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Lewis K, Lee RE, Brötz-Oesterhelt H, Hiller S, Rodnina MV, Schneider T, Weingarth M, Wohlgemuth I. Sophisticated natural products as antibiotics. Nature 2024; 632:39-49. [PMID: 39085542 DOI: 10.1038/s41586-024-07530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2024] [Indexed: 08/02/2024]
Abstract
In this Review, we explore natural product antibiotics that do more than simply inhibit an active site of an essential enzyme. We review these compounds to provide inspiration for the design of much-needed new antibacterial agents, and examine the complex mechanisms that have evolved to effectively target bacteria, including covalent binders, inhibitors of resistance, compounds that utilize self-promoted entry, those that evade resistance, prodrugs, target corrupters, inhibitors of 'undruggable' targets, compounds that form supramolecular complexes, and selective membrane-acting agents. These are exemplified by β-lactams that bind covalently to inhibit transpeptidases and β-lactamases, siderophore chimeras that hijack import mechanisms to smuggle antibiotics into the cell, compounds that are activated by bacterial enzymes to produce reactive molecules, and antibiotics such as aminoglycosides that corrupt, rather than merely inhibit, their targets. Some of these mechanisms are highly sophisticated, such as the preformed β-strands of darobactins that target the undruggable β-barrel chaperone BamA, or teixobactin, which binds to a precursor of peptidoglycan and then forms a supramolecular structure that damages the membrane, impeding the emergence of resistance. Many of the compounds exhibit more than one notable feature, such as resistance evasion and target corruption. Understanding the surprising complexity of the best antimicrobial compounds provides a roadmap for developing novel compounds to address the antimicrobial resistance crisis by mining for new natural products and inspiring us to design similarly sophisticated antibiotics.
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Affiliation(s)
- Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Boston, MA, USA.
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Tubingen, Germany
- Controlling Microbes to Fight Infection-Cluster of Excellence, Tubingen, Germany
| | | | - Marina V Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Markus Weingarth
- Chemistry Department, Utrecht University, Utrecht, the Netherlands
| | - Ingo Wohlgemuth
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
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Tambat R, Kinthada RK, Saral Sariyer A, Leus IV, Sariyer E, D'Cunha N, Zhou H, Leask M, Walker JK, Zgurskaya HI. AdeIJK Pump-Specific Inhibitors Effective against Multidrug Resistant Acinetobacter baumannii. ACS Infect Dis 2024; 10:2239-2249. [PMID: 38787939 DOI: 10.1021/acsinfecdis.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Multidrug-resistant Acinetobacter baumannii is a serious threat pathogen rapidly spreading in clinics and causing a range of complicated human infections. The major contributor to A. baumannii antibiotic resistance is the overproduction of AdeIJK and AdeABC multidrug efflux pumps of the resistance-nodulation-division (RND) superfamily of proteins. The dominant role of efflux in antibiotic resistance and the relatively high permeability of the A. baumannii outer membrane to amphiphilic compounds make this pathogen a promising target for the discovery of clinically relevant efflux pump inhibitors. In this study, we identified 4,6-diaminoquoniline analogs with inhibitory activities against A. baumannii AdeIJK efflux pump and followed up on these compounds with a focused synthetic program to improve the target specificity and to reduce cytotoxicity. We identified several candidates that potentiate antibacterial activities of antibiotics erythromycin, tetracycline, and novobiocin not only in the laboratory antibiotic susceptible strain A. baumannii ATCC17978 but also in multidrug-resistant clinical isolates AB5075 and AYE. The best analogs potentiated the activities of antibiotics in low micromolar concentrations, did not have antibacterial activities on their own, inhibited AdeIJK-mediated efflux of its fluorescent substrate ethidium ion, and had low cytotoxicity in A549 human lung epithelial cells.
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Affiliation(s)
- Rushikesh Tambat
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rama Kumar Kinthada
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Aysegul Saral Sariyer
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, 08000 Artvin, Turkey
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Emrah Sariyer
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, 08000 Artvin, Turkey
- Vocational School of Health Services, Medical Laboratory Techniques, Artvin Coruh University, 08000 Artvin, Turkey
| | - Napoleon D'Cunha
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Hinman Zhou
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Makaila Leask
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
| | - John K Walker
- School of Medicine, Saint Louis University, St. Louis, Missouri 63110, United States
- Department of Chemistry, Saint Louis University, St. Louis, Missouri 63110, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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Ramiz Uddin M, Shahriar A, Jahan Mim H, Khadiza Papia B, Rob Siddiquee MF, Bin R Q Khan A, Islam R, Fatema N, Parvez A, Kumar Roy G, Rana S. Unveiling Annona Reticulata's Bioactive Arsenal for Enhanced Antibiotic Effects. Chem Biodivers 2024; 21:e202301495. [PMID: 38282427 DOI: 10.1002/cbdv.202301495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE To study the antibacterial and phytochemical activities of bioactive elements in the leaves of Annona reticulata Linn, a historically used Bangladeshi medicinal plant. METHODS Shade-dried and crushed plant leaves were soaked with various solvents to obtain samples for different chemical analyses. All extracts were selected for antimicrobial, physicochemical, and Pharmacological investigations. The antimicrobial activity was evaluated using disc diffusion assay, and broth microdilution methods determined potentiation of the activities of the antibiotic antibacterial activity of the plant extracts was investigated using either gram-positive or gram-negative pathogenic wild-type bacteria. RESULTS From the initial phytochemical and pharmacological studies, it was clear that all extracts, methanol, chloroform, and ethyl acetate, of the leaves of A. reticulata, were proven to process potent bioactive constituents. While differential antimicrobial properties were found to be possessed by all extracts, methanolic extract was the most potent one against all tested microorganisms. It also has potentiated the activities of antibiotics in E. coli. CONCLUSION Bioactive constituents in the plant extracts were shown to possess phytochemical and antimicrobial activities. More investigation is needed to segregate the chemical components responsible for the respective phytochemical and antimicrobial activities.
