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Quantitative microscopy based on single-molecule fluorescence.
Abstract Quantitative microscopy is needed to understand reactions or phenomena carried out by biological molecules such as enzymes, receptors, and membrane-localized proteins. Counting the biomolecules of interest in single organelles or cellular compartments is critical in these approaches. In this brief perspective, we focus on the development of quantitative fluorescence microscopies that measure the precise copy numbers of proteins in cellular organelles or purified samples. We introduce recent improvements in quantitative microscopies to overcome undercounting or overcounting errors in certain conditions. We...
Source: Current Opinion in Chemical Biology - June 14, 2017 Category: Biochemistry Authors: Jung SR, Fujimoto BS, Chiu DT Tags: Curr Opin Chem Biol Source Type: research
Covalent inhibitors: an opportunity for rational target selectivity.
Abstract There is a resurging interest in compounds that engage their target through covalent interactions. Cysteine's thiol is endowed with enhanced reactivity, making it the nucleophile of choice for covalent engagement with a ligand aligning an electrophilic trap with a cysteine residue in a target of interest. The paucity of cysteine in the proteome coupled to the fact that closely related proteins do not necessarily share a given cysteine residue enable a level of unprecedented rational target selectivity. The recent demonstration that a lysine's amine can also be engaged covalently with a mild electrophile e...
Source: Current Opinion in Chemical Biology - June 10, 2017 Category: Biochemistry Authors: Lagoutte R, Patouret R, Winssinger N Tags: Curr Opin Chem Biol Source Type: research
Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors.
Abstract Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include multiplexed detection using microfluidics. Synthetic biology can be used to engineer new biological biosensors with improved characteristics. Although there have been few biosensors developed for bioprocessing thus far, emerging trends can be applied in the future. A range of new platform tech...
Source: Current Opinion in Chemical Biology - June 10, 2017 Category: Biochemistry Authors: Dekker L, Polizzi KM Tags: Curr Opin Chem Biol Source Type: research
Targeted protein knockdown using small molecule degraders.
Abstract Small molecule probes of biological systems have traditionally been designed to bind to and inhibit the active sites of their protein targets. While this class of pharmacological agents has been broadened by the development of a small number of allosteric and protein-protein interaction (PPI) inhibitors, conventional drug design still excludes 'undruggable' proteins that are neither enzymes nor receptors. Recent years have seen the emergence of new classes of small molecules that can target hitherto undruggable proteins by recruiting the cellular proteostasis machinery to selectively tag them for degradat...
Source: Current Opinion in Chemical Biology - June 9, 2017 Category: Biochemistry Authors: Raina K, Crews CM Tags: Curr Opin Chem Biol Source Type: research
Visualizing glycans on single cells and tissues-Visualizing glycans on single cells and tissues.
Abstract Metabolic oligosaccharide engineering and chemoenzymatic glycan labeling have provided powerful tools to study glycans in living systems and tissue samples. In this review article, we summarize recent advances in this field with a focus on innovative approaches for glycan imaging. The presented applications demonstrate that several of the leading imaging methods, which have revolutionized quantitative cell biology, can be adapted to imaging glycans on single cells and tissues. PMID: 28578260 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 1, 2017 Category: Biochemistry Authors: Ovryn B, Li J, Hong S, Wu P Tags: Curr Opin Chem Biol Source Type: research
Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets.
Abstract As interest in protein-protein interactions and other previously-undruggable targets increases, medicinal chemists are returning to natural products for design inspiration toward molecules that transcend the paradigm of small molecule drugs. These compounds, especially peptides, often have poor ADME properties and thus require a more nuanced understanding of structure-property relationships to achieve desirable oral bioavailability. Although there have been few clinical successes in this chemical space to date, recent work has identified opportunities to introduce favorable physicochemical properties to p...
Source: Current Opinion in Chemical Biology - May 29, 2017 Category: Biochemistry Authors: Naylor MR, Bockus AT, Blanco MJ, Lokey RS Tags: Curr Opin Chem Biol Source Type: research
Blood-brain barrier peptide shuttles.
dó M Abstract Brain delivery is hampered by the presence of the blood-brain barrier (BBB), a natural defence of the brain that protects it and allows the entrance of nutrients by several mechanisms. Taking advantage of these mechanisms is an opportunity to treat brain related diseases. Among the different alternatives, BBB peptide shuttles are gaining attention to increase brain delivery of therapeutics. The most recent advances in the field are analysed here. PMID: 28558293 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - May 27, 2017 Category: Biochemistry Authors: Sánchez-Navarro M, Giralt E, Teixidó M Tags: Curr Opin Chem Biol Source Type: research
Quantitative chemical imaging with stimulated Raman scattering microscopy.
