1
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Nonarath HJT, Jackson MA, Penoske RM, Zahrt TC, Price NPJ, Link BA. The tunicamycin derivative TunR2 exhibits potent antibiotic properties with low toxicity in an in vivo Mycobacterium marinum-zebrafish TB infection model. J Antibiot (Tokyo) 2024; 77:245-256. [PMID: 38238588 DOI: 10.1038/s41429-023-00694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 03/28/2024]
Abstract
Tunicamycins (TUN) are well-defined, Streptomyces-derived natural products that inhibit protein N-glycosylation in eukaryotes, and by a conserved mechanism also block bacterial cell wall biosynthesis. TUN inhibits the polyprenylphosphate-N-acetyl-hexosamine-1-phospho-transferases (PNPT), an essential family of enzymes found in both bacteria and eukaryotes. We have previously published the development of chemically modified TUN, called TunR1 and TunR2, that have considerably reduced activity on eukaryotes but that retain the potent antibacterial properties. A mechanism for this reduced toxicity has also been reported. TunR1 and TunR2 have been tested against mammalian cell lines in culture and against live insect cells but, until now, no in vivo evaluation has been undertaken for vertebrates. In the current work, TUN, TunR1, and TunR2 are investigated for their relative toxicity and antimycobacterial activity in zebrafish using a well-established Mycobacterium marinum (M. marinum) infection system, a model for studying human Mycobacterium tuberculosis infections. We also report the relative ability to activate the unfolded protein response (UPR), the known mechanism for the eukaryotic toxicity observed with TUN treatment. Importantly, TunR1 and TunR2 retained their antimicrobial properties, as evidenced by a reduction in M. marinum bacterial burden, compared to DMSO-treated zebrafish. In summary, findings from this study highlight the characteristics of recently developed TUN derivatives, mainly TunR2, and its potential for use as a novel anti-bacterial agent for veterinary and potential medical purposes.
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Affiliation(s)
- Hannah J T Nonarath
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael A Jackson
- USDA, Agricultural Research Service, Renewable Products Technology Research, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL, 61604, USA
| | - Renee M Penoske
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas C Zahrt
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Neil P J Price
- USDA, Agricultural Research Service, Renewable Products Technology Research, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL, 61604, USA.
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
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2
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Alexandrova LA, Oskolsky IA, Makarov DA, Jasko MV, Karpenko IL, Efremenkova OV, Vasilyeva BF, Avdanina DA, Ermolyuk AA, Benko EE, Kalinin SG, Kolganova TV, Berzina MY, Konstantinova ID, Chizhov AO, Kochetkov SN, Zhgun AA. New Biocides Based on N4-Alkylcytidines: Effects on Microorganisms and Application for the Protection of Cultural Heritage Objects of Painting. Int J Mol Sci 2024; 25:3053. [PMID: 38474298 DOI: 10.3390/ijms25053053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid increase in the antibiotic resistance of microorganisms, capable of causing diseases in humans as destroying cultural heritage sites, is a great challenge for modern science. In this regard, it is necessary to develop fundamentally novel and highly active compounds. In this study, a series of N4-alkylcytidines, including 5- and 6-methylcytidine derivatives, with extended alkyl substituents, were obtained in order to develop a new generation of antibacterial and antifungal biocides based on nucleoside derivatives. It has been shown that N4-alkyl 5- or 6-methylcytidines effectively inhibit the growth of molds, isolated from the paintings in the halls of the Ancient Russian Paintings of the State Tretyakov Gallery, Russia, Moscow. The novel compounds showed activity similar to antiseptics commonly used to protect works of art, such as benzalkonium chloride, to which a number of microorganisms have acquired resistance. It was also shown that the activity of N4-alkylcytidines is comparable to that of some antibiotics used in medicine to fight Gram-positive bacteria, including resistant strains of Staphylococcus aureus and Mycobacterium smegmatis. N4-dodecyl-5- and 6-methylcytidines turned out to be the best. This compound seems promising for expanding the palette of antiseptics used in painting, since quite often the destruction of painting materials is caused by joint fungi and bacteria infection.
