A Chemoenzymatic Strategy Toward Understanding O-Glcnac Glycosylation in the Brain
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Natural Thiopeptides As a Privileged Scaffold for Drug Discovery and Therapeutic Development
– MEDICINAL Medicinal Chemistry Research (2019) 28:1063 1098 CHEMISTRY https://doi.org/10.1007/s00044-019-02361-1 RESEARCH REVIEW ARTICLE Natural thiopeptides as a privileged scaffold for drug discovery and therapeutic development 1 1 1 1 1 Xiaoqi Shen ● Muhammad Mustafa ● Yanyang Chen ● Yingying Cao ● Jiangtao Gao Received: 6 November 2018 / Accepted: 16 May 2019 / Published online: 29 May 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Since the start of the 21st century, antibiotic drug discovery and development from natural products has experienced a certain renaissance. Currently, basic scientific research in chemistry and biology of natural products has finally borne fruit for natural product-derived antibiotics drug discovery. A batch of new antibiotic scaffolds were approved for commercial use, including oxazolidinones (linezolid, 2000), lipopeptides (daptomycin, 2003), and mutilins (retapamulin, 2007). Here, we reviewed the thiazolyl peptides (thiopeptides), an ever-expanding family of antibiotics produced by Gram-positive bacteria that have attracted the interest of many research groups thanks to their novel chemical structures and outstanding biological profiles. All members of this family of natural products share their central azole substituted nitrogen-containing six-membered ring and are fi 1234567890();,: 1234567890();,: classi ed into different series. Most of the thiopeptides show nanomolar potencies for a variety of Gram-positive bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and penicillin-resistant Streptococcus pneumonia (PRSP). They also show other interesting properties such as antiplasmodial and anticancer activities. The chemistry and biology of thiopeptides has gathered the attention of many research groups, who have carried out many efforts towards the study of their structure, biological function, and biosynthetic origin. -
Cyanobacterial Peptide Toxins
CYANOBACTERIAL PEPTIDE TOXINS CYANOBACTERIAL PEPTIDE TOXINS 1. Exposure data 1.1 Introduction Cyanobacteria, also known as blue-green algae, are widely distributed in fresh, brackish and marine environments, in soil and on moist surfaces. They are an ancient group of prokaryotic organisms that are found all over the world in environments as diverse as Antarctic soils and volcanic hot springs, often where no other vegetation can exist (Knoll, 2008). Cyanobacteria are considered to be the organisms responsible for the early accumulation of oxygen in the earth’s atmosphere (Knoll, 2008). The name ‘blue- green’ algae derives from the fact that these organisms contain a specific pigment, phycocyanin, which gives many species a slightly blue-green appearance. Cyanobacterial metabolites can be lethally toxic to wildlife, domestic livestock and even humans. Cyanotoxins fall into three broad groups of chemical structure: cyclic peptides, alkaloids and lipopolysaccharides. Table 1.1 gives an overview of the specific toxic substances within these broad groups that are produced by different genera of cyanobacteria together, with their primary target organs in mammals. However, not all cyanobacterial blooms are toxic and neither are all strains within one species. Toxic and non-toxic strains show no predictable difference in appearance and, therefore, physicochemical, biochemical and biological methods are essential for the detection of cyanobacterial toxins. The most frequently reported cyanobacterial toxins are cyclic heptapeptide toxins known as microcystins which can be isolated from several species of the freshwater genera Microcystis , Planktothrix ( Oscillatoria ), Anabaena and Nostoc . More than 70 structural variants of microcystins are known. A structurally very similar class of cyanobacterial toxins is nodularins ( < 10 structural variants), which are cyclic pentapeptide hepatotoxins that are found in the brackish-water cyanobacterium Nodularia . -
Amino Acid Building Block Models – in Brief