Abstract Chemical imaging plays an increasingly important role in studying heterogeneous biological systems. It combines molecular spectroscopy with high-resolution spatial information to create quantitative images of molecular distributions. Here I summarize recent progress in technical developments and biological applications of a specific chemical imaging technique-stimulated Raman scattering (SRS) microscopy. SRS microscopy allows for a wide range of molecules - both endogenous and exogenous - to be imaged at high spatial and temporal resolution in living cells, tissues, and organisms. I will focus on developm...
Source: Current Opinion in Chemical Biology - May 22, 2017 Category: Biochemistry Authors: Fu D Tags: Curr Opin Chem Biol Source Type: research
Development of photostable fluorophores for molecular imaging.
Abstract Advances in fluorescence microscopy promise to unlock details of biological systems with high spatiotemporal precision. These new techniques also place a heavy demand on the 'photon budget'-the number of photons one can extract from a sample. Improving the photostability of small molecule fluorophores using chemistry is a straightforward method for increasing the photon budget. Here, we review the (sometimes sparse) efforts to understand the mechanism of fluorophore photobleaching and recent advances to improve photostability through reducing the propensity for oxidation or through intramolecular triplet-...
Source: Current Opinion in Chemical Biology - May 22, 2017 Category: Biochemistry Authors: Zheng Q, Lavis LD Tags: Curr Opin Chem Biol Source Type: research
Fluorescent probes for imaging formaldehyde in biological systems.
Abstract Formaldehyde (FA) is a common environmental toxin but is also endogenously produced through a diverse array of essential biological processes, including mitochondrial one-carbon metabolism, metabolite oxidation, and nuclear epigenetic modifications. Its high electrophilicity enables reactivity with a wide variety of biological nucleophiles, which can be beneficial or detrimental to cellular function depending on the context. New methods that enable detection of FA in living systems can help disentangle the signal/stress dichotomy of this simplest reactive carbonyl species (RCS), and fluorescent probes for...
Source: Current Opinion in Chemical Biology - May 18, 2017 Category: Biochemistry Authors: Bruemmer KJ, Brewer TF, Chang CJ Tags: Curr Opin Chem Biol Source Type: research
Structure-diverse Phylomer libraries as a rich source of bioactive hits from phenotypic and target directed screens against intracellular proteins.
Abstract Phylomers are peptides derived from biodiverse protein fragments. Genetically encoded Phylomer libraries have been constructed, containing hundreds of billions of peptides derived from virtually all of the few thousand fold families found in the protein universe. They offer a rich source of high quality hits against diverse target sequences and have been used for three main purposes: firstly, to identify and validate targets in phenotypic screens; secondly, to block protein interactions with nanomolar potency binding affinities; thirdly as a source of more efficient cell penetrating peptides for the deliv...
Source: Current Opinion in Chemical Biology - May 18, 2017 Category: Biochemistry Authors: Watt PM, Milech N, Stone SR Tags: Curr Opin Chem Biol Source Type: research
Engineering genetically-encoded tools for optogenetic control of protein activity.
Abstract Optogenetic tools offer fast and reversible control of protein activity with subcellular spatial precision. In the past few years, remarkable progress has been made in engineering photoactivatable systems regulating the activity of cellular proteins. In this review, we discuss general strategies in designing and optimizing such optogenetic tools and highlight recent advances in the field, with specific focus on applications regulating protein catalytic activity. PMID: 28527343 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - May 17, 2017 Category: Biochemistry Authors: Liu Q, Tucker CL Tags: Curr Opin Chem Biol Source Type: research
Harnessing plant metabolic diversity.
Abstract Advances in DNA sequencing and synthesis technologies in the twenty-first century are now making it possible to build large-scale pipelines for engineering plant natural product pathways into heterologous production species using synthetic biology approaches. The ability to decode the chemical potential of plants by sequencing their transcriptomes and/or genomes and to then use this information as an instruction manual to make drugs and other high-value chemicals is opening up new routes to harness the vast chemical diversity of the Plant Kingdom. Here we describe recent progress in methods for pathway di...
