1
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Zhang J, Sun S, Chen H, Feng Y, Li Y, Dong Z. Advances in natural compound-based nanomedicine and the interaction with gut microbiota in ulcerative colitis therapy. Front Pharmacol 2023; 14:1197144. [PMID: 37521480 PMCID: PMC10372797 DOI: 10.3389/fphar.2023.1197144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disorder of the large intestine. Previous studies have indicated that the gut microbiota plays an important role in the triggers, development, and treatment response of UC. Natural active molecules and their nanoformulations show huge potential for treating UC. The nanoparticles can regulate the gut microbiota and metabolites, whereas gut microbiota-mediated effects on nanomedicines can also bring additional therapeutic benefits. Therefore, this review aims to integrate current research on natural active molecule-based nanomedicines for UC therapy and their interaction with the gut microbiota. Here, this discussion focuses on the effects and functions of gut microbiota and metabolites in UC. The use of active molecules and the nanoformulation from natural compounds for UC therapy have been provided. The interactions between the gut microbiota and nanomedicines are derived from natural products and elucidate the possible biological mechanisms involved. Finally, the challenges and future directions for enhancing the therapeutic efficacy of nanomedicine in treating UC are proposed.
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Affiliation(s)
- Jinlan Zhang
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuhui Sun
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huan Chen
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yifan Feng
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ying Li
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhengqi Dong
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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2
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Manrique PD, López CA, Gnanakaran S, Rybenkov VV, Zgurskaya HI. New understanding of multidrug efflux and permeation in antibiotic resistance, persistence, and heteroresistance. Ann N Y Acad Sci 2023; 1519:46-62. [PMID: 36344198 PMCID: PMC9839546 DOI: 10.1111/nyas.14921] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antibiotics effective against Gram-negative ESKAPE pathogens are a critical area of unmet need. Infections caused by these pathogens are not only difficult to treat but finding new therapies to overcome Gram-negative resistance is also a challenge. There are not enough antibiotics in development that target the most dangerous pathogens and there are not enough novel drugs in the pipeline. The major obstacle in the antibiotic discovery pipeline is the lack of understanding of how to breach antibiotic permeability barriers of Gram-negative pathogens. These barriers are created by active efflux pumps acting across both the inner and the outer membranes. Overproduction of efflux pumps alone or together with either modification of the outer membrane or antibiotic-inactivating enzymes and target mutations contribute to clinical levels of antibiotics resistance. Recent efforts have generated significant advances in the rationalization of compound efflux and permeation across the cell envelopes of Gram-negative pathogens. Combined with earlier studies and novel mathematical models, these efforts have led to a multilevel understanding of how antibiotics permeate these barriers and how multidrug efflux and permeation contribute to the development of antibiotic resistance and heteroresistance. Here, we discuss the new developments in this area.
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Affiliation(s)
- Pedro D. Manrique
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
- Present address: Physics Department, George Washington University, Washington D.C. 20052, United States
| | - Cesar A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States
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3
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Sousa CF, Kamal MAM, Richter R, Elamaldeniya K, Hartmann RW, Empting M, Lehr CM, Kalinina OV. Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. J Chem Inf Model 2022; 62:5023-5033. [PMID: 36214845 DOI: 10.1021/acs.jcim.2c00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Passive diffusion across biomembranes is an important mechanism of permeation for multiple drugs, including antibiotics. However, this process is frequently neglected while studying drug uptake and, in our view, warrants further investigation. Here, we apply molecular dynamics simulations to investigate the impact of changes in molecular hydrophobicity on the permeability of a series of inhibitors of the quorum sensing of Pseudomonas aeruginosa, previously discovered by us, across a membrane model. Overall, we show that permeation across this membrane model does not correlate with the molecule's hydrophobicity. We demonstrate that using a simple model for permeation, based on the difference between the maximum and minimum of the free energy profile, outperforms the inhomogeneous solubility-diffusion model, yielding a permeability ranking that better agrees with the experimental results, especially for hydrophobic permeants. The calculated differences in permeability could not explain differences in in bacterio activity. Nevertheless, substantial differences in molecular orientation along the permeation pathway correlate with the in bacterio activity, emphasizing the importance of analyzing, at an atomistic level, the permeation pathway of these solutes.
