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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [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: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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2
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Kamal MAM, Bassil J, Loretz B, Hirsch AKH, Lee S, Lehr CM. Arg-biodynamers as antibiotic potentiators through interacting with Gram-negative outer membrane lipopolysaccharides. Eur J Pharm Biopharm 2024:114336. [PMID: 38795784 DOI: 10.1016/j.ejpb.2024.114336] [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: 04/18/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Antimicrobial resistance is becoming more prominent day after day due to a number of mechanisms by microbes, especially the sophisticated biological barriers of bacteria, especially in Gram-negatives. There, the lipopolysaccharides (LPS) layer is a unique component of the outer leaflet of the outer membrane which is highly impermeable and prevents antibiotics from passing passively into the intracellular compartments. Biodynamers, a novel class of dynamically bio-responsive polymers, may open new perspectives to overcome this particular barrier by accommodating various secondary structures and form supramolecular structures in such bacterial microenvironments. Generally, bio-responsive polymers are not only candidates as bio-active molecules against bacteria but also carriers via their interactions with the cargo. Singh et al. (2019) [1] Based on their dynamicity, design flexibility, biodegradability, biocompatibility, and pH-responsiveness, we investigated the potential of two peptide-based biodynamers for improving antimicrobial drug delivery. By a range of experimental methods, we discovered a greater affinity of Arg-biodynamers for bacterial membranes than for mammalian membranes as well as an enhanced LPS targeting on the bacterial membrane, opening perspectives for enhancing the delivery of antimicrobials across the Gram-negative bacterial cell envelope. This could be explained by the change of the secondary structure of Arg-biodynamers into a predominant β-sheet character in the LPS microenvironment, by contrast to the α-helical structure typically observed for most lipid membrane-permeabilizing peptides. In comparison to poly-L-arginine, the intrinsic antibacterial activity of Arg-biodynamers was nearly unchanged, but its toxicity against mammalian cells was >128-fold reduced. When used in bacterio as an antibiotic potentiator, however, Arg-biodynamers improved the minimum inhibitory concentration (MIC) against Escherichia coli by 32 times compared to colistin alone. Similar effect has also been observed in two stains of Pseudomonas aeruginosa. Arg-biodynamers may therefore represent an interesting option as an adjuvant for antibiotics against Gram-negative bacteria and to overcome antimicrobial resistance.
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Affiliation(s)
- Mohamed A M Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, 66123 Saarbrücken, Germany
| | - Justine Bassil
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, 66123 Saarbrücken, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, 66123 Saarbrücken, Germany
| | - Sangeun Lee
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, 66123 Saarbrücken, Germany.
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, 66123 Saarbrücken, Germany; Saarland University, Department of Pharmacy, 66123 Saarbrücken, Germany.
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3
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Seo J, Kim JH, Ko N, Kim J, Moon K, Kim IS, Lee W. Development of novel indole-quinoline hybrid molecules targeting bacterial proton motive force. J Appl Microbiol 2024; 135:lxae104. [PMID: 38678002 DOI: 10.1093/jambio/lxae104] [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: 03/04/2024] [Revised: 04/01/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
AIMS This study aimed to develop an editable structural scaffold for improving drug development, including pharmacokinetics and pharmacodynamics of antibiotics by using synthetic compounds derived from a (hetero)aryl-quinoline hybrid scaffold. METHODS AND RESULTS In this study, 18 CF3-substituted (hetero)aryl-quinoline hybrid molecules were examined for their potential antibacterial activity against Staphylococcus aureus by determining minimal inhibitory concentrations. These 18 synthetic compounds represent modifications to key regions of the quinoline N-oxide scaffold, enabling us to conduct a structure-activity relationship analysis for antibacterial potency. Among the compounds, 3 m exhibited potency against with both methicillin resistant S. aureus strains, as well as other Gram-positive bacteria, including Enterococcus faecalis and Bacillus subtilis. We demonstrated that 3 m disrupted the bacterial proton motive force (PMF) through monitoring the PMF and conducting the molecular dynamics simulations. Furthermore, we show that this mechanism of action, disrupting PMF, is challenging for S. aureus to overcome. We also validated this PMF inhibition mechanism of 3 m in an Acinetobacter baumannii strain with weaken lipopolysaccharides. Additionally, in Gram-negative bacteria, we demonstrated that 3 m exhibited a synergistic effect with colistin that disrupts the outer membrane of Gram-negative bacteria. CONCLUSIONS Our approach to developing editable synthetic novel antibacterials underscores the utility of CF3-substituted (hetero)aryl-quinoline scaffold for designing compounds targeting the bacterial proton motive force, and for further drug development, including pharmacokinetics and pharmacodynamics.