Source: Current Opinion in Chemical Biology - May 17, 2017 Category: Biochemistry Authors: Owen C, Patron NJ, Huang A, Osbourn A Tags: Curr Opin Chem Biol Source Type: research
Synchrotron-based X-ray microscopy for sub-100nm resolution cell imaging.
Abstract Microscopic imaging provides a straightforward approach to deepen our understanding of cellular events. While the resolution of optical microscopes is generally limited to 200-300nm due to the diffraction limit, there has been ever growing interest in studying cells at the sub-100nm regime. By exploiting the short wavelength, long penetration depth and elemental specificity of X-rays, synchrotron-based X-ray microscopy (XRM) has demonstrated its power in exploring the structure and function of cells at the nanometer resolution. Here we summarize recent advances in using XRM for imaging ultrastructure of o...
Source: Current Opinion in Chemical Biology - May 15, 2017 Category: Biochemistry Authors: Zhu Y, Zhang J, Li A, Zhang Y, Fan C Tags: Curr Opin Chem Biol Source Type: research
Combinatorial chemistry in drug discovery.
Abstract Several combinatorial methods have been developed to create focused or diverse chemical libraries with a wide range of linear or macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. Each combinatorial approach has its own unique high-throughput screening and encoding strategy. In this article, we provide a brief overview of combinatorial chemistry in drug discovery with emphasis on recently developed new technologies for design, synthesis, screening and decoding of combinatorial library. Examples of successful applic...
Source: Current Opinion in Chemical Biology - May 8, 2017 Category: Biochemistry Authors: Liu R, Li X, Lam KS Tags: Curr Opin Chem Biol Source Type: research
Designer probiotics for the prevention and treatment of human diseases.
Abstract Various studies have shown the beneficial effects of probiotics in humans. The use of synthetic biology to engineer programmable probiotics that specifically targets cancer, infectious agents, or other metabolic diseases has gained much interest since the last decade. Developments made in synthetic probiotics as therapeutics within the last three years will be discussed in this review. PMID: 28478369 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - May 4, 2017 Category: Biochemistry Authors: Chua KJ, Kwok WC, Aggarwal N, Sun T, Chang MW Tags: Curr Opin Chem Biol Source Type: research
A three-step framework for programming pattern formation.
Abstract The spatial organisation of gene expression is essential to create structure and function in multicellular organisms during developmental processes. Such organisation occurs by the execution of algorithmic functions, leading to patterns within a given domain, such as a tissue. Engineering these processes has become increasingly important because bioengineers are seeking to develop tissues ex vivo. Moreover, although there are several theories on how pattern formation can occur in vivo, the biological relevance and biotechnological potential of each of these remains unclear. In this review, we will briefly...
Source: Current Opinion in Chemical Biology - April 29, 2017 Category: Biochemistry Authors: Scholes NS, Isalan M Tags: Curr Opin Chem Biol Source Type: research
Voltage imaging with genetically encoded indicators.
Abstract Membrane voltages are ubiquitous throughout cell biology. Voltage is most commonly associated with excitable cells such as neurons and cardiomyocytes, although many other cell types and organelles also support electrical signaling. Voltage imaging in vivo would offer unique capabilities in reporting the spatial pattern and temporal dynamics of electrical signaling at the cellular and circuit levels. Voltage is not directly visible, and so a longstanding challenge has been to develop genetically encoded fluorescent voltage indicator proteins. Recent advances have led to a profusion of new voltage indicator...
Source: Current Opinion in Chemical Biology - April 28, 2017 Category: Biochemistry Authors: Xu Y, Zou P, Cohen AE Tags: Curr Opin Chem Biol Source Type: research
Plant viruses and bacteriophages for delivery in medicine and biotechnology.
Abstract There are a wide variety of synthetic and naturally occurring nanomaterials under development for nanoscale cargo-delivery applications. Viruses play a special role in these developments, because they can be regarded as naturally occurring nanomaterials evolved to package and deliver cargos. While any nanomaterial has its advantage and disadvantages, viral nanoparticles (VNPs), in particular the ones derived from plant viruses and bacteriophages, are attractive options for cargo-delivery as they are biocompatible, biodegradable, and non-infectious to mammals. Their protein-based structures are often under...
