A novel multilevel statistical method for the study of the relationships between multireceptorial binding affinity profiles and in vivo endpoints

The present work introduces a novel method for drug research based on the sequential building of linked multivariate statistical models, each one introducing a different level of drug description. The use of multivariate methods allows us to overcome the traditional one-target assumption and to link in vivo endpoints with drug binding profiles, involving multiple receptors. The method starts with a set of drugs, for which in vivo or clinical observations and binding affinities for potentially relevant receptors are known, and allows obtaining predictions of the in vivo endpoints highlighting the most influential receptors. Moreover, provided that the structure of the receptor binding sites is known (experimentally or by homology modeling), the proposed method also highlights receptor regions and ligand-receptor interactions that are more likely to be linked to the in vivo endpoints, which is information of high interest for the design of novel compounds. The method is illustrated by a practical application dealing with the study of the metabolic side effects of antipsychotic drugs. Herein, the method detects related receptors confirmed by experimental results. Moreover, the use of structural models of the receptor binding sites allows identifying regions and ligand-receptor interactions that are involved in the discrimination between antipsychotic drugs that show metabolic side effects and those that do not. The structural results suggest that the topology of a hydrophobic sandwich involving residues in transmembrane helices (TM) 3, 5, and 6, as well as the assembling of polar residues in TM5, are important discriminators between target/antitarget receptors. Ultimately, this will provide useful information for the design of safer compounds inducing fewer side effects.

[Health information on the Internet and trust marks as quality indicators: vaccines case study]

OBJECTIVES

To find out the prevalence of quality trust marks present in websites and to analyse the quality of these websites displaying trust marks compared with those that do not display them, in order to put forward these trust marks as a quality indicator.

DESIGN

Cross-sectional study.

SETTING

Internet.

PARTICIPANTS

Websites on vaccines.

MAIN MEASURES

Using "vacunas OR vaccines" as key words, the features of 40 web pages were analysed. These web pages were selected from the page results of two search engines, Google and Yahoo!

RESULTS

Based on a total of 9 criteria, the average score of criteria fulfilled was 7 (95% CI 3.96-10.04) points for the web pages offered by Yahoo! and 7.3 (95% CI 3.86-10.74) offered by Google. Amongst web pages offered by Yahoo!, there were three with clearly inaccurate information, while there were four in the pages offered by Google. Trust marks were displayed in 20% and 30% medical web pages, respectively, and their presence reached statistical significance (P=0.033) when fulfilling the quality criteria compared with web pages where trust marks were not displayed.

CONCLUSIONS

A wide variety of web pages was obtained by search engines and a large number of them with useless information. Although the websites analysed had a good quality, between 15% and 20% showed inaccurate information. Websites where trust marks were displayed had more quality than those that did not display one and none of them were included amongst those where inaccurate information was found.

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

BACKGROUND

Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect of non-synonymous SNPs in the context of biological networks such as cell signalling pathways. UniProt provides curated information about the functional and phenotypic effects of sequence variation, including SNPs, as well as on mutations of protein sequences. However, no strategy has been developed to integrate this information with biological networks, with the ultimate goal of studying the impact of the functional effect of SNPs in the structure and dynamics of biological networks.

RESULTS

First, we identified the different challenges posed by the integration of the phenotypic effect of sequence variants and mutations with biological networks. Second, we developed a strategy for the combination of data extracted from public resources, such as UniProt, NCBI dbSNP, Reactome and BioModels. We generated attribute files containing phenotypic and genotypic annotations to the nodes of biological networks, which can be imported into network visualization tools such as Cytoscape. These resources allow the mapping and visualization of mutations and natural variations of human proteins and their phenotypic effect on biological networks (e.g. signalling pathways, protein-protein interaction networks, dynamic models). Finally, an example on the use of the sequence variation data in the dynamics of a network model is presented.

CONCLUSION

In this paper we present a general strategy for the integration of pathway and sequence variation data for visualization, analysis and modelling purposes, including the study of the functional impact of protein sequence variations on the dynamics of signalling pathways. This is of particular interest when the SNP or mutation is known to be associated to disease. We expect that this approach will help in the study of the functional impact of disease-associated SNPs on the behaviour of cell signalling pathways, which ultimately will lead to a better understanding of the mechanisms underlying complex diseases.

Synthesis, binding affinity and SAR of new benzolactam derivatives as dopamine D3 receptor ligands

A series of new benzolactam derivatives was synthesized and the derivatives were evaluated for their affinities at the dopamine D(1), D(2), and D(3) receptors. Some of these compounds showed high D(2) and/or D(3) affinity and selectivity over the D(1) receptor. The SAR study of these compounds revealed structural characteristics that decisively influenced their D(2) and D(3) affinities. Structural models of the complexes between some of the most representative compounds of this series and the D(2) and D(3) receptors were obtained with the aim of rationalizing the observed experimental results. Moreover, selected compounds showed moderate binding affinity on 5-HT(2A) which could contribute to reducing the occurrence of extrapyramidal side effects as potential antipsychotics.

