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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [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: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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Hayat M, Gao T, Cao Y, Rafiq M, Zhuo L, Li YZ. Identification of Prospective Ebola Virus VP35 and VP40 Protein Inhibitors from Myxobacterial Natural Products. Biomolecules 2024; 14:660. [PMID: 38927063 PMCID: PMC11201620 DOI: 10.3390/biom14060660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
The Ebola virus (EBOV) is a lethal pathogen causing hemorrhagic fever syndrome which remains a global health challenge. In the EBOV, two multifunctional proteins, VP35 and VP40, have significant roles in replication, virion assembly, and budding from the cell and have been identified as druggable targets. In this study, we employed in silico methods comprising molecular docking, molecular dynamic simulations, and pharmacological properties to identify prospective drugs for inhibiting VP35 and VP40 proteins from the myxobacterial bioactive natural product repertoire. Cystobactamid 934-2, Cystobactamid 919-1, and Cittilin A bound firmly to VP35. Meanwhile, 2-Hydroxysorangiadenosine, Enhypyrazinone B, and Sorangiadenosine showed strong binding to the matrix protein VP40. Molecular dynamic simulations revealed that, among these compounds, Cystobactamid 919-1 and 2-Hydroxysorangiadenosine had stable interactions with their respective targets. Similarly, molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations indicated close-fitting receptor binding with VP35 or VP40. These two compounds also exhibited good pharmacological properties. In conclusion, we identified Cystobactamid 919-1 and 2-Hydroxysorangiadenosine as potential ligands for EBOV that target VP35 and VP40 proteins. These findings signify an essential step in vitro and in vivo to validate their potential for EBOV inhibition.
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Affiliation(s)
- Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.H.); (T.G.); (Y.C.); (Y.-Z.L.)
| | - Tian Gao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.H.); (T.G.); (Y.C.); (Y.-Z.L.)
| | - Ying Cao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.H.); (T.G.); (Y.C.); (Y.-Z.L.)
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.H.); (T.G.); (Y.C.); (Y.-Z.L.)
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.H.); (T.G.); (Y.C.); (Y.-Z.L.)
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Wang Z, Kasper A, Takahashi M, Amador AM, Bhattacharjee A, Kan J, Hernandez Y, Ternei M, Brady SF. Tapcin, an In Vivo Active Dual Topoisomerase I/II Inhibitor Discovered by Synthetic Bioinformatic Natural Product (Syn-BNP)-Coupled Metagenomics. Angew Chem Int Ed Engl 2024; 63:e202317187. [PMID: 38231130 PMCID: PMC11018531 DOI: 10.1002/anie.202317187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportunity to identify additional natural topoisomerase inhibitors. Here we couple metagenome mining, bioinformatic structure prediction algorithms, and chemical synthesis to produce the dual topoisomerase inhibitor tapcin. Tapcin is a mixed p-aminobenzoic acid (PABA)-thiazole with a rare tri-thiazole substructure and picomolar antiproliferative activity. Tapcin reduced colorectal adenocarcinoma HT-29 cell proliferation and tumor volume in mouse hollow fiber and xenograft models, respectively. In both studies it showed similar activity to the clinically used topoisomerase I inhibitor irinotecan. The study suggests that the interrogation of soil microbiomes using synthetic bioinformatic natural product methods has the potential to be a rewarding strategy for identifying potent, biomedically relevant, antiproliferative agents.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Mai Takahashi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Adrian Morales Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Abir Bhattacharjee
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Jingbo Kan
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065
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Solga D, Wieske LHE, Wilcox S, Zeilinger C, Jansen-Olliges L, Cirnski K, Herrmann J, Müller R, Erdelyi M, Kirschning A. Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids? Chemistry 2024; 30:e202303796. [PMID: 38217886 DOI: 10.1002/chem.202303796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Cystobactamids are aromatic oligoamides that exert their natural antibacterial properties by inhibition of bacterial gyrases. Such aromatic oligoamides were proposed to inhibit α-helix-mediated protein-protein interactions and may serve for specific recognition of DNA. Based on this suggestion, we designed new derivatives that have duplicated cystobactamid triarene units as model systems to decipher the specific binding mode of cystobactamids to double stranded DNA. Solution NMR analyses revealed that natural cystobactamids as well as their elongated analogues show an overall bent shape at their central aliphatic unit, with an average CX-CY-CZ angle of ~110 degrees. Our finding is corroborated by the target-bound structure of close analogues, as established by cryo-EM very recently. Cystobactamid CN-861-2 binds directly to the bacterial gyrase with an affinity of 9 μM, and also exhibits DNA-binding properties with specificity for AT-rich DNA. Elongation/dimerization of the triarene subunit of native cystobactamids is demonstrated to lead to an increase in DNA binding affinity. This implies that cystobactamids' gyrase inhibitory activity necessitates not just interaction with the gyrase itself, but also with DNA via their triarene unit.
