1
|
Konstantinović J, Kany AM, Alhayek A, Abdelsamie AS, Sikandar A, Voos K, Yao Y, Andreas A, Shafiei R, Loretz B, Schönauer E, Bals R, Brandstetter H, Hartmann RW, Ducho C, Lehr CM, Beisswenger C, Müller R, Rox K, Haupenthal J, Hirsch AK. Inhibitors of the Elastase LasB for the Treatment of Pseudomonas aeruginosa Lung Infections. ACS Cent Sci 2023; 9:2205-2215. [PMID: 38161367 PMCID: PMC10755728 DOI: 10.1021/acscentsci.3c01102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Indexed: 01/03/2024]
Abstract
Infections caused by the Gram-negative pathogen Pseudomonas aeruginosa are emerging worldwide as a major threat to human health. Conventional antibiotic monotherapy suffers from rapid resistance development, underlining urgent need for novel treatment concepts. Here, we report on a nontraditional approach to combat P. aeruginosa-derived infections by targeting its main virulence factor, the elastase LasB. We discovered a new chemical class of phosphonates with an outstanding in vitro ADMET and PK profile, auspicious activity both in vitro and in vivo. We established the mode of action through a cocrystal structure of our lead compound with LasB and in several in vitro and ex vivo models. The proof of concept of a combination of our pathoblocker with levofloxacin in a murine neutropenic lung infection model and the reduction of LasB protein levels in blood as a proof of target engagement demonstrate the great potential for use as an adjunctive treatment of lung infections in humans.
Collapse
Affiliation(s)
- Jelena Konstantinović
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Andreas M. Kany
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alaa Alhayek
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ahmed S. Abdelsamie
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department
of Chemistry of Natural and Microbial Products, Institute of Pharmaceutical and Drug Industries Research, National
Research Centre, El-Buhouth Street, Dokki, Cairo 12622, Egypt
| | - Asfandyar Sikandar
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Katrin Voos
- Department
of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken 66123, Germany
| | - Yiwen Yao
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Anastasia Andreas
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Roya Shafiei
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Brigitta Loretz
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Esther Schönauer
- Department
of Biosciences and Medical Biology, Division of Structural Biology, University of Salzburg, Salzburg 5020, Austria
| | - Robert Bals
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Hans Brandstetter
- Department
of Biosciences and Medical Biology, Division of Structural Biology, University of Salzburg, Salzburg 5020, Austria
| | - Rolf W. Hartmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Christian Ducho
- Department
of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken 66123, Germany
| | - Claus-Michael Lehr
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
| | - Christoph Beisswenger
- Department
of Internal Medicine V − Pulmonology, Allergology and Critical
Care Medicine, Saarland University, Homburg 66421, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
- Helmholtz
International Lab for Anti-infectives, Saarbrücken 66123, Germany
| | - Katharina Rox
- Department
of Chemical Biology (CBIO), Helmholtz Centre
for Infection Research (HZI), Braunschweig 38124, Germany
- Deutsches
Zentrum für Infektionsforschung (DZIF) e.V., Braunschweig 38124, Germany
| | - Jörg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Anna K.H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS)−Helmholtz
Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarland
University, Department of Pharmacy, Saarbrücken 66123, Germany
- Helmholtz
International Lab for Anti-infectives, Saarbrücken 66123, Germany
- Deutsches
Zentrum für Infektionsforschung (DZIF) e.V., Braunschweig 38124, Germany
| |
Collapse
|
2
|
Wagdy RA, Abutaleb NS, Fathalla RK, Elgammal Y, Weck S, Pal R, Fischer PD, Ducho C, Abadi AH, N Seleem M, Engel M, Abdel-Halim M. Discovery of 1,2-diaryl-3-oxopyrazolidin-4-carboxamides as a new class of MurA enzyme inhibitors and characterization of their antibacterial activity. Eur J Med Chem 2023; 261:115789. [PMID: 37717380 DOI: 10.1016/j.ejmech.2023.115789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/19/2023]
Abstract
The cytoplasmic steps of peptidoglycan synthesis represent an important targeted pathway for development of new antibiotics. Herein, we report the synthesis of novel 3-oxopyrazolidin-4-carboxamide derivatives with variable amide side chains as potential antibacterial agents targeting MurA enzyme, the first committed enzyme in these cytosolic steps. Compounds 15 (isoindoline-1,3-dione-5-yl), 16 (4-(1H-pyrazol-4-yl)phenyl), 20 (5-cyanothiazol-2-yl), 21 and 31 (5-nitrothiazol-2-yl derivatives) exhibited the most potent MurA inhibition, with IC50 values of 9.8-12.2 μM. Compounds 15, 16 and 21 showed equipotent inhibition of the C115D MurA mutant developed by fosfomycin-resistant Escherichia coli. NMR binding studies revealed that some of the MurA residues targeted by 15 also interacted with fosfomycin, but not all, indicating an overlapping but not identical binding site. The antibacterial activity of the compounds against E. coli ΔtolC suggests that inhibition of MurA accounts for the observed effect on bacterial growth, considering that a few potent MurA inhibitors could not penetrate the bacterial outer membrane and were therefore inactive as proven by the bacterial cell uptake assay. The most promising compounds were also evaluated against a panel of Gram-positive bacteria. Remarkably, compounds 21 and 31 (MurA IC50 = 9.8 and 10.2 μM respectively) exhibited a potent activity against Clostridioides difficile strains with MIC values ranging from 0.125 to 1 μg/mL, and were also shown to be bactericidal with MBC values between 0.25 and 1 μg/mL. Furthermore, both compounds were shown to have a limited activity against human normal intestinal flora and showed high safety towards human colon cells (Caco-2) in vitro. The thiolactone derivative (compound 5) exhibited an interesting broad spectrum antibacterial activity despite its weak MurA inhibition. Altogether, the presented series provides a promising class of antibiotics that merits further investigation.
Collapse
Affiliation(s)
- Reem A Wagdy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Reem K Fathalla
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Yehia Elgammal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Stefanie Weck
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Rusha Pal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Patrick D Fischer
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Christian Ducho
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Center for One Health Research, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany.
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| |
Collapse
|
3
|
Berida T, McKee SR, Chatterjee S, Manning DL, Li W, Pandey P, Tripathi SK, Mreyoud Y, Smirnov A, Doerksen RJ, Jackson M, Ducho C, Stallings CL, Roy S. Discovery, Synthesis, and Optimization of 1,2,4-Triazolyl Pyridines Targeting Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2282-2298. [PMID: 37788674 PMCID: PMC10807233 DOI: 10.1021/acsinfecdis.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The rise in multidrug resistant tuberculosis cases underscores the urgent need to develop new treatment strategies for tuberculosis. Herein, we report the discovery and synthesis of a new series of compounds containing a 3-thio-1,2,4-triazole moiety that show inhibition of Mycobacterium tuberculosis (Mtb) growth and survival. Structure-activity relationship studies led us to identify several potent analogs displaying low micromolar to nanomolar inhibitory activity, specifically against Mtb. The potent analogs demonstrated no cytotoxicity in mammalian cells at over 100 times the effective concentration required in Mtb and were bactericidal against Mtb during infection of macrophages. In the exploratory ADME investigations, we observed suboptimal ADME characteristics, which prompted us to identify potential metabolic liabilities for further optimization. Our preliminary investigations into the mechanism of action suggest that this series is not engaging the promiscuous targets that arise from many phenotypic screens. We selected for resistant mutants with the nanomolar potent nitro-containing compound 20 and identified resistant isolates with mutations in genes required for coenzyme F420 biosynthesis and the nitroreductase Ddn. This suggests that the aromatic nitro-1,2,4-triazolyl pyridines are activated by F420-dependent Ddn activity, similar to the nitro-containing TB drug pretomanid. We were able to circumvent the requirement for F420-dependent Ddn activity using compounds that contained non-nitro groups, identifying a key feature to be modified to avoid this predominant resistance mechanism. These studies provide the foundation for the development of a new class of 1,2,4-triazole compounds for the treatment of tuberculosis.
