Current Opinion in Chemical Biology - Aktuelle Forschungsartikel
Aktuelle Forschungsartikel: Chemische Biologie
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Current Opinion in Chemical Biology - Verlag: Elsevier
Die Current Opinion Journale wurden aus der Erkenntnis heraus entwickelt, dass es immer schwieriger für Spezialisten wird, bei dem expandierenden Volumen an Informationen zu ihrem Thema auf dem Laufenden zu bleiben. Das Gebiet 'Chemischen Biologie' ist hier in thematische Abschnitte unterteilt, die regelmäßig überprüft werden und damit immer auf dem aktuellen Stand sind.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Lance C Seefeldt, Brian M Hoffman, Dennis R Dean Nitrogenase is a two-component enzyme that catalyzes the nucleotide-dependent reduction of N2 to 2NH3. This process involves three redox-active metal-containing cofactors including a [4Fe–4S] cluster, an eight-iron P cluster and a seven-iron plus molybdenum FeMo-cofactor, the site of substrate reduction. A deficit-spending model for electron transfer has recently been proposed that incorporates protein conformational gating that favors uni-directional electron transfer among the metalloclusters for the activation of the substrate-binding site. Also reviewed is a proposal that each of the metal clusters cycles through only two redox states of the metal–sulfur core as the system accumulates the multiple electrons required for substrate binding and reduction. In particular, it was suggested that as FeMo-cofactor acquires the four electrons necessary for optimal binding of N2, each successive pair of electrons is stored as an Fe–H?–Fe bridging hydride, with the FeMo-cofactor metal-ion core retaining its resting redox state. We here broaden the discussion of stable intermediates that might form when FeMo-cofactor receives an odd number of electrons.
Highlights
? The order of electron transfers between nitrogenase metal clusters is described. ? The core of each nitrogenase metal cluster cycles through a single redox couple. ? Hydrides bridging Fe ions of FeMo-cofactor ‘store’ reducing equivalents.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Gilles Gasser, Nils Metzler-Nolte Organometallic complexes have unique physico-chemical properties, which have been widely used in homogenous catalysis, for example, for the synthesis of lead compounds and drug candidates. Over the past two decades, a few scientists from all over the world have extended the use of the specific characteristics of these compounds (e.g. structural diversity, possibility of ligand exchange, redox and catalytic properties) for medicinal purposes. The results are stunning. A few organometallic compounds have already entered clinical trials and it can be anticipated that several more will follow in coming years. In this short review, we present the specific advantages that organometallic metal complexes have over purely organic and also coordination compounds. Furthermore, using specific examples, we illustrate how these particular properties can be put to good use in medicinal chemistry. The examples we present have an emphasis on, but are not restricted to, anti-cancer activity.
Highlights
? Organometallic complexes have a huge potential in medicinal chemistry. ? Organometallic compounds have specific advantages over purely organic compounds. ? The use of organometallics compounds is not limited to anti-cancer research. ? An organometallic compound could be the next anti-malarial drug on the market.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Erik T Yukl, Carrie M Wilmot Post-translational modifications of amino acids can be used to generate novel cofactors capable of chemistries inaccessible to conventional amino acid side chains. The biosynthesis of these sites often requires one or more enzyme or protein accessory factors, the functions of which are quite diverse and often difficult to isolate in cases where multiple enzymes are involved. Herein is described the current knowledge of the biosynthesis of urease and nitrile hydratase metal centers, pyrroloquinoline quinone, hypusine, and tryptophan tryptophylquinone cofactors along with the most recent work elucidating the functions of individual accessory factors in these systems. These examples showcase the breadth and diversity of this continually expanding field.
Highlights
? Maturation of metal centers with modified amino acid ligands; urease and nitrile hydratase. ? Biosynthesis of pyrroloquinoline quinone from a peptide precursor. ? Spectroscopic characterization of an enzyme required for hypusine synthesis. ? Long-range electron transfer is required for tryptophan tryptophylquinone biosynthesis.
Publication year: 2012 Source:Current Opinion in Chemical Biology Siying Ma, Nicholas Tang, Jingdong Tian The past couple of years saw exciting new developments in microchip-based gene synthesis technologies. Such technologies hold the potential for significantly increasing the throughput and decreasing the cost of gene synthesis. Together with more efficient enzymatic error correction and genome assembly methods, these new technologies are pushing the field of synthetic biology to a higher level.
Highlights
? Reviewed recent developments in DNA synthesis, gene and genome assembly technologies. ? Focused on gene synthesis technologies using microarray generated oligonucleotide pools. ? Reviewed error correction methods in gene synthesis. ? Reviewed recent applications of gene synthesis in synthetic biology.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Holger Dau, Ivelina Zaharieva, Michael Haumann Photosynthetic water oxidation chemistry at the unique manganese–calcium complex of photosystem II (PSII) is of fundamental importance and serves as a paragon in the development of efficient synthetic catalysts. A recent crystal structure of PSII shows the atoms of the water-oxidizing complex; its Mn4CaO5 core resembles inorganic manganese–calcium oxides. Merging of crystallographic and spectroscopic information reverses radiation-induced modifications at the Mn-complex in silico and facilitates discussion of the OO bond chemistry. Coordinated proton movements are promoted by a water network connecting the Mn4CaO5 core with the oxidant, a tyrosine radical and one possibly mobile chloride ion. A basic reaction-cycle model predicts an alternating proton and electron removal from the catalytic site, which facilitates energetically efficient water oxidation.
