The ELIXIR channel in F1000Research

ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate Europe's national centres, services, and core bioinformatics resources into a single, coordinated infrastructure. ELIXIR brings together Europe's major life-science data archives and connects these with national bioinformatics infrastructures  - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR's scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Advisory Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process.

[A Randomized Controlled Trial on the Effect of Earmuffs on Intermittent Hypoxia and Bradycardia in Preterm Infants]

BACKGROUND

Irregular breathing causing hypoxia and bradycardia is a common problem of preterm infants but its pathophysiology is incompletely understood. Agitation provoked by environmental noise may play a role. We wanted to know if earmuffs can at least halve the rate of intermittent hypoxia in premies.

PATIENTS AND METHODS

In this randomized controlled trial 31 infants (14 male; median [min.-max.] birth weight and gestational age: 1 323 g [560-1 990] and 30(1/7) weeks [25(5/7)-33(0/7)]) had the effect of earmuffs on the frequency of pulse oximeter desaturations (SpO(2) <80%) and bradycardia events (<80 beats per minute) tested, documented via a standard home monitor. Infants were measured 2 h each with or without earmuffs; the sequence of intervention was randomised. Measurement conditions were kept constant while a noise meter recorded sound pressure levels at a 1 Hz sampling rate.

RESULTS

Median sound pressure level was 46.8 dB(A). In a pre-study, ear muffs yielded a sound reduction by 7.2 dB. 19 infants had a total of 474 desaturations. The median (25.-75. percentile) number of desaturations was 1 (1-10.5) without, and 1 (1-10) with earmuffs. The amount of infants with at least one desaturation was equal in both treatment protocols. Only 7 bradycardias occurred.

CONCLUSION

The earmuffs had, in a rather quiet environment, no effect on intermittent hypoxia in these infants.

A quick guide for building a successful bioinformatics community

"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).

Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case

In this study, the screening collections of two major pharmaceutical companies (AstraZeneca and Bayer Pharma AG) have been compared using a 2D molecular fingerprint by a nearest neighborhood approach. Results revealed a low overlap between both collections in terms of compound identity and similarity. This emphasizes the value of screening multiple compound collections to expand the chemical space that can be accessed by high-throughput screening (HTS).

Taking Open Innovation to the Molecular Level - Strengths and Limitations

The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an 'open innovation' business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.

SARConnect: A Tool to Interrogate the Connectivity Between Proteins, Chemical Structures and Activity Data

The access and use of large-scale structure-activity relationships (SAR) is increasing as the range of targets and availability of bioactive compound-to-protein mappings expands. However, effective exploitation requires merging and normalisation of activity data, mappings to target classifications as well as visual display of chemical structure relationships. This work describes the development of the application "SARConnect" to address these issues. We discuss options for delivery and analysis of large-scale SAR data together with a set of use-cases to illustrate the design choices and utility. The main activity sources of ChEMBL,1 GOSTAR2 and AstraZeneca's internal system IBIS, had already been integrated in Chemistry Connect.3 For target relationships we selected human UniProtKB/Swiss-Prot4 as our primary source of a heuristic target classification. Similarly, to explore chemical relationships we combined several methods for framework and scaffold analysis into a unified, hierarchical classification where ease of navigation was the primary goal. An application was built on TIBCO Spotfire to retrieve data for visual display. Consequently, users can explore relationships between target, activity and structure across internal, external and commercial sources that encompass approximately 3 million compounds, 2000 human proteins and 10 million activity values. Examples showing the utility of the application are given.

Open PHACTS: semantic interoperability for drug discovery

Open PHACTS is a public-private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery research. OPS is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research. This paper lays out the challenges and how the Open PHACTS project is hoping to address these challenges technically and socially.

Combinatorial library design from reagent pharmacophore fingerprints

Combinatorial and parallel chemical synthesis technologies are powerful tools in early drug discovery projects. Over the past couple of years an increased emphasis on targeted lead generation libraries and focussed screening libraries in the pharmaceutical industry has driven a surge in computational methods to explore molecular frameworks to establish new chemical equity. In this chapter we describe a complementary technique in the library design process, termed ProSAR, to effectively cover the accessible pharmacophore space around a given scaffold. With this method reagents are selected such that each R-group on the scaffold has an optimal coverage of pharmacophoric features. This is achieved by optimising the Shannon entropy, i.e. the information content, of the topological pharmacophore distribution for the reagents. As this method enumerates compounds with a systematic variation of user-defined pharmacophores to the attachment point on the scaffold, the enumerated compounds may serve as a good starting point for deriving a structure-activity relationship (SAR).