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Affiliation(s)
- Danny Solga
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Scott Wilcox
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Carsten Zeilinger
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Linda Jansen-Olliges
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Katarina Cirnski
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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Chen C, Chen L, Mao C, Jin L, Wu S, Zheng Y, Cui Z, Li Z, Zhang Y, Zhu S, Jiang H, Liu X. Natural Extracts for Antibacterial Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306553. [PMID: 37847896 DOI: 10.1002/smll.202306553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/23/2023] [Indexed: 10/19/2023]
Abstract
Bacteria-induced epidemics and infectious diseases are seriously threatening the health of people around the world. In addition, antibiotic therapy has been inducing increasingly more serious bacterial resistance, which makes it urgent to develop new treatment strategies to combat bacteria, including multidrug-resistant bacteria. Natural extracts displaying antibacterial activity and good biocompatibility have attracted much attention due to greater concerns about the safety of synthetic chemicals and emerging drug resistance. These antibacterial components can be isolated and utilized as antimicrobials, as well as transformed, combined, or wrapped with other substances by using modern assistive technologies to fight bacteria synergistically. This review summarizes recent advances in natural extracts from three kinds of sources-plants, animals, and microorganisms-for antibacterial applications. This work discusses the corresponding antibacterial mechanisms and the future development of natural extracts in antibacterial fields.
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Affiliation(s)
- Cuihong Chen
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Lin Chen
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Congyang Mao
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
| | - Liguo Jin
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Shuilin Wu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Yufeng Zheng
- School of Materials Science & Engineering, Peking University, Yiheyuan Road 5#, Beijing, 100871, China
| | - Zhenduo Cui
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Zhaoyang Li
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Yu Zhang
- Department of Orthopedics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shengli Zhu
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Hui Jiang
- School of Materials Science & Engineering, the Key Laboratory of Advanced Ceramics and Machining Technology by the Ministry of Education of China, Tianjin University, Yaguan Road 135#, Tianjin, 300072, China
| | - Xiangmei Liu
- Biomedical Materials Engineering Research Center, Hubei Key Laboratory of Polymer Materials, Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- School of Health Science & Biomedical Engineering, Hebei University of Technology, Xiping Avenue 5340#, Tianjin, 300401, China
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Rima M, Pfennigwerth N, Cremanns M, Cirnski K, Oueslati S, Gatermann SG, d’Amélio N, Herrmann J, Müller R, Naas T. In Vitro Activity of Two Novel Antimicrobial Compounds on MDR-Resistant Clinical Isolates. Antibiotics (Basel) 2023; 12:1265. [PMID: 37627685 PMCID: PMC10451163 DOI: 10.3390/antibiotics12081265] [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: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
The development of novel antibiotics is mandatory to curb the growing antibiotic resistance problem resulting in difficult-to-treat bacterial infections. Here, we have determined the spectrum of activity of cystobactamids and chelocardins, two novel and promising classes of molecules with different modes of action. A panel of 297 clinically relevant Gram-negative and Gram-positive isolates with different antibiotic susceptibility profiles, going from wild type to multi- or even extremely drug resistant (MDR, XDR) and including carbapenem-resistant isolates, were tested using broth microdilution assays to determine the minimal inhibitory concentrations (MICs), MIC50s and MIC90s of two cystobactamids derivatives (CN-861-2 and CN-DM-861) and two chelocardin derivatives (CHD and CDCHD). Cystobactamids revealed potent activities on the