Highlights
? A stunning 1.9Å structure shows the atoms of the water-oxidizing complex. ? Spectroscopic information reverses radiation-induced modifications in-silico. ? Coordinated proton movements in water networks may promote electron transfer. ? Alternating proton and electron removal facilitates water oxidation.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Jason C Crack, Jeffrey Green, Andrew J Thomson, Nick E Le Brun Regulatory proteins that contain an iron–sulfur cluster cofactor constitute a group that is growing both in number and importance, with a range of functions that include sensing of molecular oxygen, stress response, and iron regulation. In all cases, the cluster plays a central role, as a sensory module, in controlling the activity of the regulator. In some cases, the cluster is required for the protein to attain its regulatory form, while in others the active form requires loss or modification of the cluster. In this way, nature has exploited the inherent reactivity of iron–sulfur clusters. Here, we focus on recent advances that provide new insight into the remarkable chemistries exhibited by these regulators, and how they achieve the required levels of sensitivity and specificity.
Highlights
? Evolutionary tuning of the reactivity and specificity of iron–sulfur clusters. ? The mechanism of nitrosylation of iron–sulfur clusters involved in nitric oxide sensing. ? Redox sensing by iron–sulfur clusters: the SoxR paradigm. ? Differential regulation by Rrf2 family iron–sulfur cluster regulators in different forms.
Publication year: 2012 Source:Current Opinion in Chemical Biology Benjamin Lin, Andre Levchenko Advances in synthetic biology have augmented the available toolkit of biomolecular modules, allowing engineering and manipulation of signaling in a variety of organisms, ranging in complexity from single bacteria and eukaryotic cells to multi-cellular systems. The richness of synthetic circuit outputs can be dramatically enhanced by sophisticated environmental control systems designed to precisely pattern spatial–temporally heterogeneous environmental stimuli controlling these circuits. Moreover, the performance of the synthetic modules and ‘blocks’ needed to assemble more complicated networks requires more complete characterization as a function of arbitrarily complex environmental inputs. Microfluidic technologies are poised to meet these needs through a variety of innovative designs capitalizing on the unique benefits of manipulating fluids on the micro-scales and nano-scales. This review discusses the utility of microfluidics for the study of synthetic circuits and highlights recent work in the area.
Highlights
? Microfluidic tools provide a novel means to study and control synthetic circuits. ? Microfluidic devices precisely localize cell populations and single cells. ? Microfluidic devices offer complex spatial–temporal control of synthetic circuits.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Amit S Pithadia, Mi Hee Lim Highly concentrated metals such as Cu, Zn, and Fe are found in amyloid-? (A?) plaques within the brain of Alzheimer's disease (AD). In vitro and in vivo studies have suggested that metal binding to A? could facilitate A? aggregation and generate reactive oxygen species (ROS), which could contribute to the neuropathogenesis of AD. The connection between metal–A? interaction/reactivity and AD development, however, has not been clearly revealed owing to the complexity of the disease. In this review, metal–A? interaction/reactivity and its relation to neurotoxicity are briefly discussed. Additionally, our review illustrates the recent progress of small molecules, capable of targeting metal–A? species and modulating their interaction/reactivity, which could offer a promising approach to interrogate their role in AD.
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? Generation and aggregation of amyloid-?, as well as its interaction/reactivity with metal ions in Alzheimer's disease. ? Involvement of metal ions associated with amyloid-? in the development of Alzheimer's disease. ? Current progress in the design of small molecules to target metal–amyloid-? species and modulate their interaction/reactivity.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Naoki Kato, Shunji Takahashi, Toshihiko Nogawa, Tamio Saito, Hiroyuki Osada The RIKEN Natural Products Depository (NPDepo) is a public depository of small molecules. Currently, the NPDepo chemical library contains 39,200 pure compounds, half of which are natural products and their derivatives. In order to reinforce the uniqueness of our chemical library, we have improved our strategies for the collection of microbial natural products. Firstly, a microbial metabolite fraction library coupled with an MP (microbial products) plot database provides a powerful resource for the efficient isolation of microbial metabolites. Secondly, biosynthetic studies of microbial metabolites have enabled us to not only access ingenious biosynthetic machineries, but also obtain a variety of biosynthetic intermediates. Our chemical library contributes to the discovery of molecular probes for increasing our understanding of complex biological processes and for eventually developing new drug leads.
Highlights
? NPDepo provides a chemical library that primarily focuses on natural products. ? A microbial metabolite fraction library with an MP plot database was constructed. ? The fraction library facilitates the collection of structurally unique metabolites. ? Genetically modified strains enable us to access biosynthetic intermediates. ? The microbial metabolites collected are applicable to screenings of bioactive compounds.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Michael J Smanski, Ryan M Peterson, Sheng-Xiong Huang, Ben Shen Diterpenoid biosynthesis has been extensively studied in plants and fungi, yet cloning and engineering diterpenoid pathways in these organisms remain challenging. Bacteria are emerging as prolific producers of diterpenoid natural products, and bacterial diterpene synthases are poised to make significant contributions to our understanding of terpenoid biosynthesis. Here we will first survey diterpenoid natural products of bacterial origin and briefly review their biosynthesis with emphasis on diterpene synthases (DTSs) that channel geranylgeranyl diphosphate to various diterpenoid scaffolds. We will then highlight differences of DTSs of bacterial and higher organism origins and discuss the challenges in discovering novel bacterial DTSs. We will conclude by discussing new opportunities for DTS mechanistic enzymology and applications of bacterial DTS in biocatalysis and metabolic pathway engineering.