Collapse
Affiliation(s)
- Tomayo Berida
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Samuel R McKee
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Shamba Chatterjee
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Destinee L Manning
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Pankaj Pandey
- National Center for Natural Products Research, University of Mississippi, University, Mississippi 38677, United States
| | - Siddharth Kaushal Tripathi
- National Center for Natural Products Research, University of Mississippi, University, Mississippi 38677, United States
| | - Yassin Mreyoud
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Robert J Doerksen
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken 66123, Germany
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Sudeshna Roy
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi 38677, United States
| |
Collapse
|
4
|
Fathalla RK, Engel M, Ducho C. Targeting the binding pocket of the fluorophore 8-anilinonaphthalene-1-sulfonic acid in the bacterial enzyme MurA. Arch Pharm (Weinheim) 2023; 356:e2300237. [PMID: 37464574 DOI: 10.1002/ardp.202300237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
8-Anilinonaphthalene-1-sulfonic acid (ANS) has been extensively used as a fluorescent probe to detect conformational changes of proteins. It has been cocrystallized with several of the proteins it is used to monitor, including the bacterial cell wall synthesis enzyme MurA. MurA catalyzes the first committed step of peptidoglycan biosynthesis, converting UDP-N-acetylglucosamine (UDP-GlcNAc) into enolpyruvyl UDP-GlcNAc. It has been reported before that ANS binds to MurA from Enterobacter cloacae without inhibiting the enzyme's activity up to a concentration of 1 mM ANS. In this study, we present evidence that ANS inhibits the activity of several isoforms of MurA with IC50 values of 18, 22, and 31 µM against wild-type Escherichia coli, C115D E. coli, and E. cloacae MurA, respectively. This prompted us to test a larger series of structural analogs of ANS for the inhibition of these MurA enzymes, which led to the discovery of compound 26. This ANS analog showed enhanced inhibition of MurA (WT and C115D MurA from E. coli, and E. cloacae MurA) with IC50 values of 2.7, 10, and 14 µM, respectively. Based on our results, the ANS binding pocket was identified as a novel target site for the development of potential antibiotics.
Collapse
Affiliation(s)
- Reem K Fathalla
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Matthias Engel
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| |
Collapse
|
5
|
Rohrbacher C, Zscherp R, Weck SC, Klahn P, Ducho C. Synthesis of an Antimicrobial Enterobactin-Muraymycin Conjugate for Improved Activity Against Gram-Negative Bacteria. Chemistry 2023; 29:e202202408. [PMID: 36222466 PMCID: PMC10107792 DOI: 10.1002/chem.202202408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 12/12/2022]
Abstract
Overcoming increasing antibiotic resistance requires the development of novel antibacterial agents that address new targets in bacterial cells. Naturally occurring nucleoside antibiotics (such as muraymycins) inhibit the bacterial membrane protein MraY, a clinically unexploited essential enzyme in peptidoglycan (cell wall) biosynthesis. Even though a range of synthetic muraymycin analogues has already been reported, they generally suffer from limited cellular uptake and a lack of activity against Gram-negative bacteria. We herein report an approach to overcome these hurdles: a synthetic muraymycin analogue has been conjugated to a siderophore, i. e. the enterobactin derivative EntKL , to increase the cellular uptake into Gram-negative bacteria. The resultant conjugate showed significantly improved antibacterial activity against an efflux-deficient E. coli strain, thus providing a proof-of-concept of this novel approach and a starting point for the future optimisation of such conjugates towards potent agents against Gram-negative pathogens.
Collapse
Affiliation(s)
- Christian Rohrbacher
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Robert Zscherp
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Stefanie C Weck
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Philipp Klahn
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.,Department of Chemistry and Molecular Biology, Division of Organic and Medicinal Chemistry, University of Gothenburg, Kemigården 4, 412 96, Göteborg, Sweden
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| |
Collapse
|
6
|
Fathalla RK, Fröhner W, Bader CD, Fischer PD, Dahlem C, Chatterjee D, Mathea S, Kiemer AK, Arthanari H, Müller R, Abdel-Halim M, Ducho C, Engel M. Identification and Biochemical Characterization of Pyrrolidinediones as Novel Inhibitors of the Bacterial Enzyme MurA. J Med Chem 2022; 65:14740-14763. [PMID: 36269107 PMCID: PMC9989942 DOI: 10.1021/acs.jmedchem.2c01275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.
Collapse
Affiliation(s)
- Reem K. Fathalla
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Wolfgang Fröhner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Chantal D. Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Patrick D. Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Alexandra K. Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Helmholtz International Lab for Antiinfectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Matthias Engel
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| |
Collapse
|
7
|
Alhayek A, Khan ES, Schönauer E, Däinghaus T, Shafiei R, Voos K, Han MKL, Ducho C, Posselt G, Wessler S, Brandstetter H, Haupenthal J, del Campo A, Hirsch AKH. Inhibition of Collagenase Q1 of
Bacillus cereus
as a Novel Antivirulence Strategy for the Treatment of Skin‐Wound Infections. Advanced Therapeutics 2022; 5:2100222. [PMID: 35310821 PMCID: PMC7612511 DOI: 10.1002/adtp.202100222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite the progress in surgical techniques and antibiotic prophylaxis, opportunistic wound infections with Bacillus cereus remain a public health problem. Secreted toxins are one of the main factors contributing to B. cereus pathogenicity. A promising strategy to treat such infections is to target these toxins and not the bacteria. Although the exoenzymes produced by B. cereus are thoroughly investigated, little is known about the role of B. cereus collagenases in wound infections. In this report, the collagenolytic activity of secreted collagenases (Col) is characterized in the B. cereus culture supernatant (csn) and its isolated recombinantly produced ColQ1 is characterized. The data reveals that ColQ1 causes damage on dermal collagen (COL). This results in gaps in the tissue, which might facilitate the spread of bacteria. The importance of B. cereus collagenases is also demonstrated in disease promotion using two inhibitors. Compound 2 shows high efficacy in peptidolytic, gelatinolytic, and COL degradation assays. It also preserves the fibrillar COLs in skin tissue challenged with ColQ1, as well as the viability of skin cells treated with B. cereus csn. A Galleria mellonella model highlights the significance of collagenase inhibition in vivo.
Collapse
Affiliation(s)
- Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
- Department of Pharmacy Saarland University, Saarbrücken Campus Campus E8.1 66123 Saarbrücken Germany
| | - Essak S. Khan
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Esther Schönauer
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Tobias Däinghaus
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Roya Shafiei
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Mitchell K. L. Han
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Gernot Posselt
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Silja Wessler
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology Hellbrunner Str. 34 University of Salzburg Salzburg 5020 Austria
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
| | - Aránzazu del Campo
- Leibniz Institute for New Materials (INM) Saarland University Campus D2 2 66123 Saarbrücken Germany
- Chemistry Department Saarland University 66123 Saarbrücken Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) 38124 Saarbrücken Germany
- Department of Pharmacy Saarland University, Saarbrücken Campus Campus E8.1 66123 Saarbrücken Germany
| |
Collapse
|
8
|
Cui Z, Nguyen H, Bhardwaj M, Wang X, Büschleb M, Lemke A, Schütz C, Rohrbacher C, Junghanns P, Koppermann S, Ducho C, Thorson JS, Van Lanen SG. Enzymatic C β-H Functionalization of l-Arg and l-Leu in Nonribosomally Derived Peptidyl Natural Products: A Tale of Two Oxidoreductases. J Am Chem Soc 2021; 143:19425-19437. [PMID: 34767710 DOI: 10.1021/jacs.1c08177] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Muraymycins are peptidyl nucleoside antibiotics that contain two Cβ-modified amino acids, (2S,3S)-capreomycidine and (2S,3S)-β-OH-Leu. The former is also a component of chymostatins, which are aldehyde-containing peptidic protease inhibitors that─like muraymycin─are derived from nonribosomal peptide synthetases (NRPSs). Using feeding experiments and in vitro characterization of 12 recombinant proteins, the biosynthetic mechanism for both nonproteinogenic amino acids is now defined. The formation of (2S,3S)-capreomycidine is shown to involve an FAD-dependent dehydrogenase:cyclase that requires an NRPS-bound pathway intermediate as a substrate. This cryptic dehydrogenation strategy is both temporally and mechanistically distinct in comparison to the biosynthesis of other capreomycidine diastereomers, which has previously been shown to proceed by Cβ-hydroxylation of free l-Arg catalyzed by a member of the nonheme Fe2+- and α-ketoglutarate (αKG)-dependent dioxygenase family and (eventually) a dehydration-mediated cyclization process catalyzed by a distinct enzyme(s). Contrary to our initial expectation, the sole nonheme Fe2+- and αKG-dependent dioxygenase candidate Mur15 encoded within the muraymycin gene cluster is instead demonstrated to catalyze specific Cβ hydroxylation of the Leu residue to generate (2S,3S)-β-OH-Leu that is found in most muraymycin congeners. Importantly, and in contrast to known l-Arg-Cβ-hydroxylases, the Mur15-catalyzed reaction occurs after the NRPS-mediated assembly of the peptide scaffold. This late-stage functionalization affords the opportunity to exploit Mur15 as a biocatalyst, proof of concept of which is provided.