Source: Current Opinion in Chemical Biology - April 17, 2017 Category: Biochemistry Authors: Czapar AE, Steinmetz NF Tags: Curr Opin Chem Biol Source Type: research
Peptide blockers of Kv1.3 channels in T cells as therapeutics for autoimmune disease.
We describe their structures, their binding site in the external vestibule of Kv1.3, how they have been engineered to improve Kv1.3-specificity, and their pharmacokinetic and pharmacodynamic properties. Finally, we highlight the therapeutic potential of Kv1.3 peptide inhibitors to treat autoimmune diseases without compromising protective immune responses. PMID: 28412597 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 13, 2017 Category: Biochemistry Authors: Chandy KG, Norton RS Tags: Curr Opin Chem Biol Source Type: research
Host defense antimicrobial peptides as antibiotics: design and application strategies.
Abstract This review deals with the design and application strategies of new antibiotics based on naturally occurring antimicrobial peptides (AMPs). The initial candidate can be designed based on three-dimensional structure or selected from a library of peptides from natural or laboratory sources followed by optimization via structure-activity relationship studies. There are also advanced application strategies such as induction of AMP expression from host cells by various factors (e.g., metals, amino acids, vitamin D and sunlight), the use of engineered probiotic bacteria to deliver peptides, the design of prodru...
Source: Current Opinion in Chemical Biology - April 8, 2017 Category: Biochemistry Authors: Mishra B, Reiling S, Zarena D, Wang G Tags: Curr Opin Chem Biol Source Type: research
Exploring sequence space in search of functional enzymes using microfluidic droplets.
Abstract Screening of enzyme mutants in monodisperse picoliter compartments, generated at kilohertz speed in microfluidic devices, is coming of age. After a decade of proof-of-principle experiments, workflows have emerged that combine existing microfluidic modules to assay reaction progress quantitatively and yield improved enzymes. Recent examples of the screening of libraries of randomised proteins and from metagenomic sources suggest that this approach is not only faster and cheaper, but solves problems beyond the feasibility scope of current methodologies. The establishment of new assays in this format - so fa...
Source: Current Opinion in Chemical Biology - April 5, 2017 Category: Biochemistry Authors: Mair P, Gielen F, Hollfelder F Tags: Curr Opin Chem Biol Source Type: research
Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides.
Abstract Intracellular protein-protein interactions (PPIs) are challenging targets for conventional drug modalities, because small molecules generally do not bind to their large, flat binding sites with high affinity, whereas monoclonal antibodies cannot cross the cell membrane to reach the targets. Cyclic peptides in the 700-2000 molecular-weight range have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat PPI interfaces with antibody-like affinity and specificity. Several powerful cyclic peptide library technologies were developed over the past decade to rapidly discover ...
Source: Current Opinion in Chemical Biology - April 4, 2017 Category: Biochemistry Authors: Qian Z, Dougherty PG, Pei D Tags: Curr Opin Chem Biol Source Type: research
Progress and challenges in the optimization of toxin peptides for development as pain therapeutics.
Abstract The number of new toxin peptide discoveries has been rapidly growing in the past few decades. Because of progress in proteomics, sequencing technologies, and high throughput bioassays, the search for new toxin peptides from venom collections and potency optimization has become manageable. However, to date, only six toxin peptide-derived therapeutics have been approved by the USFDA, with only one, ziconotide, for a pain indication. The challenge of venom-derived peptide therapeutic development remains in improving selectivity to the target and more importantly, in delivery of these peptides to the sites of...
Source: Current Opinion in Chemical Biology - April 1, 2017 Category: Biochemistry Authors: Netirojjanakul C, Miranda LP Tags: Curr Opin Chem Biol Source Type: research
Targeting ligand-receptor interactions for development of cancer therapeutics.
Abstract The biological importance and druggable properties of receptors and their cognate ligands have designated them as especially useful clinical targets. This significance continues to expand as new molecular insights underlying disease pathophysiology are uncovered. While both ligands and receptors have been exploited as drug targets, their differing biochemical properties require nuanced considerations for drug development, including where in the body they are located and how they are regulated on a cellular and molecular level. In this review we will discuss ligands and receptors as therapeutics targets, i...
Source: Current Opinion in Chemical Biology - March 31, 2017 Category: Biochemistry Authors: Kim JW, Cochran JR Tags: Curr Opin Chem Biol Source Type: research
Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria.