Highlights
? Cloning and engineering diterpenoid pathways in plants and fungi remain challenging. ? Bacteria are emerging as prolific producers of diterpenoid natural products. ? Bacterial diterpene synthases are poised to make significant contributions to our understanding of terpenoid biosynthesis. ? Diterpenoid biosynthesis in bacteria provides new opportunities for pathway engineering to produce complex diterpenoid natural products.
Publication year: 2012 Source:Current Opinion in Chemical Biology Lukasz J Bugaj, David V Schaffer Recent advances in synthetic biology have created genetic tools with the potential to enhance the specificity, dynamic control, efficacy, and safety of medical treatments. Interfacing these genetic devices with human patients may thus bring about more efficient treatments or entirely new solutions to presently intractable maladies. Here we review engineered circuits with clinical potential and discuss their design, implementation, and validation.
Highlights
? Synthetic biology tools are being applied towards the clinical development of enhanced therapeutics. ? Engineered genetic circuits can create ‘smart’ drugs with sensing and actuating capabilities. ? Therapeutic devices may be delivered through viral vectors, encapsulated cells, or bacteria. ? With initial clinical trials underway, safety will be the first priority.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Ivan Rivalta, Gary W Brudvig, Victor S Batista The oxygen-evolving complex (OEC) of Photosystem II (PSII) is an oxomanganese complex that catalyzes water-splitting into O2, protons and electrons. Recent breakthroughs in X-ray crystallography have resolved the cuboidal OEC structure at 1.9Å resolution, stimulating significant interest in studies of structure/function relations. This article summarizes recent advances on studies of the OEC along with studies of synthetic oxomanganese complexes for artificial photosynthesis. Quantum mechanics/molecular mechanics hybrid methods have enabled modeling the S1 state of the OEC, including the ligation proposed by the most recent X-ray data where D170 is bridging Ca and the Mn center outside the CaMn3 core. Molecular dynamics and Monte Carlo simulations have explored the structural/functional roles of chloride, suggesting that it regulates the electrostatic interactions between D61 and K317 that might be critical for proton abstraction. Furthermore, structural studies of synthetic oxomanganese complexes, including the [H2O(terpy)MnIII(?-O)2MnIV(terpy)OH2]3+ (1, terpy=2,2?:6?,2?-terpyridine) complex, provided valuable insights on the mechanistic influence of carboxylate moieties in close contact with the Mn catalyst during oxygen evolution. Covalent attachment of 1 to TiO2 has been achieved via direct deposition and by using organic chromophoric linkers. The (III,IV) oxidation state of 1 attached to TiO2 can be advanced to (IV,IV) by visible-light photoexcitation, leading to photoinduced interfacial electron transfer. These studies are particularly relevant to the development of artificial photosynthetic devices based on inexpensive materials.
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? The dark-stable S1 state of the oxygen evolving complex (OEC) of Photosystem II has been recently modeled using quantum mechanics/molecular mechanics (QM/MM) hybrid methods that explicitly describe the surrounding biomolecular environment consistently with the X-ray structure resolved at 1.9Å resolution. ? Molecular dynamics and Monte Carlo studies based on the DFT-QM/MM model of the OEC have shown that chloride regulates the formation of a salt-bridge of polar amino acids next to the OEC that are thought to be involved in proton abstraction. ? DFT studies have shown that carboxylate groups can function as redox and acid/base cofactors during oxidation state transitions of oxomanganese complexes. ? DFT QM/MM modeling and experimental studies of Mn catalysts covalently bound to TiO2 semiconductors have characterized the surface attachment mode.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Tsung-Lin Li, Yu-Chen Liu, Syue-Yi Lyu Glycopeptide antibiotics are clinically important medicines to treat serious Gram-positive bacterial infections. The emergence of glycopeptide resistance among pathogens has motivated considerable interest in expanding structural diversity of glycopeptide to counteract resistance. The complex structure of glycopeptide poses substantial barriers to conventional chemical methods for structural modifications. By contrast, biochemical approaches have attracted great attention because ample biosynthetic information and sophisticated toolboxes have been made available to change reaction specificity through protein engineering, domain swapping, pathway engineering, addition of substrate analogs, and mutagenesis.
Highlights
? Glycopeptide antibiotics are classified into five subtypes. ? Sulfation modification of glycopeptide has been achieved using sulfotransferases. ? Naturally occurring glycopeptide was modified via aglycone and sugar exchanges. ? Glycopeptide analogs were amidated and aminated on a given sugar moiety.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Alison Parkin, Frank Sargent The bacterial [NiFe]-hydrogenases have been classified as either ‘standard’ or ‘O2-tolerant’ based on their ability to function in the presence of O2. Typically, these enzymes contain four redox-active metal centers: a Ni–Fe–CO–2CN? active site and three electron-transferring Fe–S clusters. Recent research suggests that, rather than differences at the catalytic active site, it is a novel Fe–S cluster electron transfer (ET) relay that controls how [NiFe]-hydrogenases recover from O2 attack. In light of recent structural data and mutagenic studies this article reviews the molecular mechanism of O2-tolerance in [NiFe]-hydrogenases and discusses the biosynthesis of the unique Fe–S relay.
Highlights
? A novel Fe–S cluster controls how [NiFe]-hydrogenases recover from O2 attack. ? Molecular mechanism of O2-tolerance. ? Biosynthesis of the unique Fe–S relay.