Amino Acid Building Block Models – In Brief Key Teaching Points for Amino Acid Building Block Models© Overall Student Learning Objective: What Dictates How a Protein Folds? Amino acids are the building blocks of proteins. All amino acids have an identical core structure consisting of an alpha-carbon, carboxyl group, amino group and R-group (sidechain). A linear chain of amino acids is a polypeptide. The primary sequence of a protein is the linear sequence of amino acids in a polypeptide. Proteins are made up of amino acid monomers linked together by peptide bonds. Peptide bond formation between amino acids results in the release of water (dehydration synthesis or condensation reaction). The protein backbone is characterized by the “N-C-C-N-C-C. .” pattern. The “ends” of the protein can be identified by the N-terminus (amino group) end and the C-terminus (carboxyl group) end. For a more complete lesson guide, please visit: http://www.3dmoleculardesigns.com/3DMD-Files/AABB/ContentsandAssembly.pdf Amino Acid Core Structure Build an amino acid according to the diagram to the right: 1. Identify the alpha carbon, amino group, carboxyl group and R-group (sidechain representation) in the structure you have constructed. Two amino acids can be chemically linked by a reaction called “condensation” or “dehydration synthesis” to form a dipeptide bond linking the two amino acids. A chain of amino acid units (monomers) linked together by peptide bonds is called a polypeptide. General Dipeptide Structure Construct a model of a dipeptide using the amino acid models previously built. 2. What are the products of the condensation reaction (dehydration synthesis)? 3. -
Deamidation of Human Proteins
Deamidation of human proteins N. E. Robinson*† and A. B. Robinson‡ *Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and ‡Oregon Institute of Science and Medicine, Cave Junction, OR 97523 Communicated by Frederick Seitz, The Rockefeller University, New York, NY, August 31, 2001 (received for review May 8, 2001) Deamidation of asparaginyl and glutaminyl residues causes time- 3D structure is known (23). This method is more than 95% dependent changes in charge and conformation of peptides and reliable in predicting relative deamidation rates of Asn residues proteins. Quantitative and experimentally verified predictive cal- within a single protein and is also useful for the prediction of culations of the deamidation rates of 1,371 asparaginyl residues in absolute deamidation rates. a representative collection of 126 human proteins have been It is, therefore, now possible to compute the expected deami- performed. These rates suggest that deamidation is a biologically dation rate of any protein for which the primary and 3D relevant phenomenon in a remarkably large percentage of human structures are known, except for very long-lived proteins. These proteins. proteins require measurement of the 400 Gln pentapeptide rates. in vivo deamidation ͉ asparaginyl residues Materials and Methods Calculation Method. The Brookhaven Protein Data Bank (PDB) eamidation of asparaginyl (Asn) and glutaminyl (Gln) was searched to select 126 human proteins of general biochem- Dresidues to produce aspartyl (Asp) and glutamyl (Glu) ical interest and of known 3D structure without bias toward any residues causes structurally and biologically important alter- known data about their deamidation, except for 13 proteins (as ations in peptide and protein structures. -
Introduction to Proteins and Amino Acids Introduction
Introduction to Proteins and Amino Acids Introduction • Twenty percent of the human body is made up of proteins. Proteins are the large, complex molecules that are critical for normal functioning of cells. • They are essential for the structure, function, and regulation of the body’s tissues and organs. • Proteins are made up of smaller units called amino acids, which are building blocks of proteins. They are attached to one another by peptide bonds forming a long chain of proteins. Amino acid structure and its classification • An amino acid contains both a carboxylic group and an amino group. Amino acids that have an amino group bonded directly to the alpha-carbon are referred to as alpha amino acids. • Every alpha amino acid has a carbon atom, called an alpha carbon, Cα ; bonded to a carboxylic acid, –COOH group; an amino, –NH2 group; a hydrogen atom; and an R group that is unique for every amino acid. Classification of amino acids • There are 20 amino