majority of tested Enterobacterales (MIC50s ranging from 0.25 to 4 µg/mL), except for Klebsiella pneumoniae isolates (MIC50s is 128 µg/mL). Pseudomonas aeruginosa and Acinetobacter baumannii showed slightly higher MIC50s (4 µg/mL and 8 µg/mL, respectively) for cystobactamids. Chelocardins inhibited the growth of Enterobacterales and Stenotrophomas maltophilia at low to moderate MICs (0.25-16 µg/mL) and the chemically modified CDCHD was active at lower MICs. A. baumannii and P. aeruginosa were less susceptible to these molecules with MICs ranging from 0.5 to 32 µg/mL. These molecules show also interesting in vitro efficacies on clinically relevant Gram-positive bacteria with MICs of 0.125-8 µg/mL for cystobactamids and 0.5-8 µg/mL for chelocardins. Taken together, the cystobactamid CN-DM-861 and chelocardin CDCHD showed interesting antibiotic activities on MDR or XDR bacteria, without cross-resistance to clinically relevant antibiotics such as carbapenems, fluoroquinolones, and colistin.
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Affiliation(s)
- Mariam Rima
- Team “Resist”, UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, INSERM, Faculty of Medicine, Université Paris-Saclay, CEA, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France; (M.R.); (S.O.)
| | - Niels Pfennigwerth
- Department of Clinical Microbiology, Ruhr-University, 44801 Bochum, Germany; (N.P.); (M.C.); (S.G.G.)
| | - Martina Cremanns
- Department of Clinical Microbiology, Ruhr-University, 44801 Bochum, Germany; (N.P.); (M.C.); (S.G.G.)
| | - Katarina Cirnski
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; (K.C.); (J.H.); (R.M.)
- German Center for Infection Research (DZIF), Partner Site Hannover, 38124 Braunschweig, Germany
| | - Saoussen Oueslati
- Team “Resist”, UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, INSERM, Faculty of Medicine, Université Paris-Saclay, CEA, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France; (M.R.); (S.O.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Sören G. Gatermann
- Department of Clinical Microbiology, Ruhr-University, 44801 Bochum, Germany; (N.P.); (M.C.); (S.G.G.)
| | - Nicola d’Amélio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France;
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; (K.C.); (J.H.); (R.M.)
- German Center for Infection Research (DZIF), Partner Site Hannover, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; (K.C.); (J.H.); (R.M.)
- German Center for Infection Research (DZIF), Partner Site Hannover, 38124 Braunschweig, Germany
| | - Thierry Naas
- Team “Resist”, UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, INSERM, Faculty of Medicine, Université Paris-Saclay, CEA, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France; (M.R.); (S.O.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
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Kosol S, Rostock L, Barsig J, Tabarelli T, Hommernick K, Kulike M, Eulberg T, Seidel M, Behroz I, Kleebauer L, Grätz S, Mainz A, Süssmuth RD. Transcription activation by the resistance protein AlbA as a tool to evaluate derivatives of the antibiotic albicidin. Chem Sci 2023; 14:5069-5078. [PMID: 37206387 PMCID: PMC10189885 DOI: 10.1039/d3sc00955f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/15/2023] [Indexed: 05/21/2023] Open
Abstract
The rising numbers of fatal infections with resistant pathogens emphasizes the urgent need for new antibiotics. Ideally, new antibiotics should be able to evade or overcome existing resistance mechanisms. The peptide antibiotic albicidin is a highly potent antibacterial compound with a broad activity spectrum but also with several known resistance mechanisms. In order to assess the effectiveness of novel albicidin derivatives in the presence of the binding protein and transcription regulator AlbA, a resistance mechanism against albicidin identified in Klebsiella oxytoca, we designed a transcription reporter assay. In addition, by screening shorter albicidin fragments, as well as various DNA-binders and gyrase poisons, we were able to gain insights into the AlbA target spectrum. We analysed the effect of mutations in the binding domain of AlbA on albicidin sequestration and transcription activation, and found that the signal transduction mechanism is complex but can be evaded. Further demonstrating AlbA's high level of specificity, we find clues for the logical design of molecules capable of avoiding the resistance mechanism.