Publication year: 2012 Source:Current Opinion in Chemical Biology John S Chuang Without cell-to-cell communication, the organization and regulation of specialized cell types that underpin the development and physiology of multicellular organisms would be impossible. In nature, unicellular microbes have also been shown to display multicellular-like traits, such as intercellular communication, division of labor, and cooperative coordination of cellular activities. Likewise, the incorporation of artificial cell-to-cell communication into genetic circuit designs is enabling synthetic biologists to move from programming single cells towards the engineering of population-level behaviors and functions, such as diversification, spatial organization, synchronization, and coordinated information processing. The disciplined engineering goal of routinely building complex genetic circuits from well-characterized modules still poses challenges, owing to reusability and input–output matching problems resulting from information transfer being mediated through diffusible molecules. Optogenetic interfaces between circuits are considered as a possible solution.
Highlights
? Synthetic microbial populations can be programmed to exhibit multicellular traits. ? Engineered populations can diversify, spatially organize, or synchronize. ? Microbial consortia can cooperatively assemble structures or process information. ? Reusability and input–output matching problems hinder routine circuit connections. ? Optical circuit interfaces may open new possibilities for programming populations.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Vikram Saini, Aisha Farhana, Joel N Glasgow, Adrie JC Steyn All pathogenic and nonpathogenic microbes are continuously exposed to environmental or endogenous reactive oxygen and nitrogen species, which can critically effect survival and disease. Iron–sulfur [Fe–S] cluster containing prosthetic groups provide the microbial cell with a unique capacity to sense and transcriptionally respond to diatomic gases (e.g. NO and O2) and redox-cycling agents. Recent advances in our understanding of the mechanisms for how the FNR and SoxR [Fe–S] cluster proteins respond to NO and O2 have provided new insights into the biochemical mechanism of action of the Mycobacterium tuberculosis (Mtb) family of WhiB [Fe–S] cluster proteins. These insights have provided the basis for establishing a unifying paradigm for the Mtb WhiB family of proteins. Mtb is the etiological agent for tuberculosis (TB), a disease that affects nearly one-third of the world's population.
Highlights
? The repertoire of Fe–S cluster harboring proteins inmycobacterial species was examined. ? Mtb contains around 50 Fe–S cluster proteins, which is about half of thatof E. coli. ? Notably, the number of 4Fe–4S clusters motifs in Mtb correlates with that of anaerobic microbes. ? The role of WhiB proteins in mycobacterial physiology, virulence and disease was discussed.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Nan Li, Herman S Overkleeft, Bogdan I Florea Activity-based protein profiling (ABPP) is one of the main driving forces in chemical biology and one of the most visible areas where organic chemistry contributes to chemical biology research. In recent years, ABPP research has gradually made the transfer from the relatively easy target enzymes (for instance serine hydrolases, cysteine and threonine proteases) toward targeting enzymes that are intrinsically more difficult to address. These include less abundant enzymes, enzymes that do not employ a nucleophilic amino acid residue in their active site and enzymes more particular with respect to their substrate. At the same time, ABPP has started to make a tangible impact on clinical research.
Highlights
? Activity based probes covalently bind to enzymes, labeling their activity with a reporter tag. ? Activity-based protein profiling helps in unraveling biological phenomena. ? Recently ABPP has evolved from methodology development to a mature discipline in chemical biology.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Elizabeth S Millett, Igor Efimov, Jaswir Basran, Sandeep Handa, Christopher G Mowat, Emma Lloyd Raven Heme iron is often used in biology for activation of oxygen. The mechanisms of oxygen activation by heme-containing monooxygenases (the cytochrome P450s) are well known, and involve formation of a Compound I species, but information on the heme-containing dioxygenase enzymes involved in tryptophan oxidation lags far behind. In this review, we gather together information emerging recently from structural, mechanistic, spectroscopic, and computational approaches on the heme dioxygenase enzymes involved in tryptophan oxidation. We explore the subtleties that differentiate various heme enzymes from each other, and use this to piece together a developing picture for oxygen activation in this particular class of heme-containing dioxygenases.
Highlights
? This review looks at the heme-containing enzymes involved in tryptophan oxidation. ? Indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase are the main enzymes considered. ? Comparisons are made with other heme enzymes that use oxygen to activate substrates.
Publication year: 2012 Source:Current Opinion in Chemical Biology Peng Wang, Xue Gao, Yi Tang Redox enzymes such as FAD-dependent and cytochrome P450 oxygenases play indispensible roles in generating structural complexity during natural product biosynthesis. In the pre-assembly steps, redox enzymes can convert garden variety primary metabolites into unique starter and extender building blocks. In the post-assembly tailoring steps, redox cascades can transform nascent scaffolds into structurally complex final products. In this review, we will discuss several recently characterized redox enzymes in the biosynthesis of polyketides and nonribosomal peptides.
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? Redox enzymes play important roles in pre-assembly and post-assembly modifications. ? Both PKS and NRPS pathways use redox enzymes to introduce structural complexity. ? Recent discoveries of novel redox enzymes are discussed.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Hongyan Li, Hongzhe Sun Bismuth has been used in medicine for over two centuries for the treatment of various diseases, in particular for gastrointestinal disorders, owing to its antimicrobial activity. Recent structural characterization of bismuth drugs provides an insight into assembly and pharmacokinetic pathway of the drugs. Mining potential protein targets inside the pathogen via metallomic/metalloproteomic approach and further characterization on the interactions of bismuth drugs with these targets laid foundation in understanding the mechanism of action of bismuth drugs. Such studies would be beneficial in rational design of new potential drugs.
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? Bismuth anti-ulcer drugs exhibit polymeric structures. ? Bismuth complexes show potential other activities. ? Metallomic/metalloproteomic approach has been successfully used to identify bismuth binding proteins (targets). ? The metallodrug binds key proteins in the pathogen.
