Amicetin

Amicetin

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Category Antibiotics
Catalog number BBF-00536
CAS
Molecular Weight 618.68
Molecular Formula C29H42N6O9

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Description

It is produced by the strain of Streptomuces vinaceusdrappus. It is mainly resistant to gram-positive bacteria and Mycobacterium. The MIC for S.aureus 209P and Mycobacterium tuberculosis H37 Rv were 2.0 and 0.5 μg/mL, respectively, and for Mycoplasma pneumoniae was 12.5 μg/mL.

Specification

IUPAC Name 4-[(2-amino-3-hydroxy-2-methylpropanoyl)amino]-N-[1-[(2R,5S,6R)-5-[(2R,3R,4S,5S,6R)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]-2-oxopyrimidin-4-yl]benzamide
Canonical SMILES CC1C(CCC(O1)N2C=CC(=NC2=O)NC(=O)C3=CC=C(C=C3)NC(=O)C(C)(CO)N)OC4C(C(C(C(O4)C)N(C)C)O)O
InChI InChI=1S/C29H42N6O9/c1-15-19(44-26-24(38)23(37)22(34(4)5)16(2)43-26)10-11-21(42-15)35-13-12-20(33-28(35)41)32-25(39)17-6-8-18(9-7-17)31-27(40)29(3,30)14-36/h6-9,12-13,15-16,19,21-24,26,36-38H,10-11,14,30H2,1-5H3,(H,31,40)(H,32,33,39,41)/t15-,16-,19+,21-,22-,23+,24-,26-,29?/m1/s1
InChI Key HDNVYHWHCVTDIV-AUHWTNQGSA-N

Properties

Appearance Colorless Acicular Crystal
Antibiotic Activity Spectrum Gram-positive bacteria; mycobacteria
Melting Point 160-165 °C
Solubility Soluble in Water, Hydrochloric acid, Sodium hydroxide

Reference Reading

1. High Plasticity of the Amicetin Biosynthetic Pathway in Streptomyces sp. SHP 22-7 Led to the Discovery of Streptcytosine P and Cytosaminomycins F and G and Facilitated the Production of 12F-Plicacetin
Niraj Aryal, Junhong Chen, Keshab Bhattarai, Oliver Hennrich, Ira Handayani, Markus Kramer, Jan Straetener, Tatjana Wommer, Anne Berscheid, Silke Peter, Norbert Reiling, Heike Brötz-Oesterhelt, Christian Geibel, Michael Lämmerhofer, Yvonne Mast, Harald Gross J Nat Prod. 2022 Mar 25;85(3):530-539. doi: 10.1021/acs.jnatprod.1c01051. Epub 2022 Mar 9.
A chemical reinvestigation of the Indonesian strain Streptomyces sp. SHP 22-7 led to the isolation of three new pyrimidine nucleosides, along with six known analogues and zincphyrin. The structures of the new compounds (6, 7, 10) were elucidated by employing spectroscopic techniques (NMR, MS, CD, and IR) as well as enantioselective analyses of methyl branched side chain configurations. Application of the precursor-directed feeding approach led to the production and partial isolation of nine further pyrimidine analogues. The new compounds 6, 7, and 11 and three of the known compounds (2-4) were found to possess antimycobacterial and cytotoxic properties.
2. Dissecting the Nucleoside Antibiotics as Universal Translation Inhibitors
Matthew R Nelli, Kendall N Heitmeier, Ryan E Looper Acc Chem Res. 2021 Jul 6;54(13):2798-2811. doi: 10.1021/acs.accounts.1c00221. Epub 2021 Jun 21.
Without question, natural products have provided the lion share of leads, if not drugs themselves, for the treatment of bacterial infections. The bacterial arms race, fueled by selection and survival pressures has delivered a natural arsenal of small molecules targeting the most essential of life processes. Antibiotics that target these critical intracellular processes face the formidable defense of both penetrating a bacterial cell membrane and avoiding efflux to exert their effect. These challenges are especially effective in Gram-negative (Gram-(-)) bacteria, which have a double membrane structure and efficient efflux systems from the combination of outer-membrane porins and inner membrane proton pumps. In this landscape of offense and defense, our clinically used antibiotics have only successfully targeted three intracellular processes for therapeutic intervention in Gram-(-) bacteria: dihydrofolate biosynthesis, transcription, and translation. Not surprisingly, such critical survival machinery is a popular target for bacterial warfare, and eight of our 14 classes of commonly used antibiotics target translation with the bacterial ribosome remaining one the most vetted targets for antimicrobial therapy. On the plus side, its anionic character attracts cationic inhibitors, which are generally more capable of penetrating the bacterial cell wall, and clinical resistance rates are usually manageable as mutation of such a highly evolved machine is difficult. On the down side, this highly evolved machine renders it difficult to inhibit selectively, and the inhibition of prokaryotic translation versus both eukaryotic cellular and mitochondrial translation is critical for clinical development and minimization of undesired toxicities.A class of natural products known as the "nucleoside antibiotics" have historically been recognized as universal inhibitors of the ribosome and can inhibit translation in prokaryotes, eukaryotes, and archaea. While they have served an essential role in dissecting the biochemical underpinnings of the enzymatic functions of the ribosome, they have not proven therapeutically useful as they target the highly conserved rRNA in the P-site and are toxic to mammalian cells. In this Account, we describe our studies on the natural product amicetin, a nucleoside antibiotic that we have demonstrated to break the rule of being a universal translation inhibitor. While the cytosine of amicetin mimics C75 of the 3'-CCA tail of the P-site tRNA akin to other nucleoside antibiotics, we advance a hypothesis that amicetin's unique interaction with the ribosomal protein uL16 exploits an untapped mechanism for selectively targeting the bacterial ribosome. A complex molecule comprised of a nucleoside, carbohydrates and amino acids, amicetin is also chemically unstable. Our initial attempts to stabilize and simplify this scaffold are presented with the ultimate goal of rebuilding the compound with improved penetrance to bacterial cells. If successful, this scaffold would demonstrate a path forward for a new class of antibiotics capable of selectively targeting the ribosomal P-site.
3. Unifying the Aminohexopyranose- and Peptidyl-Nucleoside Antibiotics: Implications for Antibiotic Design
Catherine M Serrano, Hariprasada Reddy Kanna Reddy, Daniel Eiler, Michael Koch, Ben I C Tresco, Louis R Barrows, Ryan T VanderLinden, Charles A Testa, Paul R Sebahar, Ryan E Looper Angew Chem Int Ed Engl. 2020 Jul 6;59(28):11330-11333. doi: 10.1002/anie.202003094. Epub 2020 May 11.
In search of new anti-tuberculars compatible with anti-retroviral therapy we re-identified amicetin as a lead compound. Amicetin's binding to the 70S ribosomal subunit of Thermus thermophilus (Tth) has been unambiguously determined by crystallography and reveals it to occupy the peptidyl transferase center P-site of the ribosome. The amicetin binding site overlaps significantly with that of the well-known protein synthesis inhibitor balsticidin S. Amicetin, however, is the first compound structurally characterized to bind to the P-site with demonstrated selectivity for the inhibition of prokaryotic translation. The natural product-ribosome structure enabled the synthesis of simplified analogues that retained both potency and selectivity for the inhibition of prokaryotic translation.

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