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Affiliation(s)
- Simone Kosol
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Lida Rostock
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Jonas Barsig
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Theresa Tabarelli
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Tobias Eulberg
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Leonardo Kleebauer
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Stefan Grätz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
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8
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Testolin G, Richter J, Ritter A, Prochnow H, Köhnke J, Brönstrup M. Optical Modulation of Antibiotic Resistance by Photoswitchable Cystobactamids. Chemistry 2022; 28:e202201297. [PMID: 35771231 DOI: 10.1002/chem.202201297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 01/07/2023]
Abstract
The rise of antibiotic resistance causes a serious health care problem, and its counterfeit demands novel, innovative concepts. The combination of photopharmacology, enabling a light-controlled reversible modulation of drug activity, with antibiotic drug design has led to first photoswitchable antibiotic compounds derived from established scaffolds. In this study, we converted cystobactamids, gyrase-inhibiting natural products with an oligoaryl scaffold and highly potent antibacterial activities, into photoswitchable agents by inserting azobenzene in the N-terminal part and/or an acylhydrazone moiety near the C-terminus, yielding twenty analogs that contain mono- as well as double-switches. Antibiotic and gyrase inhibition properties could be modulated 3.4-fold and 5-fold by light, respectively. Notably, the sensitivity of photoswitchable cystobactamids towards two known resistance factors, the peptidase AlbD and the scavenger protein AlbA, was light-dependent. While irradiation of an analog with an N-terminal azobenzene with 365 nm light led to less degradation by AlbD, the AlbA-mediated inactivation was induced. This provides a proof-of-principle that resistance towards photoswitchable antibiotics can be optically controlled.
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Affiliation(s)
- Giambattista Testolin
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jana Richter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Antje Ritter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Hans Prochnow
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jesko Köhnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,German Center for Infection Research (DZIF) Site Hannover-Braunschweig, 38124, Braunschweig, Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159, Hannover, Germany
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9
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Choi HY, Kim BM, Kim YR, Yang T, Ahn S, Yong D, Kwak JH, Kim WG. Antibacterial Activity against Clinical Isolates and In Vivo Efficacy of Coralmycins. Antibiotics (Basel) 2022; 11:antibiotics11070902. [PMID: 35884156 PMCID: PMC9311539 DOI: 10.3390/antibiotics11070902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Coralmycins, such as coralmycin A and DH-coralmycin A, have novel molecular skeletons and have been reported to exhibit potent antibacterial activity against standard Gram-positive bacterial strains. Here, the in vitro antibacterial activity against an extensive clinical isolate collection, time-kill kinetics, pharmacokinetics (PK), and in vivo efficacy of coralmycins were studied. Coralmycin A showed potent antibacterial activity with an MIC90 of 1 mg/L against 73 clinical methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococci isolates, which was 2–8 times higher than the corresponding activities of DH-coralmycin A, vancomycin, daptomycin, and linezolid, and against 73 vancomycin-resistant Enterococcus and Streptococcus pneumoniae isolates, which was 4–16 times higher than the corresponding activities of DH-coralmycin A, daptomycin, and linezolid. Pharmacokinetic analysis after i.v. injection showed that coralmycins have a moderate volume of distribution and moderate-to-high clearance in mice. The coralmycin A and DH-coralmycin A bioavailability values were 61.3% and 11.7%, respectively, after s.c. administration. In a mouse respiratory tract infection model, coralmycin A showed bacteriostatic and bactericidal in vivo efficacies at an s.c. administration of 4 and 100 mg/kg bid, respectively; these efficacies were similar to those of vancomycin at 4 and 20 mg/kg bid, respectively. The present findings indicate that coralmycin A has great potential as a new class of antibiotic for treating infections caused by multidrug-resistant Gram-positive bacteria.