Knowledge environments representing molecular entities for the virtual physiological human

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

Diastereoselective synthesis of delta-aminoacids through domino Ireland-Claisen rearrangement and Michael addition

A novel domino reaction--stereoselective Ireland-Claisen rearrangement and asymmetric Michael addition--is described. A protocol starting from Baylis-Hillman adducts 3a-f using chiral lithium amide affords optically active gamma-substituted delta-amino acids 4a-f with high diastereoselectivities and enantioselectivities. The acid can be isolated easily from large-scale reactions and transformed to 2,3-disubstituted piperidines 11 or 2-substituted nipecotic acid derivates 12.

Identifying gene-specific variations in biomedical text

The influence of genetic variations on diseases or cellular processes is the main focus of many investigations, and results of biomedical studies are often only accessible through scientific publications. Automatic extraction of this information requires recognition of the gene names and the accompanying allelic variant information. In a previous work, the OSIRIS system for the detection of allelic variation in text based on a query expansion approach was communicated. Challenges associated with this system are the relatively low recall for variation mentions and gene name recognition. To tackle this challenge, we integrate the ProMiner system developed for the recognition and normalization of gene and protein names with a conditional random field (CRF)-based recognition of variation terms in biomedical text. Following the newly developed normalization of variation entities, we can link textual entities to Single Nucleotide Polymorphism database (dbSNP) entries. The performance of this novel approach is evaluated, and improved results in comparison to state-of-the-art systems are reported.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

BACKGROUND

Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.

RESULTS

Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.

CONCLUSION

OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

1-, 3- and 8-substituted-9-deazaxanthines as potent and selective antagonists at the human A2B adenosine receptor

A large series of piperazin-, piperidin- and tetrahydroisoquinolinamides of 4-(1,3-dialkyl-9-deazaxanthin-8-yl)phenoxyacetic acid were prepared through conventional or multiple parallel syntheses and evaluated for their binding affinity at the recombinant human adenosine receptors, chiefly at the hA(2B) and hA(2A) receptor subtypes. Several ligands endowed with high binding affinity at hA(2B) receptors, excellent selectivity over hA(2A) and hA(3) and a significant, but lower, selectivity over hA(1) were identified. Among them, piperazinamide derivatives 23 and 52, and piperidinamide derivative 69 proved highly potent at hA(2B) (K(i)=11, 2 and 5.5 nM, respectively) and selective towards hA(2A) (hA(2A)/hA(2B) SI=912, 159 and 630, respectively), hA(3) (hA(3)/hA(2B) SI=>100, 3090 and >180, respectively) and hA(1) (hA(1)/hA(2B) SI=>100, 44 and 120, respectively), SI being the selectivity index. A number of selected ligands tested in functional assays in vitro showed very interesting antagonist activities and efficacies at both A(2A) and A(2B) receptor subtypes, with pA(2) values close to the corresponding pK(i)s. Structure-affinity and structure-selectivity relationships suggested that the binding potency at the hA(2B) receptor may be increased by lipophilic substituents at the N4-position of piperazinamides and that an ortho-methoxy substituent at the 8-phenyl ring and alkyl groups at N1 larger than the ones at N3, in the 9-deazaxanthine ring, may strongly enhance the hA(2A)/hA(2B) SI.

[Pneumonia in the elderly population over 70 years with limited functional condition: case-control study of institutionalized patients]

OBJECTIVE

Community acquired pneumonia (CAP) of the elderly is an increasingly important growing health problem due to its prevalence and mortality. Among the factors that are usually related with poor evolution are advanced age, poor functional status and coming from a socio-health care institution such as residential homes for the elderly. In this study, we have chosen a population over 70 years of age with limited functional capacity (Barthel Index < 50) in order to know if coming from a residential home for the elderly is an isolated factor that is associated to worse prognosis of CAP.

PATIENTS AND METHODS

We selected 87 patients over 70 years from a prospective and multicenter study of the hospitalized CAPs during one year. We analyzed the evolution and course of the CAP based on place or origin and then conducted a case-control study of the elderly over 70 years with the Barthel under 50, including 21 elderly from residences and 21 from the own home.

RESULTS

In elderly patients over 70 years with CAP, those coming from the residence have a confusional picture more often and come to emergency with lower values of systolic and diastolic blood pressure, lower arterial oxygen saturation, greater involvement on the x-ray, Fine Index is worse and die more often. When we limit the population to those over 70 years with Barthel under 50, we do not find differences in institutionalized patients versus the others.

CONCLUSION

In the elderly over 70 years with CAP, patients from assisted living residences have greater mortality. However, when functional capacity is bad (Barthel < 50), place or origin (community or elderly residence) loses importance and becomes a variable that has no more influence than others in the clinical evolution and course of the CAP.