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Affiliation(s)
- Carla F Sousa
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Mohamed A M Kamal
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Robert Richter
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Kalanika Elamaldeniya
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Rolf W Hartmann
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany.,Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken66123, Germany
| | - Martin Empting
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,Antiviral & Antivirulence Drugs Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany
| | - Claus-Michael Lehr
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Olga V Kalinina
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany.,Medical Faculty, Saarland University, Homburg66421, Germany
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4
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Ooi JMF, Fairhall JM, Spangler B, Chong DJW, Feng BY, Gamble AB, Hook S. Development of a bioorthogonal fluorescence-based assay for assessing drug uptake and delivery in bacteria. RSC Adv 2022; 12:15631-15642. [PMID: 35685699 PMCID: PMC9126673 DOI: 10.1039/d2ra02272a] [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: 04/08/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
Bioorthogonal chemistry can facilitate the development of fluorescent probes that can be used to sensitively and specifically detect the presence of biological targets. In this study, such an assay was developed to evaluate the uptake and delivery of antimicrobials into Escherichia coli, building on and extending previous work which utilised more resource intensive LCMS detection. The bacteria were genetically engineered to express streptavidin in the periplasmic or cytoplasmic compartments, which was used to localise a bioorthogonal probe (BCN-biotin). Azido-compounds which are delivered to these compartments react with the localised BCN-biotin–streptavidin in a concentration-dependent manner via a strain-promoted alkyne–azide cycloaddition. The amount of azido-compound taken up by bacteria was determined by quantifying unreacted BCN-biotin–streptavidin via an inverse electron demand Diels–Alder reaction between remaining BCN-biotin and a tetrazine-containing fluorescent dye. Following optimisation and validation, the assay was used to assess uptake of liposome-formulated azide-functionalised luciferin and cefoxitin. The results demonstrated that formulation into cationic liposomes improved the uptake of azide-functionalised compounds into the periplasm of E. coli, providing insight on the uptake mechanism of liposomes in the bacteria. This newly developed bioorthogonal fluorescence plate-reader based assay provides a bioactivity-independent, medium-to-high throughput tool for screening compound uptake/delivery. Bioorthogonal alkyne–azide and alkyne–tetrazine chemistries were used to assess drug uptake in bacteria. Azido-drug reacts with streptavidin bound alkyne-biotin within bacteria, the remaining unreacted alkyne is then quantified with a tetrazine-dye.![]()
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Affiliation(s)
| | | | - Benjamin Spangler
- Novartis Institutes for BioMedical Research (NIBR) in Emeryville California USA
| | | | - Brian Y Feng
- Novartis Institutes for BioMedical Research (NIBR) in Emeryville California USA
| | - Allan B Gamble
- School of Pharmacy, University of Otago Dunedin New Zealand
| | - Sarah Hook
- School of Pharmacy, University of Otago Dunedin New Zealand
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5
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Richter R, Kamal MAM, Koch M, Niebuur B, Huber A, Goes A, Volz C, Vergalli J, Kraus T, Müller R, Schneider‐Daum N, Fuhrmann G, Pagès J, Lehr C. An Outer Membrane Vesicle-Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability. Adv Healthc Mater 2022; 11:e2101180. [PMID: 34614289 PMCID: PMC11468809 DOI: 10.1002/adhm.202101180] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/14/2021] [Indexed: 11/11/2022]
Abstract
When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound- and bacteria-specific passive uptake pathways.