Abstract The most abundant transition metal in biological systems is iron. It is incorporated into protein cofactors and serves either catalytic, redox or regulatory purposes. Anaerobic ammonium oxidizing (anammox) bacteria rely heavily on iron-containing proteins - especially cytochromes - for their energy conservation, which occurs within a unique organelle, the anammoxosome. Both their anaerobic lifestyle and the presence of an additional cellular compartment challenge our understanding of iron processing. Here, we combine existing concepts of iron uptake, utilization and metabolism, and cellular fate with geno...
Source: Current Opinion in Chemical Biology - March 29, 2017 Category: Biochemistry Authors: Ferousi C, Lindhoud S, Baymann F, Kartal B, Jetten MS, Reimann J Tags: Curr Opin Chem Biol Source Type: research
Exploring sequence space: harnessing chemical and biological diversity towards new peptide leads.
Abstract From their early roots in natural products, peptides now represent an expanding class of novel drugs. Their modular structures make them ideal candidates for pooled library screening approaches. Key technologies for library generation and screening, such as SICLOPPS, phage display and mRNA display, give unparalleled access to tight binding peptides. Through combination with genetic code reprogramming and chemical modifications, access to more natural product-like libraries, spanning non-canonical peptide space, is readily achievable. Recent advances in these fields enable introduction of diverse non-stand...
Source: Current Opinion in Chemical Biology - March 17, 2017 Category: Biochemistry Authors: Obexer R, Walport LJ, Suga H Tags: Curr Opin Chem Biol Source Type: research
Diversity of Fe(2+) entry and oxidation in ferritins.
Abstract The essential metal iron presents two major problems for life: it is potentially highly toxic due to its redox activity, and its extremely low solubility in aqueous solution in the presence of O2 can make it hard to acquire and store safely. Ferritins are part of nature's answer to these problems, as they store iron in a safe but accessible form in all types of cells. How they achieve this has been the subject of intense research for several decades. Here, we highlight recent progress in elucidating the routes by which Fe(2+) ions access the catalytic ferroxidase centers, and the mechanisms by which Fe(2+...
Source: Current Opinion in Chemical Biology - March 14, 2017 Category: Biochemistry Authors: Bradley JM, Moore GR, Le Brun NE Tags: Curr Opin Chem Biol Source Type: research
Catalytic promiscuity and heme-dependent redox regulation of H2S synthesis.
Abstract The view of enzymes as punctilious catalysts has been shifting as examples of their promiscuous behavior increase. However, unlike a number of cases where the physiological relevance of breached substrate specificity is questionable, the very synthesis of H2S relies on substrate and reaction promiscuity, which presents the enzymes with a multitude of substrate and reaction choices. The transsulfuration pathway, a major source of H2S, is inherently substrate-ambiguous. A heme-regulated switch embedded in the first enzyme in the pathway can help avert the stochastic production of cysteine versus H2S and con...
Source: Current Opinion in Chemical Biology - March 7, 2017 Category: Biochemistry Authors: Banerjee R Tags: Curr Opin Chem Biol Source Type: research
Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era.
Abstract In the past 15 years, the cost of sequencing a genome has plummeted. Consequently, the number of sequenced bacterial genomes has exponentially increased, and methods for natural product discovery have evolved rapidly to take advantage of the wealth of genomic data. This review highlights applications of genome mining software to compare and organize large-scale data sets and methods for identifying unique biosynthetic pathways amongst the thousands of ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters. We also discuss a small number of the many RiPPs discovered in the y...
Source: Current Opinion in Chemical Biology - March 2, 2017 Category: Biochemistry Authors: Hetrick KJ, van der Donk WA Tags: Curr Opin Chem Biol Source Type: research
Redesign of water networks for efficient biocatalysis.
;n PO Abstract Herein we highlight recent findings on the importance of water networks in proteins, and their redesign and reconfiguration as a new engineering strategy to generate enzymes with modulated binding affinity and improved catalytic versatility. Traditionally, enzyme engineering and drug design have focused on tailoring direct and favorable interactions between protein surfaces and ligands/transition states to achieve stronger binding, or an accelerated manufacturing of medicines, biofuels, fine chemicals and materials. In contrast, the opportunity to relocate water molecules in solvated binding pockets...
