1
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Atac N, Gunduz H, Koc I, Onbasli K, Khan M, Savani S, Sennaroglu A, Can F, Acar HY, Kolemen S. Selective antibacterial and antibiofilm activity of chlorinated hemicyanine against gram-positive bacteria. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124324. [PMID: 38676983 DOI: 10.1016/j.saa.2024.124324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/14/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
Antibiotic-free therapies are highly needed due to the limited success of conventional approaches especially against biofilm related infections. In this direction, antimicrobial phototherapy, either in the form of antimicrobial photothermal therapy (aPTT) or antimicrobial photodynamic therapy (aPDT), have appeared to be highly promising candidates in recent years. These are local and promising approaches for antibiotic resistant bacterial infections and biofilms. Organic small photosensitizers (PSs) are extensively preferred in antimicrobial phototherapy applications as they offer a great opportunity to combine therapeutic action (aPTT, aPDT or both) with fluorescence imaging on a single molecule. In this study, the bactericidal effect of cationic chlorinated hemicyanine (Cl-Hem)-based type I PS, which can function as a dual aPDT/aPTT agent, was investigated on both planktonic cells and biofilms of different gram-positive (E. faecalis and S. epidermidis) and gram-negative bacteria (P. aeruginosa and K. pneumoniae) with and without 640 nm laser irradiation. Cl-Hem was shown to induce a selective phototheranostic activity against gram-positive bacteria (E. faecalis and S. epidermidis). Cl-Hem exhibited both dose and laser irradiation time dependent bactericidal effect on planktonic and biofilms of S. epidermidis. These results clearly showed that highly potent Cl-Hem can treat resistant microbial infections, while allowing fluorescence detection at the same time. High biofilm reduction observed with combined aPDT/aPTT action of Cl-Hem together with its non-cytotoxic nature points out that Cl-Hem is a promising PS for antibacterial and antibiofilm treatments.
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Affiliation(s)
- Nazli Atac
- Koç University, School of Medicine, Medical Microbiology, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye; Koç University-İşbank Center for Infectious Diseases (KUISCID), Topkapı, Istanbul, Turkiye
| | - Hande Gunduz
- Koç University, Department of Chemistry, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye; Nanofabrication and Nanocharacterization Centre for Scientific and Technological Advanced Research, Koç University, Istanbul, Turkiye
| | - Irem Koc
- Koç University, Graduate School of Materials Science and Engineering, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye
| | - Kubra Onbasli
- Istanbul Technical University, Department of Metallurgical and Materials Engineering, Istanbul, Turkiye
| | - Minahil Khan
- Koç University, Department of Physics, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye
| | - Samira Savani
- Koç University, Department of Chemistry, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye
| | - Alphan Sennaroglu
- Koç University, Department of Physics, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye; Koç University, Department of Electrical and Electronics Engineering, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye
| | - Fusun Can
- Koç University, School of Medicine, Medical Microbiology, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye; Koç University-İşbank Center for Infectious Diseases (KUISCID), Topkapı, Istanbul, Turkiye.
| | - Havva Yagci Acar
- Koç University, Department of Chemistry, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye.
| | - Safacan Kolemen
- Koç University, Department of Chemistry, Rumelifeneri Yolu, Sarıyer, Istanbul, Turkiye.
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2
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Kumar D, Gayen A, Chandra M. Membrane Permeability Dominates over Electrostatic Interactions in Dictating Drug Transport in Osmotically Shocked Escherichia coli. J Phys Chem B 2024; 128:4911-4921. [PMID: 38736363 DOI: 10.1021/acs.jpcb.3c08426] [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: 05/14/2024]
Abstract
To combat surging multidrug-resistant Gram-negative bacterial infections, better strategies to improve the efficacy of existing drugs are critical. Because the dual membrane cell envelope is the first line of defense for these bacteria, it is crucial to understand the permeation properties of the drugs through it. Our recent study shows that isosmotic conditions prevent drug permeation inside Gram-negative bacteria, Escherichia coli, while hypoosmotic stress enhances the process. Here, we unravel the reason behind such differential drug penetration. Specifically, we dissect the roles of electrostatic screening and low membrane permeability in the penetration failure of drugs under osmotically balanced conditions. We compare the transport of a quaternary ammonium compound malachite green in the presence of an electrolyte (NaCl) and a wide variety of commonly used organic osmolytes, e.g., sucrose, proline, glycerol, sorbitol, and urea. These osmolytes of different membrane permeability (i.e., nonpermeable sucrose and NaCl, freely permeable urea and glycerol, and partially permeable proline and sorbitol) clarify the role of osmotic stress in cell envelope permeability. The results showcase that under balanced osmotic conditions, drug molecules fail to penetrate inside E. coli cells because of low membrane permeabilities and not because of electrostatic screening imposed by the osmolytes. Contribution of the electrostatic interactions, however, cannot be completely overruled as at osmotically imbalanced conditions, drug transport across the bacterial subcellular compartments is found to be dependent on the osmolytes used.
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Affiliation(s)
- Deepak Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Anindita Gayen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Manabendra Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
- Center of Excellence: Tropical and Infectious Diseases, Gangwal School of Medical Sciences and Technology, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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3
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Zhu S, Alexander MK, Paiva TO, Rachwalski K, Miu A, Xu Y, Verma V, Reichelt M, Dufrêne YF, Brown ED, Cox G. The inactivation of tolC sensitizes Escherichia coli to perturbations in lipopolysaccharide transport. iScience 2024; 27:109592. [PMID: 38628966 PMCID: PMC11019271 DOI: 10.1016/j.isci.2024.109592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
The Escherichia coli outer membrane channel TolC complexes with several inner membrane efflux pumps to export compounds across the cell envelope. All components of these complexes are essential for robust efflux activity, yet E. coli is more sensitive to antimicrobial compounds when tolC is inactivated compared to the inactivation of genes encoding the inner membrane drug efflux pumps. While investigating these susceptibility differences, we identified a distinct class of inhibitors targeting the core-lipopolysaccharide translocase, MsbA. We show that tolC null mutants are sensitized to structurally unrelated MsbA inhibitors and msbA knockdown, highlighting a synthetic-sick interaction. Phenotypic profiling revealed that tolC inactivation induced cell envelope softening and increased outer membrane permeability. Overall, this work identified a chemical probe of MsbA, revealed that tolC is associated with cell envelope mechanics and integrity, and highlighted that these findings should be considered when using tolC null mutants to study efflux deficiency.
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Affiliation(s)
- Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
| | | | - Telmo O. Paiva
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Anh Miu
- Genentech Inc, Biochemical and Cellular Pharmacology, South San Francisco, CA, USA
| | - Yiming Xu
- Genentech Inc, Infectious Diseases, South San Francisco, CA, USA
| | - Vishal Verma
- Genentech Inc, Discovery Chemistry, South San Francisco, CA, USA
| | - Mike Reichelt
- Genentech Inc, Pathology, South San Francisco, CA, USA
| | - Yves F. Dufrêne
- Institute of Life Sciences, UCLouvain, Croix du Sud, 4-5, bte L7.07.06, B-1348 Louvain-la-Neuve, Belgium
| | - Eric D. Brown
- Biochemistry and Biomedical Sciences and Degroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E, Guelph, ON N1G 2W1, Canada
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4
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Dash R, Holsinger KA, Chordia MD, Gh MS, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. ACS Infect Dis 2024; 10:1602-1611. [PMID: 38592927 DOI: 10.1021/acsinfecdis.3c00684] [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: 04/11/2024]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving the cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between the arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules in the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotic accumulation in live bacterial cells in real time.
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Affiliation(s)
- Rachita Dash
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kadie A Holsinger
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mohammad Sharifian Gh
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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5
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Wang H, Ishchenko A, Skudlarek J, Shen P, Dzhekieva L, Painter RE, Chen YT, Bukhtiyarova M, Leithead A, Tracy R, Babaoglu K, Bahnck-Teets C, Buevich A, Cabalu TD, Labroli M, Lange H, Lei Y, Li W, Liu J, Mann PA, Meng T, Mitchell HJ, Mulhearn J, Scapin G, Sha D, Shaw AW, Si Q, Tong L, Wu C, Wu Z, Xiao JC, Xu M, Zhang LK, McKenney D, Miller RR, Black TA, Cooke A, Balibar CJ, Klein DJ, Raheem I, Walker SS. Cerastecins inhibit membrane lipooligosaccharide transport in drug-resistant Acinetobacter baumannii. Nat Microbiol 2024; 9:1244-1255. [PMID: 38649414 DOI: 10.1038/s41564-024-01667-0] [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: 11/22/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024]
Abstract
Carbapenem-resistant Acinetobacter baumannii infections have limited treatment options. Synthesis, transport and placement of lipopolysaccharide or lipooligosaccharide (LOS) in the outer membrane of Gram-negative bacteria are important for bacterial virulence and survival. Here we describe the cerastecins, inhibitors of the A. baumannii transporter MsbA, an LOS flippase. These molecules are potent and bactericidal against A. baumannii, including clinical carbapenem-resistant Acinetobacter baumannii isolates. Using cryo-electron microscopy and biochemical analysis, we show that the cerastecins adopt a serpentine configuration in the central vault of the MsbA dimer, stalling the enzyme and uncoupling ATP hydrolysis from substrate flipping. A derivative with optimized potency and pharmacokinetic properties showed efficacy in murine models of bloodstream or pulmonary A. baumannii infection. While resistance development is inevitable, targeting a clinically unexploited mechanism avoids existing antibiotic resistance mechanisms. Although clinical validation of LOS transport remains undetermined, the cerastecins may open a path to narrow-spectrum treatment modalities for important nosocomial infections.