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Affiliation(s)
- Robert Richter
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Mohamed A. M. Kamal
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Marcus Koch
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
| | - Bart‐Jan Niebuur
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
| | - Anna‐Lena Huber
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Adriely Goes
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Carsten Volz
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Julia Vergalli
- UMR_MD1U‐1261Aix‐Marseille UniversitéINSERMIRBAMCTFaculté de Pharmacie27 Boulevard Jean MoulinMarseille13005France
| | - Tobias Kraus
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
- Colloid and Interface ChemistrySaarland UniversityCampus D2.2Saarbrücken66123Germany
| | - Rolf Müller
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Nicole Schneider‐Daum
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Jean‐Marie Pagès
- UMR_MD1U‐1261Aix‐Marseille UniversitéINSERMIRBAMCTFaculté de Pharmacie27 Boulevard Jean MoulinMarseille13005France
| | - Claus‐Michael Lehr
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
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6
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Ladaycia A, Passirani C, Lepeltier E. Microbiota and nanoparticles: Description and interactions. Eur J Pharm Biopharm 2021; 169:220-240. [PMID: 34736984 DOI: 10.1016/j.ejpb.2021.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/12/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The healthy human body is inhabited with a large number of bacteria, forming natural flora. It is even estimated that for a human body, its amount of DNA is less important that its bacterial genetic material. This flora plays major roles in the sickness and health of the human body and any change in its composition may lead to different diseases. Nanoparticles are widely used in numerous fields: cosmetics, food, industry, and as drug delivery carrier in the medical field. Being included in these various applications, nanoparticles may interact with the human body at various levels and with different mechanisms. These interactions differ depending on the nanoparticle nature, its structure, its concentration and manifest in different ways on the microbiota, leading to its destabilization, its restoring or showing no toxic effect. Nanoparticles may also be used as a vehicle to regulate the microbiota or to treat some of its diseases.
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Affiliation(s)
- Abdallah Ladaycia
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France
| | - Catherine Passirani
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France
| | - Elise Lepeltier
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France.
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7
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 34426795 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 576] [Impact Index Per Article: 144.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B. Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B. Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J. Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J. V. Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H. Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E. Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
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8
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma‐molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alon Golubchik
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | | | - Vikram Singh
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
| | - Sabine Kuss
- Department Chemistry University of Manitoba Winnipeg R3T 2N2 Canada
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9
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Richter R, Lehr CM. Extracellular vesicles as novel assay tools to study cellular interactions of anti-infective compounds - A perspective. Adv Drug Deliv Rev 2021; 173:492-503. [PMID: 33857554 DOI: 10.1016/j.addr.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Sudden outbreaks of novel infectious diseases and the persistent evolution of antimicrobial resistant pathogens make it necessary to develop specific tools to quickly understand pathogen-cell interactions and to study appropriate drug delivery strategies. Extracellular vesicles (EVs) are cell-specific biogenic transport systems, which are gaining more and more popularity as either diagnostic markers or drug delivery systems. Apart from that, there are emerging possibilities for EVs as tools to study drug penetration, drug-membrane interactions as well as pathogen-membrane interactions. However, it appears that the potential of EVs for such applications has not been fully exploited yet. Considering the vast variety of cells that can be involved in an infection, vesicle-based analytical methods are just emerging and the number of reported applications is still relatively small. Aim of this review is to discuss the current state of the art of EV-based assays, especially in the context of antimicrobial research and therapy, and to present some new perspectives for a more exhaustive and creative exploration in the future.
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Affiliation(s)
- Robert Richter
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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10
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Golubchik A, Lopes LC, Singh V, Kuss S. Pharma-molecule Transport across Bacterial Membranes: Detection and Quantification Approaches by Electrochemistry and Bioanalytical Methods. Angew Chem Int Ed Engl 2021; 60:22112-22124. [PMID: 33979000 DOI: 10.1002/anie.202101055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/07/2022]
Abstract
Antibiotic resistance is a significant challenge encountered by healthcare systems on a global scale. Knowledge about membrane transport of antibiotics and other pharmacologically relevant molecules in bacteria is crucial towards understanding and overcoming antibiotic resistance, as drug resistance often depends on drug transport. This comprehensive literature review discusses the detection and quantification of membrane transport of pharma-molecules in bacteria and highlights the importance of molecule transport to antibiotic resistance. This review emphasizes electrochemical and electrophysiological methods of detection and quantification. The results of this literature review reveal a substantial diversity in methods and types of quantitative information collected.