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Affiliation(s)
- Ha-Young Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon 34141, Korea; (H.-Y.C.); (B.-M.K.); (T.Y.)
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Yusong, Daejeon 34141, Korea
| | - Bo-Min Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon 34141, Korea; (H.-Y.C.); (B.-M.K.); (T.Y.)
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Yusong, Daejeon 34141, Korea
| | - Young-Rok Kim
- School of Life Science, Handong Global University, Pohang 37554, Korea; (Y.-R.K.); (J.-H.K.)
| | - Taehui Yang
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon 34141, Korea; (H.-Y.C.); (B.-M.K.); (T.Y.)
| | - Sunjoo Ahn
- Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yusong, Daejeon 34114, Korea;
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Jin-Hwan Kwak
- School of Life Science, Handong Global University, Pohang 37554, Korea; (Y.-R.K.); (J.-H.K.)
| | - Won-Gon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yusong, Daejeon 34141, Korea; (H.-Y.C.); (B.-M.K.); (T.Y.)
- Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Yusong, Daejeon 34141, Korea
- Correspondence:
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10
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Wang Z, Forelli N, Hernandez Y, Ternei M, Brady SF. Lapcin, a potent dual topoisomerase I/II inhibitor discovered by soil metagenome guided total chemical synthesis. Nat Commun 2022; 13:842. [PMID: 35149673 PMCID: PMC8837603 DOI: 10.1038/s41467-022-28292-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/21/2023] Open
Abstract
In natural product discovery programs, the power of synthetic chemistry is often leveraged for the total synthesis and diversification of characterized metabolites. The synthesis of structures that are bioinformatically predicted to arise from uncharacterized biosynthetic gene clusters (BGCs) provides a means for synthetic chemistry to enter this process at an early stage. The recent identification of non-ribosomal peptides (NRPs) containing multiple ρ-aminobenzoic acids (PABAs) led us to search soil metagenomes for BGCs that polymerize PABA. Here, we use PABA-specific adenylation-domain sequences to guide the cloning of the lap BGC directly from soil. This BGC was predicted to encode a unique N-acylated PABA and thiazole containing structure. Chemical synthesis of this structure gave lapcin, a dual topoisomerase I/II inhibitor with nM to pM IC50s against diverse cancer cell lines. The discovery of lapcin highlights the power of coupling metagenomics, bioinformatics and total chemical synthesis to unlock the biosynthetic potential contained in even complex uncharacterized BGCs. Chemical synthesis of secondary metabolites isolated from nature, and derivatives thereof, is still a paradigm of significance to drug development. Here the authors instead use bioinformatics to analyze a biosynthetic gene cluster found in the soil metagenome, and chemical synthesis of its predict product to produce lapcin, a dual topoisomerase I/II inhibitor with promising activity against cancer cell lines.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Nicholas Forelli
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Yozen Hernandez
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA.
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11
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Panjla A, Kaul G, Chopra S, Titz A, Verma S. Short Peptides and Their Mimetics as Potent Antibacterial Agents and Antibiotic Adjuvants. ACS Chem Biol 2021; 16:2731-2745. [PMID: 34779605 DOI: 10.1021/acschembio.1c00626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antimicrobial resistance (AMR) has been increasing unrelentingly worldwide, thus negatively impacting human health. The discovery and development of novel antibiotics is an urgent unmet need of the hour. However, it has become more challenging, requiring increasingly time-consuming efforts with increased commercial risks. Hence, alternative strategies are urgently needed to potentiate the existing antibiotics. In this context, short cationic peptides or peptide-based antimicrobials that mimic the activity of naturally occurring antimicrobial peptides (AMPs) could overcome the disadvantages of AMPs having evolved as potent antibacterial agents. Besides their potent antibacterial efficacy, short peptide conjugates have also gained attention as potent adjuvants to conventional antibiotics. Such peptide antibiotic combinations have become an increasingly cost-effective therapeutic option to tackle AMR. This Review summarizes the recent progress for peptide-based small molecules as promising antimicrobials and as adjuvants for conventional antibiotics to counter multidrug resistant (MDR) pathogens.
