Thiamine models and perspectives on the mechanism of action of thiamine-dependent enzymes

Thiamine dependent enzymes catalyze ligase and lyase reactions near a carbonyl moiety. Chemical models for these reactions serve as useful tools to substantiate a detailed mechanism of action. This tutorial review covers all such studies performed thus far, emphasizing the role of each part around the active site and the conformation of the cofactor during catalysis.     

Dicarbonyl reduction by single enzyme for the preparation of chiral diols

Chiral diols are a group of key building blocks useful for preparing a variety of important chiral chemicals. While the preparation of optically pure diols is generally not an easy task in synthetic organic chemistry, three classes of enzymes, namely dicarbonyl reductase, dioxygenase and epoxide hydrolase, display remarkable ability to stereoselectively introduce two hydroxyl groups in a single-step enzymatic conversion. In this tutorial review, we pay special attention to dicarbonyl reductases that directly produce chiral diols through the bio-reduction of two carbonyl groups. The dicarbonyl reductases include diketoreductase, α-acetoxy ketone reductase and sepiapterin reductase. We present these exceptional enzymes in the context of source and properties, structure and catalytic mechanism as well as biocatalytic application. In addition to the broad substrate specificity, the excellent stereoselectivity and high catalytic efficiency of these enzymes have positioned them as valuable biocatalysts. With more sophisticated understanding of the structure-function relationship, the practical utilities of these enzymes associated with their interesting chemistry will be considerably appreciated over time. Moreover, rational redesign and molecular evolution of these unusual biocatalysts will truly enable their broader applications in the synthesis of chiral diols in the future.     

Design of targeting ligands in medicinal inorganic chemistry

This tutorial review will highlight recent advances in medicinal inorganic chemistry pertaining to the use of multifunctional ligands for enhanced effect. Ligands that adequately bind metal ions and also include specific targeting features are gaining in popularity due to their ability to enhance the efficacy of less complicated metal-based agents. Moving beyond the traditional view of ligands modifying reactivity, stabilizing specific oxidation states, and contributing to substitution inertness, we will discuss recent work involving metal complexes with multifunctional ligands that target specific tissues, membrane receptors, or endogenous molecules, including enzymes.     

Probing the kinome in real time with fluorescent peptides

Protein phosphorylation is the most frequent post-translational modification used to regulate protein activity. Protein kinases, the enzymes that catalyze the phosphoryl transfer, are implicated in practically every aspect of normal as well as abnormal cell functions. Consequently, sensitive, selective, high-throughput and widely applicable methods for monitoring protein kinase activity will provide valuable tools to screen inhibitor candidates for therapeutics and chemical biology, and to unravel the diverse signaling cascades in which these enzymes are pivotal. Peptide-based chemosensors that rely on fluorescence changes upon phosphorylation are highly desirable, because these systems allow a continuous readout offering an excellent spatial and temporal resolution to observe in real time the kinase activity. This tutorial review briefly summarizes the different fluorescent continuous peptide-based strategies that are being commonly employed to sense protein phosphorylation, introduces a few novel and attractive emerging assays, discusses their advantages and limitations, and highlights possible future directions.     

Evolution in the understanding of [Fe]-hydrogenase

Hydrogenases catalyse redox reactions with molecular hydrogen, either as substrate or product. The enzymes harness hydrogen as a reductant using metals that are abundant and economical, namely, nickel and iron, and should provide new pointers for the economic use of hydrogen in manmade devices. The most recently discovered and perhaps the most enigmatic of the hydrogenases is the [Fe]-hydrogenase, used by certain microorganisms in the pathway that reduces carbon dioxide to methane. Since its discovery some twenty years ago, [Fe]-hydrogenase has consistently provided structural and mechanistic surprises, often requiring complete re-evaluation of its mechanism of action. This tutorial review combines recent advances in X-ray crystallography and other analytical techniques, as well as in computational studies and in chemical synthesis to provide a platform for understanding this remarkable enzyme type.     