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Affiliation(s)
| | - Ivan A Oskolsky
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Dmitry A Makarov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Maxim V Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Inna L Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Byazilya F Vasilyeva
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Anna A Ermolyuk
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Elizaveta E Benko
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Stanislav G Kalinin
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | | | - Maria Ya Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Alexander O Chizhov
- Zelinsky Institute of Organic Chemistry RAS 47 Leninsky Ave, Moscow 119991, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
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3
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Price NPJ, Jackson MA, Hartman TM, Bannantine JP, Naumann TA, Vermillion KE, Koch AA, Kennedy PD. Precursor-Directed Biosynthesis and Biological Testing of omega-Alicyclic- and neo-Branched Tunicamycin N-Acyl Variants. ACS Chem Biol 2023; 18:2267-2280. [PMID: 37788216 DOI: 10.1021/acschembio.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Tunicamycins (TUNs) are Streptomyces-derived natural products, widely used to block protein N-glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the N-acyl chain length and terminal branching pattern. A small molecule screen of fatty acid biosynthetic primers identified several novel alicyclic- and neo-branched TUN N-acyl variants, with primer incorporation at the terminal omega-acyl position. TUNs with unique 5- and 6-carbon ω-cycloalkane and ω-cycloalkene acyl chains are produced under fermentation and in yields comparable with the native TUN. The purification, structural assignments, and the comparable antimicrobial properties of 15 of these compounds are reported, greatly extending the structural diversity of this class of compounds for potential medicinal and agricultural applications.
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Affiliation(s)
- Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - John P Bannantine
- USDA, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave., Ames, Iowa 50010, United States
| | - Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Karl E Vermillion
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Aaron A Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
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4
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Maria C, Rauter AP. Nucleoside analogues: N-glycosylation methodologies, synthesis of antiviral and antitumor drugs and potential against drug-resistant bacteria and Alzheimer's disease. Carbohydr Res 2023; 532:108889. [PMID: 37517197 DOI: 10.1016/j.carres.2023.108889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Nucleosides have gained significant attention since the discovery of the structure of DNA. Nucleoside analogues may be synthesized through multiple synthetic pathways, however the N-glycosylation of a nucleobase is the most common method. Amongst the different classical N-glycosylation methodologies, the Vorbrüggen glycosylation is the most popular method. This review focuses on the synthesis and therapeutic applications of several FDA approved nucleoside analogues as antiviral and anticancer agents. Moreover, this review also focuses on the potential of these compounds as new antibacterial and anti-Alzheimer's disease agents, offering an overview of the most recent research in these fields.
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Affiliation(s)
- Catarina Maria
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
| | - Amélia P Rauter
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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5
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Lu S, Zhang Z, Sharma AR, Nakajima-Shimada J, Harunari E, Oku N, Trianto A, Igarashi Y. Bulbiferamide, an Antitrypanosomal Hexapeptide Cyclized via an N-Acylindole Linkage from a Marine Obligate Microbulbifer. JOURNAL OF NATURAL PRODUCTS 2023; 86:1081-1086. [PMID: 36843290 DOI: 10.1021/acs.jnatprod.2c01083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
UV absorption spectroscopy-guided fractionation of the culture extract of a marine obligate bacterium of the genus Microbulbifer yielded a novel cyclic hexapeptide, bulbiferamide (1). NMR spectroscopic and mass spectrometric analyses revealed the structure of 1 to be a cyclic tetrapeptide appending a ureido-bridged two amino acid unit. Notably, Trp is a junction residue, forming on one hand a very rare N-aminoacylated indole linkage for cyclization and on the other hand connecting the ureido-containing tail structure, which is an unprecedented way of configuring peptides. The component amino acids were determined to be l by the advanced Marfey's method. Compound 1 displayed growth inhibitory activity against Trypanosoma cruzi epimastigotes with an IC50 value of 4.1 μM, comparable to the currently approved drug benznidazole, while it was not cytotoxic to P388 murine leukemia cells at 100 μM.
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Affiliation(s)
- Shiyang Lu
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Zhiwei Zhang
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Junko Nakajima-Shimada
- Department of Molecular and Cellular Parasitology, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Agus Trianto
- Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH, Semarang, 50275 Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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6
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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7
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Walczak D, Sikorski A, Grzywacz D, Nowacki A, Liberek B. Identification of the furanose ring conformations and the factors driving their adoption. Carbohydr Res 2023; 526:108780. [PMID: 36944302 DOI: 10.1016/j.carres.2023.108780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Three groups of furanoses with restricted freedom of rotation on the C3-C4, C2-C3, and C1-C2 bonds, respectively, are presented. Conformational analysis of these furanoses is conducted based on the proton nuclear magnetic resonance (1H NMR) spectroscopy, density functional theory (DFT) calculations, and X-ray analysis. It is shown that the particular group of the presented furanoses is locked in the specific conformation. These are the 1T2-like, the 0E-like, and the 3T4-like conformation, respectively. Characteristic 1H NMR spectra of these three conformations are presented and the factors influencing the conformational preferences of the analyzed furanoses are discussed.
