Stille types cross‐coupling reactions. A series of biaryl and ter‐aryl substituted heterocycles were produced. The synthetic approach was concise and high yielding allowing large variability at the wanted side‐chain attachment points. A number of compounds were synthesised to show the versatility of the strategy.     

Detection of bio-constituents in complex biological tissue using Raman microscopy. Application to human nail clippings

Raman spectra of human nail clippings from various sources were collected and then deconvoluted to obtain the pure component spectra of the underlying constituents present. This blind-deconvolution was performed using a self-modeling curve resolution technique, namely band-target entropy minimization (BTEM). The aim was to simplify the complexity of the Raman spectra and hence to identify the underlying biological molecules in more detail. BTEM analysis could recover 13 pure component Raman spectral estimates from the collected 438 spectra measured from 113 nail samples. Six recovered pure component spectral estimates correspond to proteins or polypeptides that contain various amino acids such as phenylalanine, tyrosine, tryptophan, and cysteine. Two are associated with the secondary structures of proteins, and five are associated with two carotenoid species, lipid, ferulic acid, and calcium phosphate. Subsequently, the relative concentrations of these bio-constituents were calculated from the measured mixture spectra and the pure component BTEM estimates. These profiles indicated that the concentrations of some bio-constituents are correlated while others are not. A further analysis using target transformation factor analysis (TTFA) revealed the possible presence of curcumin in the human nails. Since the present approach and analysis is rather general, it might be extended to many other biological tissues in a rather straightforward and similar manner, thus revealing more detailed underlying biochemical information such as biomarkers that may be useful for diagnostic purposes.     

SKATE: A docking program that decouples systematic sampling from scoring

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010