Regioselective enzymatic acylation of complex natural products: expanding molecular diversity

Enzymatic catalysis has become a common tool in both academia and industrial chemistry. The efforts of chemists over recent decades have led to the rationalization of the mechanism of action of biocatalysts, which have been routinely incorporated into many synthetic sequences. Nowadays, a further step consists in expanding the application of enzymes to the modification of complex molecular scaffolds common to many pharmaceutical leads isolated from nature. Regioselective enzymatic acylation is a process which has been profitably applied for this purpose in recent times, leading to new drugs with improved activity, stability and pharmacokinetic properties. This tutorial review provides an overview of this subject employing two classes of enzymes, hydrolases and acyltransferases, in the recently concluded decade although some representative older studies are commented upon, if required. We shall place special emphasis on those examples in which the novel acylated derivatives have improved the activity or properties of the parental molecules.     

Introduction of organic/hydro-organic matrices in inductively coupled plasma optical emission spectrometry and mass spectrometry: A tutorial review. Part II. Practical considerations

Inductively coupled plasma optical emission spectrometry (ICP-OES) and mass spectrometry (ICP-MS) are increasingly used to carry out analyses in organic/hydro-organic matrices. The introduction of such matrices into ICP sources is particularly challenging and can be the cause of numerous drawbacks. This tutorial review, divided in two parts, explores the rich literature related to the introduction of organic/hydro-organic matrices in ICP sources. Part I provided theoretical considerations associated with the physico-chemical properties of such matrices, in an attempt to understand the induced phenomena. Part II of this tutorial review is dedicated to more practical considerations on instrumentation, instrumental and operating parameters, as well as analytical strategies for elemental quantification in such matrices.     

The growth of membrane technology

Not all journal articles come out of the same mold. This one is a hybrid. It has some of the elements of a review. But any comprehensive review of the membrane technology field written today would have to contain even more references than this one does. It is also partly an overview, giving my opinions of what, among all the work done in this field over the past two centuries or so, is most relevant: what were the seminal works that led to the present state of development of membrane technology. Further, in places this article is a bit tutorial, and for this I ask the informed reader's indelgence. Finally, it is a somewhat personalized story, as the interested reader who suffers through all of the References and Notes will discover.     

Enantioselective C-C bond synthesis catalysed by enzymes

The enantioselective synthesis of C-C bonds is often the pivotal step of a synthesis. Nature has made a variety of versatile enzymes available that catalyse this type of reaction very selectively under mild conditions. Cyanohydrins, acyloins (alpha-hydroxy ketones), alpha-hydroxy acids and aldols (beta-hydroxy ketones) are very efficiently synthesised enantioselectively with the aid of C-C bond forming enzymes, which we discuss in this tutorial review. In the case of the alpha-hydroxy acids the applications of nitrilases in a synthetic dkr even allows a disconnection that has no enantioselective chemical equivalent.     

Role of metal-oxo complexes in the cleavage of C-H bonds

The functionalization of C-H bonds has yet to achieve widespread use in synthetic chemistry in part because of the lack of synthetic reagents that function in the presence of other functional groups. These problems have been overcome in enzymes, which have metal-oxo active sites that efficiently and selectively cleave C-H bonds. How high-energy metal-oxo transient species can perform such difficult transformations with high fidelity is discussed in this tutorial review. Highlighted are the relationships between redox potentials and metal-oxo basicity on C-H bond activation, as seen in a series of bioinspired manganese-oxo complexes.     

The use of enzymes for construction of DNA-based objects and assemblies

DNA has found wide applications in DNA-based nanotechnology due to its simplicity and predictability of its secondary structure. Selecting DNA for the nanoconstruction of objects and assemblies bears the inherent potential for manipulations and control by DNA modifying enzymes. In this tutorial review, we present an overview of the enzyme-catalysed construction of DNA-based objects and assemblies. It is illustrated how a diversity of enzyme-based biochemical reactions are transferred in nanotechnological applications.     

Chemical biology--identification of small molecule modulators of cellular activity by natural product inspired synthesis

The aim of this tutorial review is to introduce the reader to the concept, synthesis and application of natural product-inspired compound collections as an important field in chemical biology. This review will discuss how potentially interesting scaffolds can be identified (structural classification of natural products), synthesized in an appropriate manner (including stereoselective transformations for solid phase-bound compounds) and tested in biological assays (cell-based screening as well as biochemical in vitro assays). These approaches will provide the opportunity to identify new and interesting compounds as well as new targets for chemical biology and medicinal chemistry research.     