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Affiliation(s)
- Hao Wang
- Merck & Co., Inc., West Point, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ying Lei
- Merck & Co., Inc., West Point, PA, USA
| | - Wei Li
- Merck & Co., Inc., West Point, PA, USA
| | - Jian Liu
- Merck & Co., Inc., West Point, PA, USA
| | | | - Tao Meng
- Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | - Deyou Sha
- Merck & Co., Inc., West Point, PA, USA
| | | | - Qian Si
- Merck & Co., Inc., West Point, PA, USA
| | - Ling Tong
- Merck & Co., Inc., West Point, PA, USA
| | | | - Zhe Wu
- Merck & Co., Inc., West Point, PA, USA
| | | | - Min Xu
- Merck & Co., Inc., West Point, PA, USA
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6
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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [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: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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7
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Palberg D, Kaszecki E, Dhanjal C, Kisiała A, Morrison EN, Stock N, Emery RJN. Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium. BMC PLANT BIOLOGY 2024; 24:119. [PMID: 38369476 PMCID: PMC10875822 DOI: 10.1186/s12870-024-04818-x] [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: 10/08/2023] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
Symbiotic Methylobacterium comprise a significant portion of the phyllospheric microbiome, and are known to benefit host plant growth, development, and confer tolerance to stress factors. The near ubiquitous use of the broad-spectrum herbicide, glyphosate, in farming operations globally has necessitated a more expansive evaluation of the impacts of the agent itself and formulations containing glyphosate on important components of the plant phyllosphere, including Methylobacterium.This study provides an investigation of the sensitivity of 18 strains of Methylobacterium to glyphosate and two commercially available glyphosate-based herbicides (GBH). Nearly all strains of Methylobacterium showed signs of sensitivity to the popular GBH formulations WeatherMax® and Transorb® in a modified Kirby Bauer experiment. However, exposure to pure forms of glyphosate did not show a significant effect on growth for any strain in both the Kirby Bauer test and in liquid broth, until polysorbate-20 (Tween20) was added as a surfactant. Artificially increasing membrane permeability through the introduction of polysorbate-20 caused a 78-84% reduction in bacterial cell biomass relative to controls containing glyphosate or high levels of surfactant only (0-9% and 6-37% reduction respectively). Concentrations of glyphosate as low as 0.05% w/v (500 µg/L) from both commercial formulations tested, inhibited the culturability of Methylobacterium on fresh nutrient-rich medium.To better understand the compatibility of important phyllospheric bacteria with commercial glyphosate-based herbicides, this study endeavours to characterize sensitivity in multiple strains of Methylobacterium, and explore possible mechanisms by which toxicity may be induced.
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Affiliation(s)
- Daniel Palberg
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Emma Kaszecki
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Chetan Dhanjal
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA
| | - Anna Kisiała
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Erin N Morrison
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Naomi Stock
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
- Water Quality Centre, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - R J Neil Emery
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada.
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada.
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8
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Alqahtani J, Negm WA, Elekhnawy E, Alqahtani MJ, Moglad E, Ibrahim S, El-Sherbeni SA. Outlining the Phytoconstituents of Greek Clover Herb Extract and Assessment of Its Effect against Foodborne Infections Caused by Salmonella typhimurium. Pharmaceuticals (Basel) 2024; 17:259. [PMID: 38399474 PMCID: PMC10892485 DOI: 10.3390/ph17020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Owing to the spread of resistance between pathogenic bacteria, searching for novel compounds with antibacterial activity is essential. Here, we investigated the potential antibacterial activity of Greek clover or Trigonella foenum-graecum herb extract on Salmonella typhimurium clinical isolates. The chemical profile of the herb was initially determined using LC-ESI-MS/MS, which explored 36 different compounds. Interestingly, the fenugreek extract possessed antibacterial action in vitro with minimum inhibitory concentrations of 64 to 512 µg/mL. The potential mechanism of action was studied by elucidating the effect of the fenugreek extract on the membrane properties of S. typhimurium bacteria, including the inner and outer membrane permeability and membrane integrity. Remarkably, the fenugreek extract had detrimental effects on the membrane properties in 40-60% of the isolates. Moreover, the in vivo antibacterial action was studied using a gastrointestinal infection model with S. typhimurium bacteria. Interestingly, the fenugreek extract (200 mg/kg) improved the infection outcomes in the tested mice. This was represented by the noteworthy decrease (p < 0.05) in the bacterial count in the small intestine and caecum tissues. The survival rate of the fenugreek-extract-treated mice significantly increased compared to the S. typhimurium-infected group. Additionally, there was an improvement in the histological and immunohistochemical features of tumor necrosis factor-alpha. In addition, using an ELISA and qRT-PCR, there was an improvement in the proinflammatory and oxidative stress markers in the fenugreek-extract-treated group. Consequently, fenugreek extract should be investigated further on other food pathogens.
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Affiliation(s)
- Jawaher Alqahtani
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Walaa A. Negm
- Department of Pharmacognosy, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt; (W.A.N.); (S.A.E.-S.)
| | - Engy Elekhnawy
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Moneerah J. Alqahtani
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
| | - Sarah Ibrahim
- Human Anatomy and Embryology Department, Faculty of Medicine, Tanta University, Tanta 31527, Egypt;
| | - Suzy A. El-Sherbeni
- Department of Pharmacognosy, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt; (W.A.N.); (S.A.E.-S.)
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9
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Dechsri K, Suwanchawalit C, Patrojanasophon P, Opanasopit P, Pengnam S, Charoenying T, Taesotikul T. Photodynamic Antibacterial Therapy of Gallic Acid-Derived Carbon-Based Nanoparticles (GACNPs): Synthesis, Characterization, and Hydrogel Formulation. Pharmaceutics 2024; 16:254. [PMID: 38399308 PMCID: PMC10891664 DOI: 10.3390/pharmaceutics16020254] [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: 01/25/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Carbon-based nanoparticles (CNPs) have gained recognition because of their good biocompatibility, easy preparation, and excellent phototherapy properties. In biomedicine applications, CNPs are widely applied as photodynamic agents for antibacterial purposes. Photodynamic therapy has been considered a candidate for antibacterial agents because of its noninvasiveness and minimal side effects, especially in the improvement in antibacterial activity against multidrug-resistant bacteria, compared with conventional antibiotic medicines. Here, we developed CNPs from an active polyhydroxy phenolic compound, namely, gallic acid, which has abundant hydroxyl groups that can yield photodynamic effects. Gallic acid CNPs (GACNPs) were rapidly fabricated via a microwave-assisted technique at 200 °C for 20 min. GACNPs revealed notable antibacterial properties against Gram-positive and Gram-negative bacteria, including Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). The minimum inhibitory concentrations of GACNPs in S. aureus and E. coli were equal at approximately 0.29 mg/mL and considerably lower than those in gallic acid solution. Furthermore, the GACNP-loaded hydrogel patches demonstrated an attractive photodynamic effect against S. aureus, and it was superior to that of Ag hydrofiber®, a commercial material. Therefore, the photodynamic properties of GACNPs can be potentially used in the development of antibacterial hydrogels for wound healing applications.
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Affiliation(s)
- Koranat Dechsri
- Pharmaceutical Development of Green Innovations Group (PDGIG), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand; (K.D.); (P.P.); (P.O.); (S.P.)
| | - Cheewita Suwanchawalit
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand;
| | - Prasopchai Patrojanasophon
- Pharmaceutical Development of Green Innovations Group (PDGIG), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand; (K.D.); (P.P.); (P.O.); (S.P.)
| | - Praneet Opanasopit
- Pharmaceutical Development of Green Innovations Group (PDGIG), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand; (K.D.); (P.P.); (P.O.); (S.P.)
| | - Supusson Pengnam
- Pharmaceutical Development of Green Innovations Group (PDGIG), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand; (K.D.); (P.P.); (P.O.); (S.P.)
| | - Thapakorn Charoenying
- Pharmaceutical Development of Green Innovations Group (PDGIG), Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand; (K.D.); (P.P.); (P.O.); (S.P.)
| | - Theerada Taesotikul
- Department of Biomedicine and Health Informatics, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand
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10
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Yang R, Zhang H, Sun K, Yuan C, Tao K. Nano-Emulsified Perfluorooctyl Bromide Can Infiltrate Gram-Negative Bacteria and Sensitize Them to Ultrasound. NANO LETTERS 2024; 24:501-510. [PMID: 38147357 DOI: 10.1021/acs.nanolett.3c04545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Gram-negative (G-) bacterial infections remain one of the most urgent global health threats, because the distinctive envelope structure hinders the penetration of therapeutics. Here, we showed that a perfluorooctyl bromide nanoemulsion (PFOB NE) uniquely interacts with G- bacteria. After cell envelope attachment, the PFOB can infiltrate the cell and was diffused throughout. In this process, it impaired the membranes by disintegrating phospholipid molecules, enhancing the consequent ultrasonic cavitation to break the envelope. We identified through ultrasound that the NE had remarkable bactericidal effects against various antibiotic-resistant pathogens. Using in situ sterilization, this approach accelerated the recovery of bacteria-infected murine skin wounds. Thus, combining PFOB and ultrasound might be an alternative tool for conquering the growing threat of G- pathogens.
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Affiliation(s)
- Ruihao Yang
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Haoran Zhang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Kang Sun
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Congli Yuan
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ke Tao
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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11
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Toyting J, Miura N, Utrarachkij F, Tanomsridachchai W, Belotindos LP, Suwanthada P, Kapalamula TF, Kongsoi S, Koide K, Kim H, Thapa J, Nakajima C, Suzuki Y. Exploration of the novel fluoroquinolones with high inhibitory effect against quinolone-resistant DNA gyrase of Salmonella Typhimurium. Microbiol Spectr 2023; 11:e0133023. [PMID: 37795999 PMCID: PMC10715191 DOI: 10.1128/spectrum.01330-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/24/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Quinolone-resistant nontyphoidal Salmonella is a pressing public health concern, demanding the exploration of novel treatments. In this study, we focused on two innovative synthetic fluoroquinolones, WQ-3034 and WQ-3154. Our findings revealed that these new compounds demonstrate potent inhibitory effects, even against mutant strains that cause resistance to existing quinolones. Hence, WQ-3034 and WQ-3154 could potentially be effective therapeutic agents against quinolone-resistant Salmonella Typhimurium. Furthermore, the data obtained in this study will be baseline information for antimicrobial drug development.
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Affiliation(s)
- Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Nami Miura
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Wimonrat Tanomsridachchai
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Lawrence P. Belotindos
- Biosafety and Environment Section, Research and Development Division, Philippine Carabao Center National Headquarters and Gene Pool Science City of Munoz, Munoz, Nueva Ecija, Philippines
| | - Pondpan Suwanthada
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Siriporn Kongsoi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | - Kentaro Koide
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hyun Kim
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research & Development, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research & Development, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
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12
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Dash R, Holsinger KA, Chordia MD, Sharifian Gh M, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570448. [PMID: 38106213 PMCID: PMC10723488 DOI: 10.1101/2023.12.06.570448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate into cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules into the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotics accumulation in live bacterial cells in real time.