acids. Based on the nature of their ‘R’ group, they are classified based on their polarity as: Classification based on essentiality: Essential amino acids are the amino acids which you need through your diet because your body cannot make them. Whereas non essential amino acids are the amino acids which are not an essential part of your diet because they can be synthesized by your body. Essential Non essential Histidine Alanine Isoleucine Arginine Leucine Aspargine Methionine Aspartate Phenyl alanine Cystine Threonine Glutamic acid Tryptophan Glycine Valine Ornithine Proline Serine Tyrosine Peptide bonds • Amino acids are linked together by ‘amide groups’ called peptide bonds. -
First Evidence of Production of the Lantibiotic Nisin P Enriqueta Garcia-Gutierrez1,2, Paula M
www.nature.com/scientificreports OPEN First evidence of production of the lantibiotic nisin P Enriqueta Garcia-Gutierrez1,2, Paula M. O’Connor2,3, Gerhard Saalbach4, Calum J. Walsh2,3, James W. Hegarty2,3, Caitriona M. Guinane2,5, Melinda J. Mayer1, Arjan Narbad1* & Paul D. Cotter2,3 Nisin P is a natural nisin variant, the genetic determinants for which were previously identifed in the genomes of two Streptococcus species, albeit with no confrmed evidence of production. Here we describe Streptococcus agalactiae DPC7040, a human faecal isolate, which exhibits antimicrobial activity against a panel of gut and food isolates by virtue of producing nisin P. Nisin P was purifed, and its predicted structure was confrmed by nanoLC-MS/MS, with both the fully modifed peptide and a variant without rings B and E being identifed. Additionally, we compared its spectrum of inhibition and minimum inhibitory concentration (MIC) with that of nisin A and its antimicrobial efect in a faecal fermentation in comparison with nisin A and H. We found that its antimicrobial activity was less potent than nisin A and H, and we propose a link between this reduced activity and the peptide structure. Nisin is a small peptide with antimicrobial activity against a wide range of pathogenic bacteria. It was originally sourced from a Lactococcus lactis subsp. lactis isolated from a dairy product1 and is classifed as a class I bacteri- ocin, as it is ribosomally synthesised and post-translationally modifed2. Nisin has been studied extensively and has a wide range of applications in the food industry, biomedicine, veterinary and research felds3–6. -
Deamidation, Acylation and Proteolysis of a Model Peptide in PLGA Films ⁎ M.L
Journal of Controlled Release 112 (2006) 111–119 www.elsevier.com/locate/jconrel Deamidation, acylation and proteolysis of a model peptide in PLGA films ⁎ M.L. Houchin a, K. Heppert b, E.M. Topp a, a Department of Pharmaceutical Chemistry, The University of Kansas, 2095 Constant Ave., Lawrence, KS 66047, United States b Higuchi Biosciences Centers, The University of Kansas, Lawrence, KS, United States Received 8 December 2005; accepted 30 January 2006 Available online 9 March 2006 Abstract The relative rates of deamidation, acylation and proteolysis (i.e. amide bond cleavage) were determined for a model peptide (VYPNGA) in poly (DL-lactide-co-glycolide) films. Films were stored at 70°C and either 95%, 75%, 60%, 45%, 28%, or ∼0% relative humidity and at 37°C and 95% relative humidity. Peptide degradation products were identified by ESI+MS/MS and quantitated by LC/MS/MS. Extensive overlap of degradation mechanisms occurred, producing a complex mixture of products. Acylation was the dominant peptide degradation reaction (10–20% of total peptide) at early stages of PLGA hydrolysis and at intermediate relative humidity (60–45% RH). Deamidation and proteolysis were dominant (25–50% and 20–40% of total peptide, respectively) at later stages and at high relative humidity (95–75% RH). Understanding the relative rates of each peptide degradation reaction will allow for improved design of PLGA formulations that preserve the stability of peptide and protein drugs. © 2006 Elsevier B.V. All rights reserved. Keywords: PLGA; Deamidation; Acylation; Proteolysis; Peptide stability 1. Introduction bonds produces lactic and glycolic acid, which are easily metabolized. -
Nobel Lecture by Roger Y. Tsien