Publication year: 2012 Source:Current Opinion in Chemical Biology Laura Gardner, Alexander Deiters Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.
Highlights
? Photochemical control of gene function. ? Photochemical control of cell signaling. ? Caged oligonucleotides and caged proteins. ? Light-responsive protein domains.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Jian-Xiang Liu, Guang-Biao Zhou, Sai-Juan Chen, Zhu Chen Arsenic, the 20th most abundant element in the earth crust, is one of the oldest drugs in the world. It was used in the 18th century in treating hematopoietic malignancies, discarded in 1950s in favor of chemotherapeutic agents (busulphan and others), and was revived in the 1970s due to its dramatic efficacy on acute promyelocytic leukemia (APL) driven by the t(15;17) translocation-generated PML–RAR? fusion. Arsenic represents the most potent single agent for APL, and achieves a five-year overall survival of 90% in APL patients when combined with all-trans retinoic acid (ATRA) and chemotherapy (daunorubicin and cytarabine), turning this disease from highly fatal to highly curable. Arsenic triggers sumoylation/ubiquitination and proteasomal degradation of PML–RAR? via directly binding to the C3HC4 zinc finger motif in the RBCC domain of the PML moiety and induction of its homodimerization/multimerization and interaction with the SUMO E2 conjugase Ubc9. Because of its multiplicity of targets and complex mechanisms of action, arsenic is widely tested in combination with other agents in a variety of malignancies. Other arsenic containing recipes including oral formulations and organic arsenicals are being developed and tested, and progress in these areas will definitely expand the use of arsenicals in other malignant diseases.
Highlights
? Arsenic has been shown to be the most potent single agent against APL. ? Arsenic binds PML–RAR? and induces its sumoylation/ubiquitination and degradation. ? Arsenic/ATRA/chemotherapy regimen achieves a 5-year overall survival of >90% in APL. ? Arsenic may bring new therapeutic benefits to other hematologic malignancies.
Publication year: 2012 Source:Current Opinion in Chemical Biology Hang Xing, Ngo Yin Wong, Yu Xiang, Yi Lu
Highlights
? DNA aptamer–nanomaterials combine unique optical or magnetic properties of nanomaterials with high selectivity of aptamers. ? Together they have enabled novel analytical techniques that advance our understanding of health and treatment of diseases. ? Recent work on using DNA aptamer–nanomaterials for analysis of intracellular components and metabolites are reviewed. ? Their recent applications in targeting and imaging of cancer cells and in cell-specific drug delivery are also highlighted.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Fong T Wong, Chaitan Khosla Since their discovery, polyketide synthases have been attractive targets of biosynthetic engineering to make ‘unnatural’ natural products. Although combinatorial biosynthesis has made encouraging advances over the past two decades, the field remains in its infancy. In this enzyme-centric perspective, we discuss the scientific and technological challenges that could accelerate the adoption of combinatorial biosynthesis as a method of choice for the preparation of encoded libraries of bioactive small molecules. Borrowing a page from the protein structure prediction community, we propose a periodic challenge program to vet the most promising methods in the field, and to foster the collective development of useful tools and algorithms.
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? New PKS gene clusters are being identified at an explosive rate. ? Understanding of PKS chemistry has improved, but its implications remain untested. ? DNA assembly of hybrid PKSs is easier than before, but heterologous expression and product analysis remain challenging. ? A CASP-like competition could propel combinatorial biosynthesis into mainstream engineering.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Hala A Iqbal, Zhiyang Feng, Sean F Brady The vast majority of bacteria present in environmental samples have never been cultured and therefore have not been exploited for the ability to produce useful biocatalysts or collections of biocatalysts generating interesting small molecules. Metagenomic libraries constructed using DNA extracted directly from natural bacterial communities offer access to the genetic information present in the genomes of these as yet uncultured bacteria. This review highlights recent efforts to recover both discrete enzymes and small molecules from metagenomic libraries.
Highlights
? The majority of environmental bacteria remain uncultured. ? Metagenomics provides access to the genomes of uncultured bacteria. ? Biocatalysts have been discovered using functional and sequence based screening. ? Collections of biocatalysts that produce small molecules have also been discovered.
Publication year: 2012 Source:Current Opinion in Chemical Biology Véronique Lecault, Adam K White, Anupam Singhal, Carl L Hansen Methods for single-cell analysis are critical to revealing cell-to-cell variability in biological systems, especially in cases where relevant minority cell populations can be obscured by population-averaged measurements. However, to date single cell studies have been limited by the cost and throughput required to examine large numbers of cells and the difficulties associated with analyzing small amounts of starting material. Microfluidic approaches are well suited to resolving these issues by providing increased senstitivity, economy of scale, and automation. After many years of development microfluidic systems are now finding traction in a variety of single-cell analytics including gene expression measurements, protein analysis, signaling response, and growth dynamics. With newly developed tools now being applied in fields ranging from human haplotyping and drug discovery to stem cell and cancer research, the long-heralded promise of microfluidic single cell analysis is now finally being realized.