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Affiliation(s)
- Jinbeom Seo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ji-Hoon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nayoung Ko
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jihyeon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kyeongwon Moon
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In Su Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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5
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Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chem Biol 2024; 31:712-728.e9. [PMID: 38029756 PMCID: PMC11031330 DOI: 10.1016/j.chembiol.2023.10.026] [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] [Received: 11/29/2022] [Revised: 08/13/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
There is a need to discover and develop non-toxic antibiotics that are effective against metabolically dormant bacteria, which underlie chronic infections and promote antibiotic resistance. Traditional antibiotic discovery has historically favored compounds effective against actively metabolizing cells, a property that is not predictive of efficacy in metabolically inactive contexts. Here, we combine a stationary-phase screening method with deep learning-powered virtual screens and toxicity filtering to discover compounds with lethality against metabolically dormant bacteria and favorable toxicity profiles. The most potent and structurally distinct compound without any obvious mechanistic liability was semapimod, an anti-inflammatory drug effective against stationary-phase E. coli and A. baumannii. Integrating microbiological assays, biochemical measurements, and single-cell microscopy, we show that semapimod selectively disrupts and permeabilizes the bacterial outer membrane by binding lipopolysaccharide. This work illustrates the value of harnessing non-traditional screening methods and deep learning models to identify non-toxic antibacterial compounds that are effective in infection-relevant contexts.
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Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jacqueline A Valeri
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aarti Krishnan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parijat Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melis N Anahtar
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alice Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brooke Linnehan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Felix Wong
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01062 Dresden, Germany
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA.
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6
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Su Z, Chen A, Lipkowski J. Electrochemical and Infrared Studies of a Model Bilayer of the Outer Membrane of Gram-Negative Bacteria and its Interaction with polymyxin─the Last-Resort Antibiotic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8248-8259. [PMID: 38578277 DOI: 10.1021/acs.langmuir.4c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
A model bilayer of the outer membrane (OM) of Gram-negative bacteria, composed of lipid A and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), was assembled on the β-Tg modified gold (111) single crystal surface using a combination of Langmuir-Blodgett and Langmuir-Schaefer transfer. Electrochemical and spectroscopic methods were employed to study the properties of the model bilayer and its interaction with polymyxin. The model bilayer is stable on the gold surface in the transmembrane potential region between 0.0 and -0.7 V. The presence of Mg2+ coordinates with the phosphate and carboxylate groups in the leaflet of lipid A and stabilizes the structure of the model bilayer. Polymyxin causes the model bilayer leakage and damage in the transmembrane potential region between 0.2 and -0.4 V. At transmembrane potentials lower than -0.5 V, polymyxin does not affect the membrane integrity. Polymyxin binds to the phosphate and carboxylate groups in lipid A molecules and causes the increase of the tilt angle of acyl chains and the decrease of the tilt of the C═O bond. The results in this paper indicate that the antimicrobial activity of polymyxin depends on the transmembrane potential at the model bilayer and provides useful information for the development of new antibiotics.
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Affiliation(s)
- ZhangFei Su
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Aicheng Chen
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacek Lipkowski
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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7
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Slingerland C, Martin NI. Recent Advances in the Development of Polymyxin Antibiotics: 2010-2023. ACS Infect Dis 2024; 10:1056-1079. [PMID: 38470446 PMCID: PMC11019560 DOI: 10.1021/acsinfecdis.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 03/13/2024]
Abstract
The polymyxins are nonribosomal lipopeptides produced by Paenibacillus polymyxa and are potent antibiotics with activity specifically directed against Gram-negative bacteria. While the clinical use of polymyxins has historically been limited due to their toxicity, their use is on the rise given the lack of alternative treatment options for infections due to multidrug resistant Gram-negative pathogens. The Gram-negative specificity of the polymyxins is due to their ability to target lipid A, the membrane embedded LPS anchor that decorates the cell surface of Gram-negative bacteria. Notably, the mechanisms responsible for polymyxin toxicity, and in particular their nephrotoxicity, are only partially understood with most insights coming from studies carried out in the past decade. In parallel, many synthetic and semisynthetic polymyxin analogues have been developed in recent years in an attempt to mitigate the nephrotoxicity of the natural products. Despite these efforts, to date, no polymyxin analogues have gained clinical approval. This may soon change, however, as at the moment there are three novel polymyxin analogues in clinical trials. In this context, this review provides an update of the most recent insights with regard to the structure-activity relationships and nephrotoxicity of new polymyxin variants reported since 2010. We also discuss advances in the synthetic methods used to generate new polymyxin analogues, both via total synthesis and semisynthesis.