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13
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Geddes EJ, Gugger MK, Garcia A, Chavez MG, Lee MR, Perlmutter SJ, Bieniossek C, Guasch L, Hergenrother PJ. Porin-independent accumulation in Pseudomonas enables antibiotic discovery. Nature 2023; 624:145-153. [PMID: 37993720 DOI: 10.1038/s41586-023-06760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
Gram-negative antibiotic development has been hindered by a poor understanding of the types of compounds that can accumulate within these bacteria1,2. The presence of efflux pumps and substrate-specific outer-membrane porins in Pseudomonas aeruginosa renders this pathogen particularly challenging3. As a result, there are few antibiotic options for P. aeruginosa infections4 and its many porins have made the prospect of discovering general accumulation guidelines seem unlikely5. Here we assess the whole-cell accumulation of 345 diverse compounds in P. aeruginosa and Escherichia coli. Although certain positively charged compounds permeate both bacterial species, P. aeruginosa is more restrictive compared to E. coli. Computational analysis identified distinct physicochemical properties of small molecules that specifically correlate with P. aeruginosa accumulation, such as formal charge, positive polar surface area and hydrogen bond donor surface area. Mode of uptake studies revealed that most small molecules permeate P. aeruginosa using a porin-independent pathway, thus enabling discovery of general P. aeruginosa accumulation trends with important implications for future antibiotic development. Retrospective antibiotic examples confirmed these trends and these discoveries were then applied to expand the spectrum of activity of a gram-positive-only antibiotic, fusidic acid, into a version that demonstrates a dramatic improvement in antibacterial activity against P. aeruginosa. We anticipate that these discoveries will facilitate the design and development of high-permeating antipseudomonals.
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Affiliation(s)
- Emily J Geddes
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Morgan K Gugger
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Alfredo Garcia
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Martin Garcia Chavez
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Myung Ryul Lee
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Sarah J Perlmutter
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Laura Guasch
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Paul J Hergenrother
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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14
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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15
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Kravchenko SV, Domnin PA, Grishin SY, Vershinin NA, Gurina EV, Zakharova AA, Azev VN, Mustaeva LG, Gorbunova EY, Kobyakova MI, Surin AK, Fadeev RS, Ostroumova OS, Ermolaeva SA, Galzitskaya OV. Enhancing the Antimicrobial Properties of Peptides through Cell-Penetrating Peptide Conjugation: A Comprehensive Assessment. Int J Mol Sci 2023; 24:16723. [PMID: 38069046 PMCID: PMC10706425 DOI: 10.3390/ijms242316723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Combining antimicrobial peptides (AMPs) with cell-penetrating peptides (CPPs) has shown promise in boosting antimicrobial potency, especially against Gram-negative bacteria. We examined the CPP-AMP interaction with distinct bacterial types based on cell wall differences. Our investigation focused on AMPs incorporating penetratin CPP and dihybrid peptides containing both cell-penetrating TAT protein fragments from the human immunodeficiency virus and Antennapedia peptide (Antp). Assessment of the peptides TAT-AMP, AMP-Antp, and TAT-AMP-Antp revealed their potential against Gram-positive strains (Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus cereus). Peptides TAT-AMP and AMP-Antp using an amyloidogenic AMP from S1 ribosomal protein Thermus thermophilus, at concentrations ranging from 3 to 12 μM, exhibited enhanced antimicrobial activity against B. cereus. TAT-AMP and TAT-AMP-Antp, using an amyloidogenic AMP from the S1 ribosomal protein Pseudomonas aeruginosa, at a concentration of 12 µM, demonstrated potent antimicrobial activity against S. aureus and MRSA. Notably, the TAT-AMP, at a concentration of 12 µM, effectively inhibited Escherichia coli (E. coli) growth and displayed antimicrobial effects similar to gentamicin after 15 h of incubation. Peptide characteristics determined antimicrobial activity against diverse strains. The study highlights the intricate relationship between peptide properties and antimicrobial potential. Mechanisms of AMP action are closely tied to bacterial cell wall attributes. Peptides with the TAT fragment exhibited enhanced antimicrobial activity against S. aureus, MRSA, and P. aeruginosa. Peptides containing only the Antp fragment displayed lower activity. None of the investigated peptides demonstrated cytotoxic or cytostatic effects on either BT-474 cells or human skin fibroblasts. In conclusion, CPP-AMPs offer promise against various bacterial strains, offering insights for targeted antimicrobial development.
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Affiliation(s)
- Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (S.Y.G.); (N.A.V.); (E.V.G.)
| | - Pavel A. Domnin
- Biology Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Gamaleya Research Centre of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Sergei Y. Grishin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (S.Y.G.); (N.A.V.); (E.V.G.)
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Nikita A. Vershinin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (S.Y.G.); (N.A.V.); (E.V.G.)
| | - Elena V. Gurina
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (S.Y.G.); (N.A.V.); (E.V.G.)
| | - Anastasiia A. Zakharova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (A.A.Z.); (O.S.O.)
| | - Viacheslav N. Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (V.N.A.); (L.G.M.); (E.Y.G.)
| | - Leila G. Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (V.N.A.); (L.G.M.); (E.Y.G.)
| | - Elena Y. Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (V.N.A.); (L.G.M.); (E.Y.G.)
| | - Margarita I. Kobyakova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
- Research Institute of Clinical and Experimental Lymphology—Branch of the Institute of Cytology and Genetics Siberian Branch of Russian Academy of Sciences, 630060 Novosibirsk, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia;
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (V.N.A.); (L.G.M.); (E.Y.G.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Roman S. Fadeev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
| | - Olga S. Ostroumova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (A.A.Z.); (O.S.O.)
| | | | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia;
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
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16
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Allgood SC, Su CC, Crooks AL, Meyer CT, Zhou B, Betterton MD, Barbachyn MR, Yu EW, Detweiler CS. Bacterial efflux pump modulators prevent bacterial growth in macrophages and under broth conditions that mimic the host environment. mBio 2023; 14:e0249223. [PMID: 37921493 PMCID: PMC10746280 DOI: 10.1128/mbio.02492-23] [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: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
New approaches for combating microbial infections are needed. One strategy for disrupting pathogenesis involves developing compounds that interfere with bacterial virulence. A critical molecular determinant of virulence for Gram-negative bacteria are efflux pumps of the resistance-nodulation-division family, which includes AcrAB-TolC. We previously identified small molecules that bind AcrB, inhibit AcrAB-TolC, and do not appear to damage membranes. These efflux pump modulators (EPMs) were discovered in an in-cell screening platform called SAFIRE (Screen for Anti-infectives using Fluorescence microscopy of IntracellulaR Enterobacteriaceae). SAFIRE identifies compounds that disrupt the growth of a Gram-negative human pathogen, Salmonella enterica serotype Typhimurium (S. Typhimurium), in macrophages. We used medicinal chemistry to iteratively design ~200 EPM35 analogs and test them for activity in SAFIRE, generating compounds with nanomolar potency. Analogs were demonstrated to bind AcrB in a substrate binding pocket by cryo-electron microscopy. Despite having amphipathic structures, the EPM analogs do not disrupt membrane voltage, as monitored by FtsZ localization to the cell septum. The EPM analogs had little effect on bacterial growth in standard Mueller Hinton Broth. However, under broth conditions that mimic the micro-environment of the macrophage phagosome, acrAB is required for growth, the EPM analogs are bacteriostatic, and the EPM analogs increase the potency of antibiotics. These data suggest that under macrophage-like conditions, the EPM analogs prevent the export of a toxic bacterial metabolite(s) through AcrAB-TolC. Thus, compounds that bind AcrB could disrupt infection by specifically interfering with the export of bacterial toxic metabolites, host defense factors, and/or antibiotics.IMPORTANCEBacterial efflux pumps are critical for resistance to antibiotics and for virulence. We previously identified small molecules that inhibit efflux pumps (efflux pump modulators, EPMs) and prevent pathogen replication in host cells. Here, we used medicinal chemistry to increase the activity of the EPMs against pathogens in cells into the nanomolar range. We show by cryo-electron microscopy that these EPMs bind an efflux pump subunit. In broth culture, the EPMs increase the potency (activity), but not the efficacy (maximum effect), of antibiotics. We also found that bacterial exposure to the EPMs appear to enable the accumulation of a toxic metabolite that would otherwise be exported by efflux pumps. Thus, inhibitors of bacterial efflux pumps could interfere with infection not only by potentiating antibiotics, but also by allowing toxic waste products to accumulate within bacteria, providing an explanation for why efflux pumps are needed for virulence in the absence of antibiotics.
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Affiliation(s)
- Samual C. Allgood
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Amy L. Crooks
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Christian T. Meyer
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, USA
- Duet Biosystems, Nashville, Tennessee, USA
- Antimicrobial Research Consortium (ARC) Labs, Boulder, Colorado, USA
| | - Bojun Zhou
- Department of Physics, University of Colorado, Boulder, Colorado, USA
| | - Meredith D. Betterton
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Physics, University of Colorado, Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, New York, USA
| | | | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Corrella S. Detweiler
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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17
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Waite R, Adams CT, Chisholm DR, Sims CHC, Hughes JG, Dias E, White EA, Welsby K, Botchway SW, Whiting A, Sharples GJ, Ambler CA. The antibacterial activity of a photoactivatable diarylacetylene against Gram-positive bacteria. Front Microbiol 2023; 14:1243818. [PMID: 37808276 PMCID: PMC10556703 DOI: 10.3389/fmicb.2023.1243818] [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: 06/21/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
The emergence of antibiotic resistance is a growing threat to human health, and therefore, alternatives to existing compounds are urgently needed. In this context, a novel fluorescent photoactivatable diarylacetylene has been identified and characterised for its antibacterial activity, which preferentially eliminates Gram-positive over Gram-negative bacteria. Experiments confirmed that the Gram-negative lipopolysaccharide-rich outer surface is responsible for tolerance, as strains with reduced outer membrane integrity showed increased susceptibility. Additionally, bacteria deficient in oxidative damage repair pathways also displayed enhanced sensitivity, confirming that reactive oxygen species production is the mechanism of antibacterial activity. This new diarylacetylene shows promise as an antibacterial agent against Gram-positive bacteria that can be activated in situ, potentially for the treatment of skin infections.