CONSTRUCTING AND EXPLOITING THE FLUORESCENT PROTEIN PAINTBOX Nobel Lecture, December 8, 2008 by Roger Y. Tsien Howard Hughes Medical Institute, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0647, USA. MOTIVATION My first exposure to visibly fluorescent proteins (FPs) was near the end of my time as a faculty member at the University of California, Berkeley. Prof. Alexander Glazer, a friend and colleague there, was the world’s expert on phycobiliproteins, the brilliantly colored and intensely fluorescent proteins that serve as light-harvesting antennae for the photosynthetic apparatus of blue-green algae or cyanobacteria. One day, probably around 1987–88, Glazer told me that his lab had cloned the gene for one of the phycobilipro- teins. Furthermore, he said, the apoprotein produced from this gene became fluorescent when mixed with its chromophore, a small molecule cofactor that could be extracted from dried cyanobacteria under conditions that cleaved its bond to the phycobiliprotein. I remember becoming very excited about the prospect that an arbitrary protein could be fluorescently tagged in situ by genetically fusing it to the phycobiliprotein, then administering the chromophore, which I hoped would be able to cross membranes and get inside cells. Unfortunately, Glazer’s lab then found out that the spontane- ous reaction between the apoprotein and the chromophore produced the “wrong” product, whose fluorescence was red-shifted and five-fold lower than that of the native phycobiliprotein1–3. An enzyme from the cyanobacteria was required to insert the chromophore correctly into the apoprotein. This en- zyme was a heterodimer of two gene products, so at least three cyanobacterial genes would have to be introduced into any other organism, not counting any gene products needed to synthesize the chromophore4. -
BOSTON UNIVERSITY SCHOOL of MEDICINE Dissertation
BOSTON UNIVERSITY SCHOOL OF MEDICINE Dissertation DEAMIDATION AND RELATED PROBLEMS IN STRUCTURAL ANALYSIS OF PEPTIDES AND PROTEINS by NADEZDA P. SARGAEVA B.S., St. Petersburg State Polytechnical University, 2002 M.S., St. Petersburg State Polytechnical University, 2004 Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2012 Approved by First Reader Peter B. O’Connor, Ph.D. Associate Professor of Biochemistry Second Reader Cheng Lin, Ph.D. Assistant Professor of Biochemistry Dedications I dedicate this thesis to my Family iii Acknowledgments I would like to express my deepest gratitude to my advisor, Prof. Peter B. O’Connor. We met in St. Petersburg, Russia in 2004 and you believed in my abilities and you gave me an opportunity to be a part of such a great mass spectrometry program. I also want to thank you for your support and your guidance throughout my Ph.D. studies. Thank you for pushing me to achieve my goals of learning and becoming a better scientist, and for the opportunity you gave me to build up my professional and scientific network. Your help, your advice, and your encouragement in building up my professional career are very much appreciated. Prof. Cheng Lin, thank you for being my second reader and mentor. Working with you has always been a pleasure – I highly value your well thought out ideas, your constant use of the scientific principle, and your willingness to follow up regarding the data, the future directions, etc. I truly appreciate your attention to details, your regular availability and willingness to help me hands on. -
Introduction 1.1 Post-Translational Modifications
Chapter I: Introduction 1.1 Post-translational modifications Post-translational modifications (PTMs) are responsible for dynamic regulation of protein structure and function (Jensen et al., 2006). One example of the function of post-translational modifications in the dynamic regulation of protein structure and function is signal transduction; post-translational modification of key regulatory proteins in signal transduction pathways controls cellular proliferation, metabolism, gene expression, cytoskeletal organization and apoptosis (Jensen et al., 2006). Post-translational modifications not only change the mass of the protein, they are also often responsible for changes in charge, structure and conformation. This leads to changes in the biological activity of proteins like enzymes, the binding affinity of proteins to receptors and other protein-protein interactions (Hoffmann et al., 2008) (Murray et al., 1998). For example, the interaction of the