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Affiliation(s)
- Apurva Panjla
- Department of Chemistry, IIT Kanpur, Kanpur-208016, Uttar Pradesh, India
| | - Grace Kaul
- Department of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sidharth Chopra
- Department of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), 38124, Standort Hannover-Braunschweig, Germany
| | - Sandeep Verma
- Department of Chemistry, IIT Kanpur, Kanpur-208016, Uttar Pradesh, India
- Center for Nanoscience, IIT Kanpur, Kanpur-208016, Uttar Pradesh, India
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12
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Zborovsky L, Kleebauer L, Seidel M, Kostenko A, von Eckardstein L, Gombert FO, Weston J, Süssmuth RD. Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms. Chem Sci 2021; 12:14606-14617. [PMID: 34881013 PMCID: PMC8580050 DOI: 10.1039/d1sc04019g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/17/2021] [Indexed: 01/22/2023] Open
Abstract
The worrisome development and spread of multidrug-resistant bacteria demands new antibacterial agents with strong bioactivities particularly against Gram-negative bacteria. Albicidins were recently structurally characterized as highly active antibacterial natural products from the bacterium Xanthomonas albilineans. Albicidin, which effectively targets the bacterial DNA-gyrase, is a lipophilic hexapeptide mostly consisting of para amino benzoic acid units and only one α-amino acid. In this study, we report on the design and synthesis of new albicidins, containing N-atoms on each of the 5 different phenyl rings. We systematically introduced N-atoms into the aromatic backbone to monitor intramolecular H-bonds and for one derivative correlated them with a significant enhancement of the antibacterial activity and activity spectrum, particularly also towards Gram-positive bacteria. In parallel we conducted DFT calculations to find the most stable conformation of each derivative. A drastic angle-change was observed for the lead compound and shows a preferred planarity through H-bonding with the introduced N-atom at the D-fragment of albicidin. Finally, we went to the next level and conducted the first in vivo experiments with an albicidin analogue. Our lead compound was evaluated in two different mouse experiments: In the first we show a promising PK profile and the absence of toxicity and in the second very good efficiency and reduction of the bacterial titre in an E. coli infection model with FQ-resistant clinically relevant strains. These results qualify albicidins as active antibacterial substances with the potential to be developed as a drug for treatment of infections caused by Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Lieby Zborovsky
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Leonardo Kleebauer
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Maria Seidel
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Arseni Kostenko
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Leonard von Eckardstein
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Frank Otto Gombert
- Gombert Pharma Research Solutions (GPRS) Dornacherstrasse 120 CH 4053 Basel Switzerland
| | - John Weston
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institut für Organische Chemie, Technische Universität Berlin Straße des 17. Juni 124 10623 Berlin Germany
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13
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Wang Z, Kasper A, Mehmood R, Ternei M, Li S, Freundlich JS, Brady SF. Metagenome-Guided Analogue Synthesis Yields Improved Gram-Negative-Active Albicidin- and Cystobactamid-Type Antibiotics. Angew Chem Int Ed Engl 2021; 60:22172-22177. [PMID: 34355488 DOI: 10.1002/anie.202104874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/05/2021] [Indexed: 11/11/2022]
Abstract
Natural products are a major source of new antibiotics. Here we utilize biosynthetic instructions contained within metagenome-derived congener biosynthetic gene clusters (BGCs) to guide the synthesis of improved antibiotic analogues. Albicidin and cystobactamid are the first members of a new class of broad-spectrum ρ-aminobenzoic acid (PABA)-based antibiotics. Our search for PABA-specific adenylation domain sequences in soil metagenomes revealed that BGCs in this family are common in nature. Twelve BGCs that were bio-informatically predicted to encode six new congeners were recovered from soil metagenomic libraries. Synthesis of these six predicted structures led to the identification of potent antibiotics with changes in their spectrum of activity and the ability to circumvent resistance conferred by endopeptidase cleavage enzymes.
