Preparative isolation of (+)-beta-eudesmol fromAmyris balsamifera

Summary Optically pure (+)-beta-eudesmol is a possible starting material for the synthesis of several termite defense compounds. A two step procedure for the isolation of gram quantities of (+)-beta-eudesmol from commercially availableAmyris balsamifera oil (syn. West Indian sandalwood oil), containing 8% beta-eudesmol, was developed. Step one consisted of an efficient vacuum distillation of the total oil. Step two was a medium pressure LC separation with an AgNO₃ impregnated silica gel stationary phase. Several other separation procedures failed due to the presence of many closely related sesquiterpene alcohols (75% of the oil).     

Technique for generating three-dimensional alignments of multiple ligands from one-dimensional alignments

We describe and demonstrate a method for the simultaneous, fully flexible alignment of multiple molecules with a common biological activity. The key aspect of the algorithm is that the alignment problem is first solved in a lower dimensional space, in this case using the one-dimensional representations of the molecules. The three-dimensional alignment is then guided by constraints derived from the one-dimensional alignment. We demonstrate using 10 hERG channel blockers, with a total of 72 rotatable bonds, that the one-dimensional alignment is able to effectively isolate key conserved pharmacophoric features and that these conserved features can effectively guide the three-dimensional alignment. Further using 10 estrogen receptor agonists and 5 estrogen receptor antagonists with publicly available cocrystal structures we show that the method is able to produce superpositions comparable to those derived from crystal structures. Finally, we demonstrate, using examples from peptidic CXCR3 agonists, that the method is able to generate reasonable binding hypotheses.     

Application of machine learning to improve the results of high-throughput docking against the HIV-1 protease

We have previously reported that the application of a Laplacian-modified naive Bayesian (NB) classifier may be used to improve the ranking of known inhibitors from a random database of compounds after High-Throughput Docking (HTD). The method relies upon the frequency of substructural features among the active and inactive compounds from 2D fingerprint information of the compounds. Here we present an investigation of the role of extended connectivity fingerprints in training the NB classifier against HTD studies on the HIV-1 protease using three docking programs: Glide, FlexX, and GOLD. The results show that the performance of the NB classifier is due to the presence of a large number of features common to the set of known active compounds rather than a single structural or substructural scaffold. We demonstrate that the Laplacian-modified naive Bayesian classifier trained with data from high-throughput docking is superior at identifying active compounds from a target database in comparison to conventional two-dimensional substructure search methods alone.     

Library fingerprints: a novel approach to the screening of virtual libraries

We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a na?ve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.     

Transplant-insert-constrain-relax-assemble (TICRA): protein-ligand complex structure modeling and application to kinases

We introduce TICRA (transplant-insert-constrain-relax-assemble), a method for modeling the structure of unknown protein-ligand complexes using the X-ray crystal structures of homologous proteins and ligands with known activity. We present results from modeling the structures of protein kinase-inhibitor complexes using p38 and Lck as examples. These examples show that the TICRA method may be used prospectively to create and refine models for protein kinase-inhibitor complexes with an overall backbone rmsd of less than 0.75 ? for the kinase domain, when compared to published X-ray crystal structures. Further refinement of the models of the kinase domains of p38 and Lck in complex with their cognate ligands from the published crystal structures was able to improve the rmsd's of the model complexes to below 0.5 ?. Our results show that TICRA is a useful approach to the problem of structure-based drug design in cases where little structural information is available for the target proteins and the binding mode of active compounds is unknown.     

Investigations into beam monitors at the AEg ̄ IS experiment

Detailed diagnostic of antiproton beams at low energies is required for essentially all experiments at the Antiproton Decelerator (AD), but will be particularly important for the future Extra Low ENergy Antiproton ring (ELENA) and its keV beam lines to the different experiments. Many monitors have been successfully developed and operated at the AD, but in particular beam profile monitoring remains a challenge. A dedicated beam instrumentation and detector test stand has recently been setup at the AE \(\bar {g}\) IS experiment (Antimatter Experiment: Gravity, Interferometry, Spectroscopy). Located behind the actual experiment, it allows for parasitic use of the antiproton beam at different energies for testing and calibration. With the aim to explore and validate different candidate technologies for future low energy beam lines, as well as the downstream antihydrogen detector in AE \(\bar {g}\) IS, measurements have been carried out using Silicon strip and pixel detectors, a purpose-built secondary emission monitor and emulsions. Here, results from measurements and characterization of the different detector types with regard to their future use at the AD complex are presented.