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Affiliation(s)
- Cornelis
J. Slingerland
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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8
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Fu J, Cai W, Pan S, Chen L, Fang X, Shang Y, Xu J. Developments and Trends of Nanotechnology Application in Sepsis: A Comprehensive Review Based on Knowledge Visualization Analysis. ACS NANO 2024; 18:7711-7738. [PMID: 38427687 DOI: 10.1021/acsnano.3c10458] [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: 03/03/2024]
Abstract
Sepsis, a common life-threatening clinical condition, continues to have high morbidity and mortality rates, despite advancements in management. In response, significant research efforts have been directed toward developing effective strategies. Within this scope, nanotechnology has emerged as a particularly promising field, attracting significant interest for its potential to enhance disease diagnosis and treatment. While several reviews have highlighted the use of nanoparticles in sepsis, comprehensive studies that summarize and analyze the hotspots and research trends are lacking. To identify and further promote the development of nanotechnology in sepsis, a bibliometric analysis was conducted on the relevant literature, assessing research trends and hotspots in the application of nanomaterials for sepsis. Next, a comprehensive review of the subjectively recognized research hotspots in sepsis, including nanotechnology-enhanced biosensors and nanoscale imaging for sepsis diagnostics, and nanoplatforms designed for antimicrobial, immunomodulatory, and detoxification strategies in sepsis therapy, is elucidated, while the potential side effects and toxicity risks of these nanomaterials were discussed. Particular attention is given to biomimetic nanoparticles, which mimic the biological functions of source cells like erythrocytes, immune cells, and platelets to evade immune responses and effectively deliver therapeutic agents, demonstrating substantial translational potential. Finally, current challenges and future perspectives of nanotechnology applications in sepsis with a view to maximizing their great potential in the research of translational medicine are also discussed.
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Affiliation(s)
- Jiaji Fu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430023, China
| | - Wentai Cai
- The First Clinical College, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shangwen Pan
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lang Chen
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaowei Fang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - You Shang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430023, China
| | - Jiqian Xu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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9
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Lee TH, Charchar P, Separovic F, Reid GE, Yarovsky I, Aguilar MI. The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes. Chem Sci 2024; 15:3408-3427. [PMID: 38455013 PMCID: PMC10915831 DOI: 10.1039/d3sc04523d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Patrick Charchar
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
| | - Gavin E Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
- Department of Biochemistry and Pharmacology, University of Melbourne Parkville VIC 3010 Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
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10
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Baijal K, Abramchuk I, Herrera CM, Mah TF, Trent MS, Lavallée-Adam M, Downey M. Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli. PLoS Biol 2024; 22:e3002558. [PMID: 38478588 PMCID: PMC10962826 DOI: 10.1371/journal.pbio.3002558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, Ontario, Canada
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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11
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Álvarez-Martínez FJ, Díaz-Puertas R, Barrajón-Catalán E, Micol V. Plant-Derived Natural Products for the Treatment of Bacterial Infections. Handb Exp Pharmacol 2024. [PMID: 38418668 DOI: 10.1007/164_2024_706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Bacterial infections are a significant public health concern, and the emergence of antibiotic-resistant bacteria (ARB) has become a major challenge for modern medicine. The overuse and misuse of antibiotics have contributed to the development of ARB, which has led to the need for alternative therapies. Plant-derived natural products (PNPs) have been extensively studied for their potential as alternative therapies for the treatment of bacterial infections. The diverse chemical compounds found in plants have shown significant antibacterial properties, making them a promising source of novel antibacterial agents. The use of PNPs as antibacterial agents is particularly appealing because they offer a relatively safe and cost-effective approach to the treatment of bacterial infections. This chapter aims to provide an overview of the current state of research on PNPs as antibacterial agents. It will cover the mechanisms of action of the main PNPs against bacterial pathogens and discuss their potential to be used as complementary therapies to combat ARB. This chapter will also highlight the most common screening methodologies to discover new PNPs and the challenges and future prospects in the development of these compounds as antibacterial agents.
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Affiliation(s)
- Francisco Javier Álvarez-Martínez
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
- Institute of Sanitary and Biomedical Research of Alicante (ISABIAL), Alicante, Spain
| | - Rocío Díaz-Puertas
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
| | - Enrique Barrajón-Catalán
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain.