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Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Rabia Mehmood
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Shaogang Li
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, 07103, USA
| | - Joel S Freundlich
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, 07103, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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14
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Kleebauer L, Zborovsky L, Hommernick K, Seidel M, Weston JB, Süssmuth RD. Overcoming AlbD Protease Resistance and Improving Potency: Synthesis and Bioactivity of Antibacterial Albicidin Analogues with Amide Bond Isosteres. Org Lett 2021; 23:7023-7027. [PMID: 34398605 DOI: 10.1021/acs.orglett.1c02312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albicidin is a potent antibacterial oligoaromatic peptide that is susceptible to the protease AlbD, a resistance factor. This potentially restricts the use of albicidin as a drug. To overcome this obstacle, we synthesized and evaluated six analogues with isosteric replacement of the key amide link. Protease stability was established while maintaining the antibacterial activity, including three analogues with up to eight times higher activity compared with the natural albicidin.
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Affiliation(s)
- Leonardo Kleebauer
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Lieby Zborovsky
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
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15
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Wang Z, Kasper A, Mehmood R, Ternei M, Li S, Freundlich JS, Brady SF. Metagenome‐Guided Analogue Synthesis Yields Improved Gram‐Negative‐Active Albicidin‐ and Cystobactamid‐Type Antibiotics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zongqiang Wang
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Amanda Kasper
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Rabia Mehmood
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
| | - Shaogang Li
- Department of Medicine, Center for Emerging and Re-emerging Pathogens Rutgers University—New Jersey Medical School Newark NJ 07103 USA
| | - Joel S. Freundlich
- Department of Medicine, Center for Emerging and Re-emerging Pathogens Rutgers University—New Jersey Medical School Newark NJ 07103 USA
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules The Rockefeller University 1230 York Avenue New York NY 10065 USA
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16
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Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa. mSystems 2021; 6:e0061021. [PMID: 34254824 PMCID: PMC8407119 DOI: 10.1128/msystems.00610-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The design of novel antibiotics relies on a profound understanding of their mechanism of action. While it has been shown that cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins, and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at subinhibitory concentrations could be distinguished clearly by RNA sequencing as well as metabolomics. We observed a strong (2.8- to 212-fold) induction of autolysis-triggering pyocins in all gyrase inhibitors, which correlated with extracellular DNA (eDNA) release. Gyrase B-binding aminocoumarins induced the most pronounced changes, including a strong downregulation of phenazine and rhamnolipid virulence factors. Cystobactamids led to a downregulation of a glucose catabolism pathway. The study implies that clustering cellular mechanisms of action according to the primary target needs to take class-dependent variances into account. IMPORTANCE Novel antibiotics are urgently needed to tackle the growing worldwide problem of antimicrobial resistance. Bacterial pathogens possess few privileged targets for a successful therapy: the majority of existing antibiotics as well as current candidates in development target the complex bacterial machinery for cell wall synthesis, protein synthesis, or DNA replication. An important mechanistic question addressed by this study is whether inhibiting such a complex target at different sites with different compounds has similar or differentiated cellular consequences. Using transcriptomics and metabolomics, we demonstrate that three different classes of gyrase inhibitors can be distinguished by their molecular signatures in P. aeruginosa. We describe the cellular effects of a promising, recently identified gyrase inhibitor class, the cystobactamids, in comparison to those of the established gyrase A-binding fluoroquinolones and the gyrase B-binding aminocoumarins. The study results have implications for mode-of-action discovery approaches based on target-specific reference compounds, as they highlight the intraclass variability of cellular compound effects.
