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Current Opinion in Chemical Biology

Soham Mandal, Jens Müller
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids...
February 16, 2017: Current Opinion in Chemical Biology
Megan R Showalter, Tomas Cajka, Oliver Fiehn
Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism...
February 14, 2017: Current Opinion in Chemical Biology
Conor J Zeer-Wanklyn, Deborah B Zamble
Nickel enzymes allow microorganisms to access chemistry that can be vital for survival and virulence. In this review we highlight recent work on several systems that import nickel ions and deliver them to the active sites of these enzymes. Small molecules, in particular l-His and derivatives, may chelate nickel ions before import at TonB-dependent outer-membrane and ABC-type inner-membrane transporters. Inside the cell, nickel ions are used by maturation factors required to produce nickel enzymes such as [NiFe]-hydrogenase, urease and lactate racemase...
February 14, 2017: Current Opinion in Chemical Biology
Jennifer Bridwell-Rabb, Catherine L Drennan
The ability of cobalamin to coordinate different upper axial ligands gives rise to a diversity of reactivity. Traditionally, adenosylcobalamin is associated with radical-based rearrangements, and methylcobalamin with methyl cation transfers. Recently, however, a new role for adenosylcobalamin has been discovered as a light sensor, and a methylcobalamin-dependent enzyme has been identified that is suggested to transfer a methyl anion. Additionally, recent studies have provided a wealth of new information about a third class of cobalamin-dependent enzymes that do not appear to use an upper ligand...
February 3, 2017: Current Opinion in Chemical Biology
Tobias J Erb, Patrik R Jones, Arren Bar-Even
Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic 'copy, paste and fine-tuning' approaches are limited to the structure of naturally existing pathways. 'Mix and match' approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products...
January 30, 2017: Current Opinion in Chemical Biology
David M Upp, Jared C Lewis
Catalytic CH bond functionalization has become an important tool for organic synthesis. Metalloenzymes offer a solution to one of the foremost challenges in this field, site-selective CH functionalization, but they are only capable of catalyzing a subset of the CH functionalization reactions known to small molecule catalysts. To overcome this limitation, metalloenzymes have been repurposed by exploiting the reactivity of their native cofactors toward substrates not found in nature. Additionally, new reactivity has been accessed by incorporating synthetic metal cofactors into protein scaffolds to form artificial metalloenzymes...
January 27, 2017: Current Opinion in Chemical Biology
Maria João Romão, Catarina Coelho, Teresa Santos-Silva, Alessandro Foti, Mineko Terao, Enrico Garattini, Silke Leimkühler
Aldehyde oxidases (AOXs) are molybdo-flavoenzymes characterized by broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into the corresponding carboxylic acids and hydroxylating various heteroaromatic rings. Mammals are characterized by a complement of species-specific AOX isoenzymes, that varies from one in humans (AOX1) to four in rodents (AOX1, AOX2, AOX3 and AOX4). The physiological function of mammalian AOX isoenzymes is unknown, although human AOX1 is an emerging enzyme in phase-I drug metabolism...
January 23, 2017: Current Opinion in Chemical Biology
Mark R Viant, Irwin J Kurland, Martin R Jones, Warwick B Dunn
The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here, we review the status of metabolome annotation and describe advances in the analytical methodologies being applied...
January 20, 2017: Current Opinion in Chemical Biology
Claire L Windle, Alan Berry, Adam Nelson
The introduction of fluorine has been widely exploited to tune the biological functions of small molecules. Indeed, around 20% of leading drugs contain at least one fluorine atom. Yet, despite profound effects of fluorination on conformation, there is only a limited toolkit of reactions that enable stereoselective synthesis of fluorinated compounds. Aldolases are useful catalysts for the stereoselective synthesis of bioactive small molecules; however, despite fluoropyruvate being a viable nucleophile for some aldolases, the potential of aldolases to control the formation of fluorine-bearing stereocentres has largely been untapped...
January 20, 2017: Current Opinion in Chemical Biology
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
Shannon E Stone, Weslee S Glenn, Graham D Hamblin, David A Tirrell
Cells alter the proteome to respond to environmental and developmental cues. Global analysis of proteomic responses is of limited value in heterogeneous environments, where there is no 'average' cell. Advances in sequencing, protein labeling, mass spectrometry, and data analysis have fueled recent progress in the investigation of specific subpopulations of cells in complex systems. Here we highlight recently developed chemical tools that enable cell-selective proteomic analysis of complex biological systems, from bacterial pathogens to whole animals...