- Department of Pharmacy, Elche University Hospital-FISABIO, Elche, Spain.
| | - Vicente Micol
- Institute for Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Miguel Hernández University (UMH), Elche, Spain
- CIBER, Pathophysiology of Obesity and Nutrition, CIBERobn, Carlos III Health Institute (CB12/03/30038), Madrid, Spain
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12
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Choi Y, Choe HW, Kook M, Choo S, Park TW, Bae S, Kim H, Yang J, Jeong WS, Yu J, Lee KR, Kim YS, Yu J. Proline-Hinged α-Helical Peptides Sensitize Gram-Positive Antibiotics, Expanding Their Physicochemical Properties to Be Used as Gram-Negative Antibiotics. J Med Chem 2024; 67:1825-1842. [PMID: 38124427 PMCID: PMC10860147 DOI: 10.1021/acs.jmedchem.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is the most difficult obstacle for small-molecule antibiotics to reach their targets in the cytosol. The molecular features of Gram-negative antibiotics required for passing through the OM are that they should be positively charged rather than neutral, flat rather than globular, less flexible, or more increased amphiphilic moment. Because of these specific molecular characteristics, developing Gram-negative antibiotics is difficult. We focused on sensitizer peptides to facilitate the passage of hydrophobic Gram-positive antibiotics through the OM. We explored ways of improving the sensitizing ability of proline-hinged α-helical peptides by adjusting their length, hydrophobicity, and N-terminal groups. A novel peptide, 1403, improves the potentiation of rifampicin in vitro and in vivo and potentiates most Gram-positive antibiotics. The "sensitizer" approach is more plausible than those that rely on conventional drug discovery methods concerning drug development costs and the development of drug resistance.
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Affiliation(s)
- Yoonhwa Choi
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
- CAMP
Therapeutics, Seoul 08826, Republic of Korea
| | - Hyeong Woon Choe
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Minsoo Kook
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Seolah Choo
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Tae Woo Park
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Soeun Bae
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Heeseung Kim
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jihye Yang
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Woo-Seong Jeong
- Laboratory
Animal Resource Center, Korea Research Institute
of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jiyoung Yu
- Asan
Medical Center, Seoul 05505, Republic
of Korea
| | - Kyeong-Ryoon Lee
- Laboratory
Animal Resource Center, Korea Research Institute
of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yang Soo Kim
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jaehoon Yu
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
- CAMP
Therapeutics, Seoul 08826, Republic of Korea
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13
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He S, Deber CM. Interaction of designed cationic antimicrobial peptides with the outer membrane of gram-negative bacteria. Sci Rep 2024; 14:1894. [PMID: 38253659 PMCID: PMC10803810 DOI: 10.1038/s41598-024-51716-1] [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: 07/27/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The outer membrane (OM) is a hallmark feature of gram-negative bacteria that provides the species with heightened resistance against antibiotic threats while cationic antimicrobial peptides (CAPs) are natural antibiotics broadly recognized for their ability to disrupt bacterial membranes. It has been well-established that lipopolysaccharides present on the OM are among major targets of CAP activity against gram-negative species. Here we investigate how the relative distribution of charged residues along the primary peptide sequence, in conjunction with its overall hydrophobicity, affects such peptide-OM interactions in the natural CAP Ponericin W1. Using a designed peptide library derived from Ponericin W1, we determined that the consecutive placement of Lys residues at the peptide N- or C-terminus (ex. "PonN": KKKKKKWLGSALIGALLPSVVGLFQ) enhances peptide binding affinity to OM lipopolysaccharides compared to constructs where Lys residues are interspersed throughout the primary sequence (ex. "PonAmp": WLKKALKIGAKLLPSVVKLFKGSGQ). Antimicrobial activity against multidrug resistant strains of Pseudomonas aeruginosa was similarly found to be highest among Lys-clustered sequences. Our findings suggest that while native Ponericin W1 exerts its initial activity at the OM, Lys-clustering may be a promising means to enhance potency towards this interface, thereby augmenting peptide entry and activity at the IM, with apparent advantage against multidrug-resistant species.
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Affiliation(s)
- Shelley He
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada.
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14
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Mandal S, Patra D, Mandal S, Das GK, Sahoo P. Insights into colistin-mediated fluorescence labelling of bacterial LPS. RSC Adv 2024; 14:2770-2777. [PMID: 38234867 PMCID: PMC10792355 DOI: 10.1039/d3ra07107c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
Gram-negative bacterial infections are becoming untreatable due to their ability to mutate, and the gradual development of their resistance to the available antimicrobials. In recent times colistin, a drug of last resort, started losing its efficacy towards multidrug-resistant bacterial infections. Colistin targets bacterial endotoxin lipopolysaccharides (LPS) and destabilises the cytoplasmic membrane by disrupting the outer LPS membrane. In this study, we have tried to label the bacterial LPS, the main constituent of the cytoplasmic membrane of bacterial cells, to try to understand the interaction mechanism of LPS with colistin. The chemosensor, naphthaldehyde appended furfural (NAF) that selectively recognises colistin can label LPS, by showing its fluorescence signals. The computationally derived three-dimensional structure of LPS has been introduced to speculate on the possible binding mode of colistin with LPS, and this was also thoroughly studied with the help of quantum mechanics and molecular dynamics energy minimisation. Fluorescence microscopy and FE-SEM microscopic studies were also used to observe the change in the structural morphology of colistin-sensitive and resistant Salmonella typhi in different experimental conditions.