Collapse
Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Han Nguyen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Xiachang Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Martin Büschleb
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University, GöTammannstr. 2, 37077 Göttingen, Germany
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Schütz
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Rohrbacher
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Pierre Junghanns
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| |
Collapse
|
9
|
Yahiaoui S, Voos K, Haupenthal J, Wichelhaus TA, Frank D, Weizel L, Rotter M, Brunst S, Kramer JS, Proschak E, Ducho C, Hirsch AKH. N-Aryl mercaptoacetamides as potential multi-target inhibitors of metallo-β-lactamases (MBLs) and the virulence factor LasB from Pseudomonas aeruginosa. RSC Med Chem 2021; 12:1698-1708. [PMID: 34778771 PMCID: PMC8528214 DOI: 10.1039/d1md00187f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/23/2021] [Indexed: 12/18/2022] Open
Abstract
Increasing antimicrobial resistance is evolving to be one of the major threats to public health. To reduce the selection pressure and thus to avoid a fast development of resistance, novel approaches aim to target bacterial virulence instead of growth. Another strategy is to restore the activity of antibiotics already in clinical use. This can be achieved by the inhibition of resistance factors such as metallo-β-lactamases (MBLs). Since MBLs can cleave almost all β-lactam antibiotics, including the “last resort” carbapenems, their inhibition is of utmost importance. Here, we report on the synthesis and in vitro evaluation of N-aryl mercaptoacetamides as inhibitors of both clinically relevant MBLs and the virulence factor LasB from Pseudomonas aeruginosa. All tested N-aryl mercaptoacetamides showed low micromolar to submicromolar activities on the tested enzymes IMP-7, NDM-1 and VIM-1. The two most promising compounds were further examined in NDM-1 expressing Klebsiella pneumoniae isolates, where they restored the full activity of imipenem. Together with their LasB-inhibitory activity in the micromolar range, this class of compounds can now serve as a starting point for a multi-target inhibitor approach against both bacterial resistance and virulence, which is unprecedented in antibacterial drug discovery. Simultaneous inhibition of metallo-β-lactamases (MBLs) and virulence factors such as LasB from Pseudomonas aeruginosa offers a new approach to combat antibiotic-resistant pathogens.![]()
Collapse
Affiliation(s)
- Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Marco Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University Campus Building E8 1 66123 Saarbrücken Germany
| |
Collapse
|
10
|
Voos K, Schönauer E, Alhayek A, Haupenthal J, Andreas A, Müller R, Hartmann RW, Brandstetter H, Hirsch AKH, Ducho C. Front Cover: Phosphonate as a Stable Zinc‐Binding Group for “Pathoblocker” Inhibitors of Clostridial Collagenase H (ColH) (ChemMedChem 8/2021). ChemMedChem 2021. [DOI: 10.1002/cmdc.202100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katrin Voos
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Esther Schönauer
- Department of Biosciences and Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization Division of Structural Biology University of Salzburg Billrothstrasse 11 5020 Salzburg Austria
| | - Alaa Alhayek
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Anastasia Andreas
- Department of Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Rolf Müller
- Department of Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Hans Brandstetter
- Department of Biosciences and Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization Division of Structural Biology University of Salzburg Billrothstrasse 11 5020 Salzburg Austria
| | - Anna K. H. Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
- Department of Pharmacy Saarland University Campus E8 1 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
11
|
Voos K, Schönauer E, Alhayek A, Haupenthal J, Andreas A, Müller R, Hartmann RW, Brandstetter H, Hirsch AKH, Ducho C. Phosphonate as a Stable Zinc-Binding Group for "Pathoblocker" Inhibitors of Clostridial Collagenase H (ColH). ChemMedChem 2021; 16:1257-1267. [PMID: 33506625 PMCID: PMC8251769 DOI: 10.1002/cmdc.202000994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/05/2023]
Abstract
Microbial infections are a significant threat to public health, and resistance is on the rise, so new antibiotics with novel modes of action are urgently needed. The extracellular zinc metalloprotease collagenase H (ColH) from Clostridium histolyticum is a virulence factor that catalyses tissue damage, leading to improved host invasion and colonisation. Besides the major role of ColH in pathogenicity, its extracellular localisation makes it a highly attractive target for the development of new antivirulence agents. Previously, we had found that a highly selective and potent thiol prodrug (with a hydrolytically cleavable thiocarbamate unit) provided efficient ColH inhibition. We now report the synthesis and biological evaluation of a range of zinc-binding group (ZBG) variants of this thiol-derived inhibitor, with the mercapto unit being replaced by other zinc ligands. Among these, an analogue with a phosphonate motif as ZBG showed promising activity against ColH, an improved selectivity profile, and significantly higher stability than the thiol reference compound, thus making it an attractive candidate for future drug development.
Collapse
Affiliation(s)
- Katrin Voos
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Esther Schönauer
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Alaa Alhayek
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Jörg Haupenthal
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
| | - Anastasia Andreas
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Hans Brandstetter
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Christian Ducho
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| |
Collapse
|
12
|
Fischer PD, Papadopoulos E, Dempersmier JM, Wang ZF, Nowak RP, Donovan KA, Kalabathula J, Gorgulla C, Junghanns PPM, Kabha E, Dimitrakakis N, Petrov OI, Mitsiades C, Ducho C, Gelev V, Fischer ES, Wagner G, Arthanari H. A biphenyl inhibitor of eIF4E targeting an internal binding site enables the design of cell-permeable PROTAC-degraders. Eur J Med Chem 2021; 219:113435. [PMID: 33892272 DOI: 10.1016/j.ejmech.2021.113435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
Abstract
The eukaryotic translation initiation factor 4E (eIF4E) is the master regulator of cap-dependent protein synthesis. Overexpression of eIF4E is implicated in diseases such as cancer, where dysregulation of oncogenic protein translation is frequently observed. eIF4E has been an attractive target for cancer treatment. Here we report a high-resolution X-ray crystal structure of eIF4E in complex with a novel inhibitor (i4EG-BiP) that targets an internal binding site, in contrast to the previously described inhibitor, 4EGI-1, which binds to the surface. We demonstrate that i4EG-BiP is able to displace the scaffold protein eIF4G and inhibit the proliferation of cancer cells. We provide insights into how i4EG-BiP is able to inhibit cap-dependent translation by increasing the eIF4E-4E-BP1 interaction while diminishing the interaction of eIF4E with eIF4G. Leveraging structural details, we designed proteolysis targeted chimeras (PROTACs) derived from 4EGI-1 and i4EG-BiP and characterized these on biochemical and cellular levels. We were able to design PROTACs capable of binding eIF4E and successfully engaging Cereblon, which targets proteins for proteolysis. However, these initial PROTACs did not successfully stimulate degradation of eIF4E, possibly due to competitive effects from 4E-BP1 binding. Our results highlight challenges of targeted proteasomal degradation of eIF4E that must be addressed by future efforts.
Collapse
Affiliation(s)
- Patrick D Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, 66123, Germany
| | - Evangelos Papadopoulos
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Jon M Dempersmier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zi-Fu Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joann Kalabathula
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Christoph Gorgulla
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Pierre P M Junghanns
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, 66123, Germany
| | - Eihab Kabha
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Nikolaos Dimitrakakis
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
| | - Ognyan I Petrov
- Faculty of Chemistry and Pharmacy, Sofia University, 1 James Bourchier Blvd., 1164, Sofia, Bulgaria
| | | | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, 66123, Germany
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy, Sofia University, 1 James Bourchier Blvd., 1164, Sofia, Bulgaria
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
13
|
Hawner M, Ducho C. Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules. Molecules 2020; 25:molecules25245963. [PMID: 33339365 PMCID: PMC7766908 DOI: 10.3390/molecules25245963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022] Open
Abstract
Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular 'targeting', i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.