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Affiliation(s)
- Ryan Waite
- Department of Biosciences, Durham University, Science Site, Durham, United Kingdom
| | | | | | | | - Joshua G. Hughes
- Department of Biosciences, Durham University, Science Site, Durham, United Kingdom
- LightOx Limited, Newcastle, United Kingdom
- Department of Physics, Durham University, Science Site, Durham, United Kingdom
| | - Eva Dias
- LightOx Limited, Newcastle, United Kingdom
| | - Emily A. White
- Department of Biosciences, Durham University, Science Site, Durham, United Kingdom
| | - Kathryn Welsby
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, United Kingdom
| | - Stanley W. Botchway
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, United Kingdom
| | - Andrew Whiting
- LightOx Limited, Newcastle, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Gary J. Sharples
- Department of Biosciences, Durham University, Science Site, Durham, United Kingdom
| | - Carrie A. Ambler
- Department of Biosciences, Durham University, Science Site, Durham, United Kingdom
- LightOx Limited, Newcastle, United Kingdom
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18
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Allgood SC, Su CC, Crooks AL, Meyer CT, Zhou B, Betterton MD, Barbachyn MR, Yu EW, Detweiler CS. Bacterial Efflux Pump Modulators Prevent Bacterial Growth in Macrophages and Under Broth Conditions that Mimic the Host Environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558466. [PMID: 37786697 PMCID: PMC10541609 DOI: 10.1101/2023.09.20.558466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
New approaches for combatting microbial infections are needed. One strategy for disrupting pathogenesis involves developing compounds that interfere with bacterial virulence. A critical molecular determinant of virulence for Gram-negative bacteria are efflux pumps of the resistance-nodulation-division (RND) family, which includes AcrAB-TolC. We previously identified small molecules that bind AcrB, inhibit AcrAB-TolC, and do not appear to damage membranes. These efflux pump modulators (EPMs) were discovered in an in-cell screening platform called SAFIRE (Screen for Anti-infectives using Fluorescence microscopy of IntracellulaR Enterobacteriaceae). SAFIRE identifies compounds that disrupt the growth of a Gram-negative human pathogen, Salmonella enterica serotype Typhimurium (S. Typhimurium) in macrophages. We used medicinal chemistry to iteratively design ~200 EPM35 analogs and test them for activity in SAFIRE, generating compounds with nanomolar potency. Analogs were demonstrated to bind AcrB in a substrate binding pocket by cryo-electron microscopy (cryo-EM). Despite having amphipathic structures, the EPM analogs do not disrupt membrane voltage, as monitored by FtsZ localization to the cell septum. The EPM analogs had little effect on bacterial growth in standard Mueller Hinton Broth. However, under broth conditions that mimic the micro-environment of the macrophage phagosome, acrAB is required for growth, the EPM analogs are bacteriostatic, and increase the potency of antibiotics. These data suggest that under macrophage-like conditions the EPM analogs prevent the export of a toxic bacterial metabolite(s) through AcrAB-TolC. Thus, compounds that bind AcrB could disrupt infection by specifically interfering with the export of bacterial toxic metabolites, host defense factors, and/or antibiotics.
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Affiliation(s)
- Samual C Allgood
- Molecular, Cellular Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Amy L Crooks
- Molecular, Cellular Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Christian T Meyer
- Molecular, Cellular Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
- Duet Biosystems, Nashville, TN, USA
- Antimicrobial Research Consortium (ARC) Labs, Boulder, CO, USA
| | - Bojun Zhou
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Meredith D Betterton
- Molecular, Cellular Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Corrella S Detweiler
- Molecular, Cellular Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
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19
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Lee MMS, Yu EY, Yan D, Chau JHC, Wu Q, Lam JWY, Ding D, Kwok RTK, Wang D, Tang BZ. The Role of Structural Hydrophobicity on Cationic Amphiphilic Aggregation-Induced Emission Photosensitizer-Bacterial Interaction and Photodynamic Efficiency. ACS NANO 2023; 17:17004-17020. [PMID: 37594229 DOI: 10.1021/acsnano.3c04266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The aggregation-induced emission photosensitizer (AIE PS) has stood out as an alternative and competent candidate in bacterial theranostics, particularly with the use of cationic AIE PS in bacterial discrimination and elimination. Most reported work emphasizes the role of electrostatic interaction between cationic AIE PS and negatively charged bacterial surfaces, enabling broad applications from bacterial discrimination to bacterial killing. However, the underlying targeting mechanism and the design rationale of the cationic AIE PS for effective bacterial labeling remain poorly investigated. In this Article, we designed and synthesized a series of cationic amphiphilic AIE PSs with different calculated log P values. Then, we systemically studied the relationship between the hydrophobicity variation of AIE PS and bacterial targeting outcomes, the dose of AIE PS needed to label various species of bacteria, and their photodynamic antibacterial efficiency. The findings in this work provide a better understanding of the unclear AIE PS-bacterial interaction mechanism and some insights into the structural design strategies of cationic amphiphilic AIE PS for better development in bacterial theranostics.
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Affiliation(s)
- Michelle M S Lee
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Eric Y Yu
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Dingyuan Yan
- Centre for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518061, People's Republic of China
| | - Joe H C Chau
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Qian Wu
- Centre for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518061, People's Republic of China
| | - Jacky W Y Lam
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Dan Ding
- Key Laboratory of Bioactive Materials, Ministry of Education and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ryan T K Kwok
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Dong Wang
- Centre for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518061, People's Republic of China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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20
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Wen L, Luo C, Chen X, Liu T, Li X, Wang M. In vitro Activity of Cefepime/Avibactam Against Carbapenem Resistant Klebsiella pneumoniae and Integrative Metabolomics-Proteomics Approach for Resistance Mechanism: A Single-Center Study. Infect Drug Resist 2023; 16:6061-6077. [PMID: 37719649 PMCID: PMC10503517 DOI: 10.2147/idr.s420898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
Purpose We aimed to evaluate the in vitro antibacterial effects of combination of cefepime/avibactam against carbapenem-resistant Klebsiella pneumonia (CRKP) and explore the resistance mechanism of FEP/AVI. Patients and Methods This study explored the in vitro antibacterial activities of ceftazidime/avibactam (CAZ/AVI) and cefepime/avibactam (FEP/AVI) against 40 and 76 CRKP clinical isolates. Proteomics and metabolomics were employed to investigate the resistance mechanisms of CRKP to FEP/AVI. Results FEP/AVI (MIC50/MIC90 0.5/4-64/4 μg/mL, resistance rate 17.1%) showed better antibacterial activity against CRKP than CAZ/AVI (MIC50/MIC90 4/4-128/4 μg/mL, resistance rate 20%) in vitro. Bioinformatics analysis showed that the differentially expressed proteins (DEPs) were enriched in alanine, aspartate and glutamate metabolism, and ribosome. Remarkably, transcriptional and translational activity-related pathways were inhibited in FEP/AVI resistant CRKP. Overlap analysis suggested that H-NS might play an important role in resistance to FEP/AVI in CRKP. The mRNA levels of DEPs-related genes (adhE, gltB, purA, ftsI and hns) showed the same trends as DEPs in FEP/AVI susceptible and resistant strains. FEP/AVI resistant isolates demonstrated stronger biofilm formation capacity than susceptible isolates. Metabolomics results showed that disturbed metabolites were mainly lipids, and adenine was decreased in FEP/AVI resistant CRKP. Conclusion These results indicated that H-NS, GltB and SpoT may directly or indirectly promote biofilm formation of CRKP and led to FEP/AVI resistance, but inhibited ribosomal function. Our study provides a mechanistic insight into the acquisition of resistance to FEP/AVI in Klebsiella pneumoniae.
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Affiliation(s)
- Lingjun Wen
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Can Luo
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xinyi Chen
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Tianyao Liu
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China
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21
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Lapierre J, Hub JS. Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy. J Chem Inf Model 2023; 63:5319-5330. [PMID: 37560945 DOI: 10.1021/acs.jcim.3c00880] [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: 08/11/2023]
Abstract
The emergence of multidrug-resistant pathogens led to a critical need for new antibiotics. A key property of effective antibiotics against Gram-negative bacteria is their ability to permeate through the bacterial outer membrane via transmembrane porin proteins. Molecular dynamics (MD) simulations are, in principle, capable of modeling antibiotic permeation across outer membrane porins (OMPs). However, owing to sampling problems, it has remained challenging to obtain converged potentials of mean force (PMFs) for antibiotic permeation across OMPs. Here, we investigated the convergence of PMFs along a single collective variable aimed at quantifying the permeation of the antibiotic fosmidomycin across the OprO porin. We compared standard umbrella sampling (US) with three advanced flavors of the US technique: (i) Hamiltonian replica exchange with solute tempering in combination with US, (ii) simulated tempering-enhanced US, and (iii) replica-exchange US. To quantify the PMF convergence and to reveal hysteresis problems, we computed several independent sets of US simulations starting from pulling simulations in the outward and inward permeation directions. We find that replica-exchange US in combination with well-chosen restraints is highly successful for obtaining converged PMFs of fosmidomycin permeation through OprO, reaching PMFs converged to subkilocalorie per mole accuracy.
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Affiliation(s)
- Jeremy Lapierre
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
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22
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Han YY, Wang JT, Cheng WC, Chen KL, Chi Y, Teng LJ, Wang JK, Wang YL. SERS-based rapid susceptibility testing of commonly administered antibiotics on clinically important bacteria species directly from blood culture of bacteremia patients. World J Microbiol Biotechnol 2023; 39:282. [PMID: 37589866 PMCID: PMC10435613 DOI: 10.1007/s11274-023-03717-x] [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: 06/05/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Bloodstream infections are a growing public health concern due to emerging pathogens and increasing antimicrobial resistance. Rapid antibiotic susceptibility testing (AST) is urgently needed for timely and optimized choice of antibiotics, but current methods require days to obtain results. Here, we present a general AST protocol based on surface-enhanced Raman scattering (SERS-AST) for bacteremia caused by eight clinically relevant Gram-positive and Gram-negative pathogens treated with seven commonly administered antibiotics. Our results show that the SERS-AST protocol achieves a high level of agreement (96% for Gram-positive and 97% for Gram-negative bacteria) with the widely deployed VITEK 2 diagnostic system. The protocol requires only five hours to complete per blood-culture sample, making it a rapid and effective alternative to conventional methods. Our findings provide a solid foundation for the SERS-AST protocol as a promising approach to optimize the choice of antibiotics for specific bacteremia patients. This novel protocol has the potential to improve patient outcomes and reduce the spread of antibiotic resistance.