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Affiliation(s)
- Saurodeep Mandal
- Department of Chemistry, Siksha Bhavana, Visva-Bharati Santiniketan 731235 West Bengal India
| | - Dipanwita Patra
- Department of Microbiology, University of Calcutta Kolkata 700019 West Bengal India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta Kolkata 700019 West Bengal India
| | - Gourab Kanti Das
- Department of Chemistry, Siksha Bhavana, Visva-Bharati Santiniketan 731235 West Bengal India
| | - Prithidipa Sahoo
- Department of Chemistry, Siksha Bhavana, Visva-Bharati Santiniketan 731235 West Bengal India
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15
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Jiang X, Patil NA, Xu Y, Wickremasinghe H, Zhou QT, Zhou F, Thompson PE, Wang L, Xiao M, Roberts KD, Velkov T, Li J. Structure-Interaction Relationship of Polymyxins with Lung Surfactant. J Med Chem 2023; 66:16109-16119. [PMID: 38019899 DOI: 10.1021/acs.jmedchem.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Multidrug-resistant Gram-negative bacteria present an urgent and formidable threat to the global public health. Polymyxins have emerged as a last-resort therapy against these 'superbugs'; however, their efficacy against pulmonary infection is poor. In this study, we integrated chemical biology and molecular dynamics simulations to examine how the alveolar lung surfactant significantly reduces polymyxin antibacterial activity. We discovered that lung surfactant is a phospholipid-based permeability barrier against polymyxins, compromising their efficacy against target bacteria. Next, we unraveled the structure-interaction relationship between polymyxins and lung surfactant, elucidating the thermodynamics that govern the penetration of polymyxins through this critical surfactant layer. Moreover, we developed a novel analog, FADDI-235, which exhibited potent activity against Gram-negative bacteria, both in the presence and absence of lung surfactant. These findings shed new light on the sequestration mechanism of lung surfactant on polymyxins and importantly pave the way for the rational design of new-generation lipopeptide antibiotics to effectively treat Gram-negative bacterial pneumonia.
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Affiliation(s)
- Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Nitin A Patil
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Yuwen Xu
- Shandong Institute for Food and Drug Control, Jinan 250000, China
| | - Hasini Wickremasinghe
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette 47907, United States of America
| | - Fanfan Zhou
- Faculty of Medicine and Health, Sydney Pharmacy School, The University of Sydney, Sydney 2006, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne 3052, Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Kade D Roberts
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne 3010, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne 3800, Australia
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16
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Materon IC, Palzkill T. Structural biology of MCR-1-mediated resistance to polymyxin antibiotics. Curr Opin Struct Biol 2023; 82:102647. [PMID: 37399693 PMCID: PMC10527939 DOI: 10.1016/j.sbi.2023.102647] [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: 04/01/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023]
Abstract
Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.
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Affiliation(s)
- Isabel Cristina Materon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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17
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Gadar K, de Dios R, Kadeřábková N, Prescott TAK, Mavridou DAI, McCarthy RR. Disrupting iron homeostasis can potentiate colistin activity and overcome colistin resistance mechanisms in Gram-Negative Bacteria. Commun Biol 2023; 6:937. [PMID: 37704838 PMCID: PMC10499790 DOI: 10.1038/s42003-023-05302-2] [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: 01/26/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative priority pathogen that can readily overcome antibiotic treatment through a range of intrinsic and acquired resistance mechanisms. Treatment of carbapenem-resistant A. baumannii largely relies on the use of colistin in cases where other treatment options have been exhausted. However, the emergence of resistance against this last-line drug has significantly increased amongst clinical strains. In this study, we identify the phytochemical kaempferol as a potentiator of colistin activity. When administered singularly, kaempferol has no effect on growth but does impact biofilm formation. Nonetheless, co-administration of kaempferol with sub-inhibitory concentrations of colistin exposes bacteria to a metabolic Achilles heel, whereby kaempferol-induced dysregulation of iron homeostasis leads to bacterial killing. We demonstrate that this effect is due to the disruption of Fenton's reaction, and therefore to a lethal build-up of toxic reactive oxygen species in the cell. Furthermore, we show that this vulnerability can be exploited to overcome both intrinsic and acquired colistin resistance in clinical strains of A. baumannii and E. coli in vitro and in the Galleria mellonella model of infection. Overall, our findings provide a proof-of-principle demonstration that targeting iron homeostasis is a promising strategy for enhancing the efficacy of colistin and overcoming colistin-resistant infections.