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Affiliation(s)
- Dominik Walczak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Artur Sikorski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Daria Grzywacz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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8
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Walczak D, Sikorski A, Grzywacz D, Nowacki A, Liberek B. Characteristic 1H NMR spectra of β-d-ribofuranosides and ribonucleosides: factors driving furanose ring conformations. RSC Adv 2022; 12:29223-29239. [PMID: 36320749 PMCID: PMC9557318 DOI: 10.1039/d2ra04274f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
A series of β-d-ribofuranosides and ribonucleosides fused with 2,3-O-isopropylidene ring was synthesized and studied in terms of their conformational preferences. Based on the 1H NMR spectra, DFT calculations, and X-ray analysis the E0-like and E4-like conformations adopted by these furanosides are identified. The 3E-like and 2E-like conformations are assigned to ribonucleosides without the 2,3-O-isopropylidene group. The studies are supported by analysis of the structural data of β-d-ribofuranosides and ribonucleosides deposited in the Cambridge Crystallographic Data Center (CCDC) database.† Finally, the factors influencing the conformational preferences of the furanose ring with the β-d-ribo configuration are indicated. These are the unfavorable ecliptic orientation of the 2-OH and 3-OH groups, the 1,3-pseudodiaxial interaction of the aglycone and terminal hydroxymethyl group and the endo-anomeric effect. It is also proved that the exo-anomeric effect acts in β-d-ribofuranosides. The 2,3-O-isopropylidene group locks β-d-ribofuranosides in the E0-like conformation whereas ribonucleosides in the E4-like conformation. The conformational preferences of β-d-ribofuranosides are determined by the anomeric effect.![]()
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Affiliation(s)
- Dominik Walczak
- Faculty of Chemistry, University of GdańskWita Stwosza 6380-308 GdańskPoland
| | - Artur Sikorski
- Faculty of Chemistry, University of GdańskWita Stwosza 6380-308 GdańskPoland
| | - Daria Grzywacz
- Faculty of Chemistry, University of GdańskWita Stwosza 6380-308 GdańskPoland
| | - Andrzej Nowacki
- Faculty of Chemistry, University of GdańskWita Stwosza 6380-308 GdańskPoland
| | - Beata Liberek
- Faculty of Chemistry, University of GdańskWita Stwosza 6380-308 GdańskPoland
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9
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Kusaka S, Yamamoto K, Shinohara M, Minato Y, Ichikawa S. Design, synthesis and conformation-activity relationship analysis of LNA/BNA-type 5'-O-aminoribosyluridine as MraY inhibitors. Bioorg Med Chem 2022; 65:116744. [PMID: 35500521 DOI: 10.1016/j.bmc.2022.116744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
It is important to understand and control the biologically active conformation in medicinal chemistry. Muraymycins and caprazamycins, which are strong inhibitors of MraY, are promising antibacterial agents with a novel mode of action. Focusing on a sugar puckering and a dihedral angle ϕ of the uridine moiety of these natural products, LNA/BNA-type 5'-O-aminoribosyluridine analogues, whose puckering of the ribose moiety are completely restricted to the N-type, were designed and synthesized as simplified MraY inhibitors. Their conformation-activity relationship was further investigated in details. The conformation-activity relationship analysis investigated in this study could be a general guideline for simplification and rational drug design of MraY inhibitory nucleoside natural products.