Highlights
? Microfluidics provides cost-effective, high-throughput single-cell analysis. ? Small volumes increase the concentration of template DNA, RNA, or secreted proteins. ? Microfluidic RT-qPCR arrays perform multiple gene measurements in individual cells. ? Automated microfluidic cell culture allows single cell tracking and dynamic stimulation. ? Applications in protein or signaling studies, and personal and environmental genomics.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Hak Joong Kim, Mark W Ruszczycky, Hung-wen Liu Only a very few examples of enzymes known to catalyze pericyclic reactions have been reported, and presently no enzyme has been demonstrated unequivocally to catalyze a Diels-Alder reaction. Nevertheless, research into secondary metabolism has led to the discovery of numerous natural products exhibiting the structural hallmarks of [4+2] cycloadditions, prompting efforts to characterize the responsible enzymatic processes. These efforts have resulted in a growing collection of enzymes believed to catalyze pericyclic [4+2] cycloaddition reactions; however, in each case the complexity of the substrates and catalytic properties of these enzymes poses significant challenges in substantiating these hypotheses. Herein we consider the principles motivating these efforts and the enzymological systems currently under investigation.
Highlights
? No enzyme has presently been identified unequivocally as a bona fide Diels-Alderase. ? Structural features of many natural products imply the existence of such an enzyme. ? Interest in these enzymes stems from uncertainty in how catalysis might be achieved. ? Several enzymes are currently under investigation as putative Diels-Alderases. ? Complexity of the substrates and reactions involved has made their study challenging.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Madan K Kharel, Jürgen Rohr The exact sequence of events in biosyntheses of natural products is essential not only to understand and learn from nature's strategies and tricks to assemble complex natural products, but also for yield optimization of desired natural products, and for pathway engineering and muta-synthetic preparation of analogues of bioactive natural products. Biosyntheses of natural products were classically studied applying in vivo experiments, usually by combining incorporation experiments with stable-isotope labeled precursors with cross-feeding experiments of putative intermediates. Later genetic studies were dominant, which consist of gene cluster determination and analysis of gene inactivation experiments. From such studies various biosynthetic pathways were proposed, to a large extent just through in silico analyses of the biosynthetic gene clusters after DNA sequencing. Investigations of the complex biosyntheses of the angucycline group anticancer drugs landomycin, jadomycin and gilvocarcin revealed that in vivo and in silico studies were insufficient to delineate the true biosynthetic sequence of events. Neither was it possible to unambiguously assign enzyme activities, especially where multiple functional enzymes were involved. However, many of the intriguing ambiguities could be solved after in vitro reconstitution of major segments of these pathways, and subsequent systematic variations of the used enzyme mixtures. This method has been recently termed ‘combinatorial biosynthetic enzymology’.
Highlights
? The exact sequence of biosynthetic events is essential for the preparation of bioactive natural product analogues. ? Biosynthetic investigation of landomycin and gilvocarcin using classical methods led to many ambiguities. ? The combinatorial biosynthetic enzymology approach turned out to be the superior way to delineate the complex post-polyketide tailoring steps of landomycin, gilvocarcin and jadomycin biosyntheses. ? Previously impossible unambiguous assignments could be made for the function of many of the involved enzymes. ? Many of the earlier drawn hypotheses and conclusions were revised.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Kento Koketsu, Atsushi Minami, Kenji Watanabe, Hiroki Oguri, Hideaki Oikawa Nonribosomal peptide synthetase (NRPS) is a programmable modular machinery that produces a number of biologically active small-molecule peptides. Saframycin A is a potent antitumor antibiotic with a unique pentacyclic tetrahydroisoquinoline scaffold. We found that the nonribosomal peptide synthetase SfmC catalyzes a seven-step transformation of readily synthesized dipeptidyl substrates with long acyl chains into a complex saframycin scaffold. Based on a series of enzymatic reactions, we proposed a detailed mechanism involving the reduction of various peptidyl thioesters by a single R domain followed by iterative C domain-mediated Pictet-Spengler reactions. This shows that NRPSs possess a remarkable capability to acquire novel function for diversifying structures of peptide natural products.
Highlights
? Remarkable multiple-catalysis of NRPS: construction of complex saframycin scaffold. ? Novel functions of nonribosomal peptide synthetase found in saframycin biosynthesis. ? Pictet-Spenglerase involved in tetrahydroisoquinoline antibiotic biosynthesis.
Publication year: 2012 Source:Current Opinion in Chemical Biology Felix Kurth, Klaus Eyer, Alfredo Franco-Obregón, Petra S Dittrich Fueled by technological advances in micromanipulation methodologies, the field of mechanobiology has boomed in the last decade. Increasing needs for clinical solutions to better maintain our major mechanosensitive tissues (muscle, bone, and cartilage) with increasing age and new insights into cellular adaptations to mechanical stresses beckon for novel approaches to meet the needs of the future. In particular, the emergence of microfluidics has inspired new interdisciplinary strategies to decipher cellular mechanotransduction on the biochemical as well as macromolecular level. Cellular actuation by locally varying fluid shear can serve to accurately alter membrane surface tension as well as produce direct compressive and strain forces onto cells. Moreover, incorporating microelectronic technologies into microfluidic platforms has led to further advances in actuation and readout possibilities. In this review, we discuss the application of microfluidics to mechanobiological research with particular focus on microfluidic platforms that are able to simultaneously monitor cellular adaptation to mechanical forces and interpret biochemical mechanotransduction.
Highlights
? Microfluidic methods facilitate investigations of mechanotransduction processes. ? Methods to apply shear stress, mechanical loads and gravity are discussed. ? Various mechanical forces can simultaneously be applied to cells or tissues. ? Biomechanical forces exerted by cells can be determined by means of microtechnology.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Heather L Condurso, Steven D Bruner Nonribosomal peptide and polyketide natural products are structurally diverse small molecules synthesized on complex enzyme assemblies. The ability to rationally engineer secondary metabolic pathways is a promising approach to novel therapeutics. Atomic resolution structures of biosynthetic enzymes provide information on active site architecture and macromolecular assembly that can aid in the engineering of new compounds. This review surveys recent applications toward biosynthetic engineering of natural products guided by structural biology.