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Affiliation(s)
- Kavita Gadar
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Rubén de Dios
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
- John Ring LaMontagne Centre for Infectious Diseases, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ronan R McCarthy
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK.
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18
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Manioglu S, Modaresi SM, Thoma J, Overall SA, Upert G, Luther A, Barnes AB, Obrecht D, Müller DJ, Hiller S. Reply to: Antibiotics and hexagonal order in the bacterial outer membrane. Nat Commun 2023; 14:4773. [PMID: 37558675 PMCID: PMC10412578 DOI: 10.1038/s41467-023-40276-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Affiliation(s)
- Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | | | - Johannes Thoma
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, 405 30 Göteborg, Sweden
| | - Sarah A Overall
- Laboratory of Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | | | | | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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19
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Benn G, Silhavy TJ, Kleanthous C, Hoogenboom BW. Antibiotics and hexagonal order in the bacterial outer membrane. Nat Commun 2023; 14:4772. [PMID: 37558670 PMCID: PMC10412626 DOI: 10.1038/s41467-023-40275-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023] Open
Affiliation(s)
- Georgina Benn
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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20
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Bekale LA, Sharma D, Bacacao B, Chen J, Santa Maria PL. Eradication of Bacterial Persister Cells By Leveraging Their Low Metabolic Activity Using Adenosine Triphosphate Coated Gold Nanoclusters. NANO TODAY 2023; 51:101895. [PMID: 37575958 PMCID: PMC10421611 DOI: 10.1016/j.nantod.2023.101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Bacteria first develop tolerance after antibiotic exposure; later genetic resistance emerges through the population of tolerant bacteria. Bacterial persister cells are the multidrug-tolerant subpopulation within an isogenic bacteria culture that maintains genetic susceptibility to antibiotics. Because of this link between antibiotic tolerance and resistance and the rise of antibiotic resistance, there is a pressing need to develop treatments to eradicate persister cells. Current anti persister cell strategies are based on the paradigm of "awakening" them from their low metabolic state before attempting eradication with traditional antibiotics. Herein, we demonstrate that the low metabolic activity of persister cells can be exploited for eradication over their metabolically active counterparts. We engineered gold nanoclusters coated with adenosine triphosphate (AuNC@ATP) as a benchmark nanocluster that kills persister cells over exponential growth bacterial cells and prove the feasibility of this new concept. Finally, using AuNC@ATP as a new research tool, we demonstrated that it is possible to prevent the emergence of antibiotic-resistant superbugs with an anti-persister compound. Eradicating persister cells with AuNC@ATP in an isogenic culture of bacteria stops the emergence of superbug bacteria mediated by the sub-lethal dose of conventional antibiotics. Our findings lay the groundwork for developing novel nano-antibiotics targeting persister cells, which promise to prevent the emergence of superbugs and prolong the lifespan of currently available antibiotics.
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Affiliation(s)
- Laurent A. Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Devesh Sharma
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Jing Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Peter L. Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
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21
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Chan DK, Dykema K, Fatima M, Harvey H, Qaderi I, Burrows LL. Nutrient Limitation Sensitizes Pseudomonas aeruginosa to Vancomycin. ACS Infect Dis 2023; 9:1408-1423. [PMID: 37279282 PMCID: PMC10353551 DOI: 10.1021/acsinfecdis.3c00167] [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: 04/14/2023] [Indexed: 06/08/2023]
Abstract
Traditional antibacterial screens rely on growing bacteria in nutrient-replete conditions which are not representative of the natural environment or sites of infection. Instead, screening in more physiologically relevant conditions may reveal novel activity for existing antibiotics. Here, we screened a panel of antibiotics reported to lack activity against the opportunistic Gram-negative bacterium, Pseudomonas aeruginosa, under low-nutrient and low-iron conditions, and discovered that the glycopeptide vancomycin inhibited the growth of P. aeruginosa at low micromolar concentrations through its canonical mechanism of action, disruption of peptidoglycan crosslinking. Spontaneous vancomycin-resistant mutants underwent activating mutations in the sensor kinase of the two-component CpxSR system, which induced cross-resistance to almost all classes of β-lactams, including the siderophore antibiotic cefiderocol. Other mutations that conferred vancomycin resistance mapped to WapR, an α-1,3-rhamnosyltransferase involved in lipopolysaccharide core biosynthesis. A WapR P164T mutant had a modified LPS profile compared to wild type that was accompanied by increased susceptibility to select bacteriophages. We conclude that screening in nutrient-limited conditions can reveal novel activity for existing antibiotics and lead to discovery of new and impactful resistance mechanisms.