Collapse
|
14
|
Niro G, Weck SC, Ducho C. Merging Natural Products: Muraymycin-Sansanmycin Hybrid Structures as Novel Scaffolds for Potential Antibacterial Agents. Chemistry 2020; 26:16875-16887. [PMID: 32897546 PMCID: PMC7756498 DOI: 10.1002/chem.202003387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/07/2020] [Indexed: 02/01/2023]
Abstract
To overcome bacterial resistances, the need for novel antimicrobial agents is urgent. The class of so-called nucleoside antibiotics furnishes promising candidates for the development of new antibiotics, as these compounds block a clinically unexploited bacterial target: the integral membrane protein MraY, a key enzyme in cell wall (peptidoglycan) biosynthesis. Nucleoside antibiotics exhibit remarkable structural diversity besides their uridine-derived core motifs. Some sub-classes also show specific selectivities towards different Gram-positive and Gram-negative bacteria, which are poorly understood so far. Herein, the synthesis of a novel hybrid structure is reported, derived from the 5'-defunctionalized uridine core moiety of muraymycins and the peptide chain of sansanmycin B, as a new scaffold for the development of antimicrobial agents. The reported muraymycin-sansanmycin hybrid scaffold showed nanomolar activity against the bacterial target enzyme MraY, but displayed no significant antibacterial activity against S. aureus, E. coli, and P. aeruginosa.
Collapse
Affiliation(s)
- Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Stefanie C. Weck
- Department of Pharmacy, Pharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| |
Collapse
|
15
|
Wojtyniak M, Schmidtgall B, Kirsch P, Ducho C. Cover Feature: Towards Zwitterionic Oligonucleotides with Improved Properties: the NAA/LNA‐Gapmer Approach (ChemBioChem 22/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Melissa Wojtyniak
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Boris Schmidtgall
- Department of Chemistry University of Paderborn Warburger Str. 100 33098 Paderborn Germany
| | - Philine Kirsch
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
- Department of Chemistry University of Paderborn Warburger Str. 100 33098 Paderborn Germany
| |
Collapse
|
16
|
Abstract
Oligonucleotides (ON) are promising therapeutic candidates, for instance by blocking endogenous mRNA (antisense mechanism). However, ON usually require structural modifications of the native nucleic acid backbone to ensure satisfying pharmacokinetic properties. One such strategy to design novel antisense oligonucleotides is to replace native phosphate diester units by positively charged artificial linkages, thus leading to (partially) zwitterionic backbone structures. Herein, we report a "gapmer" architecture comprised of one zwitterionic central segment ("gap") containing nucleosyl amino acid (NAA) modifications and two outer segments of locked nucleic acid (LNA). This NAA/LNA-gapmer approach furnished a partially zwitterionic ON with optimised properties: i) the formation of stable ON-RNA duplexes with base-pairing fidelity and superior target selectivity at 37 °C; and ii) excellent stability in complex biological media. Overall, the NAA/LNA-gapmer approach is thus established as a strategy to design partially zwitterionic ON for the future development of novel antisense agents.
Collapse
Affiliation(s)
- Melissa Wojtyniak
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Boris Schmidtgall
- Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
| | - Philine Kirsch
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Christian Ducho
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
- Department of ChemistryUniversity of PaderbornWarburger Str. 10033098PaderbornGermany
| |
Collapse
|
17
|
Cui Z, Overbay J, Wang X, Liu X, Zhang Y, Bhardwaj M, Lemke A, Wiegmann D, Niro G, Thorson JS, Ducho C, Van Lanen SG. Pyridoxal-5'-phosphate-dependent alkyl transfer in nucleoside antibiotic biosynthesis. Nat Chem Biol 2020; 16:904-911. [PMID: 32483377 PMCID: PMC7377962 DOI: 10.1038/s41589-020-0548-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/10/2020] [Indexed: 11/09/2022]
Abstract
Several nucleoside antibiotics are structurally characterized by a 5′′-amino-5′′-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside, (5′S,6′S)-5′-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origins of which have yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR-GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-l-methionine (AdoMet) as the direct precursor of the N-alkylamine, but unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5′-phophosate (PLP)-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to utilizing a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway.
Collapse
Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Xiaodong Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Yinan Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.
| |
Collapse
|
18
|
Saady A, Wojtyniak M, Varon E, Böttner V, Kinor N, Shav-Tal Y, Ducho C, Fischer B. Specific, Sensitive, and Quantitative Detection of HER-2 mRNA Breast Cancer Marker by Fluorescent Light-Up Hybridization Probes. Bioconjug Chem 2020; 31:1188-1198. [DOI: 10.1021/acs.bioconjchem.0c00130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Noa Kinor
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
19
|
Saady A, Steinman NY, Wojtyniak M, Ducho C, Fischer B. Synthesis of 2'-Deoxyuridine Modified with a 3,5-Difluoro-4-Methoxybenzylidene Imidazolinone Derivative for Incorporation into Oligonucleotide Probes for Detection of HER2 Breast Cancer Marker. ACTA ACUST UNITED AC 2020; 80:e104. [PMID: 32032480 DOI: 10.1002/cpnc.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleoside intercalator conjugates (NICs) describe an innovative methodology developed in our research group for preparation of fluorescence turn-on DNA hybridization probes targeting specific mRNA sequences (e.g., breast cancer markers). In this methodology, we conjugate a non-fluorescent intercalator to the base of a nucleic acid (e.g., uracil) via a flexible spacer. This modified monomer can be incorporated into oligonucleotides by solid-phase synthesis and a large fluorescence enhancement is observed when the modified oligonucleotide is hybridized with its complementary strand due to intercalation of the fluorophore between the two strands. 5-(6-p-Methoxybenzylidene imidazolinone-1-hexene)-2'-deoxyuridine (dUMBI ) is a synthetic monomer to which 4-methoxybenzylidene imidazolinone (MBI), the fluorescent chromophore of green fluorescent protein (GFP), has been conjugated via a flexible spacer. The detection of human epidermal growth factor receptor 2 (HER2) mRNA by this probe has already been established by our group. The fluorescent intensity of the single-strand DNA can be considered as negligible due to the free rotation of the fluorophore. Upon hybridization, however, the flexible spacer allows for the intercalation of the fluorophore between the hybridized strands, giving rise to enhanced fluorescence and indicating the presence of target mRNA. 3,5-Difluoro-4-methoxybenzylidene (DFMBI) has enhanced photophysical properties compared to MBI fluorophore. This protocol describes a simple, reliable, efficient, and general method for the synthesis of improved derivative dUDFMBI as a monomer of fluorescent turn-on DNA hybridization probe with application for detection of HER2 mRNA. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Synthesis of 5-[(6)-3,5-difluoro-4-methoxybenzylidene imidazolinone-1-hexene]-2'-deoxyuridine.
Collapse
Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| | - Noam Y Steinman
- Institute of Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
20
|
Heib A, Niro G, Weck SC, Koppermann S, Ducho C. Muraymycin Nucleoside Antibiotics: Structure-Activity Relationship for Variations in the Nucleoside Unit. Molecules 2019; 25:molecules25010022. [PMID: 31861655 PMCID: PMC6983020 DOI: 10.3390/molecules25010022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/04/2022] Open
Abstract
Muraymycins are a subclass of naturally occurring nucleoside antibiotics with promising antibacterial activity. They inhibit the bacterial enzyme translocase I (MraY), a clinically yet unexploited target mediating an essential intracellular step of bacterial peptidoglycan biosynthesis. Several structurally simplified muraymycin analogues have already been synthesized for structure–activity relationship (SAR) studies. We now report on novel derivatives with unprecedented variations in the nucleoside unit. For the synthesis of these new muraymycin analogues, we employed a bipartite approach facilitating the introduction of different nucleosyl amino acid motifs. This also included thymidine- and 5-fluorouridine-derived nucleoside core structures. Using an in vitro assay for MraY activity, it was found that the introduction of substituents in the 5-position of the pyrimidine nucleobase led to a significant loss of inhibitory activity towards MraY. The loss of nucleobase aromaticity (by reduction of the uracil C5-C6 double bond) resulted in a ca. tenfold decrease in inhibitory potency. In contrast, removal of the 2′-hydroxy group furnished retained activity, thus demonstrating that modifications of the ribose moiety might be well-tolerated. Overall, these new SAR insights will guide the future design of novel muraymycin analogues for their potential development towards antibacterial drug candidates.