Highlights
? Using structure to guide natural product bioengineering is an emerging strategy. ? Recent reports related nonribsomal peptide and polyketide pathways are reviewed. ? Studies have provided significant approaches to generating novel small molecules.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Seok Joon Kwon, Mauricio Mora-Pale, Moo-Yeal Lee, Jonathan S Dordick The enormous pool of chemical diversity found in nature serves as an excellent inventory for accessing biologically active compounds. This chemical inventory, primarily found in microorganisms and plants, is generated by a broad range of enzymatic pathways under precise genetic and protein-level control. In vitro pathway reconstruction can be used to characterize individual pathway enzymes, identify pathway intermediates, and gain an increased understanding of how pathways can be manipulated to generate natural product analogs. Moreover, through in vitro approaches, it is possible to achieve a diversification that is not restricted by toxicity, limited availability of intracellular precursors, or preconceived (by nature) regulatory controls. Additionally, combinatorial biosynthesis and high-throughput techniques can be used to generate both known natural products and analogs that would not likely be generated naturally. This current opinion review will focus on recent advances made in performing in vitro pathway-driven natural product diversification and opportunities for exploiting this approach for elucidating and entering this new chemical biology space.
Highlights
? Natural product pathways can be performed in vitro to generate new complex chemical and biological diversity. ? Core scaffold generating enzymes followed by tailoring enzymes can be exploited to yield novel bioactive compounds. ? High-throughput methodologies will play an increasingly important role in yielding unique chemical and biological diversity.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Ikuro Abe The structurally and mechanistically simple type III polyketide synthases (PKSs) catalyze iterative condensations of CoA thioesters to produce a variety of polyketide scaffolds with remarkably diverse structures and biological activities. By exploiting the enzymes, we combined precursor-directed biosynthesis with nitrogen-containing substrates and structure-based enzyme engineering and generated unnatural, novel polyketide–alkaloid scaffolds with promising biological activities. The nucleophilic nitrogen atom and the engineered enzymes thus facilitated the formation of additional CC and CN bonds during the enzymatic transformations. The methodology will contribute to the further production of chemically and structurally divergent, unnatural natural products, as well as the rational design of novel biocatalysts with unprecedented catalytic functions.
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Graphical abstractHighlights
? By exploiting type III polyketide synthases, we generated unnatural novel polyketide–alkaloids. ? We used a combination of the precursor-directed biosynthesis and structure-based mutagenesis. ? The basic nitrogen atom facilitated the formation of additional CC and CN bonds during the enzyme reactions. ? The methodology will contribute to the further production of unnatural natural products. ? The methodology will contribute to the further production of novel biocatalysts.
Publication year: 2012 Source:Current Opinion in Chemical Biology Haesik Yang Signal amplification in conventional enzyme-based biosensors is not high enough to achieve the ultrasensitive detection of biomolecules. In recent years, signal amplification has been improved by combining enzymatic reactions with redox cycling or employing multienzyme labels per detection probe. Electrochemical–chemical redox cycling and electrochemical–chemical–chemical redox cycling allow ultrasensitive detection simply by including one or two more chemicals in a solution without the use of an additional enzyme and/or electrode. Multiple horseradish peroxidase labels on magnetic bead carriers provide high signal enhancement along with a multiplex detection possibility. In both cases, the detection procedures are the same as those in conventional enzyme-based electrochemical sensors.
Highlights
? Signal amplification for the ultrasensitive electrochemical detection of biomolecules. ? Combining enzymatic reactions with redox cycling. ? Use of multienzyme labels per detection probe. ? The same detection procedures as those in conventional biosensors.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Christopher J Hipolito, Hiroaki Suga Bioactive natural product peptides have diverse architectures such as non-standard sidechains and a macrocyclic backbone bearing modifications. In vitro translation of peptides bearing these features would provide the research community with a diverse collection of natural product peptide-like molecules with a potential for drug development. The ordinary in vitro translation system, however, is not amenable to the incorporation of non-proteinogenic amino acids or genetic encoding of macrocyclic backbones. To circumvent this problem, flexible tRNA-acylation ribozymes (flexizymes) were combined with a custom-made reconstituted translation system to produce the flexible in vitro translation (FIT) system. The FIT system was integrated with mRNA display to devise an in vitro selection technique, referred to as the random non-standard peptide integrated discovery (RaPID) system. It has recently yielded an N-methylated macrocyclic peptide having high affinity (Kd=0.60nM) for its target protein, E6AP.
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Graphical abstractHighlights
? Flexizymes are used to produce tRNA charged with non-standard amino acids. ? Flexizymes were integrated with genetic code reprogramming to create the FIT system. ? The FIT system was integrated with mRNA display to create the RaPID system. ? E6AP-binding non-standard cyclic peptides were selected from a random library. ? Selected peptides possess a d-amino acid and an N-methylated cyclic backbone.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Daniel Kolarich, Bernd Lepenies, Peter H Seeberger Glycomics and glycoproteomics have become indispensible tools in the study of glycoconjugates. Mass spectrometry based methods are standardly used to study the proteome and/or glycome and these approaches are capable of providing both, qualitative and quantitative information using top down techniques. The human immune system marks a particular area of interest for glycomics and glycoproteomics research since a large number of key proteins in innate and adaptive immunity are glycoproteins. In numerous examples, the crucial influence of glycosylation on critical steps such as receptor interaction and binding has been demonstrated. In this review, we focus on different glycomics and glycoproteomics approaches and their application for studying protein glycosylation in the immune system.