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Affiliation(s)
- Derek
C. K. Chan
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Katherine Dykema
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Mahrukh Fatima
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Hanjeong Harvey
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Ikram Qaderi
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Lori L. Burrows
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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22
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Melcrová A, Maity S, Melcr J, de Kok NAW, Gabler M, van der Eyden J, Stensen W, Svendsen JSM, Driessen AJM, Marrink SJ, Roos WH. Lateral membrane organization as target of an antimicrobial peptidomimetic compound. Nat Commun 2023; 14:4038. [PMID: 37419980 PMCID: PMC10328936 DOI: 10.1038/s41467-023-39726-5] [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: 12/23/2022] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Antimicrobial resistance is one of the leading concerns in medical care. Here we study the mechanism of action of an antimicrobial cationic tripeptide, AMC-109, by combining high speed-atomic force microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on negatively charged membranes derived from Staphylococcus aureus consists of two crucial steps. First, AMC-109 self-assembles into stable aggregates consisting of a hydrophobic core and a cationic surface, with specificity for negatively charged membranes. Second, upon incorporation into the membrane, individual peptides insert into the outer monolayer, affecting lateral membrane organization and dissolving membrane nanodomains, without forming pores. We propose that membrane domain dissolution triggered by AMC-109 may affect crucial functions such as protein sorting and cell wall synthesis. Our results indicate that the AMC-109 mode of action resembles that of the disinfectant benzalkonium chloride (BAK), but with enhanced selectivity for bacterial membranes.
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Affiliation(s)
- Adéla Melcrová
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Josef Melcr
- Molecular Dynamics, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Niels A W de Kok
- Molecular Microbiology, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Mariella Gabler
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Jonne van der Eyden
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wenche Stensen
- Department of Chemistry, UiT Arctic University of Norway, Tromsø, Norway
| | - John S M Svendsen
- Department of Chemistry, UiT Arctic University of Norway, Tromsø, Norway
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
- Molecular Dynamics, Groningen Biomolecular Sciences & Biotechnology Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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23
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Baijal K, Abramchuk I, Herrera CM, Stephen Trent M, Lavallée-Adam M, Downey M. Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.546892. [PMID: 37461725 PMCID: PMC10350021 DOI: 10.1101/2023.07.06.546892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (∆ppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and ∆ppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks. From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in ∆ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in ∆ppk cells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that ∆ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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24
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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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25
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Pandit S, Jacquemin L, Zhang J, Gao Z, Nishina Y, Meyer RL, Mijakovic I, Bianco A, Pang C. Polymyxin B complexation enhances the antimicrobial potential of graphene oxide. Front Cell Infect Microbiol 2023; 13:1209563. [PMID: 37415828 PMCID: PMC10321305 DOI: 10.3389/fcimb.2023.1209563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction The antibacterial activity of graphene oxide (GO) has been widely explored and tested against various pathogenic bacterial strains. Although antimicrobial activity of GO against planktonic bacterial cells was demonstrated, its bacteriostatic and bactericidal effect alone is not sufficient to damage sedentary and well protected bacterial cells inside biofilms. Thus, to be utilized as an effective antibacterial agent, it is necessary to improve the antibacterial activity of GO either by integration with other nanomaterials or by attachment of antimicrobial agents. In this study, antimicrobial peptide polymyxin B (PMB) was adsorbed onto the surface of pristine GO and GO functionalized with triethylene glycol. Methods The antibacterial effects of the resulting materials were examined by evaluating minimum inhibitory concentration, minimum bactericidal concentration, time kill assay, live/dead viability staining and scanning electron microscopy. Results and discussion PMB adsorption significantly enhanced the bacteriostatic and bactericidal activity of GO against both planktonic cells and bacterial cells in biofilms. Furthermore, the coatings of PMB-adsorbed GO applied to catheter tubes strongly mitigated biofilm formation, by preventing bacterial adhesion and killing the bacterial cells that managed to attach. The presented results suggest that antibacterial peptide absorption can significantly enhance the antibacterial activity of GO and the resulting material can be effectively used not only against planktonic bacteria but also against infectious biofilms.