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Affiliation(s)
- Yin-Yi Han
- Department of Anesthesiology, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
- Department of Surgery, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
- Department of Traumatology, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan.
| | - Jann-Tay Wang
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, 7 Zhongshan S. Road, Taipei, 100225, Taiwan
- Taiwan National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli, 35053, Taiwan
| | - Wei-Chih Cheng
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Ko-Lun Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Yi Chi
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, 1, Roosevelt Road Sec. 4, Taipei, 10048, Taiwan
| | - Juen-Kai Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan.
- Center for Condensed Matter Sciences, National Taiwan University, 1 Roosevelt Road Sec. 4, Taipei, 106319, Taiwan.
| | - Yuh-Lin Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Road Sec. 4, Taipei, 10617, Taiwan.
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23
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Di Bonaventura G, Lupetti V, Di Giulio A, Muzzi M, Piccirilli A, Cariani L, Pompilio A. Repurposing High-Throughput Screening Identifies Unconventional Drugs with Antibacterial and Antibiofilm Activities against Pseudomonas aeruginosa under Experimental Conditions Relevant to Cystic Fibrosis. Microbiol Spectr 2023; 11:e0035223. [PMID: 37306577 PMCID: PMC10433973 DOI: 10.1128/spectrum.00352-23] [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: 01/22/2023] [Accepted: 05/13/2023] [Indexed: 06/13/2023] Open
Abstract
Pseudomonas aeruginosa is the most common pathogen infecting cystic fibrosis (CF) lungs, causing acute and chronic infections. Intrinsic and acquired antibiotic resistance allow P. aeruginosa to colonize and persist despite antibiotic treatment, making new therapeutic approaches necessary. Combining high-throughput screening and drug repurposing is an effective way to develop new therapeutic uses for drugs. This study screened a drug library of 3,386 drugs, mostly FDA approved, to identify antimicrobials against P. aeruginosa under physicochemical conditions relevant to CF-infected lungs. Based on the antibacterial activity, assessed spectrophotometrically against the prototype RP73 strain and 10 other CF virulent strains, and the toxic potential evaluated toward CF IB3-1 bronchial epithelial cells, five potential hits were selected for further analysis: the anti-inflammatory and antioxidant ebselen, the anticancer drugs tirapazamine, carmofur, and 5-fluorouracil, and the antifungal tavaborole. A time-kill assay showed that ebselen has the potential to cause rapid and dose-dependent bactericidal activity. The antibiofilm activity was evaluated by viable cell count and crystal violet assays, revealing carmofur and 5-fluorouracil as the most active drugs in preventing biofilm formation regardless of the concentration. In contrast, tirapazamine and tavaborole were the only drugs actively dispersing preformed biofilms. Tavaborole was the most active drug against CF pathogens other than P. aeruginosa, especially against Burkholderia cepacia and Acinetobacter baumannii, while carmofur, ebselen, and tirapazamine were particularly active against Staphylococcus aureus and B. cepacia. Electron microscopy and propidium iodide uptake assay revealed that ebselen, carmofur, and tirapazamine significantly damage cell membranes, with leakage and cytoplasm loss, by increasing membrane permeability. IMPORTANCE Antibiotic resistance makes it urgent to design new strategies for treating pulmonary infections in CF patients. The repurposing approach accelerates drug discovery and development, as the drugs' general pharmacological, pharmacokinetic, and toxicological properties are already well known. In the present study, for the first time, a high-throughput compound library screening was performed under experimental conditions relevant to CF-infected lungs. Among 3,386 drugs screened, the clinically used drugs from outside infection treatment ebselen, tirapazamine, carmofur, 5-fluorouracil, and tavaborole showed, although to different extents, anti-P. aeruginosa activity against planktonic and biofilm cells and broad-spectrum activity against other CF pathogens at concentrations not toxic to bronchial epithelial cells. The mode-of-action studies revealed ebselen, carmofur, and tirapazamine targeted the cell membrane, increasing its permeability with subsequent cell lysis. These drugs are strong candidates for repurposing for treating CF lung P. aeruginosa infections.
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Affiliation(s)
- Giovanni Di Bonaventura
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Veronica Lupetti
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
| | | | | | - Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L’Aquila, Italy
| | - Lisa Cariani
- Microbiology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Arianna Pompilio
- Department of Medical, Oral, and Biotechnological Sciences, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
- Center for Advanced Studies and Technology, G. d’Annunzio University of Chieti-Pescara, Chieti, Italy
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24
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Krajnc A, Gobec S. Conjugates of monocyclic β-lactams and siderophore mimetics: a patent evaluation (WO2023023393). Expert Opin Ther Pat 2023; 33:471-476. [PMID: 37902072 DOI: 10.1080/13543776.2023.2262135] [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: 04/25/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023]
Abstract
INTRODUCTION β-Lactams, which include monobactams, remain the most important class of antibiotics worldwide. Aztreonam, the only monobactam in clinical use, has remarkable activity against many Gram-negative bacteria, but limited activity against some of the most problematic multidrug-resistant (MDR) pathogens, such as MDR Pseudomonas aeruginosa and Acinetobacter baumannii co-expressing extended-spectrum- and metallo-β-lactamases, which can inactivate aztreonam by hydrolysis. AREAS COVERED Structurally novel siderophore-conjugated aztreonam derivatives with improved antibacterial properties against several high-priority pathogens are claimed. This invention reports that sidechain extension of aztreonam is tolerated; the coupling of its aminothiazoloxime carboxylic acid part with a siderophore mimetic significantly improved the antibacterial activity against several problematic strains, including MDR A. baumannii isolates with carbapenemase/cephalosporinase activity. EXPERT OPINION Finding new strategies to tackle bacterial resistance to β-lactam antibiotics is critical. Considering that β lactams are validated and safe drugs, this research may stimulate the field to develop new ideas in the arena of antimicrobial drug discovery, particularly with respect to siderophore mimetics.
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Affiliation(s)
- Alen Krajnc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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25
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Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
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Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
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26
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Oi KK, Moehle K, Schuster M, Zerbe O. Early Molecular Insights into Thanatin Analogues Binding to A. baumannii LptA. Molecules 2023; 28:4335. [PMID: 37298811 PMCID: PMC10254193 DOI: 10.3390/molecules28114335] [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: 05/04/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
The cationic antimicrobial ß-hairpin, thanatin, was recently developed into drug-like analogues active against carbapenem-resistant Enterobacteriaceae (CRE). The analogues represent new antibiotics with a novel mode of action targeting LptA in the periplasm and disrupting LPS transport. The compounds lose antimicrobial efficacy when the sequence identity to E. coli LptA falls below 70%. We wanted to test the thanatin analogues against LptA of a phylogenetic distant organism and investigate the molecular determinants of inactivity. Acinetobacter baumannii (A. baumannii) is a critical Gram-negative pathogen that has gained increasing attention for its multi-drug resistance and hospital burden. A. baumannii LptA shares 28% sequence identity with E. coli LptA and displays an intrinsic resistance to thanatin and thanatin analogues (MIC values > 32 µg/mL) through a mechanism not yet described. We investigated the inactivity further and discovered that these CRE-optimized derivatives can bind to LptA of A. baumannii in vitro, despite the high MIC values. Herein, we present a high-resolution structure of A. baumannii LptAm in complex with a thanatin derivative 7 and binding affinities of selected thanatin derivatives. Together, these data offer structural insights into why thanatin derivatives are inactive against A. baumannii LptA, despite binding events in vitro.
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Affiliation(s)
| | | | | | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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27
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Draveny M, Rose C, Pinet A, Ferrié L, Figadère B, Brunel JM, Masi M. Scope and Limitations of Exploiting the Ability of the Chemosensitizer NV716 to Enhance the Activity of Tetracycline Derivatives against Pseudomonas aeruginosa. Molecules 2023; 28:molecules28114262. [PMID: 37298737 DOI: 10.3390/molecules28114262] [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: 04/27/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The spread of antibiotic resistance is an urgent threat to global health that requires new therapeutic approaches. Treatments for pathogenic Gram-negative bacteria are particularly challenging to identify due to the robust OM permeability barrier in these organisms. One strategy is to use antibiotic adjuvants, a class of drugs that have no significant antibacterial activity on their own but can act synergistically with certain antibiotics. Previous studies described the discovery and development of polyaminoisoprenyl molecules as antibiotic adjuvants with an OM effect. In particular, the compound NV716 has been shown to sensitize Pseudomonas aeruginosa to tetracycline antibiotics such as doxycycline. Here, we sought to explore the disruption of OM to sensitize P. aeruginosa to otherwise inactive antimicrobials using a series of tetracycline derivatives in the presence of NV716. We found that OM disruption expands the hydrophobicity threshold consistent with antibacterial activity to include hydrophobic molecules, thereby altering permeation rules in Gram-negative bacteria.
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Affiliation(s)
- Margot Draveny
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
| | - Clémence Rose
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Alexis Pinet
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Laurent Ferrié
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Bruno Figadère
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Jean-Michel Brunel
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Muriel Masi
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
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28
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 188] [Impact Index Per Article: 188.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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29
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Maingot M, Bourotte M, Vetter AC, Schellhorn B, Antraygues K, Scherer H, Gitzinger M, Kemmer C, Dale GE, Defert O, Lociuro S, Brönstrup M, Willand N, Trebosc V. Structure-activity relationships of actively FhuE transported rifabutin derivatives with potent activity against Acinetobacter baumannii. Eur J Med Chem 2023; 252:115257. [PMID: 36948128 DOI: 10.1016/j.ejmech.2023.115257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
Abstract
Hospital-acquired infections are on the rise and represent both, a clinical and financial burden. With resistance emerging and an ever-dwindling armamentarium at hand, infections caused by Acinetobacter baumannii are particularly problematic, since these bacteria have a high level of resistance and resilience to traditional and even last-resort antibiotics. The antibiotic rifabutin was recently found to show potent in vitro and in vivo activity against extensively drug resistant A. baumannii. Building on this discovery, we report on the synthesis and activity of rifabutin analogs, with a focus on N-functionalization of the piperidine ring. The antimicrobial testing uncovered structure activity relationships (SAR) for A. baumannii that were not reflected in Staphylococcus aureus. The cellular activity did not correlate with cell-free transcription inhibition, but with bacterial intracellular compound accumulation. Mass spectrometry-based accumulation studies confirmed the involvement of the siderophore receptor FhuE in active compound translocation at low concentrations, and they showed a strong impact of the culture medium on the accumulation of rifabutin. Overall, the study underlines the structural feature required for strong accumulation of rifabutin in A. baumannii and identifies analogs as or more potent than rifabutin against A. baumannii.