Source: Current Opinion in Chemical Biology - March 1, 2017 Category: Biochemistry Authors: Fink MJ, Syrén PO Tags: Curr Opin Chem Biol Source Type: research
Recent advances in methyltransferase biocatalysis.
Abstract S-adenosyl-L-methionine-dependent methyltransferses are ubiquitous in nature, methylating a vast range of small molecule metabolites, as well as biopolymers. This review covers the recent advances in the development of methyltransferase enzymes for synthetic applications, focusing on the methyltransferase catalyzed transformations with S-adenosyl methionine analogs, as well as non-native substrates. We discuss how metabolic engineering approaches have been used to enhance S-adenosyl methionine production in vivo. Enzymatic approaches that enable the more efficient generation of S-adenosyl methionine analo...
Source: Current Opinion in Chemical Biology - March 1, 2017 Category: Biochemistry Authors: Bennett MR, Shepherd SA, Cronin VA, Micklefield J Tags: Curr Opin Chem Biol Source Type: research
SICLOPPS cyclic peptide libraries in drug discovery.
Abstract Cyclic peptide libraries have demonstrated significant potential when employed against challenging targets such as protein-protein interactions. While a variety of methods for library generation exist, genetically encoded libraries hold several advantages over their chemically synthesized counterparts; they are more readily accessible and allow straightforward hit deconvolution. One method for the intracellular generation of such libraries is split-intein circular ligation of peptides and proteins (SICLOPPS). Here we detail and discuss the deployment of SICLOPPS libraries for the identification of cyclic ...
Source: Current Opinion in Chemical Biology - February 28, 2017 Category: Biochemistry Authors: Tavassoli A Tags: Curr Opin Chem Biol Source Type: research
Cyclic peptide therapeutics: past, present and future.
Abstract Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that make them an attractive modality for the development of therapeutics. Over 40 cyclic peptide drugs are currently in clinical use and around one new cyclic peptide drug enters the market every year on average. The vast majority of clinically approved cyclic peptides are derived from natural products, such as antimicrobials or human peptide hormones. New powerful techniques based on rational design and in vitro evolution have enabled the de novo development of cyclic peptide ligands t...
Source: Current Opinion in Chemical Biology - February 26, 2017 Category: Biochemistry Authors: Zorzi A, Deyle K, Heinis C Tags: Curr Opin Chem Biol Source Type: research
Cyclotides as drug design scaffolds.
This article describes recent developments in this field, particularly developments over the last two years relating to the grafting of bioactive peptide sequences into the cyclic cystine knot framework of cyclotides to stabilize the sequences. Grafted cyclotides have now been developed that interact with protein or enzyme targets, both extracellular and intracellular, as well as with cell surface receptors and membranes. PMID: 28249194 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - February 26, 2017 Category: Biochemistry Authors: Craik DJ, Du J Tags: Curr Opin Chem Biol Source Type: research
Expression and functional evaluation of biopharmaceuticals made in plant chloroplasts.
Abstract After approval of the first plant-made biopharmaceutical by FDA for human use, many protein drugs are now in clinical development. Within the last decade, significant advances have been made in expression of heterologous complex/large proteins in chloroplasts of edible plants using codon optimized human or viral genes. Furthermore, advances in quantification enable determination of in-planta drug dosage. Oral delivery of plastid-made biopharmaceuticals (PMB) is affordable because it eliminates prohibitively expensive fermentation, purification processes addressing major challenges of short shelf-life afte...
Source: Current Opinion in Chemical Biology - February 21, 2017 Category: Biochemistry Authors: Zhang B, Shanmugaraj B, Daniell H Tags: Curr Opin Chem Biol Source Type: research
Computational tools for enzyme improvement: why everyone can - and should - use them.
Abstract This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists. These methods guide efficient experimental planning and all...
Source: Current Opinion in Chemical Biology - February 20, 2017 Category: Biochemistry Authors: Ebert MC, Pelletier JN Tags: Curr Opin Chem Biol Source Type: research
Enzyme-mediated ligation technologies for peptides and proteins.
Abstract With the steadily increasing complexity and quantity requirements for peptides in industry and academia, the efficient and site-selective ligation of peptides and proteins represents a highly desirable goal. Within this context, enzyme-mediated ligation technologies for peptides and proteins have attracted great interest in recent years as they represent an extremely powerful extension to the scope of chemical methodologies (e.g. native chemical ligation) in basic and applied research. Compared to chemical ligation methods, enzymatic strategies using ligases such as sortase, butelase, peptiligase or omnil...