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Affiliation(s)
- Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoko Shinohara
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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10
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Shao X, Zheng C, Xu P, Shiraishi T, Kuzuyama T, Molinaro A, Silipo A, Yu B. Total Synthesis and Stereochemistry Assignment of Nucleoside Antibiotic A‐94964. Angew Chem Int Ed Engl 2022; 61:e202200818. [DOI: 10.1002/anie.202200818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Xiaofei Shao
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
| | - Chang Zheng
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
| | - Taro Shiraishi
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Antonio Molinaro
- Department of Chemical Sciences University of Naples Federico II Napoli Italy
| | - Alba Silipo
- Department of Chemical Sciences University of Naples Federico II Napoli Italy
| | - Biao Yu
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
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11
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Shao X, Zheng C, Xu P, Shiraishi T, Kuzuyama T, Molinaro A, Silipo A, Yu B. Total Synthesis and Stereochemistry Assignment of Nucleoside Antibiotic A‐94964. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaofei Shao
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
| | - Chang Zheng
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
| | - Peng Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
| | - Taro Shiraishi
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Tokyo Japan
| | - Antonio Molinaro
- Department of Chemical Sciences University of Naples Federico II Napoli Italy
| | - Alba Silipo
- Department of Chemical Sciences University of Naples Federico II Napoli Italy
| | - Biao Yu
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou China
- State Key Laboratory of Bioorganic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai China
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12
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Kerr RV, Fairbairn JA, Merritt AT, Bugg TDH. Peptidomimetic analogues of an Arg-Trp-x-x-Trp motif responsible for interaction of translocase MraY with bacteriophage ϕX174 lysis protein E. Bioorg Med Chem 2021; 52:116502. [PMID: 34808406 DOI: 10.1016/j.bmc.2021.116502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022]
Abstract
Translocase MraY is the target for bacteriophage ϕX174 lysis protein E, which interacts via a protein-protein interaction mediated by Phe-288 and Glu-287 of E. coli MraY, and an Arg-Trp-x-x-Trp motif on protein E, also found in several cationic antimicrobial peptides. Analogues of Arg-Trp-octyl ester, found previously to show antimicrobial activity, were tested for antimicrobial activity, with Lys-Trp-oct (MIC50P. fluorescens 5 µg/mL) and Arg-Trp-decyl ester (MIC50P. fluorescens 3 µg/mL) showing enhanced antimicrobial activity. Synthesis and testing of α-helix peptidomimetic analogues for this motif revealed improved antibacterial activity (MIC50E. coli 4-7 µg/mL) for analogues containing two aromatic substituents, mimicking the Arg-Trp-x-x-Trp motif, and MraY inhibition (IC50 140 µM) by one such peptidomimetic. Investigation of mechanism of action using the Alamar Blue membrane permeabilisation assay revealed bacteriostatic and bacteriocidal mechanisms in different members of this set of compounds, raising the possibility of more than one biological target. The observed antimicrobial activity and MraY inhibition shown by peptidomimetic compounds confirms that this site could be targeted by drug-like molecules.
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Affiliation(s)
- Rachel V Kerr
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Julia A Fairbairn
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew T Merritt
- LifeArc, SBC Open Innovation Campus, Stevenage, Herts SG1 2FX, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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13
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Liu J, Xing WY, Zhang JY, Zeng X, Yang Y, Zhang CC. Functions of the Essential Gene mraY in Cellular Morphogenesis and Development of the Filamentous Cyanobacterium Anabaena PCC 7120. Front Microbiol 2021; 12:765878. [PMID: 34745074 PMCID: PMC8566892 DOI: 10.3389/fmicb.2021.765878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022] Open
Abstract
Bacterial cell shape is determined by the peptidoglycan (PG) layer. The cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a filamentous strain with ovoid-shaped cells connected together with incomplete cell constriction. When deprived of combined nitrogen in the growth medium, about 5–10% of the cells differentiate into heterocysts, cells devoted to nitrogen fixation. It has been shown that PG synthesis is modulated during heterocyst development and some penicillin-binding proteins (PBPs) participating in PG synthesis are required for heterocyst morphogenesis or functioning. Anabaena has multiple PBPs with functional redundancy. In this study, in order to examine the function of PG synthesis and its relationship with heterocyst development, we created a conditional mutant of mraY, a gene necessary for the synthesis of the PG precursor, lipid I. We show that mraY is required for cell and filament integrity. Furthermore, when mraY expression was being limited, persistent septal PG synthetic activity was observed, resulting in increase in cell width. Under non-permissive conditions, filaments and cells were rapidly lysed, and no sign of heterocyst development within the time window allowed was detected after nitrogen starvation. When mraY expression was being limited, a high percentage of heterocyst doublets were found. These doublets are formed likely as a consequence of delayed cell division and persistent septal PG synthesis. MraY interacts with components of both the elongasome and the divisome, in particular those directly involved in PG synthesis, including HetF, which is required for both cell division and heterocyst formation.
