Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

A Convenient One-Pot Preparation of Symmetrical Polymethoxyanthracenes

Symmetrical polymethoxyanthracenes are rapidly made and easily isolated in moderate yield by treatment of appropriately substituted (methoxy)_n halobenzenes with lithium 2,2,6,6-tetramethylpiperidide (LTMP) in refluxing THF.     

The carbenoid approach to peptide synthesis

A different approach to the synthesis of dipeptides is described based on the formation of the NHCHR1CONH-CHR2CO bond by carbenoid N-H insertion, rather than the formation of the peptide bond itself. Thus decomposition of triethyl diazophosphonoacetate catalysed by rhodium(II) acetate in the presence of N-protected amino acid amides 8 gives the phosphonates 9. Subsequent Wadsworth-Emmons reaction of 9 with aldehydes in the presence of DBU gives dehydro dipeptides 10. The reaction has been extended to a simple two-step procedure, without the isolation of the intermediate phosphonate, for conversion of a range of amino acid amides 11 into dehydro dipeptides 12 and to an N-methylamide 11 h, and for conversion of a dipeptide to tripeptide (13-->14). Direct conversion, by using methyl diazophenylacetate, of amino acid amides to phenylglycine-containing dipeptides 19 proceeds in good chemical yield, but with poor diastereoselectivity.     

A synthetic approach to kingianin A based on biosynthetic speculation

A synthetic approach towards the structurally complex dimer, kingianin A is reported. The strategy involved a cascade of complexity generating reactions, inspired through biosynthetic speculation. A concise protecting group free synthesis of the proposed monomeric precursor pre-kingianin A has been achieved using a tandem Stille cross-coupling reaction and electrocyclisation process. However, preliminary studies of the key dimerisation reaction have been conducted, which indicate that the process is not spontaneous, raising questions as to the origin of this complex natural product.     

Room temperature palladium catalysed coupling of acyl chlorides with terminal alkynes

Conditions are reported for the facile, high-yielding coupling of acyl chlorides with terminal alkynes in a reaction involving palladium and copper iodide; the reaction is tolerant of a wide variety of acyl chlorides and terminal alkynes and provides a convenient one-pot route to acetylenic ketones.     

Improvements in the Sensitivity of Time Resolved Fluorescence Energy Transfer Assays

The effect on fluorescence resonance energy transfer (FRET) of multiple labelling of DNA oligonucleotides with donor lanthanide chelate and acceptor CyDye fluors has been investigated. It is shown that using a multiple donor lanthanide chelate with a single acceptor Cy or Cy5 can increase sensitivity and fluorescence output. The enhanced FRET observed in the multiple donor label system has been utilised in two different DNA based assay formats to demonstrate the advantages over a steady state fluorescence assay and a radiometric assay.     

Approximation of an open polygonal curve with a minimum number of circular arcs and biarcs

We present an algorithm for approximating a given open polygonal curve with a minimum number of circular arcs. In computer-aided manufacturing environments, the paths of cutting tools are usually described with circular arcs and straight line segments. Greedy algorithms for approximating a polygonal curve with curves of higher order can be found in the literature. Without theoretical bounds it is difficult to say anything about the quality of these algorithms. We present an algorithm which finds a series of circular arcs that approximate the polygonal curve while remaining within a given tolerance region. This series contains the minimum number of arcs of any such series. Our algorithm takes O(n²logn) time for an original polygonal chain with n vertices. Using a similar approach, we design an algorithm with a runtime of O(n²logn), for computing a tangent-continuous approximation with the minimum number of biarcs, for a sequence of points with given tangent directions.