Collapse
|
21
|
Leyerer K, Koppermann S, Ducho C. Front Cover: Solid Phase-Supported Synthesis of Muraymycin Analogues (Eur. J. Org. Chem. 45/2019). European J Org Chem 2019. [DOI: 10.1002/ejoc.201901640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kristin Leyerer
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Stefan Koppermann
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
22
|
Affiliation(s)
- Kristin Leyerer
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Stefan Koppermann
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
23
|
Saady A, Böttner V, Meng M, Varon E, Shav-Tal Y, Ducho C, Fischer B. An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker. Eur J Med Chem 2019; 173:99-106. [PMID: 30991278 DOI: 10.1016/j.ejmech.2019.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/05/2019] [Accepted: 04/04/2019] [Indexed: 01/15/2023]
Abstract
Diagnosis and treatment of breast cancer can be greatly enhanced and personalized based on the quantitative detection of mRNA markers. Here, we targeted the development of a fluorescent oligonucleotide probe to detect specifically the HER-2 mRNA breast cancer marker. We have selected the chromophore of the Green Fluorescent Protein (GFP), 4-hydroxybenzylidene imidazolinone (HBI), as a fluorophore covalently bound to an oligonucleotide probe and potentially capable of intercalating within a probe-mRNA duplex. We first synthesized the two-ring scaffold of the HBI chromophore 5 and coupled it to 2'-deoxyuridine at C5-position via a 7-atom-spacer, to give 4. Indeed, in the highly viscous glycerol used to mimic the reduced conformational flexibility of the intercalated HBI, chromophore 4 displayed a quantum yield of 0.29 and brightness of 20600 M-1cm-1, while no fluorescent signal was observed in methanol. Next, we synthesized a 20-mer oligonucleotide probe incorporating 4 at position 6 (5'-CCCGTUTCAACAGGAGTTTC-3'), ONHBI, targeting nucleotides 1233-1253 of HER-2 mRNA. A 16-fold enhancement of ONHBI emission intensity upon hybridization with the complementary RNA vs that of the oligonucleotide probe alone indicated the presence of target oligonucleotide and proved the intercalation of the chromophore (quantum yield 0.52; brightness 23500 M-1cm-1). Even more, an 11-fold enhancement of ONHBI emission (quantum yield 0.50; brightness 23200 M-1cm-1) was observed when the probe was mixed with total RNA extract from a human cell line that has high levels of HER2 mRNA expression. Thus, we propose ONHBI as a promising probe potentially useful for the sensitive and specific detection of HER2 mRNA breast cancer marker.
Collapse
Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| |
Collapse
|
24
|
Linder R, Ducho C. Unified Synthesis of Densely Functionalized Amino Acid Building Blocks for the Preparation of Caprazamycin Nucleoside Antibiotics. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ruth Linder
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
25
|
Wiegmann D, Koppermann S, Ducho C. Aminoribosylated Analogues of Muraymycin Nucleoside Antibiotics. Molecules 2018; 23:molecules23123085. [PMID: 30486316 PMCID: PMC6320880 DOI: 10.3390/molecules23123085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Nucleoside antibiotics are uridine-derived natural products that inhibit the bacterial membrane protein MraY. MraY is a key enzyme in the membrane-associated intracellular stages of peptidoglycan biosynthesis and therefore considered to be a promising, yet unexploited target for novel antibacterial agents. Muraymycins are one subclass of such naturally occurring MraY inhibitors. As part of structure-activity relationship (SAR) studies on muraymycins and their analogues, we now report on novel derivatives with different attachment of one characteristic structural motif, i.e., the aminoribose moiety normally linked to the muraymycin glycyluridine core unit. Based on considerations derived from an X-ray co-crystal structure, we designed and synthesised muraymycin analogues having the aminoribose attached (via a linker) to either the glycyluridine amino group or to the uracil nucleobase. Reference compounds bearing the non-aminoribosylated linker units were also prepared. It was found that the novel aminoribosylated analogues were inactive as MraY inhibitors in vitro, but that the glycyluridine-modified reference compound retained most of the inhibitory potency relative to the unmodified parent muraymycin analogue. These results point to 6′-N-alkylated muraymycin analogues as a potential novel variation of the muraymycin scaffold for future SAR optimisation.
Collapse
Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| |
Collapse
|
26
|
Meng M, Schmidtgall B, Ducho C. Enhanced Stability of DNA Oligonucleotides with Partially Zwitterionic Backbone Structures in Biological Media. Molecules 2018; 23:molecules23112941. [PMID: 30423832 PMCID: PMC6278555 DOI: 10.3390/molecules23112941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 11/16/2022] Open
Abstract
Deficient stability towards nuclease-mediated degradation is one of the most relevant tasks in the development of oligonucleotide-derived biomedical agents. This hurdle can be overcome through modifications to the native oligonucleotide backbone structure, with the goal of simultaneously retaining the unique hybridization properties of nucleic acids. The nucleosyl amino acid (NAA)-modification is a recently introduced artificial cationic backbone linkage. Partially zwitterionic NAA-modified oligonucleotides had previously shown hybridization with DNA strands with retained base-pairing fidelity. In this study, we report the significantly enhanced stability of NAA-modified oligonucleotides towards 3′- and 5′-exonuclease-mediated degradation as well as in complex biological media such as human plasma and whole cell lysate. This demonstrates the potential versatility of the NAA-motif as a backbone modification for the development of biomedically active oligonucleotide analogues.
Collapse
Affiliation(s)
- Melissa Meng
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Boris Schmidtgall
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Christian Ducho
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| |
Collapse
|
27
|
Abstract
Their unique ability to selectively bind specific nucleic acid sequences makes oligonucleotides promising bioactive agents. However, modifications of the nucleic acid structure are an essential prerequisite for their application in vivo or even in cellulo. The oligoanionic backbone structure of oligonucleotides mainly hampers their ability to penetrate biological barriers such as cellular membranes. Hence, particular attention has been given to structural modifications of oligonucleotides which reduce their overall number of negative charges. One such approach is the site-specific replacement of the negatively charged phosphate diester linkage with alternative structural motifs which are positively charged at physiological pH, thus resulting in zwitterionic or even oligocationic backbone structures. This review provides a general overview of this concept and summarizes research on four according artificial backbone linkages: aminoalkylated phosphoramidates (and related systems), guanidinium groups, S-methylthiourea motifs, and nucleosyl amino acid (NAA)-derived modifications. The synthesis and properties of the corresponding oligonucleotide analogues are described.
Collapse
Affiliation(s)
- Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| |
Collapse
|
28
|
Cui Z, Liu X, Overbay J, Cai W, Wang X, Lemke A, Wiegmann D, Niro G, Thorson JS, Ducho C, Van Lanen SG. Enzymatic Synthesis of the Ribosylated Glycyl-Uridine Disaccharide Core of Peptidyl Nucleoside Antibiotics. J Org Chem 2018; 83:7239-7249. [PMID: 29768920 DOI: 10.1021/acs.joc.8b00855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Muraymycins belong to a family of nucleoside antibiotics that have a distinctive disaccharide core consisting of 5-amino-5-deoxyribofuranose (ADR) attached to 6'- N-alkyl-5'- C-glycyluridine (GlyU). Here, we functionally assign and characterize six enzymes from the muraymycin biosynthetic pathway involved in the core assembly that starts from uridine monophosphate (UMP). The biosynthesis is initiated by Mur16, a nonheme Fe(II)- and α-ketoglutarate-dependent dioxygenase, followed by four transferase enzymes: Mur17, a pyridoxal-5'-phosphate (PLP)-dependent transaldolase; Mur20, an aminotransferase; Mur26, a pyrimidine phosphorylase; and Mur18, a nucleotidylyltransferase. The pathway culminates in glycosidic bond formation in a reaction catalyzed by an additional transferase enzyme, Mur19, a ribosyltransferase. Analysis of the biochemical properties revealed several noteworthy discoveries including that (i) Mur16 and downstream enzymes can also process 2'-deoxy-UMP to generate a 2-deoxy-ADR, which is consistent with the structure of some muraymycin congeners; (ii) Mur20 prefers l-Tyr as the amino donor source; (iii) Mur18 activity absolutely depends on the amine functionality of the ADR precursor consistent with the nucleotidyltransfer reaction occurring after the Mur20-catalyzed aminotransfer reaction; and (iv) the bona fide sugar acceptor for Mur19 is (5' S,6' S)-GlyU, suggesting that ribosyltransfer occurs prior to N-alkylation of GlyU. Finally, a one-pot, six-enzyme reaction was utilized to generate the ADR-GlyU disaccharide core starting from UMP.