Highlights
? Glycomics by PGC LC ESI MS enables isobaric glycan separation. ? Modifications in the N-glycans can completely reverse IgG function. ? Glycoproteomics investigates glycan structures in a site-specific manner. ? Glycomics and glycoproteomics are key technologies for probing glycoprotein function. ? Glycan structures on immune cells interact with lectins (C-type lectins, galectins, siglecs, among others).
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 AF Maarten Altelaar, Albert JR Heck Here we review recent developments and trends in sample preparation, pre-fractionation, chromatography and mass spectrometry contributing towards the ultra-sensitive global analysis of proteins. Highly sensitive MS-based proteomics is not only beneficiary for the proteome analysis of single cells, an aim which is getting into reach, but also clearly relevant for the analysis of (a) subcellular organelles, (b) specific low-abundant cell-types such as adult stem cells, and (c) smaller but more homogeneous cell populations sorted or dissected from (diseased) tissue.
Highlights
? Proteomics provides a tool to understand molecular regulatory mechanisms. ? Several biological questions require improved dynamic range and sensitivity. ? Better sample handling and LC–MS performance enables small sample volume analysis. ? Proteomics of about a 1000 cells is becoming feasible, permitting FACS LC–MS. ? Encouraging single cell results have been obtained with chips and mass cytometry.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 H Alex Brown Lipidomics is a branch of the field of metabolomics. Although only about a decade since its inception, lipidomics has already had a major influence on the way in which questions about lipid metabolism and signaling are posed. The field is intertwined in the culture and rich history of mass spectrometry. Early work emphasized analytical issues such as limits of detection and numbers of molecular species quantitated in single injections. Increased sophistication in applications of lipidomic analysis and emerging technologies, such as imaging mass spectrometry, are facilitating the study of lipid metabolism and signaling species in cellular functions and human diseases. In the coming years we anticipate a richer understanding of how specific lipid species mediate complex biological processes and interconnections between cellular pathways that were thought to be disparate.
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Graphical abstractHighlights
? Lipidomics has developed well established methodologies and updated nomenclature. ? Several major challenges lie ahead for the field of lipidomics. ? Lipidomics identifies the roles of lipid species in complex biological processes.
Publication year: 2012 Source:Current Opinion in Chemical Biology, Volume 16, Issues 1–2 Yu M Foong, Jiaqi Fu, Shao Q Yao, Mahesh Uttamchandani Microarrays offer a compact solution for massively parallel screening. In recent years, microarrays have branched away from the exclusive pursuit of small molecule ‘hits’ in target centric screens, towards the sophisticated dissection of disease biology and comparative profiling of cellular states. This has led to innovative and instructive ways in which the platform may be deployed, providing new-found methods with which to harness the throughput achievable. Library design and diversity continues to drive success with peptide and small molecule microarrays. Newer synthesis and immobilization strategies extend the already wide repertoire of fabrication methods available. Herein we describe the latest advances in the small molecule and peptide microarray arena, which herald even more exciting breakthroughs in the coming decade.
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Graphical abstractHighlights
? Microarrays are rapid screening tools leveraging on miniaturization and automation. ? A wide range of tags and surfaces enable screening many small molecule classes. ? On-chip kinetics facilitates quantitative assessments of interactions en masse. ? SMMs are well established in ligand discovery and enzyme profiling. ? Newer applications include immunological screens and biomarker discovery.
Publication year: 2011 Source:Current Opinion in Chemical Biology, Volume 15, Issue 6 Laura M Wysocki, Luke D Lavis Small molecule fluorophores are essential tools for chemical biology. A benefit of synthetic dyes is the ability to employ chemical approaches to control the properties and direct the position of the fluorophore. Applying modern synthetic organic chemistry strategies enables efficient tailoring of the chemical structure to obtain probes for specific biological experiments. Chemistry can also be used to activate fluorophores; new fluorogenic enzyme substrates and photoactivatable compounds with improved properties have been prepared that facilitate advanced imaging experiments with low background fluorescence. Finally, chemical reactions in live cells can be used to direct the spatial distribution of the fluorophore, allowing labeling of defined cellular regions with synthetic dyes.
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Graphical abstractHighlights
? Modern synthetic chemistry techniques enable the efficient construction of fluorophores. ? Controlling dye properties with enzymes or light facilitates advanced imaging experiments. ? Specific fluorophore labeling is achieved through orthogonal chemical reactions inside cells.
Publication year: 2011 Source:Current Opinion in Chemical Biology, Volume 15, Issue 6 Jun-Seok Lee, Marc Vendrell, Young-Tae Chang The development of optical probes is receiving considerable attention due to their rising adaptation in diagnostics and medical imaging. Diversity-oriented approaches make use of combinatorial chemistry and high-throughput screenings to enrich the spectral and structural variety of these probes and effectively identify those with specific properties (e.g. molecular affinity, cellular selectivity, high photostability, and sensitivity). Herein we review recent examples in which diversity-driven strategies have assisted the discovery of new molecular imaging probes.
Highlights
? Diversity generating methods differ depending on the material of imaging probe. ? Unbiased screening of fluorophore and binding enzyme revealed novel imaging tags. ? High-throughput screening of diversity-oriented library disclose novel imaging probes. ? Careful design of screening platform is crucial step in diversity-oriented approach. ? We reviewed in vitro spectrum-based, fluorescent image-based, and FACS-based screenings.
Posted on 27 May 2012 | 1:09 am
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