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Affiliation(s)
- Jing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Yue Xing
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institut WUT-AMU, Aix-Marseille University and Wuhan University of Technology, Wuhan, China
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14
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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15
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Guo Z, Tang Y, Tang W, Chen Y. Heptose-containing bacterial natural products: structures, bioactivities, and biosyntheses. Nat Prod Rep 2021; 38:1887-1909. [PMID: 33704304 DOI: 10.1039/d0np00075b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2020Glycosylated natural products hold great potential as drugs for the treatment of human and animal diseases. Heptoses, known as seven-carbon-chain-containing sugars, are a group of saccharides that are rarely observed in natural products. Based on the structures of the heptoses, the heptose-containing natural products can be divided into four groups, characterized by heptofuranose, highly-reduced heptopyranose, d-heptopyranose, and l-heptopyranose. Many of them possess remarkable biological properties, including antibacterial, antifungal, antitumor, and pain relief activities, thereby attracting great interest in biosynthesis and chemical synthesis studies to understand their construction mechanisms and structure-activity relationships. In this review, we summarize the structural properties, biological activities, and recent progress in the biosynthesis of bacterial natural products featuring seven-carbon-chain-containing sugars. The biosynthetic origins of the heptose moieties are emphasized.
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Affiliation(s)
- Zhengyan Guo
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
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16
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Kwak SH, Lim WY, Hao A, Mashalidis EH, Kwon DY, Jeong P, Kim MJ, Lee SY, Hong J. Synthesis and evaluation of cyclopentane-based muraymycin analogs targeting MraY. Eur J Med Chem 2021; 215:113272. [PMID: 33607457 DOI: 10.1016/j.ejmech.2021.113272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance is one of the most challenging global health issues and presents an urgent need for the development of new antibiotics. In this regard, phospho-MurNAc-pentapeptide translocase (MraY), an essential enzyme in the early stages of peptidoglycan biosynthesis, has emerged as a promising new antibiotic target. We recently reported the crystal structures of MraY in complex with representative members of naturally occurring nucleoside antibiotics, including muraymycin D2. However, these nucleoside antibiotics are synthetically challenging targets, which limits the scope of medicinal chemistry efforts on this class of compounds. To gain access to active muraymycin analogs with reduced structural complexity and improved synthetic tractability, we prepared and evaluated cyclopentane-based muraymycin analogs for targeting MraY. For the installation of the 1,2-syn-amino alcohol group of analogs, the diastereoselective isocyanoacetate aldol reaction was explored. The structure-activity relationship analysis of the synthesized analogs suggested that a lipophilic side chain is essential for MraY inhibition. Importantly, the analog 20 (JH-MR-23) showed antibacterial efficacy against Staphylococcus aureus. These findings provide insights into designing new muraymycin-based MraY inhibitors with improved chemical tractability.
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Affiliation(s)
- Seung-Hwa Kwak
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Won Young Lim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Pyeonghwa Jeong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Mi Jung Kim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States.
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17
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Alexandrova LA, Jasko MV, Negrya SD, Solyev PN, Shevchenko OV, Solodinin AP, Kolonitskaya DP, Karpenko IL, Efremenkova OV, Glukhova AA, Boykova YV, Efimenko TA, Kost NV, Avdanina DA, Nuraeva GK, Volkov IA, Kochetkov SN, Zhgun AA. Discovery of novel N 4-alkylcytidines as promising antimicrobial agents. Eur J Med Chem 2021; 215:113212. [PMID: 33582576 DOI: 10.1016/j.ejmech.2021.113212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/18/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
The emergence of drug-resistant strains of pathogenic microorganisms necessitates the creation of new drugs. In order to find new compounds that effectively inhibit the growth of pathogenic bacteria and fungi, we synthesized a set of N4-derivatives of cytidine, 2'-deoxycytidine and 5-metyl-2'-deoxycytidine bearing extended N4-alkyl and N4-phenylalkyl groups. The derivatives demonstrate activity against a number of Gram-positive bacteria, including Mycobacterium smegmatis (MIC = 24-200 μM) and Staphylococcus aureus (MIC = 50-200 μM), comparable with the activities of some antibiotics in medical use. The most promising compound appeared to be N4-dodecyl-5-metyl-2'-deoxycytidine 4h with activities of 24 and 48 μM against M. smegmatis and S. aureus, respectively, and high inhibitory activity of 0.5 mM against filamentous fungi that can, among other things, damage works of art, such as tempera painting. Noteworthy, some of other synthesized compounds are active against fungal growth with the inhibitory concentration in the range of 0.5-3 mM.
