1
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Weerakoon D, Marzinek JK, Pedebos C, Bond PJ, Khalid S. Polymyxin B1 in the E. coli inner membrane: a complex story of protein and lipopolysaccharide mediated insertion. J Biol Chem 2024:107754. [PMID: 39260694 DOI: 10.1016/j.jbc.2024.107754] [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: 02/10/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for 'last-resort' antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD) including long-timescale coarse-grained (CG) and all-atom (AA) simulations to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.
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Affiliation(s)
- Dhanushka Weerakoon
- School of Chemistry, University of Southampton, SO17 1BJ, UK; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, OX1 3QU, UK; Programa de Pós-Graduação em Biociências (PPGBio), Universidade Federal de Ciências da Saudé de Porto Alegre - UFCSPA, Brazil
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, OX1 3QU, UK
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2
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Thombare VJ, Wu Y, Pamulapati K, Han M, Tailhades J, Cryle MJ, Roberts KD, Velkov T, Li J, Patil NA. Advancing Nitrile-Aminothiol Strategy for Dual and Sequential Bioconjugation. Chemistry 2024; 30:e202401674. [PMID: 38839567 DOI: 10.1002/chem.202401674] [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: 04/29/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Nitrile-aminothiol conjugation (NATC) stands out as a promising biocompatible ligation technique due to its high chemo-selectivity. Herein we investigated the reactivity and substrate scope of NAT conjugation chemistry, thus developing a novel pH dependent orthogonal NATC as a valuable tool for chemical biology. The study of reaction kinetics elucidated that the combination of heteroaromatic nitrile and aminothiol groups led to the formation of an optimal bioorthogonal pairing, which is pH dependent. This pairing system was effectively utilized for sequential and dual conjugation. Subsequently, these rapid (≈1 h) and high yield (>90 %) conjugation strategies were successfully applied to a broad range of complex biomolecules, including oligonucleotides, chelates, small molecules and peptides. The effectiveness of this conjugation chemistry was demonstrated by synthesizing a fluorescently labelled antimicrobial peptide-oligonucleotide complex as a dual conjugate to imaging in live cells. This first-of-its-kind sequential NATC approach unveils unprecedented opportunities in modern chemical biology, showcasing exceptional adaptability in rapidly creating structurally complex bioconjugates. Furthermore, the results highlight its potential for versatile applications across fundamental and translational biomedical research.
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Affiliation(s)
- Varsha J Thombare
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Yimin Wu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Kavya Pamulapati
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Meiling Han
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Julien Tailhades
- Department of Biochemistry Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Max J Cryle
- Department of Biochemistry Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Kade D Roberts
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Tony Velkov
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Jian Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Nitin A Patil
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
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3
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Kloula Ben Ghorbal S, Dhaya I, Ouzari IH, Chatti A. Cyclopropanation and membrane unsaturation improve antibiotic resistance of swarmer Pseudomonas and its sod mutants exposed to radiations, in vitro and in silico approch. World J Microbiol Biotechnol 2024; 40:243. [PMID: 38869625 DOI: 10.1007/s11274-024-04033-8] [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: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024]
Abstract
It was known that UVc irradiation increases the reactive oxygen species' (ROS) levels in bacteria hence the intervention of antioxidant enzymes and causes also changes in fatty acids (FAs) composition enabling bacteria to face antibiotics. Here, we intended to elucidate an interrelationship between SOD and susceptibility to antibiotics by studying FA membrane composition of UVc-treated P. aeruginosa PAO1 and its isogenic mutants (sodM, sodB and sod MB) membrane, after treatment with antibiotics. Swarmer mutants defective in genes encoding superoxide dismutase were pre-exposed to UVc radiations and then tested by disk diffusion method for their contribution to antibiotic tolerance in comparison with the P. aeruginosa wild type (WT). Moreover, fatty acid composition of untreated and UVc-treated WT and sod mutants was examined by Gaz chromatography and correlated to antibiotic resistance. Firstly, it has been demonstrated that after UVc exposure, swarmer WT strain, sodM and sodB mutants remain resistant to polymixin B, a membrane target antibiotic, through membrane unsaturation supported by the intervention of Mn-SOD after short UVc exposure and cyclopropanation of unsaturated FAs supported by the action of Fe-SOD after longer UVc exposure. However, resistance for ciprofloxacin is correlated with increase in saturated FAs. This correlation has been confirmed by a molecular docking approach showing that biotin carboxylase, involved in the initial stage of FA biosynthesis, exhibits a high affinity for ciprofloxacin. This investigation has explored the correlation of antibiotic resistance with FA content of swarmer P.aeruginosa pre-exposed to UVc radiations, confirmed to be antibiotic target dependant.