January 12, 2017: Current Opinion in Chemical Biology
Pierre-Marie Allard, Grégory Genta-Jouve, Jean-Luc Wolfender
Natural products (NPs) research is changing and rapidly adopting cutting-edge tools, which radically transform the way to characterize extracts and small molecules. With the innovations in metabolomics, early integration of deep metabolome annotation information allows to efficiently guide the isolation of valuable NPs only and, in parallel, to generate massive metadata sets for the study of given extracts under various perspectives. This is the case for chemotaxonomy studies where common biosynthetic traits among species can be evidenced, but also for drug discovery purpose where such traits, in combination with bioactivity studies on extracts, may evidence bioactive molecules even before their isolation...
January 12, 2017: Current Opinion in Chemical Biology
L Safak Yilmaz, Albertha Jm Walhout
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases...
January 12, 2017: Current Opinion in Chemical Biology
Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein
Spatial information in the form of 3D digital content has been increasingly integrated into our daily lives. Metabolomic studies parallel this trend with spatial and time resolved information being acquired. Mass spectrometry imaging (MSI), which combines qualitative and quantitative molecular information with spatial information, plays a crucial role in mass spectrometry-based metabolomics. The lateral spatial resolution obtained by MSI continues to improve and allows mass spectrometers to be used as molecular microscopes-enabling the exploration of the cellular and subcellular metabolome...
January 10, 2017: Current Opinion in Chemical Biology
Mattia Zampieri, Karthik Sekar, Nicola Zamboni, Uwe Sauer
Large scale metabolomics studies are increasingly used to investigate genetically different individuals and time-dependent responses to environmental stimuli. New mass spectrometric approaches with at least an order of magnitude more rapid analysis of small molecules within the cell's metabolome are now paving the way towards true high-throughput metabolomics, opening new opportunities in systems biology, functional genomics, drug discovery, and personalized medicine. Here we discuss the impact and advantages of the progress made in profiling large cohorts and dynamic systems with high temporal resolution and automated sampling...
January 5, 2017: Current Opinion in Chemical Biology
Claire M Weekley, Chuan He
Metal dyshomeostasis is involved in the pathogenesis and progression of diseases including cancer and neurodegenerative diseases. Metal chelators and ionophores are well known modulators of transition metal homeostasis, and a number of these molecules are in clinical trials. Metal-binding compounds are not the only drugs capable of targeting transition metal homeostasis. This review presents recent highlights in the development of chelators and ionophores for the treatment of cancer and neurodegenerative disease...
December 29, 2016: Current Opinion in Chemical Biology
Juan Mangas-Sanchez, Scott P France, Sarah L Montgomery, Godwin A Aleku, Henry Man, Mahima Sharma, Jeremy I Ramsden, Gideon Grogan, Nicholas J Turner
Imine reductases (IREDs) have emerged as a valuable new set of biocatalysts for the asymmetric synthesis of optically active amines. The development of bioinformatics tools and searchable databases has led to the identification of a diverse range of new IRED biocatalysts that have been characterised and employed in different synthetic processes. This review describes the latest developments in the structural and mechanistic aspects of IREDs, together with synthetic applications of these enzymes, and identifies ongoing and future challenges in the field...
December 27, 2016: Current Opinion in Chemical Biology
Laura K Reed, Charles F Baer, Arthur S Edison
Model organisms are important in many areas of chemical biology. In metabolomics, model organisms can provide excellent samples for methods development as well as the foundation of comparative phylometabolomics, which will become possible as metabolomics applications expand. Comparative studies of conserved and unique metabolic pathways will help in the annotation of metabolites as well as provide important new targets of investigation in biology and biomedicine. However, most chemical biologists are not familiar with genetics, which needs to be considered when choosing a model organism...
December 22, 2016: Current Opinion in Chemical Biology
Sebastian Böcker
Untargeted metabolomics experiments usually rely on tandem mass spectrometry (MS/MS) to identify the thousands of compounds in a complex sample. Spectral libraries used for identification are incomplete, and many metabolites remain unknown. There has been a recent development to replace spectral libraries by molecular structure databases when searching the MS/MS data of the unknown compound. Several tools have been developed for this task, including CFM-ID, MetFrag, MAGMa(+), FingerID and CSI:FingerID. These methods are already helpful for everyday metabolomics; with further advances, these methods can become indispensable tools for tomorrow's metabolomics...
December 22, 2016: Current Opinion in Chemical Biology
Wilma Neumann, Anmol Gulati, Elizabeth M Nolan
A tug-of-war between the mammalian host and bacterial pathogen for nutrients, including first-row transition metals (e.g. Mn, Fe, Zn), occurs during infection. Here we present recent advances about three metal-chelating metabolites that bacterial pathogens deploy when invading the host: staphylopine, staphyloferrin B, and enterobactin. These highlights provide new insights into the mechanisms of bacterial metal acquisition and regulation, as well as the contributions of host-defense proteins during the human innate immune response...
December 16, 2016: Current Opinion in Chemical Biology
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