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Affiliation(s)
| | - Maxim V Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Sergey D Negrya
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia.
| | - Oleg V Shevchenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Andrei P Solodinin
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Daria P Kolonitskaya
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Inna L Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Alla A Glukhova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Yuliya V Boykova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Tatiana A Efimenko
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Natalya V Kost
- Federal State Budgetary Scientific Institution "Mental Health Research Centre", 34 Kashirskoe Highway, 115522, Moscow, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071, Moscow, Russia
| | - Gulgina K Nuraeva
- Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Alley, 141700, Dolgoprudny, Russia
| | - Ivan A Volkov
- Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Alley, 141700, Dolgoprudny, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071, Moscow, Russia
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18
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Price NPJ, Jackson MA, Hartman TM, Brändén G, Ek M, Koch AA, Kennedy PD. Branched Chain Lipid Metabolism As a Determinant of the N-Acyl Variation of Streptomyces Natural Products. ACS Chem Biol 2021; 16:116-124. [PMID: 33411499 DOI: 10.1021/acschembio.0c00799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Branched-chain fatty acids (BCFA) are encountered in Gram-positive bacteria, but less so in other organisms. The bacterial BCFA in membranes are typically saturated, with both odd- and even-numbered carbon chain lengths, and with methyl branches at either the ω-1 (iso) or ω-2 (anteiso) positions. The acylation with BCFA also contributes to the structural diversity of microbial natural products and potentially modulates biological activity. For the tunicamycin (TUN) family of natural products, the toxicity toward eukaryotes is highly dependent upon N-acylation with trans-2,3-unsaturated BCFA. The loss of the 2,3-unsaturation gives modified TUN with reduced eukaryotic toxicity but crucially with retention of the synergistic enhancement of the β-lactam group of antibiotics. Here, we infer from genomics, mass spectrometry, and deuterium labeling that the trans-2,3-unsaturated TUN variants and the saturated cellular lipids found in TUN-producing Streptomyces are derived from the same pool of BCFA metabolites. Moreover, non-natural primers of BCFA metabolism are selectively incorporated into the cellular lipids of TUN-producing Streptomyces and concomitantly produce structurally novel neo-branched TUN N-acyl variants.
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Affiliation(s)
- Neil P. J. Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A. Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics & FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Aaron A. Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D. Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
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19
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Hering J, Dunevall E, Snijder A, Eriksson PO, Jackson MA, Hartman TM, Ting R, Chen H, Price NPJ, Brändén G, Ek M. Exploring the Active Site of the Antibacterial Target MraY by Modified Tunicamycins. ACS Chem Biol 2020; 15:2885-2895. [PMID: 33164499 DOI: 10.1021/acschembio.0c00423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The alarming growth of antibiotic resistance that is currently ongoing is a serious threat to human health. One of the most promising novel antibiotic targets is MraY (phospho-MurNAc-pentapeptide-transferase), an essential enzyme in bacterial cell wall synthesis. Through recent advances in biochemical research, there is now structural information available for MraY, and for its human homologue GPT (GlcNAc-1-P-transferase), that opens up exciting possibilities for structure-based drug design. The antibiotic compound tunicamycin is a natural product inhibitor of MraY that is also toxic to eukaryotes through its binding to GPT. In this work, we have used tunicamycin and modified versions of tunicamycin as tool compounds to explore the active site of MraY and to gain further insight into what determines inhibitor potency. We have investigated tunicamycin variants where the following motifs have been modified: the length and branching of the tunicamycin fatty acyl chain, the saturation of the fatty acyl chain, the 6″-hydroxyl group of the GlcNAc ring, and the ring structure of the uracil motif. The compounds are analyzed in terms of how potently they bind to MraY, inhibit the activity of the enzyme, and affect the protein thermal stability. Finally, we rationalize these results in the context of the protein structures of MraY and GPT.
