Multilevel component analysis of time-resolved metabolic fingerprinting data

Genomics-based technologies in systems biology have gained a lot of popularity in recent years. These technologies generate large amounts of data. To obtain information from this data, multivariate data analysis methods are required. Many of the datasets generated in genomics are multilevel datasets, in which the variation occurs on different levels simultaneously (e.g. variation between organisms and variation in time). We introduce multilevel component analysis (MCA) into the field of metabolic fingerprinting to separate these different types of variation. This is in contrast to the commonly used principal component analysis (PCA) that is not capable of doing this: in a PCA model the different types of variation in a multilevel dataset are confounded.

MCA generates different submodels for different types of variation. These submodels are lower-dimensional component models in which the variation is approximated. These models are easier to interpret than the original data. Multilevel simultaneous component analysis (MSCA) is a method within the class of MCA models with increased interpretability, due to the fact that the time-resolved variation of all individuals is expressed in the same subspace.

MSCA is applied on a time-resolved metabolomics dataset. This dataset contains ¹H NMR spectra of urine collected from 10 monkeys at 29 time-points during 2 months. The MSCA model contains a submodel describing the biorhythms in the urine composition and a submodel describing the variation between the animals. Using MSCA the largest biorhythms in the urine composition and the largest variation between the animals are identified.

Comparison of the MSCA model to a PCA model of this data shows that the MSCA model is better interpretable: the MSCA model gives a better view on the different types of variation in the data since they are not confounded.     

Solid-phase synthesis of heterocyclic aromates: applicability towards combinatorial chemistry; a review

Because of their biological activity, stability in vivo, the rigid spatial positioning of their substituents, and their synthetic challenges, heterocyclic aromates continue to be of interest to both academic and industrial medicinal chemists. Currently, many drug-like heterocyclic aromates are prepared via solid-phase organic chemistry methods. This review examines the applicability of those methods towards combinatorial chemistry with respect to the basic demands of such an approach: 1) synthesis, work-up and subsequent purification should be easily automated enabling the efficient simultaneous synthesis of large numbers of highly pure compounds in a minimum amount of time, 2) large diversity among the ligands to be synthesized, 3) high conversion rates of the individual reaction steps, and 4) the use of commercially available starting materials. Although many methods have been developed for the synthesis of heterocyclic aromates, very few of the available methods enable the synthesis of highly diverse heteroaromatic libraries.     

Proximally functionalized cavitands and synthesis of a flexible hemicarcerand

A general study on the synthesis of partly bridged octols3a-d and4c-d is described. Tri-bridged diol3c can be prepared in 54% yield in DMSO at 70°C with excess CH₂BrCl or in 52% yield in DMF at 70°C with only 4 equiv. of CH₂BrCl. 1,3-Di-bridged tetrol4a, one of the two possible di-bridged isomers formed in preference to the other, was obtained in 30% yield. Tri-bridged diols3c andd can be selectively debrominated in one step by treatment with 5 equiv. ofn-BuLi in THF to afford the corresponding dibromo derivatives8a andb in 77% and 76% yields, respectively. After incorporation of the fourth bridge, the remaining two bromines can be replaced by C(O)OMe to give9c (60%), by OH to give9d (62%) or by CN to give9f (>95%). When the lithiated derivatives of3c andd are quenched with electrophiles other thanH ⁺, a selectively functionalized tri-bridged diol with hydroxyl (8c, 47%) and selectively functionalized cavitands with thiomethyl (9g, 25%) or iodo (9h, 20%) groups can be synthesized. Two molecules of9d were coupled with CH₂BrCl in DMSO/THF under high dilution conditions to give the flexible hemicarcerand10 in 71% yield. Supplementary Data. A list of observed and calculated structure factors have been deposited with the British Document Supply Centre as Supplementary Publication No. SUP 82170 (50 pages)This paper is dedicated to the commemorative issue on the 50th anniversary of calixarenes.     

The agonistic binding site at the histamine H2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven α-helical transmembrane domain

Summary In the first part (pp. 461–478 in this issue) of this study regarding the histamine H₂ receptor agonistic binding site, the best possible interactions of histamine with an -helical oligopeptide, mimicking a part of the fifth transmembrane -helical domain (TM5) of the histamine H₂ receptor, were considered. It was established that histamine can only bind via two H-bonds with a pure -helical TM5, when the binding site consists of Tyr¹⁸²/Asp¹⁸⁶ and not of the Asp¹⁸⁶/Thr¹⁹⁰ couple. In this second part, two particular three-dimensional models of G-protein-coupled receptors previously reported in the literature are compared in relation to agonist binding at the histamine H₂ receptor. The differences between these two receptor models are discussed in relation to the general benefits and limitations of such receptor models. Also the pros and cons of simplifying receptor models to a relatively easy-to-deal-with oligopeptide for mimicking agonistic binding to an agonistic binding site are addressed. Within complete receptor models, the simultaneous interaction of histamine with both TM3 and TM5 can be analysed. The earlier suggested three-point interaction of histamine with the histamine H₂ receptor can be explored. Our results demonstrate that a three-point interaction cannot be established for the Asp⁹⁸/Asp¹⁸⁶/Thr¹⁹⁰ binding site in either of the investigated receptor models, whereas histamine can form three H-bonds in case the agonistic binding site is constituted by the Asp⁹⁸/Tyr¹⁸²/Asp¹⁸⁶ triplet. Furthermore this latter triplet is seen to be able to accommodate a series of substituted histamine analogues with known histamine H₂ agonistic activity as well.     

Nanostructures via noncovalent synthesis: 144 hydrogen bonds bring together 27 components.

This paper describes the spontaneous and reversible assembly of approximately 20 kDa synthetic hydrogen-bonded assemblies via the formation of 144 cooperative hydrogen bonds. These nanostructures ( approximately 3.0 x 5.5 nm), consisting of 27 different components, have been carefully characterized using a combination of (1)H NMR spectroscopy, MALDI-TOF MS using Ag(+)-labeling, gel permeation chromatography, and CD spectroscopy.