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17
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Yuwen L, Qiu Q, Xiu W, Yang K, Li Y, Xiao H, Yang W, Yang D, Wang L. Hyaluronidase-responsive phototheranostic nanoagents for fluorescence imaging and photothermal/photodynamic therapy of methicillin-resistant Staphylococcus aureus infections. Biomater Sci 2021; 9:4484-4495. [PMID: 34002742 DOI: 10.1039/d1bm00406a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infectious diseases associated with antibiotic-resistant bacteria are ever-growing threats to public health. Effective treatment and detection methods of bacterial infections are in urgent demand. Herein, novel phototheranostic nanoagents (MoS2@HA-Ce6 nanosheets, MHC NSs) with hyaluronidase (HAase)-responsive fluorescence imaging (FLI) and photothermal/photodynamic therapy (PTT/PDT) functions were prepared. In this design, Ce6 is used as both a photosensitizer and a fluorescent probe, while MoS2 nanosheets (MoS2 NSs) serve as both a fluorescence quencher and a photothermal agent. Hyaluronic acid conjugated with Ce6 (HA-Ce6) was assembled on the surface of MoS2 NSs to form MHC NSs. Without the HAase secreted by methicillin-resistant Staphylococcus aureus (MRSA), the fluorescence of Ce6 is quenched by MoS2 NSs, while in the presence of MRSA, HAase can degrade the HA and release Ce6, which restores the fluorescence and photodynamic activity of Ce6. The experimental results show that MHC NSs can fluorescently image the MRSA both in vitro and in vivo by HAase activation. Meanwhile, MHC NSs can serve as PTT/PDT dual-mode antibacterial agents for MRSA. In vitro antibacterial results show that MHC NSs can kill 99.97% MRSA under 635 nm and 785 nm laser irradiation. In vivo study further shows that MHC NSs can kill 99.9% of the bacteria in MRSA infected tissues in mice and prompt wound healing by combined PTT/PDT. This work provides novel HAase-responsive phototheranostic nanoagents for effective detection and treatment of bacterial infections.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Qiu Qiu
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Weijun Xiu
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Kaili Yang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Yuqing Li
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Hang Xiao
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Wenjing Yang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
| | - Dongliang Yang
- School of Physical and Mathematical Sciences & Institute of Advanced Materials (IAM), Nanjing Tech University, Nanjing 211800, China
| | - Lianhui Wang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Centre for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
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18
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Seedorf T, Kirschning A, Solga D. Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications. Chemistry 2021; 27:7321-7339. [PMID: 33481284 PMCID: PMC8251530 DOI: 10.1002/chem.202005086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
The term "privileged structure" refers to a single molecular substructure or scaffold that can serve as a starting point for high-affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well-defined scaffolds capable of specifically binding to conformationally well-defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein-protein and nucleic acid-protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications.
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Affiliation(s)
- Tim Seedorf
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Danny Solga
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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19
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Hawkins PME, Liu DY, Linington RG, Payne RJ. Solid-phase synthesis of coralmycin A/ epi-coralmycin A and desmethoxycoralmycin A. Org Biomol Chem 2021; 19:6291-6300. [PMID: 34212970 DOI: 10.1039/d1ob01062j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The total synthesis of the natural product coralmycin A/epi-coralmycin A, as well as a desmethoxy analogue is described. Synthesis was achieved via a divergent, bidirectional solid-phase strategy, including a key on-resin O-acylation, O to N acyl shift, and O-alkylation protocol to incorporate the unusual 4-amino-2-hydroxy-3-isopropoxybenzoic acid motifs. The synthetic natural product was generated as a 1 : 1 mixture of epimers at the central β-methoxyasparagine residue and exhibited potent antibacterial activity against a panel of ten Gram-negative and seven Gram-positive organisms. The desmethoxy analogue possessed significantly more potent antimicrobial activity against this panel with minimal inhibitory concentrations (MICs) as low as 50 nM.
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Affiliation(s)
- Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW 2006, Australia
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