Organocatalysis with endogenous compounds: Towards novel non-enzymatic reactions

The aldol reaction of the endogeneous compounds acetone and methylglyoxal has been studied using organocatalysis in relation to biologically relevant non-enzymatic reactions. Under preparative conditions, 3-hydroxy-2,5-hexadione, known as Henze’s ketol, is formed in high yield and with enantioselectivities up to 88% ee. Furthermore, Henze’s ketol is also formed under simulated physiological conditions at micromolar scale, indicating that this reaction might take place in living organisms.     

'Five at one stroke': proline and small peptides in the stereoselective de novo synthesis and enantiotopic functionalization of carbohydrates

Asymmetric catalysis with the simple amino acid proline (so called 'enamine catalysis') arrested big attention in the last few years since the re-discovery of the Hajos-Parrish-Eder-Sauer-Wiechert reaction. After basic mechanistic studies, probing scope and limitations of the catalyst and the corresponding reactions, this concept has now emerged to a state where it is applied to the assembly of up to five stereogenic centers of carbohydrates, not really 'at one stroke', but in only two simple synthetic operations. Beyond, it is not only possible to build up complicated natural products elegantly, but also to address selectively the similar functional groups of carbohydrates by small peptidic catalysts. This short review covers the recent developments of organocatalysis in both fields, with special emphasis on the asymmetric assembly and selective derivatization of carbohydrates.     

Novel phenyl(thio)ureas bearing (thio)oxothiazoline group as potential BACE-1 inhibitors: synthesis and biological evaluation

We report the synthesis and the β-site amyloid precursor protein cleaving enzyme-1 inhibitory properties of novel phenyl(thio)ureas bearing 2-(thio)oxothiazoline derivatives. A library of analogues was prepared according to specific synthetic schemes and the inhibitory activity was monitored using a fluorescence resonance energy transfer assay. Several analogues show potent inhibitory activities ranging between 1 and 0.01 µM and the activity is related to the NH acidity of the (thio)urea motif. Our results illustrate once again the close relationship between molecular recognition, complexation of the active site in enzymatic system, and organocatalysis utilizing explicit hydrogen bonding.     

Medical image registration: a review

This paper presents a review of automated image registration methodologies that have been used in the medical field. The aim of this paper is to be an introduction to the field, provide knowledge on the work that has been developed and to be a suitable reference for those who are looking for registration methods for a specific application. The registration methodologies under review are classified into intensity or feature based. The main steps of these methodologies, the common geometric transformations, the similarity measures and accuracy assessment techniques are introduced and described.     

Characterisation framework development for the SIMPASS (Singapore IMPact ASSessment) methodology

Purpose  

Life cycle assessment (LCA) practitioners in Singapore currently rely on foreign life cycle impact assessment (LCIA) methodologies when conducting studies, despite the fact that foreign methodologies may not be relevant, adaptable and sensitive to Singapore's circumstances. As a result, work has been undertaken to develop the Singapore IMPact ASSessment (SIMPASS) methodology by adapting and modifying existing LCIA methodologies to suit the Singaporean context. It is envisioned that the use of SIMPASS will improve the accuracy of LCA studies conducted for industries operating in Singapore.     

Lessons from a decade of integrating cancer copy number alterations with gene expression profiles

Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression profiles and somatic copy number alterations (CNA) information on the same patients identified using microarray platforms. In response, many algorithms and software packages are available for integrating these paired data. Surprisingly, there has been no serious attempt to review the currently available methodologies or the novel insights brought using them. In this work, we discuss the quantitative relationships observed between CNA and gene expression in multiple cancer types and biological milestones achieved using the available methodologies. We discuss the conceptual evolution of both, the step-wise and the joint data integration methodologies over the last decade. We conclude by providing suggestions for building efficient data integration methodologies and asking further biological questions.     

Methodology capture: discriminating between the "best" and the rest of community practice

Background  

The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field.     

Air filled porosity measurements by air pycnometry in the composting process: A review and a correlation analysis

Air filled porosity (AFP) appears as the best measure to determine the available porosity in a composting material or, in general, in an organic matrix. Several methodologies, including theoretical and empirical approaches have been developed to estimate AFP. Among them, air pycnometry has been considered the most suitable and accurate technique to obtain reliable measures of AFP. In this review, the published methodologies to determine AFP by air pycnometry are explained in detail, and the main advantages and disadvantages of such methodologies are discussed. Also, a massive sampling of several organic wastes and mixtures intended for composting has been characterized by air pycnometry, and the theoretical and empirical correlations proposed in literature are compared in terms of accuracy in AFP measurement. Results obtained show that some theoretical correlations are suitable for estimating AFP in the majority of organic wastes studied. However, some waste samples need an experimental determination to obtain a realistic value of AFP.     

The need for co-product allocation in the life cycle assessment of agricultural systems—is “biophysical” allocation progress?