cytokine TGF-beta with its receptor complex results in the phosphorylation of SMAD family proteins which activates these proteins to regulate target gene expression (Massague et al., 2000). Post-translational modified amino acid residues can act as binding sites on proteins for a specific recognition domain on other proteins. For example, phosphorylated tyrosine residues can bind to SH2 or PTB domains (Pawson et al., 1997). Depending on the type of PTM they can be very abundant and have a large number of target proteins, whereas other PTM`s have only a few target proteins. Moreover, some PTM`s are connected with several different residues and not only with one residue. For example multi-site phosphorylation that primarily targets Serine, Threonine and Tyrosine residues is a crucial mechanism for the regulation of protein localization and functional activity (Cohen et al., 2000). -
Peptides & Proteins
Peptides & Proteins (thanks to Hans Börner) 1 Proteins & Peptides Proteuos: Proteus (Gr. mythological figure who could change form) proteuo: „"first, ref. the basic constituents of all living cells” peptos: „Cooked referring to digestion” Proteins essential for: Structure, metabolism & cell functions 2 Bacterium Proteins (15 weight%) 50% (without water) • Construction materials Collagen Spider silk proteins 3 Proteins Structural proteins structural role & mechanical support "cell skeleton“: complex network of protein filaments. muscle contraction results from action of large protein assemblies Myosin und Myogen. Other organic material (hair and bone) are also based on proteins. Collagen is found in all multi cellular animals, occurring in almost every tissue. • It is the most abundant vertebrate protein • approximately a quarter of mammalian protein is collagen 4 Proteins Storage Various ions, small molecules and other metabolites are stored by complexation with proteins • hemoglobin stores oxygen (free O2 in the blood would be toxic) • iron is stored by ferritin Transport Proteins are involved in the transportation of particles ranging from electrons to macromolecules. • Iron is transported by transferrin • Oxygen via hemoglobin. • Some proteins form pores in cellular membranes through which ions pass; the transport of proteins themselves across membranes also depends on other proteins. Beside: Regulation, enzymes, defense, functional properties 5 Our universal container system: Albumines 6 zones: IA, IB, IIA, IIB, IIIA, IIIB; IIB and -
Structure and Synthesis of Antifungal Disulfide
microorganisms Review Structure and Synthesis of Antifungal Disulfide β-Strand Proteins from Filamentous Fungi Györgyi Váradi 1,*, Gábor K. Tóth 1,2 and Gyula Batta 3 1 Department of Medical Chemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; [email protected] 2 MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Hungary 3 Department of Organic Chemistry, University of Debrecen, H-4032 Debrecen, Hungary; [email protected] * Correspondence: [email protected]; Tel.: +36-62-545-142; Fax: +36-62-545-971 Received: 20 November 2018; Accepted: 24 December 2018; Published: 27 December 2018 Abstract: The discovery and understanding of the mode of action of new antimicrobial agents is extremely urgent, since fungal infections cause 1.5 million deaths annually. Antifungal peptides and proteins represent a significant group of compounds that are able to kill pathogenic fungi. Based on phylogenetic analyses the ascomycetous, cysteine-rich antifungal proteins can be divided into three different groups: Penicillium chrysogenum antifungal protein (PAF), Neosartorya fischeri antifungal protein 2 (NFAP2) and “bubble-proteins” (BP) produced, for example, by P. brevicompactum. They all dominantly have β-strand secondary structures that are stabilized by several disulfide bonds. The PAF group (AFP antifungal protein from Aspergillus giganteus, PAF and PAFB from P. chrysogenum, Neosartorya fischeri antifungal protein (NFAP)) is the best characterized with their common β-barrel tertiary structure. These proteins and variants can efficiently be obtained either from fungi production or by recombinant expression. However, chemical synthesis may be a complementary aid for preparing unusual modifications, e.g., the incorporation of non-coded amino acids, fluorophores, or even unnatural disulfide bonds.