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Affiliation(s)
- Alon Golubchik
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | | | - Vikram Singh
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Sabine Kuss
- Department Chemistry, University of Manitoba, Winnipeg, R3T 2N2, Canada
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11
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 PMCID: PMC8369882 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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12
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Mastering the Gram-negative bacterial barrier - Chemical approaches to increase bacterial bioavailability of antibiotics. Adv Drug Deliv Rev 2021; 172:339-360. [PMID: 33705882 DOI: 10.1016/j.addr.2021.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
To win the battle against resistant, pathogenic bacteria, novel classes of anti-infectives and targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of antibiotics in Gram-negative bacteria determine what we here refer to as bacterial bioavailability. Understanding these mechanisms from a chemical perspective is essential for anti-infective activity and hence, drug discovery as well as drug delivery. A systematic and critical discussion of in bacterio, in vitro and in silico assays reveals that a sufficiently accurate holistic approach is still missing. We expect new findings based on Gram-negative bacterial bioavailability to guide future anti-infective research.
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13
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Horstmann JC, Thorn CR, Carius P, Graef F, Murgia X, de Souza Carvalho-Wodarz C, Lehr CM. A Custom-Made Device for Reproducibly Depositing Pre-metered Doses of Nebulized Drugs on Pulmonary Cells in vitro. Front Bioeng Biotechnol 2021; 9:643491. [PMID: 33968912 PMCID: PMC8096921 DOI: 10.3389/fbioe.2021.643491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/16/2021] [Indexed: 12/20/2022] Open
Abstract
The deposition of pre-metered doses (i.e., defined before and not after exposition) at the air-liquid interface of viable pulmonary epithelial cells remains an important but challenging task for developing aerosol medicines. While some devices allow quantification of the deposited dose after or during the experiment, e.g., gravimetrically, there is still no generally accepted way to deposit small pre-metered doses of aerosolized drugs or pharmaceutical formulations, e.g., nanomedicines. Here, we describe a straightforward custom-made device, allowing connection to commercially available nebulizers with standard cell culture plates. Designed to tightly fit into the approximately 12-mm opening of either a 12-well Transwell® insert or a single 24-well plate, a defined dose of an aerosolized liquid can be directly deposited precisely and reproducibly (4.8% deviation) at the air-liquid interface (ALI) of pulmonary cell cultures. The deposited dose can be controlled by the volume of the nebulized solution, which may vary in a range from 20 to 200 μl. The entire nebulization-deposition maneuver is completed after 30 s and is spatially homogenous. After phosphate-buffered saline (PBS) deposition, the viability and barrier properties transepithelial electrical resistance (TEER) of human bronchial epithelial Calu-3 cells were not negatively affected. Straightforward in manufacture and use, the device enables reproducible deposition of metered doses of aerosolized drugs to study the interactions with pulmonary cell cultures grown at ALI conditions.
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Affiliation(s)
- Justus C Horstmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Chelsea R Thorn
- Clinical and Health Science, University of South Australia, Adelaide, SA, Australia
| | - Patrick Carius
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Florian Graef
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
| | - Xabier Murgia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
| | | | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Saarbrücken, Germany
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14
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Montefusco-Pereira CV, Carvalho-Wodarz CDS, Seeger J, Kloft C, Michelet R, Lehr CM. Decoding (patho-)physiology of the lung by advanced in vitro models for developing novel anti-infectives therapies. Drug Discov Today 2020; 26:148-163. [PMID: 33232842 DOI: 10.1016/j.drudis.2020.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/11/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
Advanced lung cell culture models provide physiologically-relevant and complex data for mathematical models to exploit host-pathogen responses during anti-infective drug testing.