A review and tutorial discussion of noise and signal-to-noise ratios in analytical spectrometry—II. Fundamental principles of signal-to-noise ratios

This part of the review links up with the tutorial discussion in Part I and gives general signal-to-noise expressions for emission and luminescence spectrometric systems. Tabular presentations are used for the expressions and for comparison of noise sources.     

Olefin metathesis in ionic liquids

This tutorial review covers the use of ionic liquids as (co)solvents for the olefin metathesis reaction. Olefin metathesis is a simple and effective synthetic tool used to create many compounds which otherwise would require complex multistep syntheses. It is expected that the application of ionic liquids (IL) as well as the development of IL-enabled catalysts and separation techniques will create a green aspect to this important methodology.     

Recent progress on polymer-based fluorescent and colorimetric chemosensors

Recently, fluorescent or colorimetric chemosensors based on polymers have attracted great attention due to several important advantages, such as their simplicity of use, signal amplification, easy fabrication into devices, and combination of different outputs, etc. This tutorial review will cover polymer-based optical chemosensors from 2007 to 2010.     

Fundamentals of green chemistry: efficiency in reaction design

In this tutorial review, the fundamental concepts underlying the principles of green and sustainable chemistry--atom and step economy and the E factor--are presented, within the general context of efficiency in organic synthesis. The importance of waste minimisation through the widespread application of catalysis in all its forms--homogeneous, heterogeneous, organocatalysis and biocatalysis--is discussed. These general principles are illustrated with simple practical examples, such as alcohol oxidation and carbonylation and the asymmetric reduction of ketones. The latter reaction is exemplified by a three enzyme process for the production of a key intermediate in the synthesis of the cholesterol lowering agent, atorvastatin. The immobilisation of enzymes as cross-linked enzyme aggregates (CLEAs) as a means of optimizing operational performance is presented. The use of immobilised enzymes in catalytic cascade processes is illustrated with a trienzymatic process for the conversion of benzaldehyde to (S)-mandelic acid using a combi-CLEA containing three enzymes. Finally, the transition from fossil-based chemicals manufacture to a more sustainable biomass-based production is discussed.     

The tandem Claisen rearrangement in the construction of building blocks for supramolecular chemistry

The tandem Claisen rearrangement is a simple but highly efficient reaction to synthesize useful building blocks for supramolecular chemistry. It provides in one step two new C-C bonds in very high yield. The scope and limits of this reaction will be discussed in this review and it will be shown, how macrocyclic compounds as well as rotaxanes or helicates can be formed by use of butenylidene bridged aromatic compounds obtained after the rearrangement reaction. Special aspects will cover the search for new receptors and sensors or for energy transfer properties. The contents of this tutorial review are within the field of preparative organic synthesis but in addition cover aspects of inorganic and supramolecular chemistry.     

From C(sp(2))-H to C(sp(3))-H: systematic studies on transition metal-catalyzed oxidative C-C formation

In this tutorial review, we will summarize our recent efforts in transition metal-catalyzed oxidative coupling via C-H functionalization of aromatic, benzylic and allylic C-H bonds. Related works from other laboratories will be cited where suitable, aiming to give the readers a flavor of this field. Special emphasis is placed on the reaction design and development.     

Vitamin B12-derivatives-enzyme cofactors and ligands of proteins and nucleic acids

B(12)-cofactors play important roles in the metabolism of microorganisms, animals and humans. Microorganisms are the only natural sources of B(12)-derivatives, and the latter are "vitamins" for other B(12)-requiring organisms. Some B(12)-dependent enzymes catalyze complex isomerisation reactions, such as methylmalonyl-CoA mutase. They need coenzyme B(12), an organometallic B(12)-derivative, to induce enzymatic radical reactions. Another group of widely relevant enzymes catalyzes the transfer of methyl groups, such as methionine synthase, which uses methylcobalamin as cofactor. This tutorial review covers structure and reactivity of B(12)-derivatives and structural aspects of their interactions with proteins and nucleotides, which are crucial for the efficient catalysis by the important B(12)-dependent enzymes, and for achieving and regulating uptake and transport of B(12)-derivatives.