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Affiliation(s)
- Jenny Hering
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Olof Eriksson
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Michael A. Jackson
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Ran Ting
- Chemistry and Chemical Biology Centre, Bioland Laboratory, Guangzhou, China
| | - Hongming Chen
- Chemistry and Chemical Biology Centre, Bioland Laboratory, Guangzhou, China
| | - Neil P. J. Price
- U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics and FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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20
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Bege M, Bereczki I, Molnár DJ, Kicsák M, Pénzes-Daku K, Bereczky Z, Ferenc G, Kovács L, Herczegh P, Borbás A. Synthesis and oligomerization of cysteinyl nucleosides. Org Biomol Chem 2020; 18:8161-8178. [PMID: 33020786 DOI: 10.1039/d0ob01890b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nucleoside and nucleic acid analogues are known to possess a considerable therapeutic potential. In this work, by coupling cysteine to nucleosides, we successfully synthesized compounds that may not only have interesting biological properties in their monomeric form, but can be used beyond that, for oligomerization, in order to produce new types of synthetic nucleic acids. We elaborated different strategies for the synthesis of cysteinyl nucleosides as monomers of cysteinyl nucleic acids using nucleophilic substitution or thiol-ene coupling as a synthetic tool, and utilised on two complementary nucleosides, uridine and adenosine. Dipeptidyl dinucleosides and pentameric cysteinyl uridine were prepared from the monomeric building blocks, which are the first members of a new class of peptide nucleic acids containing the entire ribofuranosyl nucleoside units bound to the peptide backbone.
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Affiliation(s)
- Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary. and Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, H-4032, Hungary and MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Debrecen, H-4032, Hungary
| | - Ilona Bereczki
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary.
| | - Dénes J Molnár
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary.
| | - Máté Kicsák
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary.
| | - Krisztina Pénzes-Daku
- Division of Clinical Laboratory Science, University of Debrecen, Debrecen, H-4032, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, University of Debrecen, Debrecen, H-4032, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Center, Szeged, H-6726, Hungary
| | - Lajos Kovács
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Debrecen, H-4032, Hungary.
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21
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Patel B, Kerr RV, Malde AK, Zunk M, Bugg TDH, Grant G, Rudrawar S. Simplified Novel Muraymycin Analogues; using a Serine Template Strategy for Linking Key Pharmacophores. ChemMedChem 2020; 15:1429-1438. [PMID: 32476294 DOI: 10.1002/cmdc.202000033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/25/2020] [Indexed: 12/15/2022]
Abstract
The present status of antibiotic research requires the urgent invention of novel agents that act on multidrug-resistant bacteria. The World Health Organization has classified antibiotic-resistant bacteria into critical, high and medium priority according to the urgency of need for new antibiotics. Naturally occurring uridine-derived "nucleoside antibiotics" have shown promising activity against numerous priority resistant organisms by inhibiting the transmembrane protein MraY (translocase I), which is yet to be explored in a clinical context. The catalytic activity of MraY is an essential process for bacterial cell viability and growth including that of priority organisms. Muraymycins are one subclass of naturally occurring MraY inhibitors. Despite having potent antibiotic properties, the structural complexity of muraymycins advocates for simplified analogues as potential lead structures. Herein, we report a systematic structure-activity relationship (SAR) study of serine template-linked, simplified muraymycin-type analogues. This preliminary SAR lead study of serine template analogues successfully revealed that the complex structure of naturally occurring muraymycins could be easily simplified to afford bioactive scaffolds against resistant priority organisms. This study will pave the way for the development of novel antibacterial lead compounds based on a simplified serine template.
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Affiliation(s)
- Bhautikkumar Patel
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Rachel V Kerr
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Alpeshkumar K Malde
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia.,MaldE Scientific, Australia
| | - Matthew Zunk
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Gary Grant
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia.,School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia.,Quality Use of Medicines Network, Griffith University, Gold Coast, QLD 4222, Australia
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22
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Negrya SD, Jasko MV, Solyev PN, Karpenko IL, Efremenkova OV, Vasilyeva BF, Sumarukova IG, Kochetkov SN, Alexandrova LA. Synthesis of water-soluble prodrugs of 5-modified 2ʹ-deoxyuridines and their antibacterial activity. J Antibiot (Tokyo) 2020; 73:236-246. [DOI: 10.1038/s41429-019-0273-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/09/2019] [Accepted: 12/15/2019] [Indexed: 12/14/2022]
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