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Affiliation(s)
- Carlos Victor Montefusco-Pereira
- Department of Pharmacy, Saarland University, Saarbruecken, Germany; Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, Germany
| | | | - Johanna Seeger
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, Germany
| | - Charlotte Kloft
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, Germany
| | - Robin Michelet
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universitaet Berlin, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbruecken, Germany; Department of Pharmacy, Saarland University, Saarbruecken, Germany
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15
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Richter R, Kamal M, García-Rivera MA, Kaspar J, Junk M, Elgaher WA, Srikakulam SK, Gress A, Beckmann A, Grißmer A, Meier C, Vielhaber M, Kalinina O, Hirsch AK, Hartmann RW, Brönstrup M, Schneider-Daum N, Lehr CM. A hydrogel-based in vitro assay for the fast prediction of antibiotic accumulation in Gram-negative bacteria. Mater Today Bio 2020; 8:100084. [PMID: 33313504 PMCID: PMC7720078 DOI: 10.1016/j.mtbio.2020.100084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 11/30/2022] Open
Abstract
The pipeline of antibiotics has been for decades on an alarmingly low level. Considering the steadily emerging antibiotic resistance, novel tools are needed for early and easy identification of effective anti-infective compounds. In Gram-negative bacteria, the uptake of anti-infectives is especially limited. We here present a surprisingly simple in vitro model of the Gram-negative bacterial envelope, based on 20% (w/v) potato starch gel, printed on polycarbonate 96-well filter membranes. Rapid permeability measurements across this polysaccharide hydrogel allowed to correctly predict either high or low accumulation for all 16 tested anti-infectives in living Escherichia coli. Freeze-fracture TEM supports that the macromolecular network structure of the starch hydrogel may represent a useful surrogate of the Gram-negative bacterial envelope. A random forest analysis of in vitro data revealed molecular mass, minimum projection area, and rigidity as the most critical physicochemical parameters for hydrogel permeability, in agreement with reported structural features needed for uptake into Gram-negative bacteria. Correlating our dataset of 27 antibiotics from different structural classes to reported MIC values of nine clinically relevant pathogens allowed to distinguish active from nonactive compounds based on their low in vitro permeability specifically for Gram-negatives. The model may help to identify poorly permeable antimicrobial candidates before testing them on living bacteria.
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Affiliation(s)
- Robert Richter
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Mohamed.A.M. Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Mariel A. García-Rivera
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Jerome Kaspar
- Institute of Engineering Design, Saarland University, 66123 Saarbrücken, Germany
| | - Maximilian Junk
- Institute of Engineering Design, Saarland University, 66123 Saarbrücken, Germany
| | - Walid A.M. Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Sanjay Kumar Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Alexander Gress
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Anja Beckmann
- Department of Anatomy and Cell Biology, Saarland University, 66421 Homburg, Germany
| | - Alexander Grißmer
- Department of Anatomy and Cell Biology, Saarland University, 66421 Homburg, Germany
| | - Carola Meier
- Department of Anatomy and Cell Biology, Saarland University, 66421 Homburg, Germany
| | - Michael Vielhaber
- Institute of Engineering Design, Saarland University, 66123 Saarbrücken, Germany
| | - Olga Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
- Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Anna K.H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Nicole Schneider-Daum
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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16
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Ferreira RJ, Kasson PM. Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics. ACS Infect Dis 2019; 5:2096-2104. [PMID: 31593635 DOI: 10.1021/acsinfecdis.9b00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crossing the Gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay of outer membrane vesicle swelling. Parallel molecular dynamics simulations of compound uptake through Escherichia coli (E. coli) OmpF are used to successfully and quantitatively predict experimental permeabilities measured via either outer membrane swelling or prior liposome-swelling measurements. These simulations are analyzed using an inhomogeneous solubility-diffusion model to yield predictions of permeability. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer membrane permeability.