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Affiliation(s)
| | - Asif Shahriar
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh
| | - Halima Jahan Mim
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Bibi Khadiza Papia
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Mohd Faijanur Rob Siddiquee
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Ahnaf Bin R Q Khan
- Department of Applied Chemistry and Chemical Engineering, University of Dhaka, Dhaka, Bangladesh
| | - Rahatul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nour Fatema
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh
| | - Anwar Parvez
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | | | - Sohel Rana
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
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Kong J, Wang Y, Yao Z, Lin Y, Zhang Y, Han Y, Zhou T, Ye J, Cao J. Eugenol works synergistically with colistin against colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae isolates by enhancing membrane permeability. Microbiol Spectr 2023; 11:e0366622. [PMID: 37707450 PMCID: PMC10581171 DOI: 10.1128/spectrum.03666-22] [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: 09/16/2022] [Accepted: 07/20/2023] [Indexed: 09/15/2023] Open
Abstract
Colistin is a potent antibiotic for the treatment of carbapenem-resistant Gram-negative bacteria and is considered a last-resort drug. Unfortunately, the incidence of colistin-resistant bacteria isolated from patients is continuously growing due to clinical reuse of colistin. In this study, we found that the combination of colistin and eugenol has a significant synergistic antibacterial effect and reverses the sensitivity of colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae against colistin, as confirmed by checkerboard and time-kill assays. Crystal violet staining and scanning electron microscopy revealed colistin and eugenol's synergistic antibiofilm action. Concerning the synergy mechanism, the results revealed that the combination of eugenol and colistin increases membrane permeability and causes considerable membrane damage, further inhibiting bacteria synergistically. Meanwhile, up to 500 µg/mL of eugenol is non-toxic to RAW 264.7 cells, and the colistin/eugenol combination is also efficacious in vivo, as demonstrated by the Galleria mellonella infection model. Our findings indicate that the colistin/eugenol combination is a viable treatment option for colistin-resistant P. aeruginosa and K. pneumoniae clinical infections. IMPORTANCE Colistin is used as a last resort for severe infections caused by multidrug-resistant Gram-negative bacteria, however, colistin resistance is increasing. As a result, we investigated the synergistic effect of eugenol/colistin combination, and the results revealed significant antibacterial and antibiofilm action. Eugenol may help clinical colistin-resistant Pseudomonas aeruginosa and Klebsiella pneumoniae recover their susceptibility. These findings suggest that combining eugenol and colistin may be a viable treatment option for colistin-resistant pathogen clinical infections.
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Affiliation(s)
- Jingchun Kong
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yue Wang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zhuocheng Yao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yishuai Lin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yi Zhang
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yijia Han
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Szal T, Chauhan SS, Lewe P, Rachad FZ, Madre M, Paunina L, Witt S, Parthasarathi R, Windshügel B. Efflux Pump-Binding 4(3-Aminocyclobutyl)Pyrimidin-2-Amines Are Colloidal Aggregators. Biomolecules 2023; 13:1000. [PMID: 37371580 DOI: 10.3390/biom13061000] [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: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Efflux pumps are a relevant factor in antimicrobial resistance. In E. coli, the tripartite efflux pump AcrAB-TolC removes a chemically diverse set of antibiotics from the bacterium. Therefore, small molecules interfering with efflux pump function are considered adjuvants for improving antimicrobial therapies. Several compounds targeting the periplasmic adapter protein AcrA and the efflux pump AcrB have been identified to act synergistically with different antibiotics. Among those, several 4(3-aminocyclobutyl)pyrimidin-2-amines have been shown to bind to both proteins. In this study, we intended to identify analogs of these substances with improved binding affinity to AcrA using virtual screening followed by experimental validation. While we succeeded in identifying several compounds showing a synergistic effect with erythromycin on E. coli, biophysical studies suggested that 4(3-aminocyclobutyl)pyrimidin-2-amines form colloidal aggregates that do not bind specifically to AcrA. Therefore, these substances are not suited for further development. Our study emphasizes the importance of implementing additional control experiments to identify aggregators among bioactive compounds.
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Affiliation(s)
- Tania Szal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
| | - Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Fatima-Zahra Rachad
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
| | - Marina Madre
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Laura Paunina
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
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