Collapse
Affiliation(s)
| | | | | | | | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing 210023 , People's Republic of China
| | - Anke Lemke
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2 3 , 66123 Saarbrücken , Germany
| | - Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2 3 , 66123 Saarbrücken , Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2 3 , 66123 Saarbrücken , Germany
| | | | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2 3 , 66123 Saarbrücken , Germany
| | | |
Collapse
|
29
|
Abstract
Muraymycins are nucleoside antibiotics isolated from Streptomyces sp. NRRL 30471 and several mutant strains thereof that were generated by random, chemical mutagenesis. Reinvestigation of two mutant strains using new media conditions led to the isolation of three new muraymycin congeners, named B8, B9, and C6 (1-3), as well as a known muraymycin, C1. Structures of the compounds were elucidated by HRMS and 1D and 2D NMR spectroscopic analyses. Complete 2D NMR assignments for the known muraymycin C1 are also provided for the first time. Compounds 1 and 2, which differ from other muraymycins by having an elongated, terminally branched fatty acid side chain, had picomolar IC50 values against Staphylococcus aureus and Aquifex aeolicus MraY and showed good antibacterial activity against S. aureus (MIC = 2 and 6 μg/mL, respectively) and Escherichia coli Δ tolC (MIC = 4 and 2 μg/mL, respectively). Compound 3, which is characterized by an N-acetyl modification of the primary amine of the dissacharide core that is shared among nearly all of the reported muraymycin congeners, greatly reduced its inhibitory and antibacterial activity compared to nonacylated muraymycin C1, which possibly indicates this modification is used for self-resistance.
Collapse
Affiliation(s)
- Zheng Cui
- Department of Pharmaceutical Sciences, College of
Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Xiachang Wang
- Center for Pharmaceutical Research and Innovation,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United
States
- Jiangsu Key Laboratory for Functional Substance of
Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine,
Nanjing 210023, People’s Republic of China
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal
Chemistry, Saarland University Campus C2 3, 66123 Saarbrücken, Germany
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of
Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center for Pharmaceutical Research and Innovation,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United
States
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal
Chemistry, Saarland University Campus C2 3, 66123 Saarbrücken, Germany
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of
Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| |
Collapse
|
30
|
Koppermann S, Cui Z, Fischer PD, Wang X, Ludwig J, Thorson JS, Van Lanen SG, Ducho C. Insights into the Target Interaction of Naturally Occurring Muraymycin Nucleoside Antibiotics. ChemMedChem 2018; 13:779-784. [PMID: 29438582 PMCID: PMC6019934 DOI: 10.1002/cmdc.201700793] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/02/2018] [Indexed: 11/08/2022]
Abstract
Muraymycins are a subclass of antimicrobially active uridine-derived natural products. Biological data on several muraymycin analogues have been reported, including some inhibitory in vitro activities toward their target protein, the bacterial membrane enzyme MraY. However, a structure-activity relationship (SAR) study on naturally occurring muraymycins based on such in vitro data has been missing so far. In this work, we report a detailed SAR investigation on representatives of the four muraymycin subgroups A-D using a fluorescence-based in vitro MraY assay. For some muraymycins, inhibition of MraY with IC50 values in the low-picomolar range was observed. These inhibitory potencies were compared with antibacterial activities and were correlated to modelling data derived from a previously reported X-ray crystal structure of MraY in complex with a muraymycin inhibitor. Overall, these results will pave the way for the development of muraymycin analogues with optimized properties as antibacterial drug candidates.
Collapse
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Patrick D Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, P.R. China
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Jannine Ludwig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| |
Collapse
|
31
|
Koppermann S, Cui Z, Fischer PD, Wang X, Ludwig J, Thorson JS, Van Lanen SG, Ducho C. Cover Feature: Insights into the Target Interaction of Naturally Occurring Muraymycin Nucleoside Antibiotics (ChemMedChem 8/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy; University of Kentucky; 789 S. Limestone Street Lexington KY 40536 USA
| | - Patrick D. Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy; Nanjing University of Chinese Medicine; Nanjing 210023 P.R. China
- Center for Pharmaceutical Research and Innovation, College of Pharmacy; University of Kentucky; 789 S. Limestone Street Lexington KY 40536 USA
| | - Jannine Ludwig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy; University of Kentucky; 789 S. Limestone Street Lexington KY 40536 USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy; University of Kentucky; 789 S. Limestone Street Lexington KY 40536 USA
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy; University of Kentucky; 789 S. Limestone Street Lexington KY 40536 USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
32
|
El-Sharkawy LY, El-Sakhawy RA, Abdel-Halim M, Lee K, Piazza GA, Ducho C, Hartmann RW, Abadi AH. Design and synthesis of novel annulated thienopyrimidines as phosphodiesterase 5 (PDE5) inhibitors. Arch Pharm (Weinheim) 2018; 351:e1800018. [DOI: 10.1002/ardp.201800018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Lina Y. El-Sharkawy
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry; German University in Cairo; Cairo Egypt
| | - Rowaida A. El-Sakhawy
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry; German University in Cairo; Cairo Egypt
| | - Mohammad Abdel-Halim
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry; German University in Cairo; Cairo Egypt
| | - Kevin Lee
- Drug Discovery Research Center, Mitchell Cancer Institute; University of South Alabama; Mobile Alabama USA
| | - Gary A. Piazza
- Drug Discovery Research Center, Mitchell Cancer Institute; University of South Alabama; Mobile Alabama USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Saarbrücken Germany
| | - Rolf W. Hartmann
- Department of Drug Design and Optimization; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Saarbrücken Germany
| | - Ashraf H. Abadi
- Faculty of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry; German University in Cairo; Cairo Egypt
| |
Collapse
|
33
|
Schmidtgall B, Kuepper A, Meng M, Grossmann TN, Ducho C. Frontispiece: Oligonucleotides with Cationic Backbone and Their Hybridization with DNA: Interplay of Base Pairing and Electrostatic Attraction. Chemistry 2018. [DOI: 10.1002/chem.201880764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Boris Schmidtgall
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
- Department of Chemistry; University of Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Arne Kuepper
- Chemical Genomics Centre (CGC) of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Melissa Meng
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Tom N. Grossmann
- Chemical Genomics Centre (CGC) of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Christian Ducho
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
- Department of Chemistry; University of Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| |
Collapse
|
34
|
Schmidtgall B, Kuepper A, Meng M, Grossmann TN, Ducho C. Oligonucleotides with Cationic Backbone and Their Hybridization with DNA: Interplay of Base Pairing and Electrostatic Attraction. Chemistry 2017; 24:1544-1553. [PMID: 29048135 PMCID: PMC5814856 DOI: 10.1002/chem.201704338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Indexed: 01/01/2023]
Abstract
Non‐natural oligonucleotides represent important (bio)chemical tools and potential therapeutic agents. Backbone modifications altering hybridization properties and biostability can provide useful analogues. Here, we employ an artificial nucleosyl amino acid (NAA) motif for the synthesis of oligonucleotides containing a backbone decorated with primary amines. An oligo‐T sequence of this cationic DNA analogue shows significantly increased affinity for complementary DNA. Notably, hybridization with DNA is still governed by Watson–Crick base pairing. However, single base pair mismatches are tolerated and some degree of sequence‐independent interactions between the cationic NAA backbone and fully mismatched DNA are observed. These findings demonstrate that a high density of positive charges directly connected to the oligonucleotide backbone can affect Watson–Crick base pairing. This provides a paradigm for the design of therapeutic oligonucleotides with altered backbone charge patterns.