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Affiliation(s)
- M Maingot
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - M Bourotte
- BioVersys SAS, 1 rue du Professeur Calmette, 59000, Lille, France
| | - A C Vetter
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - B Schellhorn
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - K Antraygues
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - H Scherer
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France
| | - M Gitzinger
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - C Kemmer
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - G E Dale
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - O Defert
- BioVersys SAS, 1 rue du Professeur Calmette, 59000, Lille, France
| | - S Lociuro
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland
| | - M Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - N Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000, Lille, France.
| | - V Trebosc
- BioVersys AG, 60C Hochbergerstrasse, 4057, Basel, Switzerland.
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30
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Bali K, Guffick C, McCoy R, Lu Z, Kaminski CF, Mela I, Owens RM, van Veen HW. Biosensor for Multimodal Characterization of an Essential ABC Transporter for Next-Generation Antibiotic Research. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12766-12776. [PMID: 36866935 PMCID: PMC10020959 DOI: 10.1021/acsami.2c21556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 05/21/2023]
Abstract
As the threat of antibiotic resistance increases, there is a particular focus on developing antimicrobials against pathogenic bacteria whose multidrug resistance is especially entrenched and concerning. One such target for novel antimicrobials is the ATP-binding cassette (ABC) transporter MsbA that is present in the plasma membrane of Gram-negative pathogenic bacteria where it is fundamental to the survival of these bacteria. Supported lipid bilayers (SLBs) are useful in monitoring membrane protein structure and function since they can be integrated with a variety of optical, biochemical, and electrochemical techniques. Here, we form SLBs containing Escherichia coli MsbA and use atomic force microscopy (AFM) and structured illumination microscopy (SIM) as high-resolution microscopy techniques to study the integrity of the SLBs and incorporated MsbA proteins. We then integrate these SLBs on microelectrode arrays (MEA) based on the conducting polymer poly(3,4-ethylenedioxy-thiophene) poly(styrene sulfonate) (PEDOT:PSS) using electrochemical impedance spectroscopy (EIS) to monitor ion flow through MsbA proteins in response to ATP hydrolysis. These EIS measurements can be correlated with the biochemical detection of MsbA-ATPase activity. To show the potential of this SLB approach, we observe not only the activity of wild-type MsbA but also the activity of two previously characterized mutants along with quinoline-based MsbA inhibitor G907 to show that EIS systems can detect changes in ABC transporter activity. Our work combines a multitude of techniques to thoroughly investigate MsbA in lipid bilayers as well as the effects of potential inhibitors of this protein. We envisage that this platform will facilitate the development of next-generation antimicrobials that inhibit MsbA or other essential membrane transporters in microorganisms.
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Affiliation(s)
- Karan Bali
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Charlotte Guffick
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
| | - Reece McCoy
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Zixuan Lu
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Ioanna Mela
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Róisín M. Owens
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U. K.
| | - Hendrik W. van Veen
- Department
of Pharmacology, University of Cambridge, CB2 1PD Cambridge, U. K.
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Dhiman S, Ramirez D, Li Y, Kumar A, Arthur G, Schweizer F. Chimeric Tobramycin-Based Adjuvant TOB-TOB-CIP Potentiates Fluoroquinolone and β-Lactam Antibiotics against Multidrug-Resistant Pseudomonas aeruginosa. ACS Infect Dis 2023; 9:864-885. [PMID: 36917096 DOI: 10.1021/acsinfecdis.2c00549] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
According to the World Health Organization, antibiotic resistance is a global health threat. Of particular importance are infections caused by multidrug-resistant Gram-negative bacteria including Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa for which limited treatment options exist. Multiple and simultaneously occurring resistance mechanisms including outer membrane impermeability, overexpression of efflux pumps, antibiotic-modifying enzymes, and modification of genes and antibiotic targets have made antibiotic drug development more difficult against these pathogens. One strategy to cope with these challenges is the use of outer membrane permeabilizers that increase the intracellular concentration of antibiotics when used in combination. In some circumstances, this approach can rescue antibiotics from resistance or repurpose currently marketed antibiotics. Tobramycin-based hybrid antibiotic adjuvants that combine two outer membrane-active components have been previously shown to potentiate antibiotics by facilitating transit through the outer membrane, resulting in increased antibiotic accumulation within the cell. Herein, we extended the concept of tobramycin-based hybrid antibiotic adjuvants to tobramycin-based chimeras by engineering up to three different membrane-active antibiotic warheads such as tobramycin, 1-(1-naphthylmethyl)-piperazine, ciprofloxacin, and cyclam into a central 1,3,5-triazine scaffold. Chimera 4 (TOB-TOB-CIP) consistently synergized with ciprofloxacin, levofloxacin, and moxifloxacin against wild-type and fluoroquinolone-resistant P. aeruginosa. Moreover, the susceptibility breakpoints of ceftazidime, aztreonam, and imipenem were reached using the triple combination of chimera 4 with ceftazidime/avibactam, aztreonam/avibactam, and imipenem/relebactam, respectively, against β-lactamase-harboring P. aeruginosa. Our findings demonstrate that tobramycin-based chimeras form a novel class of antibiotic potentiators capable of restoring the activity of antibiotics against P. aeruginosa.
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Affiliation(s)
- Shiv Dhiman
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Manitoba, Canada
| | - Danyel Ramirez
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Manitoba, Canada
| | - Yanqi Li
- Department of Microbiology, University of Manitoba, Winnipeg R3T 2N2, Manitoba, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg R3T 2N2, Manitoba, Canada
| | - Gilbert Arthur
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg R3E 0J9, Manitoba, Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Manitoba, Canada
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32
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Lai YH, Franke R, Pinkert L, Overwin H, Brönstrup M. Molecular Signatures of the Eagle Effect Induced by the Artificial Siderophore Conjugate LP-600 in E. coli. ACS Infect Dis 2023; 9:567-581. [PMID: 36763039 PMCID: PMC10012262 DOI: 10.1021/acsinfecdis.2c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Achieving cellular uptake is a central challenge for novel antibiotics targeting Gram-negative bacterial pathogens. One strategy is to hijack the bacterial iron transport system by siderophore-antibiotic conjugates that are actively imported into the cell. This was realized with the MECAM-ampicillin conjugate LP-600 we recently reported that was highly active against E. coli. In the present study, we investigate a paradoxical regrowth of E. coli upon treatment of LP-600 at concentrations 16-32 times above the minimum inhibitory concentration (MIC). The phenomenon, coined "Eagle-effect" in other systems, was not due to resistance formation, and it occurred for the siderophore conjugate but not for free ampicillin. To investigate the molecular imprint of the Eagle effect, a combined transcriptome and untargeted metabolome analysis was conducted. LP-600 induced the expression of genes involved in iron acquisition, SOS response, and the e14 prophage upon regrowth conditions. The Eagle effect was diminished in the presence of sulbactam, which we ascribe to a putative synergistic antibiotic action but not to β-lactamase inhibition. The study highlights the relevance of the Eagle effect for siderophore conjugates. Through the first systematic -omics investigations, it also demonstrates that the Eagle effect manifests not only in a paradoxical growth but also in unique gene expression and metabolite profiles.
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Affiliation(s)
- Yi-Hui Lai
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Heike Overwin
- 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), Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159 Hannover, Germany
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33
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Kim C, Tomoshige S, Lee M, Zgurskaya HI, Mobashery S. Penetration through Outer Membrane and Efflux Potential in Pseudomonas aeruginosa of Bulgecin A as an Adjuvant to β-Lactam Antibiotics. Antibiotics (Basel) 2023; 12:antibiotics12020358. [PMID: 36830269 PMCID: PMC9952357 DOI: 10.3390/antibiotics12020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
The treatment of infections by Gram-negative bacteria remains a difficult clinical challenge. In the light of the dearth of discovery of novel antibiotics, one strategy that is being explored is the use of adjuvants to enhance antibacterial activities of existing antibiotics. One such adjuvant is bulgecin A, which allows for the lowering of minimal-inhibitory concentrations for β-lactam antibiotics. We have shown that bulgecin A inhibits three of the pseudomonal lytic transglycosylases in its mode of action, yet high concentrations are needed for potentiation activity. Herein, we document that bulgecin A is not a substrate for pseudomonal efflux pumps, whose functions could have been a culprit in the need for high concentrations. We present evidence that the penetration barrier into the periplasm is at the root of the need for high concentrations of bulgecin A in its potentiation of β-lactam antibiotics.
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Affiliation(s)
- Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shusuke Tomoshige
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
- Correspondence: ; Tel.: +1-574-631-2933
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34
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Shabatina TI, Vernaya OI, Melnikov MY. Hybrid Nanosystems of Antibiotics with Metal Nanoparticles-Novel Antibacterial Agents. Molecules 2023; 28:molecules28041603. [PMID: 36838591 PMCID: PMC9959110 DOI: 10.3390/molecules28041603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
The appearance and increasing number of microorganisms resistant to the action of antibiotics is one of the global problems of the 21st century. Already, the duration of therapeutic treatment and mortality from infectious diseases caused by pathogenic microorganisms have increased significantly over the last few decades. Nanoscale inorganic materials (metals and metal oxides) with antimicrobial potential are a promising solution to this problem. Here we discuss possible mechanisms of pathogenic microorganisms' resistance to antibiotics, proposed mechanisms of action of inorganic nanoparticles on bacterial cells, and the possibilities and benefits of their combined use with antibacterial drugs. The prospects of using metal and metal oxide nanoparticles as carriers in targeted delivery systems for antibacterial compositions are also discussed.