Physicochemical property profiles of marketed drugs, clinical candidates and bioactive compounds

We performed a comparison of several simple physicochemical properties between marketed drugs, clinical candidates and bioactive compounds using commercially available databases (GVKBIO, Hyderabad, India). In contrast to previous studies this comparison was performed at the individual target level. Confirming earlier studies this shows that marketed drugs have, on average and taken as a single set, lower physicochemical property values than the corresponding clinical candidates and bioactive compounds but that there is considerable variation between drug targets. This work complements earlier studies by using a much larger annotated dataset and confirms that there is a shift in physicochemical properties for targets with launched drugs and clinical candidates compared to bioactive compounds.

Structure-based organic synthesis of unnatural aeruginosin hybrids as potent inhibitors of thrombin

Based on X-ray crystallographic data of complexes of chlorodysinosin A with the enzyme thrombin, a series of analogs were synthesized varying the nature of the P(1), P(2), and P(3) pharmacophoric sites and the central octahydroindole carboxyamide core. In general, introduction of a hydrophobic substituent on the d-leucine amide residue dramatically improved the inhibition of the enzyme. This is rationalized based on a better fit of the P(3) subunit in the hydrophobic S(3) enzyme site. Single digit nanomolar inhibition expressed as IC(50) was observed for several analogs.

Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data

A 'global' model of hERG K(+) channel was built to satisfy three basic criteria for QSAR models in drug discovery: (1) assessment of the applicability domain, (2) assuring that model decisions can be interpreted by medicinal chemists and (3) assessment of model performance after the model was built. A combination of D-optimal onion design and hierarchical partial least squares modelling was applied to construct a global model of hERG blockade in order to maximize the applicability domain of the model and to enhance its interpretability. Additionally, easily interpretable hERG specific fragment-based descriptors were developed. Model performance was monitored, throughout a time period of 15 months, after model implementation. It was found that after this time duration a greater proportion of molecules were outside the model's applicability domain and that these compounds had a markedly higher average prediction error than those from molecules within the model's applicability domain. The model's predictive performance deteriorated within 4 months after building, illustrating the necessity of regular updating of global models within a drug discovery environment.

Total Synthesis and Structural Confirmation of Chlorodysinosin A

The first enantiocontrolled total synthesis of the marine sponge metabolite chlorodysinosin A is described. The structure and absolute configuration are identical to those of dysinosin A except for the presence of a novel 2S,3R-3-chloroleucine residue in the former. A concise stereocontrolled synthesis of the new chlorine-containing amino acid fragment was developed. An X-ray cocrystal structure of synthetic chlorodysinosin A with the enzyme thrombin confirms the structure and configuration assignment achieved through total synthesis. Within the aeruginosin family of natural products, chlorodysinosin A is the most potent inhibitor of the serine proteases thrombin, factor VIIa, and factor Xa, which are critical enzymes in the process leading to platelet aggregation and fibrin mesh formation in humans.

Multifingerprint Based Similarity Searches for Targeted Class Compound Selection

Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules by similarity searching against a set of query compounds. For this purpose, we used biological data from HTS screening campaigns of four protein families (GPCRs, kinases, ion channels, and proteases). We have established threshold values for the similarity index (Tanimoto index) to be used as starting points for similarity searches. Based on the complementarities between the selections made by using different fingerprints we propose a multifingerprint approach as an efficient tool to balance the strengths and weaknesses of various fingerprints.

Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family

BACKGROUND

The peroxisome proliferator-activated receptors (PPAR) are ligand-activated transcription factors belonging to the nuclear receptor family. The roles of PPARalpha in fatty acid oxidation and PPARgamma in adipocyte differentiation and lipid storage have been characterized extensively. PPARs are activated by fatty acids and eicosanoids and are also targets for antidyslipidemic drugs, but the molecular interactions governing ligand selectivity for specific subtypes are unclear due to the lack of a PPARalpha ligand binding domain structure.

RESULTS

We have solved the crystal structure of the PPARalpha ligand binding domain (LBD) in complex with the combined PPARalpha and -gamma agonist AZ 242, a novel dihydro cinnamate derivative that is structurally different from thiazolidinediones. In addition, we present the crystal structure of the PPARgamma_LBD/AZ 242 complex and provide a rationale for ligand selectivity toward the PPARalpha and -gamma subtypes. Heteronuclear NMR data on PPARalpha in both the apo form and in complex with AZ 242 shows an overall stabilization of the LBD upon agonist binding. A comparison of the novel PPARalpha/AZ 242 complex with the PPARgamma/AZ 242 complex and previously solved PPARgamma structures reveals a conserved hydrogen bonding network between agonists and the AF2 helix.

CONCLUSIONS

The complex of PPARalpha and PPARgamma with the dual specificity agonist AZ 242 highlights the conserved interactions required for receptor activation. Together with the NMR data, this suggests a general model for ligand activation in the PPAR family. A comparison of the ligand binding sites reveals a molecular explanation for subtype selectivity and provides a basis for rational drug design.