Source: Current Opinion in Chemical Biology - February 18, 2017 Category: Biochemistry Authors: Schmidt M, Toplak A, Quaedflieg PJ, Nuijens T Tags: Curr Opin Chem Biol Source Type: research
Metal-mediated DNA assembly with ligand-based nucleosides.
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. It particularly focuses on recently developed metal-mediated base pairs with purine-derived nucleosides, gives an overview of metal-responsive systems relying on metal-mediated base pairs and summarizes various applications beyond metal-ion sensors. PMID: 28214670 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - February 16, 2017 Category: Biochemistry Authors: Mandal S, Müller J Tags: Curr Opin Chem Biol Source Type: research
Microbial nickel: cellular uptake and delivery to enzyme centers.
Abstract 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. These accessory proteins often exhibit metal selectivit...
Source: Current Opinion in Chemical Biology - February 14, 2017 Category: Biochemistry Authors: Zeer-Wanklyn CJ, Zamble DB Tags: Curr Opin Chem Biol Source Type: research
Epimetabolites: discovering metabolism beyond building and burning.
Abstract 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. Epimetabolites are discovered by untargeted metabolomics using liquid- or gas chromat...
Source: Current Opinion in Chemical Biology - February 14, 2017 Category: Biochemistry Authors: Showalter MR, Cajka T, Fiehn O Tags: Curr Opin Chem Biol Source Type: research
Vitamin B12 in the spotlight again.
Abstract 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. They func...
Source: Current Opinion in Chemical Biology - February 3, 2017 Category: Biochemistry Authors: Bridwell-Rabb J, Drennan CL Tags: Curr Opin Chem Biol Source Type: research
Synthetic metabolism: metabolic engineering meets enzyme design.
Abstract 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. The spa...
Source: Current Opinion in Chemical Biology - January 30, 2017 Category: Biochemistry Authors: Erb TJ, Jones PR, Bar-Even A Tags: Curr Opin Chem Biol Source Type: research
Selective C-H bond functionalization using repurposed or artificial metalloenzymes.
Abstract 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 arti...
Source: Current Opinion in Chemical Biology - January 27, 2017 Category: Biochemistry Authors: Upp DM, Lewis JC Tags: Curr Opin Chem Biol Source Type: research
Structural basis for the role of mammalian aldehyde oxidases in the metabolism of drugs and xenobiotics.
ml;hler S Abstract 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. Indeed, the number of therapeutic molecules under development which act as AOX...
Source: Current Opinion in Chemical Biology - January 23, 2017 Category: Biochemistry Authors: Romão MJ, Coelho C, Santos-Silva T, Foti A, Terao M, Garattini E, Leimkühler S Tags: Curr Opin Chem Biol Source Type: research
Aldolase-catalysed stereoselective synthesis of fluorinated small molecules.
Abstract 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 ...
Source: Current Opinion in Chemical Biology - January 20, 2017 Category: Biochemistry Authors: Windle CL, Berry A, Nelson A Tags: Curr Opin Chem Biol Source Type: research
How close are we to complete annotation of metabolomes?
Abstract 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. In...
Source: Current Opinion in Chemical Biology - January 20, 2017 Category: Biochemistry Authors: Viant MR, Kurland IJ, Jones MR, Dunn WB Tags: Curr Opin Chem Biol Source Type: research
Global open data management in metabolomics.
Abstract 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...
Source: Current Opinion in Chemical Biology - January 13, 2017 Category: Biochemistry Authors: Haug K, Salek RM, Steinbeck C Tags: Curr Opin Chem Biol Source Type: research
Metabolic network modeling with model organisms.
Abstract 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...
Source: Current Opinion in Chemical Biology - January 12, 2017 Category: Biochemistry Authors: Yilmaz LS, Walhout AJ Tags: Curr Opin Chem Biol Source Type: research
Deep metabolome annotation in natural products research: towards a virtuous cycle in metabolite identification.
Abstract 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 combinat...
Source: Current Opinion in Chemical Biology - January 12, 2017 Category: Biochemistry Authors: Allard PM, Genta-Jouve G, Wolfender JL Tags: Curr Opin Chem Biol Source Type: research