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Affiliation(s)
- Tatyana I. Shabatina
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Fundamental Sciences, N.E. Bauman Moscow Technical University, 105005 Moscow, Russia
- Correspondence:
| | - Olga I. Vernaya
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Fundamental Sciences, N.E. Bauman Moscow Technical University, 105005 Moscow, Russia
| | - Mikhail Y. Melnikov
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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35
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Rogers PD, Lee RE. Editorial overview: Recent advances in antimicrobial drug discovery and resistance. Curr Opin Microbiol 2023; 71:102242. [PMID: 36423503 PMCID: PMC10364994 DOI: 10.1016/j.mib.2022.102242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, USA.
| | - Richard E Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, USA
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36
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Update on the Discovery of Efflux Pump Inhibitors against Critical Priority Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:antibiotics12010180. [PMID: 36671381 PMCID: PMC9854755 DOI: 10.3390/antibiotics12010180] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance (AMR) has become a major problem in public health leading to an estimated 4.95 million deaths in 2019. The selective pressure caused by the massive and repeated use of antibiotics has led to bacterial strains that are partially or even entirely resistant to known antibiotics. AMR is caused by several mechanisms, among which the (over)expression of multidrug efflux pumps plays a central role. Multidrug efflux pumps are transmembrane transporters, naturally expressed by Gram-negative bacteria, able to extrude and confer resistance to several classes of antibiotics. Targeting them would be an effective way to revive various options for treatment. Many efflux pump inhibitors (EPIs) have been described in the literature; however, none of them have entered clinical trials to date. This review presents eight families of EPIs active against Escherichia coli or Pseudomonas aeruginosa. Structure-activity relationships, chemical synthesis, in vitro and in vivo activities, and pharmacological properties are reported. Their binding sites and their mechanisms of action are also analyzed comparatively.
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37
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Synthesis, characterization of 1,2,4-triazolidine-3-thione tethered beta-aryl butanoic acid and butanoate derivatives as potent antimicrobial and antioxidant agents and their molecular docking studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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38
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Forward or backward, that is the question: phospholipid trafficking by the Mla system. Emerg Top Life Sci 2022; 7:125-135. [PMID: 36459067 DOI: 10.1042/etls20220087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022]
Abstract
The distinctive feature of Gram-negative bacteria is the presence of an asymmetric outer membrane (OM), which acts as a permeation barrier blocking the diffusion of noxious components such as antibiotics that could compromise cell survival. The outer membrane has an inner leaflet, mainly formed by phospholipids (PLs), and the outer leaflet, composed of molecules of lipopolysaccharide (LPS). Building this membrane is a very complex process as every OM element needs to be transported from the cytoplasm or the inner membrane and properly placed in the OM. In addition, the asymmetry needs to be maintained to guarantee the barrier function of the membrane. The presence of misplaced PLs in the outer leaflet of the OM causes increased permeability, endangering cell survival. The Mla system (maintenance of OM lipid asymmetry) has been linked to the removal of the misplaced PLs, restoring OM asymmetry. The Mla system has elements in all compartments of the cell envelope: the lipoprotein MlaA in complex with the trimeric porins OmpC/F in the OM, MlaC in the periplasmic space and an ABC transporter in the inner membrane called MlaFEDB. While genetic and structural work suggest that the Mla pathway is retrograde (PL movement from OM to IM), several groups have advocated that transport could happen in an anterograde fashion (from IM to OM). However, recent biochemical studies strongly support retrograde transport. This review provides an overview of the current knowledge of the Mla system from a structural point of view and addresses the latest biochemical findings and their impact in transport directionality.
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Goetz JA, Kuehfuss NM, Botschner AJ, Zhu S, Thompson LK, Cox G. Exploring functional interplay amongst Escherichia coli efflux pumps. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36318669 DOI: 10.1099/mic.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial efflux pumps exhibit functional interplay that can translate to additive or multiplicative effects on resistance to antimicrobial compounds. In diderm bacteria, two different efflux pump structural types - single-component inner membrane efflux pumps and cell envelope-spanning multicomponent systems - cooperatively export antimicrobials with cytoplasmic targets from the cell. Harnessing our recently developed efflux platform, which is built upon an extensively efflux-deficient strain of Escherichia coli, here we explore interplay amongst a panel of diverse E. coli efflux pumps. Specifically, we assessed the effect of simultaneously expressing two efflux pump-encoding genes on drug resistance, including single-component inner membrane efflux pumps (MdfA, MdtK and EmrE), tripartite complexes (AcrAB, AcrAD, MdtEF and AcrEF), and the acquired TetA(C) tetracycline resistance pump. Overall, the expression of two efflux pump-encoding genes from the same structural type did not enhance resistance levels regardless of the antimicrobial compound or efflux pump under investigation. In contrast, a combination of the tripartite efflux systems with single-component pumps sharing common substrates provided multiplicative increases to antimicrobial resistance levels. In some instances, resistance was increased beyond the product of resistance provided by the two pumps individually. In summary, the developed efflux platform enables the isolation of efflux pump function, facilitating the identification of interactions between efflux pumps.
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Affiliation(s)
- James A Goetz
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Noah M Kuehfuss
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Alexander J Botschner
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
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40
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Villanueva JA, Crooks AL, Nagy TA, Quintana JLJ, Dalebroux ZD, Detweiler CS. Salmonella enterica Infections Are Disrupted by Two Small Molecules That Accumulate within Phagosomes and Differentially Damage Bacterial Inner Membranes. mBio 2022; 13:e0179022. [PMID: 36135367 PMCID: PMC9601186 DOI: 10.1128/mbio.01790-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
Gram-negative bacteria have a robust cell envelope that excludes or expels many antimicrobial agents. However, during infection, host soluble innate immune factors permeabilize the bacterial outer membrane. We identified two small molecules that exploit outer membrane damage to access the bacterial cell. In standard microbiological media, neither compound inhibited bacterial growth nor permeabilized bacterial outer membranes. In contrast, at micromolar concentrations, JAV1 and JAV2 enabled the killing of an intracellular human pathogen, Salmonella enterica serovar Typhimurium. S. Typhimurium is a Gram-negative bacterium that resides within phagosomes of cells from the monocyte lineage. Under broth conditions that destabilized the lipopolysaccharide layer, JAV2 permeabilized the bacterial inner membrane and was rapidly bactericidal. In contrast, JAV1 activity was more subtle: JAV1 increased membrane fluidity, altered reduction potential, and required more time than JAV2 to disrupt the inner membrane barrier and kill bacteria. Both compounds interacted with glycerophospholipids from Escherichia coli total lipid extract-based liposomes. JAV1 preferentially interacted with cardiolipin and partially relied on cardiolipin production for activity, whereas JAV2 generally interacted with lipids and had modest affinity for phosphatidylglycerol. In mammalian cells, neither compound significantly altered mitochondrial membrane potential at concentrations that killed S. Typhimurium. Instead, JAV1 and JAV2 became trapped within acidic compartments, including macrophage phagosomes. Both compounds improved survival of S. Typhimurium-infected Galleria mellonella larvae. Together, these data demonstrate that JAV1 and JAV2 disrupt bacterial inner membranes by distinct mechanisms and highlight how small, lipophilic, amine-substituted molecules can exploit host soluble innate immunity to facilitate the killing of intravesicular pathogens. IMPORTANCE Innovative strategies for developing new antimicrobials are needed. Combining our knowledge of host-pathogen interactions and relevant drug characteristics has the potential to reveal new approaches to treating infection. We identified two compounds with antibacterial activity specific to infection and with limited host cell toxicity. These compounds appeared to exploit host innate immunity to access the bacterium and differentially damage the bacterial inner membrane. Further, both compounds accumulated within Salmonella-containing and other acidic vesicles, a process known as lysosomal trapping, which protects the host and harms the pathogen. The compounds also increased host survival in an insect infection model. This work highlights the ability of host innate immunity to enable small molecules to act as antibiotics and demonstrates the feasibility of antimicrobial targeting of the inner membrane. Additionally, this study features the potential use of lysosomal trapping to enhance the activities of compounds against intravesicular pathogens.
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Affiliation(s)
- Joseph A. Villanueva
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Amy L. Crooks
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Toni A. Nagy
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Joaquin L. J. Quintana
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Zachary D. Dalebroux
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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Poulton NC, Rock JM. Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:997283. [PMID: 36325467 PMCID: PMC9618640 DOI: 10.3389/fcimb.2022.997283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/30/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis (TB) is among the most difficult infections to treat, requiring several months of multidrug therapy to produce a durable cure. The reasons necessitating long treatment times are complex and multifactorial. However, one major difficulty of treating TB is the resistance of the infecting bacterium, Mycobacterium tuberculosis (Mtb), to many distinct classes of antimicrobials. This review will focus on the major gaps in our understanding of intrinsic drug resistance in Mtb and how functional and chemical-genetics can help close those gaps. A better understanding of intrinsic drug resistance will help lay the foundation for strategies to disarm and circumvent these mechanisms to develop more potent antitubercular therapies.
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New Multidrug Efflux Systems in a Microcystin-Degrading Bacterium Blastomonas fulva and Its Genomic Feature. Int J Mol Sci 2022; 23:ijms231810856. [PMID: 36142771 PMCID: PMC9505733 DOI: 10.3390/ijms231810856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
A microcystin-degrading bacterial strain, Blastomonas fulva T2, was isolated from the culture of a microalgae Microcystis. The strain B. fulva T2 is Gram-stain-negative, non-motile, aerobic, non-spore-forming and phototrophic. The cells of B. fulva T2 are able to grow in ranges of temperature from 15 to 37 °C, with a pH of 6 to 8 and a salinity of 0 to 1% NaCl. Here, we sequenced the complete genome of B. fulva T2, aiming to better understand the evolutionary biology and the function of the genus Blastomonas at the molecular level. The complete genome of B. fulva T2 contained a circular chromosome (3,977,381 bp) with 64.3% GC content and a sizable plasmid (145.829 bp) with 60.7% GC content which comprises about 3.5% of the total genetic content. A total of 3842 coding genes, including 46 tRNAs and 6 rRNAs, were predicted in the genome. The genome contains genes for glycolysis, citric acid cycle, Entner–Doudoroff pathways, photoreaction center and bacteriochlorophylla synthesis. A 7.9 K gene cluster containing mlrA, mlrB, mlrC and mlrD1,2,3,4 of microcystin-degrading enzymes was identified. Notably, eight different efflux pumps categorized into RND, ABC and MFS types have been identified in the genome of strain T2. Our findings should provide new insights of the alternative reaction pathway as well as the enzymes which mediated the degradation of microcystin by bacteria, as well as the evolution, architectures, chemical mechanisms and physiological roles of the new bacterial multidrug efflux system.