Collapse
Affiliation(s)
- Boris Schmidtgall
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Arne Kuepper
- Chemical Genomics Centre (CGC) of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre (CGC) of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| |
Collapse
|
35
|
Ducho C, Wiegmann D, Spork A, Niro G. Thieme Chemistry Journals Awardees – Where Are They Now? Ribosylation of an Acid-Labile Glycosyl Acceptor as a Potential Key Step for the Synthesis of Nucleoside Antibiotics. Synlett 2017. [DOI: 10.1055/s-0036-1591517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Naturally occurring nucleoside antibiotics (e.g., muraymycins and caprazamycins) represent attractive lead structures for the development of urgently needed novel antibacterial agents. One major challenge in the total synthesis of muraymycins, caprazamycins, and their analogues is the efficient construction of the densely functionalized aminoribosylated uridine-derived core unit. In order to avoid tedious protecting-group manipulations, we have aimed to conduct the aminoribosylation step with an acid-labile glycosyl acceptor. Therefore, different glycosylation approaches have been studied, with pentenyl glycosides giving the best results.
Collapse
Affiliation(s)
- Christian Ducho
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry
- Georg-August-University Göttingen, Department of Chemistry, Institute of Organic and Biomolecular Chemistry
| | - Daniel Wiegmann
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry
| | - Anatol Spork
- Georg-August-University Göttingen, Department of Chemistry, Institute of Organic and Biomolecular Chemistry
| | - Giuliana Niro
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry
| |
Collapse
|
36
|
Schönauer E, Kany AM, Haupenthal J, Hüsecken K, Hoppe IJ, Voos K, Yahiaoui S, Elsässer B, Ducho C, Brandstetter H, Hartmann RW. Discovery of a Potent Inhibitor Class with High Selectivity toward Clostridial Collagenases. J Am Chem Soc 2017; 139:12696-12703. [PMID: 28820255 PMCID: PMC5607459 DOI: 10.1021/jacs.7b06935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Secreted virulence
factors like bacterial collagenases are conceptually
attractive targets for fighting microbial infections. However, previous
attempts to develop potent compounds against these metalloproteases
failed to achieve selectivity against human matrix metalloproteinases
(MMPs). Using a surface plasmon resonance-based screening complemented
with enzyme inhibition assays, we discovered an N-aryl mercaptoacetamide-based inhibitor scaffold that showed
sub-micromolar affinities toward collagenase H (ColH) from the human
pathogen Clostridium histolyticum. Moreover, these
inhibitors also efficiently blocked the homologous bacterial collagenases,
ColG from C. histolyticum, ColT from C. tetani, and ColQ1 from the Bacillus cereus strain Q1,
while showing negligible activity toward human MMPs-1, -2, -3, -7,
-8, and -14. The most active compound displayed a more than 1000-fold
selectivity over human MMPs. This selectivity can be rationalized
by the crystal structure of ColH with this compound, revealing a distinct
non-primed binding mode to the active site. The non-primed binding
mode presented here paves the way for the development of selective
broad-spectrum bacterial collagenase inhibitors with potential therapeutic
application in humans.
Collapse
Affiliation(s)
- Esther Schönauer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Andreas M Kany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kristina Hüsecken
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabel J Hoppe
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Samir Yahiaoui
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Brigitta Elsässer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| |
Collapse
|
37
|
Wohnig S, Spork AP, Koppermann S, Mieskes G, Gisch N, Jahn R, Ducho C. Total Synthesis of Dansylated Park's Nucleotide for High-Throughput MraY Assays. Chemistry 2016; 22:17813-17819. [PMID: 27791327 DOI: 10.1002/chem.201604279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/11/2022]
Abstract
The membrane protein translocase I (MraY) is a key enzyme in bacterial peptidoglycan biosynthesis. It is therefore frequently discussed as a target for the development of novel antibiotics. The screening of compound libraries for the identification of MraY inhibitors is enabled by an established fluorescence-based MraY assay. However, this assay requires a dansylated derivative of the bacterial biosynthetic intermediate Park's nucleotide as the MraY substrate. Isolation of Park's nucleotide from bacteria and subsequent dansylation only furnishes limited amounts of this substrate, thus hampering the high-throughput screening for MraY inhibitors. Accordingly, the efficient provision of dansylated Park's nucleotide is a major bottleneck in the exploration of this promising drug target. In this work, we present the first total synthesis of dansylated Park's nucleotide, affording an unprecedented amount of the target compound for high-throughput MraY assays.
Collapse
Affiliation(s)
- Stephanie Wohnig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Anatol P Spork
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany.,Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Gottfried Mieskes
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845, Borstel, Germany
| | - Reinhard Jahn
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| |
Collapse
|
38
|
Graef F, Vukosavljevic B, Michel JP, Wirth M, Ries O, De Rossi C, Windbergs M, Rosilio V, Ducho C, Gordon S, Lehr CM. The bacterial cell envelope as delimiter of anti-infective bioavailability - An in vitro permeation model of the Gram-negative bacterial inner membrane. J Control Release 2016; 243:214-224. [PMID: 27769806 DOI: 10.1016/j.jconrel.2016.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/11/2016] [Accepted: 10/15/2016] [Indexed: 11/26/2022]
Abstract
Gram-negative bacteria possess a unique and complex cell envelope, composed of an inner and outer membrane separated by an intermediate cell wall-containing periplasm. This tripartite structure acts intrinsically as a significant biological barrier, often limiting the permeation of anti-infectives, and so preventing such drugs from reaching their target. Furthermore, identification of the specific permeation-limiting envelope component proves difficult in the case of many anti-infectives, due to the challenges associated with isolation of individual cell envelope structures in bacterial culture. The development of an in vitro permeation model of the Gram-negative inner membrane, prepared by repeated coating of physiologically-relevant phospholipids on Transwell® filter inserts, is therefore reported, as a first step in the development of an overall cell envelope model. Characterization and permeability investigations of model compounds as well as anti-infectives confirmed the suitability of the model for quantitative and kinetically-resolved permeability assessment, and additionally confirmed the importance of employing bacteria-specific base materials for more accurate mimicking of the inner membrane lipid composition - both advantages compared to the majority of existing in vitro approaches. Additional incorporation of further elements of the Gram-negative bacterial cell envelope could ultimately facilitate model application as a screening tool in anti-infective drug discovery or formulation development.
Collapse
Affiliation(s)
- Florian Graef
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany.
| | - Branko Vukosavljevic
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany.
| | - Jean-Philippe Michel
- Institut Galien Paris Sud, UMR 8612, Univ Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.B. Clément, F-92290 Châtenay-Malabry, France.
| | - Marius Wirth
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Oliver Ries
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany
| | - Chiara De Rossi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany.
| | - Maike Windbergs
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany.
| | - Véronique Rosilio
- Institut Galien Paris Sud, UMR 8612, Univ Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.B. Clément, F-92290 Châtenay-Malabry, France.
| | - Christian Ducho
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Sarah Gordon
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany.
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Department of Drug Delivery, Campus E8 1, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, Biopharmacy and Pharmaceutical Technology, Campus E8 1, 66123 Saarbrücken, Germany.
| |
Collapse
|
39
|
Koppermann S, Ducho C. Natural Products at Work: Structural Insights into Inhibition of the Bacterial Membrane Protein MraY. Angew Chem Int Ed Engl 2016; 55:11722-4. [DOI: 10.1002/anie.201606396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
40
|
Koppermann S, Ducho C. Naturstoffe bei der Arbeit: strukturelle Einblicke in die Inhibition des bakteriellen Membranproteins MraY. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stefan Koppermann
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| | - Christian Ducho
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| |
Collapse
|
41
|
Wiegmann D, Koppermann S, Wirth M, Niro G, Leyerer K, Ducho C. Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents. Beilstein J Org Chem 2016; 12:769-795. [PMID: 27340469 PMCID: PMC4902027 DOI: 10.3762/bjoc.12.77] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/23/2022] Open
Abstract
Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure-activity relationship (SAR) studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.