Purpose

Several new “biophysical” co-product allocation methodologies have been developed for LCA studies of agricultural systems based on proposed physical or causal relationships between inputs and outputs (i.e. co-products). These methodologies are thus meant to be preferable to established allocation methodologies such as economic allocation under the ISO 14044 standard. The aim here was to examine whether these methodologies really represent underlying physical relationships between the material and energy flows and the co-products in such systems, and hence are of value.

Methods

Two key components of agricultural LCAs which involve co-product allocation were used to provide examples of the methodological challenges which arise from adopting biophysical allocation in agricultural LCA: (1) the crop production chain and (2) the multiple co-products produced by animals. The actual “causal” relationships in these two systems were illustrated, the energy flows within them detailed, and the existing biophysical allocation methods, as found in literature, were critically evaluated in the context of such relationships.

Results and discussion

The premise of many biophysical allocation methodologies has been to define relationships which describe how the energy input to agricultural systems is partitioned between co-products. However, we described why none of the functional outputs from animal or crop production can be considered independently from the rest on the basis of the inputs to the system. Using the example of manure in livestock systems, we also showed why biophysical allocation methodologies are still sensitive to whether a system output has economic value or not. This sensitivity is a longstanding criticism of economic allocation which is not resolved by adopting a biophysical approach.

Conclusions

The biophysical allocation methodologies for various aspects of agricultural systems proposed to date have not adequately explained how the physical parameters chosen in each case represent causal physical mechanisms in these systems. Allocation methodologies which are based on shared (but not causal) physical properties between co-products are not preferable to allocation based on non-physical properties within the ISO hierarchy on allocation methodologies and should not be presented as such.

     

METHODOLOGIES FOR THE STEREOSELECTIVE SYNTHESIS OF ADRENERGIC β-BLOCKERS: AN OVERVIEW

The importance of the adrenergic β-blockers with structure of (S) 1-aryloxy-3-amino-2-propanol in the treatment of different diseases has led the development of a variety of stereoselective synthetic methodologies for this stereoisomer. In this review we present several methodologies to obtain this compound using (i) chiral substrates, (ii) chiral catalysts (organometallic or enzymes) and (iii) preparative chiral chromatography, showing the advantages and disadvantages of each methodology.     

Methods to drive systems biology forward

The development of new methodologies has driven the expansion of systems biology over the past decades. Technological breakthroughs in sequencing, in quantitative proteomics, in single‐cell measurements, to name only a few, have each opened up whole new fields of research. To highlight the importance of new experimental and computational methodologies in enabling novel biological discoveries, we are pleased to announce the introduction of a new Methods section in Molecular Systems Biology ( http://msb.embopress.org/authorguide#methodsguide ).     

Detection and characterization of single biomolecules at surfaces

The investigation of bio-molecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states, occurring as highly correlated in space and time within an arrangement of various elements. In order to resolve such dynamical changes in ensemble average techniques, one would have to synchronize all molecules, which is hard to achieve and might interfere with important system properties. Single molecule studies, in contrast, do not require pretreatment of the system and resume, therefore, much less invasive methodologies. Here, we review recent employments for the investigation of bio-molecules on surfaces, in which the high local and temporal resolution of two complementary techniques, atomic force microscopy and single molecule fluorescence microscopy, is used to address single molecules. Novel methodologies for the characterization of biologically relevant parameters, functions and dynamical aspects of individual molecules are described.     

Complementary double-stranded helical oligomers bearing achiral bifunctional groups that catalyze asymmetric aldol reaction

Two novel chiral dimer and trimer strands composed of m-terphenyl groups linked through p-diethynylbenzene units with the chiral amidine group and achiral piperazine group introduced at the terminus or center of the strands, respectively, and its complementary achiral carboxylic acid dimer and trimer were synthesized. The complementary chiral/achiral strands form an excess-handed double-helical structure as supported by intense split-type Cotton effects in the absorption regions of the conjugated backbones biased by the chiral amidinium–carboxylate salt bridges. The double-helical trimer was found to catalyze the direct aldol reaction of cyclohexanone with 4-nitrobenzaldehyde and produce the products with a moderate enantioselectivity despite the fact that the catalytically active bifunctional piperazine/carboxylic acid pair introduced in the middle is achiral, indicating the key role of the one-handed double-helical framework for supramolecular bifunctional organocatalysis.     

User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation

Journal of Microbiology - Due to accumulating protein structure information and advances in computational methodologies, it has now become possible to predict protein-compound interactions. In...     