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Affiliation(s)
- Santosh Pandit
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lucas Jacquemin
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Jian Zhang
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Zhengfeng Gao
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Yuta Nishina
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alberto Bianco
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Chengfang Pang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- The Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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26
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. J Biol Chem 2023:104894. [PMID: 37286040 PMCID: PMC10331486 DOI: 10.1016/j.jbc.2023.104894] [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: 05/02/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg2+ as a cofactor. Mn2+, but not other divalent cations, could substitute for Mg2+. Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (Km,app=19.2 ± 5.5 μM; Vmax,app=2590 ± 230 pmol/min/mg enzyme) and ATP (Km,app=0.29 ± 0.07 mM; Vmax,app=10100 ± 996 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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Affiliation(s)
| | - Geordan Stukey
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - George M Carman
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric A Klein
- Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA; Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA.
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27
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Carfrae LA, Rachwalski K, French S, Gordzevich R, Seidel L, Tsai CN, Tu MM, MacNair CR, Ovchinnikova OG, Clarke BR, Whitfield C, Brown ED. Inhibiting fatty acid synthesis overcomes colistin resistance. Nat Microbiol 2023:10.1038/s41564-023-01369-z. [PMID: 37127701 DOI: 10.1038/s41564-023-01369-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Treating multidrug-resistant infections has increasingly relied on last-resort antibiotics, including polymyxins, for example colistin. As polymyxins are given routinely, the prevalence of their resistance is on the rise and increases mortality rates of sepsis patients. The global dissemination of plasmid-borne colistin resistance, driven by the emergence of mcr-1, threatens to diminish the therapeutic utility of polymyxins from an already shrinking antibiotic arsenal. Restoring sensitivity to polymyxins using combination therapy with sensitizing drugs is a promising approach to reviving its clinical utility. Here we describe the ability of the biotin biosynthesis inhibitor, MAC13772, to synergize with colistin exclusively against colistin-resistant bacteria. MAC13772 indirectly disrupts fatty acid synthesis (FAS) and restores sensitivity to the last-resort antibiotic, colistin. Accordingly, we found that combinations of colistin and other FAS inhibitors, cerulenin, triclosan and Debio1452-NH3, had broad potential against both chromosomal and plasmid-mediated colistin resistance in chequerboard and lysis assays. Furthermore, combination therapy with colistin and the clinically relevant FabI inhibitor, Debio1452-NH3, showed efficacy against mcr-1 positive Klebsiella pneumoniae and colistin-resistant Escherichia coli systemic infections in mice. Using chemical genomics, lipidomics and transcriptomics, we explored the mechanism of the interaction. We propose that inhibiting FAS restores colistin sensitivity by depleting lipid synthesis, leading to changes in phospholipid composition. In all, this work reveals a surprising link between FAS and colistin resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Laura Seidel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Caressa N Tsai
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Craig R MacNair
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Olga G Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Bradley R Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Eric D Brown
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
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28
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538943. [PMID: 37205603 PMCID: PMC10187206 DOI: 10.1101/2023.05.01.538943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg 2+ as a cofactor. Mn 2+ , but not other divalent cations, could substitute for Mg 2+ . Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (K m,app =19.2 ± 5.5 μM; V max,app =2586.29 ± 231.99 pmol/min/mg enzyme) and ATP (K m,app =0.29 ± 0.07 mM; V max,app =10067.57 ± 996.85 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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29
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Whitehead B, Antennuci F, Boysen AT, Nejsum P. Polymyxin B inhibits pro-inflammatory effects of E. coli outer membrane vesicles whilst increasing immune cell uptake and clearance. J Antibiot (Tokyo) 2023; 76:360-364. [PMID: 37016014 DOI: 10.1038/s41429-023-00615-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 04/06/2023]
Abstract
Polymyxin B (PMB) is a peptide based antibiotic that binds the lipid A moiety of lipopolysaccharide (LPS) with a resultant bactericidal effect. The interaction of PMB with LPS presented on outer membrane vesicles (OMVs) is not fully known, however, a sacrificial role of OMVs in protecting bacterial cells by sequestering PMB has been described. Here we assess the ability of PMB to neutralize the immune-stimulatory properties of OMVs whilst modulating the uptake of OMVs in human immune cells. We show for the first time that PMB increases immune cell uptake of Escherichia coli derived OMVs whilst inhibiting TNF and IL-1β production. Therefore, we present a potential new role for PMB in the neutralization of OMVs via LPS masking and increased immune cell uptake.
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Affiliation(s)
- Bradley Whitehead
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Fabio Antennuci
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders T Boysen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Peter Nejsum
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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