Collapse
Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Marius Wirth
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Kristin Leyerer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| |
Collapse
|
42
|
Lemke A, Ducho C. Synthesis of Deuterium-Labelled 3-Hydroxy- L-arginine: Comparative Studies on Different Protecting-Group Strategies. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
43
|
Ducho C. Enzymatically Cleavable siRNA Prodrugs: a New Paradigm for the Intracellular Delivery of RNA-Based Therapeutics. ChemMedChem 2015; 10:1625-7. [DOI: 10.1002/cmdc.201500279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Indexed: 11/06/2022]
|
44
|
Schmidtgall B, Spork AP, Wachowius F, Höbartner C, Ducho C. Synthesis and properties of DNA oligonucleotides with a zwitterionic backbone structure. Chem Commun (Camb) 2015; 50:13742-5. [PMID: 25251903 DOI: 10.1039/c4cc06371f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The nucleosyl amino acid (NAA)-modification of oligonucleotides is introduced, which enables the preparation of oligonucleotides with zwitterionic backbone structures. It is demonstrated that partially zwitterionic NAA-modified DNA oligonucleotides are capable of duplex formation with native polyanionic counterstrands and show retained sensitivity towards base-pairing mismatches.
Collapse
Affiliation(s)
- Boris Schmidtgall
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33 098 Paderborn, Germany
| | | | | | | | | |
Collapse
|
45
|
Rodolis MT, Mihalyi A, Ducho C, Eitel K, Gust B, Goss RJM, Bugg TDH. Mechanism of action of the uridyl peptide antibiotics: an unexpected link to a protein-protein interaction site in translocase MraY. Chem Commun (Camb) 2015; 50:13023-5. [PMID: 25222373 DOI: 10.1039/c4cc06516f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pacidamycin and muraymycin uridyl peptide antibiotics show some structural resemblance to an Arg-Trp-x-x-Trp sequence motif for protein-protein interaction between bacteriophage ϕX174 protein E and E. coli translocase MraY. Members of the UPA class, and a synthetic uridine-peptide analogue, were found to show reduced levels of inhibition to F288L or E287A mutant MraY enzymes, implying that the UPAs interact at this extracellular site as part of the enzyme inhibition mechanism.
Collapse
Affiliation(s)
- Maria T Rodolis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
| | | | | | | | | | | | | |
Collapse
|
46
|
Cai W, Goswami A, Yang Z, Liu X, Green KD, Barnard-Britson S, Baba S, Funabashi M, Nonaka K, Sunkara M, Morris AJ, Spork AP, Ducho C, Garneau-Tsodikova S, Thorson JS, Van Lanen SG. The Biosynthesis of Capuramycin-type Antibiotics: IDENTIFICATION OF THE A-102395 BIOSYNTHETIC GENE CLUSTER, MECHANISM OF SELF-RESISTANCE, AND FORMATION OF URIDINE-5'-CARBOXAMIDE. J Biol Chem 2015; 290:13710-24. [PMID: 25855790 DOI: 10.1074/jbc.m115.646414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Indexed: 11/06/2022] Open
Abstract
A-500359s, A-503083s, and A-102395 are capuramycin-type nucleoside antibiotics that were discovered using a screen to identify inhibitors of bacterial translocase I, an essential enzyme in peptidoglycan cell wall biosynthesis. Like the parent capuramycin, A-500359s and A-503083s consist of three structural components: a uridine-5'-carboxamide (CarU), a rare unsaturated hexuronic acid, and an aminocaprolactam, the last of which is substituted by an unusual arylamine-containing polyamide in A-102395. The biosynthetic gene clusters for A-500359s and A-503083s have been reported, and two genes encoding a putative non-heme Fe(II)-dependent α-ketoglutarate:UMP dioxygenase and an l-Thr:uridine-5'-aldehyde transaldolase were uncovered, suggesting that C-C bond formation during assembly of the high carbon (C6) sugar backbone of CarU proceeds from the precursors UMP and l-Thr to form 5'-C-glycyluridine (C7) as a biosynthetic intermediate. Here, isotopic enrichment studies with the producer of A-503083s were used to indeed establish l-Thr as the direct source of the carboxamide of CarU. With this knowledge, the A-102395 gene cluster was subsequently cloned and characterized. A genetic system in the A-102395-producing strain was developed, permitting the inactivation of several genes, including those encoding the dioxygenase (cpr19) and transaldolase (cpr25), which abolished the production of A-102395, thus confirming their role in biosynthesis. Heterologous production of recombinant Cpr19 and CapK, the transaldolase homolog involved in A-503083 biosynthesis, confirmed their expected function. Finally, a phosphotransferase (Cpr17) conferring self-resistance was functionally characterized. The results provide the opportunity to use comparative genomics along with in vivo and in vitro approaches to probe the biosynthetic mechanism of these intriguing structures.
Collapse
Affiliation(s)
- Wenlong Cai
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Anwesha Goswami
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Zhaoyong Yang
- the Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China
| | - Xiaodong Liu
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Keith D Green
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Sandra Barnard-Britson
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Satoshi Baba
- the New Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Masanori Funabashi
- the Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co., Ltd., Tokyo, Japan
| | - Koichi Nonaka
- the Biologics Technology Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Tokyo 103-8426, Japan
| | - Manjula Sunkara
- the Division of Cardiovascular Medicine and Gill Heart Institute, College of Medicine, University of Kentucky, Lexington, Kentucky 40506, and
| | - Andrew J Morris
- the Division of Cardiovascular Medicine and Gill Heart Institute, College of Medicine, University of Kentucky, Lexington, Kentucky 40506, and
| | - Anatol P Spork
- the Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Christian Ducho
- the Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Sylvie Garneau-Tsodikova
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Jon S Thorson
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506
| | - Steven G Van Lanen
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506,
| |
Collapse
|
47
|
Schmidtgall B, Höbartner C, Ducho C. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks. Beilstein J Org Chem 2015; 11:50-60. [PMID: 25670992 PMCID: PMC4311628 DOI: 10.3762/bjoc.11.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022] Open
Abstract
Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.
Collapse
Affiliation(s)
- Boris Schmidtgall
- Department of Chemistry, University of Paderborn, Warburger Str. 100, 33 098 Paderborn, Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66 123 Saarbrücken, Germany
| | - Claudia Höbartner
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37 077 Göttingen, Germany
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37 077 Göttingen, Germany
| | - Christian Ducho
- Department of Chemistry, University of Paderborn, Warburger Str. 100, 33 098 Paderborn, Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66 123 Saarbrücken, Germany
| |
Collapse
|
48
|
Ries O, Carnarius C, Steinem C, Ducho C. Membrane-interacting properties of the functionalised fatty acid moiety of muraymycin antibiotics. Med Chem Commun 2015. [DOI: 10.1039/c4md00526k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simplified model system is introduced to elucidate the significance of the ω-functionalised fatty acid moiety of muraymycin nucleoside antibiotics for membrane interaction and penetration.
Collapse
Affiliation(s)
- Oliver Ries
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Christian Carnarius
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Claudia Steinem
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| | - Christian Ducho
- Georg-August-University Göttingen
- Department of Chemistry
- Institute of Organic and Biomolecular Chemistry
- 37 077 Göttingen
- Germany
| |
Collapse
|
49
|
Spork AP, Büschleb M, Ries O, Wiegmann D, Boettcher S, Mihalyi A, Bugg TDH, Ducho C. Frontispiece: Lead Structures for New Antibacterials: Stereocontrolled Synthesis of a Bioactive Muraymycin Analogue. Chemistry 2014. [DOI: 10.1002/chem.201484761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
50
|
Spork AP, Büschleb M, Ries O, Wiegmann D, Boettcher S, Mihalyi A, Bugg TDH, Ducho C. Lead structures for new antibacterials: stereocontrolled synthesis of a bioactive muraymycin analogue. Chemistry 2014; 20:15292-7. [PMID: 25318977 DOI: 10.1002/chem.201404775] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 11/10/2022]
Abstract
Naturally occurring muraymycin nucleoside antibiotics represent a promising class of novel antibacterial agents. The structural complexity suggests the investigation of simplified analogues as potential lead structures, which can then be further optimized towards highly potent antimicrobials. Herein we report studies on muraymycin-derived potential lead structures lacking an aminoribose motif found in most naturally occurring muraymycins. We have identified a 5'-defunctionalized motif to be ideal in terms of stability and chemical accessibility and have synthesized a full-length muraymycin analogue based on this structure using a novel fully stereocontrolled route. The obtained 5'-deoxy analogue of the natural product muraymycin C4 showed good inhibitory properties towards the bacterial target protein MraY, sufficient pharmacokinetic stability and no cytotoxicity against human cells, thus making it a promising lead for antibacterial drug development.
Collapse
Affiliation(s)
- Anatol P Spork
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken (Germany); Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077 Göttingen (Germany)
| | | | | | | | | | | | | | | |
Collapse
|