Multistructure 3D-QSAR studies on a series of conformationally constrained butyrophenones docked into a new homology model of the 5-HT2A receptor

The present study is part of a long-term research project aiming to gain insight into the mechanism of action of atypical antipsychotics. Here we describe a 3D-QSAR study carried out on a series of butyrophenones with affinity for the serotonin-2A receptor, aligned by docking into the binding site of a receptor model. The series studied has two peculiarities: (i) all the compounds have a chiral center and can be represented by two enantiomeric structures, and (ii) many of the structures can bind the receptor in two alternative orientations, posing the problem of how to select a single representative structure for every compound. We have used an original solution consisting of the simultaneous use of multiple structures, representing different configurations, binding conformations, and positions. The final model showed good statistical quality (n = 426, r2 = 0.84, q2LOO = 0.81) and its interpretation provided useful information, not obtainable from the simple inspection of the ligand-receptor complexes.

Synthesis of novel antitumoural analogues of dysidiolide from ent-halimic acid

Several sesterterpenolides analogues of dysidiolide have been synthesized and their in vitro antitumoural activity against human HeLa, A549, HT-29 and HL-60 carcinoma cells is presented. The proliferation inhibition data showed a significant antitumour activity of the compounds 1b, 2a, 2b, 3a, 3b, 4a, 4b, 5, inhibiting proliferation of distinct cancer cell types with an IC(50) in the low micromolar range.

PM10 speciation and determination of air quality target levels. A case study in a highly industrialized area of Spain

The paper shows how PM speciation studies allow the evaluation of the strategies to be followed to diminish PM pollution in highly industrialized areas with a large number of potential pollution sources. Evolution of levels and speciation of PM10 in the ceramic producing area of Castelló (East Spain) was studied from April 2002 until December 2005. PM10 levels were measured at one rural (Borriana-rural), two suburban (Almassora and Onda) and three urban (Borriana-urban, L'Alcora and Vila-real) sites, all influenced by the ceramics industry. Average PM10 levels varied between 27 and 36 microg/m3 for the study period. Evaluation of 1996-2005 PM data from Onda shows a clear decrease of PM levels since the beginning of 2002. Summer peak levels and winter minima occurred at both rural and suburban sites, whereas urban sites had no clear seasonal trend, with high PM10 episodes being due variously to local, regional, and African dust intrusion events. PM10 chemical analysis at four of the sites showed the dominant constituent to be mineral matter, exceeding by 5-12 microg/m3 the usual ranges of annual mineral loadings in PM10 at comparable Spanish urban or regional background sites with no industrial influence. Given current PM10 loadings, we recommend a lowering target of 3-5 microg/m3 of the annual mean at the urban sites, which should be achievable given available emission abatement techniques.

Characterization of Langmuir and Langmuir–Blodgett films of a thiomacrocyclic ionophore by surface pressure and AFM

The new synthesized thiomacrocyclic ionophore 4-phenyl-4-sulfide-11-(1-oxodecyl)-1,7-dithia-11-aza-4-phosphacyclotetradecane has proven to form Langmuir and Langmuir-Blodgett (LB) films. This ionophore shows a large affinity for copper(II) ions. Thus, the influence of the subphase composition on the surface pressure-area isotherms has been studied. The LB films have been observed by AFM and the effect of the subphase composition and the deposition surface pressure on the LB films is discussed. AFM image morphology has been correlated to the ionophore molecular structure. Surface pressure-area isotherms and AFM images show that the presence of copper(II) ions has an important role in the film structure.

OSIRIS: a tool for retrieving literature about sequence variants

Sequence variants, in particular single nucleotide polymorphisms (SNPs), are key elements for the identification of genes associated with complex diseases and with particular drug responses. The search for literature about sequence variation is hampered by the large number of allelic variants reported for many genes and by the variability in both gene and sequence variants nomenclatures. We describe OSIRIS, a search tool that integrates different sources of information with the aim to retrieve literature about sequence variation of a gene. In addition, it provides a method to link a dbSNP entry with the articles referring to it.

AVAILABILITY

OSIRIS is available for public use at http://ibi.imim.es/

QF2004B, a potential antipsychotic butyrophenone derivative with similar pharmacological properties to clozapine

The aim of the present work was to characterize a lead compound displaying relevant multi-target interactions, and with an in vivo behavioral profile predictive of atypical antipsychotic activity. Synthesis, molecular modeling and in vitro and in vivo pharmacological studies were carried out for 2-[4-(6-fluorobenzisoxazol-3-yl)piperidinyl]methyl-1,2,3,4-tetrahydro-carbazol-4-one (QF2004B), a conformationally constrained butyrophenone analogue. This compound showed a multi-receptor profile with affinities similar to those of clozapine for serotonin (5-HT2A, 5-HT1A, and 5-HT2C), dopamine (D1, D2, D3 and D4), alpha-adrenergic (alpha1, alpha2), muscarinic (M1, M2) and histamine H1 receptors. In addition, QF2004B mirrored the antipsychotic activity and atypical profile of clozapine in a broad battery of in vivo tests including locomotor activity (ED50 = 1.19 mg/kg), apomorphine-induced stereotypies (ED50 = 0.75 mg/kg), catalepsy (ED50 = 2.13 mg/kg), apomorphine- and DOI (2,5-dimethoxy-4-iodoamphetamine)-induced prepulse inhibition (PPI) tests. These results point to QF2004B as a new lead compound with a relevant multi-receptor interaction profile for the discovery and development of new antipsychotics.