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Affiliation(s)
- Ricardo J. Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Peter M. Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Departments of Biomedical Engineering and Molecular Physiology and Biological Physics, University of Virginia, Box 800886, Charlottesville, Virginia 22908, United States
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17
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Prochnow H, Fetz V, Hotop SK, García-Rivera MA, Heumann A, Brönstrup M. Subcellular Quantification of Uptake in Gram-Negative Bacteria. Anal Chem 2018; 91:1863-1872. [PMID: 30485749 DOI: 10.1021/acs.analchem.8b03586] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Infections by Gram-negative pathogens represent a major health care issue of growing concern due to a striking lack of novel antibacterial agents over the course of the last decades. The main scientific problem behind the rational optimization of novel antibiotics is our limited understanding of small molecule translocation into, and their export from, the target compartments of Gram-negative species. To address this issue, a versatile, label-free assay to determine the intracellular localization and concentration of a given compound has been developed for Escherichia coli and its efflux-impaired ΔTolC mutant. The assay applies a fractionation procedure to antibiotic-treated bacterial cells to obtain periplasm, cytoplasm, and membrane fractions of high purity, as demonstrated by Western Blots of compartment-specific marker proteins. This is followed by an LC-MS/MS-based quantification of antibiotic content in each compartment. Antibiotic amounts could be converted to antibiotic concentrations by assuming that an E. coli cell is a cylinder flanked by two half spheres and calculating the volumes of bacterial compartments. The quantification of antibiotics from different classes, namely ciprofloxacin, tetracycline, trimethoprim, and erythromycin, demonstrated pronounced differences in uptake quantities and distribution patterns across the compartments. For example, in the case of ciprofloxacin, a higher amount of compound was located in the cytoplasm than in the periplasm (592 ± 50 pg vs 277 ± 13 pg per 3.9 × 109 cells), but owing to the smaller volume of the periplasmic compartment, its concentration in the cytoplasm was much lower (37 ± 3 vs 221 ± 10 pg/μL for the periplasm). For erythromycin and tetracycline, differences in MICs between WT and ΔTolC mutant strains were not reflected by equal differences in uptake, illustrating that additional experimental data are needed to predict antibiotic efficacy. We believe that our assay, providing the antibiotic concentration at the compartment in which the drug target is expressed, constitutes an essential piece of information for a more rational optimization of novel antibiotics against Gram-negative infections.
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Affiliation(s)
- Hans Prochnow
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Verena Fetz
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany.,School of Engineering and Science , Jacobs University Bremen , 28759 Bremen , Germany
| | - Sven-Kevin Hotop
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Mariel A García-Rivera
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Axel Heumann
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Mark Brönstrup
- Department of Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 Braunschweig , Germany.,German Center for Infection Research (DZIF) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
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18
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Iyer R, Ye Z, Ferrari A, Duncan L, Tanudra MA, Tsao H, Wang T, Gao H, Brummel CL, Erwin AL. Evaluating LC-MS/MS To Measure Accumulation of Compounds within Bacteria. ACS Infect Dis 2018; 4:1336-1345. [PMID: 29961312 DOI: 10.1021/acsinfecdis.8b00083] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A general method for determining bacterial uptake of compounds independent of antibacterial activity would be a valuable tool in antibacterial drug discovery. LC-MS/MS assays have been described, but it has not been shown whether the data can be used directly to inform medicinal chemistry. We describe the evaluation of an LC-MS/MS assay measuring association of compounds with bacteria, using a set of over a hundred compounds (inhibitors of NAD-dependent DNA ligase, LigA) for which in vitro potency and antibacterial activity had been determined. All compounds were active against an efflux-deficient strain of Escherichia coli with reduced LigA activity ( E. coli ligA251 Δ tolC). Testing a single compound concentration and incubation time, we found that, for equipotent compounds, LC-MS/MS values were not predictive of antibacterial activity. This indicates that measured bacteria-associated compound was not necessarily exposed to the target enzyme. Our data suggest that, while exclusion from bacteria is a major reason for poor antibacterial activity of potent compounds, the distribution of compound within the bacterial cell may also be a problem. The relative importance of these factors is likely to vary from one chemical series to another. Our observations provide directions for further study of this difficult issue.
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Affiliation(s)
- Ramkumar Iyer
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Zhengqi Ye
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Annette Ferrari
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Leonard Duncan
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - M. Angela Tanudra
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Hong Tsao
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Tiansheng Wang
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Hong Gao
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Christopher L. Brummel
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Alice L. Erwin
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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