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The Exploration of Complement-Resistance Mechanisms of Pathogenic Gram-Negative Bacteria to Support the Development of Novel Therapeutics. Pathogens 2022; 11:pathogens11080931. [PMID: 36015050 PMCID: PMC9412335 DOI: 10.3390/pathogens11080931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Resistance to antibiotics in Bacteria is one of the biggest threats to human health. After decades of attempting to isolate or design antibiotics with novel mechanisms of action against bacterial pathogens, few approaches have been successful. Antibacterial drug discovery is now moving towards targeting bacterial virulence factors, especially immune evasion factors. Gram-negative bacteria present some of the most significant challenges in terms of antibiotic resistance. However, they are also able to be eliminated by the component of the innate immune system known as the complement system. In response, Gram-negative bacteria have evolved a variety of mechanisms by which they are able to evade complement and cause infection. Complement resistance mechanisms present some of the best novel therapeutic targets for defending against highly antibiotic-resistant pathogenic bacterial infections.
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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45
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Wilson A, Ruiz N. The transmembrane α-helix of LptC participates in LPS extraction by the LptB 2 FGC transporter. Mol Microbiol 2022; 118:61-76. [PMID: 35678757 PMCID: PMC9544173 DOI: 10.1111/mmi.14952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022]
Abstract
Lipopolysaccharide (LPS) is an essential component of the outer membrane of most Gram‐negative bacteria that provides resistance to various toxic compounds and antibiotics. Newly synthesized LPS is extracted from the inner membrane by the ATP‐binding cassette (ABC) transporter LptB2FGC, which places the glycolipid onto a periplasmic protein bridge that connects to the outer membrane. This ABC transporter is structurally unusual in that it associates with an additional protein, LptC. The periplasmic domain of LptC is part of the transporter's bridge while its transmembrane α‐helix intercalates into the LPS‐binding cavity of the core LptB2FG transporter. LptC’s transmembrane helix affects the in vitro ATPase activity of LptB2FG, but its role in LPS transport in cells remains undefined. Here, we describe two roles of LptC’s transmembrane helix in Escherichia coli. We demonstrate that it is required to maintain proper levels of LptC and participates in coupling the activity of the ATPase LptB to that of its transmembrane partners LptF/LptG prior to loading LPS onto the periplasmic bridge. Our data support a model in which the association of LptC’s transmembrane helix with LptFG creates a nonessential step that slows down the LPS transporter.
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Affiliation(s)
- Andrew Wilson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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46
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Dombach JL, Quintana JLJ, Allgood SC, Nagy TA, Gustafson DL, Detweiler CS. A small molecule that disrupts S. Typhimurium membrane voltage without cell lysis reduces bacterial colonization of mice. PLoS Pathog 2022; 18:e1010606. [PMID: 35687608 PMCID: PMC9223311 DOI: 10.1371/journal.ppat.1010606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022] Open
Abstract
As pathogenic bacteria become increasingly resistant to antibiotics, antimicrobials with mechanisms of action distinct from current clinical antibiotics are needed. Gram-negative bacteria pose a particular problem because they defend themselves against chemicals with a minimally permeable outer membrane and with efflux pumps. During infection, innate immune defense molecules increase bacterial vulnerability to chemicals by permeabilizing the outer membrane and occupying efflux pumps. Therefore, screens for compounds that reduce bacterial colonization of mammalian cells have the potential to reveal unexplored therapeutic avenues. Here we describe a new small molecule, D66, that prevents the survival of a human Gram-negative pathogen in macrophages. D66 inhibits bacterial growth under conditions wherein the bacterial outer membrane or efflux pumps are compromised, but not in standard microbiological media. The compound disrupts voltage across the bacterial inner membrane at concentrations that do not permeabilize the inner membrane or lyse cells. Selection for bacterial clones resistant to D66 activity suggested that outer membrane integrity and efflux are the two major bacterial defense mechanisms against this compound. Treatment of mammalian cells with D66 does not permeabilize the mammalian cell membrane but does cause stress, as revealed by hyperpolarization of mitochondrial membranes. Nevertheless, the compound is tolerated in mice and reduces bacterial tissue load. These data suggest that the inner membrane could be a viable target for anti-Gram-negative antimicrobials, and that disruption of bacterial membrane voltage without lysis is sufficient to enable clearance from the host.
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Affiliation(s)
- Jamie L. Dombach
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (JLD); (CSD)
| | - Joaquin LJ Quintana
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Samual C. Allgood
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Toni A. Nagy
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Daniel L. Gustafson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail: (JLD); (CSD)
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47
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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48
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Selim S, Almuhayawi MS, Alharbi MT, Al Jaouni SK, Alharthi A, Abdel-Wahab BA, Ibrahim MAR, Alsuhaibani AM, Warrad M, Rashed K. Insights into the Antimicrobial, Antioxidant, Anti-SARS-CoV-2 and Cytotoxic Activities of Pistacia lentiscus Bark and Phytochemical Profile; In Silico and In Vitro Study. Antioxidants (Basel) 2022; 11:antiox11050930. [PMID: 35624793 PMCID: PMC9138067 DOI: 10.3390/antiox11050930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022] Open
Abstract
Foodborne infections and antibiotic resistance pose a serious threat to public health and must be addressed urgently. Pistacia lentiscus is a wild-growing shrub and has been utilized for medicinal applications as well as for culinary purposes. The antibacterial and antioxidant activities of P. lentiscus bark in vitro, as well as the phytochemical composition, are the focus of this inquiry. The bark extract of P. lentiscus showed significant antimicrobial activity in experiments on bacteria and yeast isolated from human and food sources. The exposure time for the complete inhibition of cell viability of P. aeruginosa in the extracts was found to be 5% at 15 min. Phytochemical inquiry of the methanol extract demonstrates the existence of carbohydrates, flavonoids, tannins, coumarins, triterpenes, and alkaloids. Deep phytochemical exploration led to the identification of methyl gallate, gallic acid, kaempferol, quercetin, kaempferol 3-O-α-rhamnoside, kaempferol 3-O-β-glucoside, and Quercetin-3-O-β-glucoside. When tested using the DPPH assay, the methanol extracts of P. lentiscus bark demonstrated a high free radical scavenging efficiency. Further, we have performed a molecular modelling study which revealed that the extract of P. lentiscus bark could be a beneficial source for novel flavonoid glycosides inhibitors against SARS-CoV-2 infection. Taken together, this study highlights the Pistacia lentiscus bark methanol extract as a promising antimicrobial and antiviral agent.
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Affiliation(s)
- Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
- Correspondence: (S.S.); (M.S.A.); (K.R.)
| | - Mohammed S. Almuhayawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (S.S.); (M.S.A.); (K.R.)
| | - Mohanned T. Alharbi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Jeddah, Jeddah 23218, Saudi Arabia;
| | - Soad K. Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Afaf Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia;
| | - Basel A. Abdel-Wahab
- Department of Medical Pharmacology, College of Medicine, Assiut University, Assiut 71515, Egypt;
- Department of Pharmacology, College of Pharmacy, Najran University, Najran 55461, Saudi Arabia
| | - Mervat A. R. Ibrahim
- Biochemistry Department, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt;
| | - Amnah Mohammed Alsuhaibani
- Department of Physical Sport Science, College of Education, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Mona Warrad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Quriat, Jouf University, Al Qurayyat 77425, Saudi Arabia;
| | - Khaled Rashed
- Pharmacognosy Department, National Research Centre, 33El Bohouth Str., Dokki, Giza 12622, Egypt
- Correspondence: (S.S.); (M.S.A.); (K.R.)
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49
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Govender P, Müller R, Singh K, Reddy V, Eyermann CJ, Fienberg S, Ghorpade SR, Koekemoer L, Myrick A, Schnappinger D, Engelhart C, Meshanni J, Byl JAW, Osheroff N, Singh V, Chibale K, Basarab GS. Spiropyrimidinetrione DNA Gyrase Inhibitors with Potent and Selective Antituberculosis Activity. J Med Chem 2022; 65:6903-6925. [PMID: 35500229 DOI: 10.1021/acs.jmedchem.2c00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotics with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The present study profiles new spiropyrimidinetriones (SPTs), DNA gyrase inhibitors having activity against drug-resistant Mycobacterium tuberculosis (Mtb), the causative agent of TB. While the clinical candidate zoliflodacin has progressed to phase 3 trials for the treatment of gonorrhea, compounds herein demonstrated higher inhibitory potency against Mtb DNA gyrase (e.g., compound 42 with IC50 = 2.0) and lower Mtb minimum inhibitor concentrations (0.49 μM for 42). Notably, 42 and analogues showed selective Mtb activity relative to representative Gram-positive and Gram-negative bacteria. DNA gyrase inhibition was shown to involve stabilization of double-cleaved DNA, while on-target activity was supported by hypersensitivity against a gyrA hypomorph. Finally, a docking model for SPTs with Mtb DNA gyrase was developed, and a structural hypothesis was built for structure-activity relationship expansion.
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Affiliation(s)
- Preshendren Govender
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Rudolf Müller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kawaljit Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Virsinha Reddy
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Charles J Eyermann
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Stephen Fienberg
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Sandeep R Ghorpade
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Lizbé Koekemoer
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Alissa Myrick
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Curtis Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jaclynn Meshanni
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, Cape Town, 7935, South Africa
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50
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Gurvic D, Leach AG, Zachariae U. Data-Driven Derivation of Molecular Substructures That Enhance Drug Activity in Gram-Negative Bacteria. J Med Chem 2022; 65:6088-6099. [PMID: 35427114 PMCID: PMC9059115 DOI: 10.1021/acs.jmedchem.1c01984] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The complex cell
envelope of Gram-negative bacteria creates a formidable
barrier to antibiotic influx. Reduced drug uptake impedes drug development
and contributes to a wide range of drug-resistant bacterial infections,
including those caused by extremely resistant species prioritized
by the World Health Organization. To develop new and efficient treatments,
a better understanding of the molecular features governing Gram-negative
permeability is essential. Here, we present a data-driven approach,
using matched molecular pair analysis and machine learning on minimal
inhibitory concentration data from Gram-positive and Gram-negative
bacteria to uncover chemical features that influence Gram-negative
bioactivity. We find recurring chemical moieties, of a wider range
than previously known, that consistently improve activity and suggest
that this insight can be used to optimize compounds for increased
Gram-negative uptake. Our findings may help to expand the chemical
space of broad-spectrum antibiotics and aid the search for new antibiotic
compound classes.
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Affiliation(s)
- Dominik Gurvic
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Andrew G. Leach
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Medchemica Limited, Mereside, Alderley Park, Macclesfield, SK10 4TG, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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