Natural product-inspired cascade synthesis yields modulators of centrosome integrity

In biology-oriented synthesis, the scaffolds of biologically relevant compound classes inspire the synthesis of focused compound collections enriched in bioactivity. This criterion is, in particular, met by the scaffolds of natural products selected in evolution. The synthesis of natural product-inspired compound collections calls for efficient reaction sequences that preferably combine multiple individual transformations in one operation. Here we report the development of a one-pot, twelve-step cascade reaction sequence that includes nine different reactions and two opposing kinds of organocatalysis. The cascade sequence proceeds within 10-30 min and transforms readily available substrates into complex indoloquinolizines that resemble the core tetracyclic scaffold of numerous polycyclic indole alkaloids. Biological investigation of a corresponding focused compound collection revealed modulators of centrosome integrity, termed centrocountins, which caused fragmented and supernumerary centrosomes, chromosome congression defects, multipolar mitotic spindles, acentrosomal spindle poles and multipolar cell division by targeting the centrosome-associated proteins nucleophosmin and Crm1.     

Analysis of the human saliva proteome

Interest in the characterization of the salivary proteome has increased in the last few years. This review discusses the different techniques and methodologies applied to the separation and identification of salivary proteins. Nowadays, proteomic techniques are the state of the art for the analysis of biologic materials and saliva is no exception. 2D electrophoresis and tryptic digest analysis by mass spectrometry are the typical methodology, but new approaches using 2D liquid chromatography/mass spectrometry methods have already been introduced for saliva analysis. Due to their important physiologic role in the oral cavity, low-molecular-weight proteins and peptides are also included in this article and the methodologies discussed.     

A Practical and Stereoselective Organocatalytic Alkylation of Aldehydes with Benzodithiolylium Tetrafluoroborate

Recently, the direct substitution of allylic, benzylic, and tertiary alcohols has been achieved via S_N1‐type reactions with catalytic amounts of Brønsted or Lewis acids. When a new stereogenic center is formed most of these transformations produce the desired product as a racemate, as these reactions proceed through carbenium ions. The arsenal of activation modes available in organocatalysis can be used to set up suitable reaction conditions in which chiral nucleophiles (enamine catalysis) or chiral electrophiles (iminium catalysis, chiral counterion catalysis) can easily be generated. Recently, we have used stabilized carbenium ions, directly available or obtained from the corresponding alcohols, in new organocatalytic stereoselective S_N1‐type reactions. The commercially available carbenium ion benzodithiolylium tetrafluoroborate 1 can be used for the straightforward organocatalytic stereoselective alkylation of aldehydes. In this account we will illustrate the application of this methodology in the total synthesis of natural products and the preparation of valuable starting materials. Chirality 26:607–613, 2014. © 2014 Wiley Periodicals, Inc.     

Analysis of the human saliva proteome

Interest in the characterization of the salivary proteome has increased in the last few years. This review discusses the different techniques and methodologies applied to the separation and identification of salivary proteins. Nowadays, proteomic techniques are the state of the art for the analysis of biologic materials and saliva is no exception. 2D electrophoresis and tryptic digest analysis by mass spectrometry are the typical methodology, but new approaches using 2D liquid chromatography/mass spectrometry methods have already been introduced for saliva analysis. Due to their important physiologic role in the oral cavity, low-molecular-weight proteins and peptides are also included in this article and the methodologies discussed.     

Preclinical cardio-safety assessment of torsadogenic risk and alternative methods to animal experimentation: The inseparable twins

The last decade has been marked by the withdrawal from the market of several medicines whose use in patients has been associated with the development of torsade de pointes (TdP), a potentially life-threatening polymorphic tachycardia. In a few cases, TdP can degenerate into ventricular fibrillation and lead to sudden death, thus constituting a real problem of public health. The recently finalized ICH S7B guideline defines the prolongation of the QT interval on the electrocardiogram as the best biomarker for predicting the torsadogenic risk of a given compound. However, a growing body of evidence suggests that drugs’ torsadogenic potential may not necessarily be proportional to their ability to prolong the QT interval. It is a dynamic combination of multiple predisposing factors and components rather than a single particular event that can trigger this particular tachycardia. Following recommendations of the guideline, pharmaceutical companies have intensively implemented methodologies to assess the possible risk of QT prolongation and TdP in humans. The main problem in cardiac safety pharmacology is how best to combine the capabilities of different methodologies with their strengths and limitations in order to detect the potential of one molecular entity to induce a lethal arrhythmia of very low clinical incidence. This publication will review the current methodologies, focusing on the alternative methods to animal experimentation, including an overview of cardiac modeling.     

The rise of high throughput

The realization that gene, protein, and metabolite space is vast has led to the development of novel high-throughput methodologies aimed directly at interrogating biomolecules and their interactions at previously impossible depths. In this special focus section, the editors of BioTechniques explore the development of high-throughput applications in five areas of life science (page 27), while a primary research article by Kapetis et al. details an enhanced software platform capable of automated cross-platform microarray data analysis (page 33). It is our hope that through the articles in this section, readers will obtain a deeper understanding of high-throughput methodologies and their evolution.