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Affiliation(s)
- Salma Kloula Ben Ghorbal
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et Technologies des Eaux Usées, Technopole Borj Cedria, BP 273, 8020, Soliman, Tunisia.
| | - Ibtihel Dhaya
- LR18ES03- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecules Valorization, University of Tunis El Manar, Tunis, Tunisia
| | - Imene-Hadda Ouzari
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Physiques et Naturelles de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Abdelwaheb Chatti
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et Technologies des Eaux Usées, Technopole Borj Cedria, BP 273, 8020, Soliman, Tunisia
- Unite de Biochimie des Lipides et Interactions des Macromolécules en Biologie (03/UR/0902), Laboratoire de Biochimie et Biologie Moléculaire, Faculté des Sciences de Bizerte, Zarzouna, 7021, Bizerte, Tunisia
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4
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Romano KP, Bagnall J, Warrier T, Sullivan J, Ferrara K, Orzechowski M, Nguyen P, Raines K, Livny J, Shoresh N, Hung D. Perturbation-Specific Transcriptional Mapping for unbiased target elucidation of antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590978. [PMID: 38712067 PMCID: PMC11071498 DOI: 10.1101/2024.04.25.590978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The rising prevalence of antibiotic resistance threatens human health. While more sophisticated strategies for antibiotic discovery are being developed, target elucidation of new chemical entities remains challenging. In the post-genomic era, expression profiling can play an important role in mechanism-of-action (MOA) prediction by reporting on the cellular response to perturbation. However, the broad application of transcriptomics has yet to fulfill its promise of transforming target elucidation due to challenges in identifying the most relevant, direct responses to target inhibition. We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether chemical or genetic, will elicit similar transcriptional responses. Using this approach, we elucidated the MOAs of three new molecules with activity against Pseudomonas aeruginosa by comparing their expression profiles to those of a reference set of antimicrobial compounds with known MOAs. We also show that transcriptional responses to small molecule inhibition resemble those resulting from genetic depletion of essential targets by CRISPRi by PerSpecTM, demonstrating proof-of-concept that correlations between expression profiles of small molecule and genetic perturbations can facilitate MOA prediction when no chemical entities exist to serve as a reference. Empowered by PerSpecTM, this work lays the foundation for an unbiased, readily scalable, systematic reference-based strategy for MOA elucidation that could transform antibiotic discovery efforts.
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5
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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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6
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Dini S, Bekhit AEDA, Roohinejad S, Vale JM, Agyei D. The Physicochemical and Functional Properties of Biosurfactants: A Review. Molecules 2024; 29:2544. [PMID: 38893420 PMCID: PMC11173842 DOI: 10.3390/molecules29112544] [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: 04/05/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Surfactants, also known as surface-active agents, have emerged as an important class of compounds with a wide range of applications. However, the use of chemical-derived surfactants must be restricted due to their potential adverse impact on the ecosystem and the health of human and other living organisms. In the past few years, there has been a growing inclination towards natural-derived alternatives, particularly microbial surfactants, as substitutes for synthetic or chemical-based counterparts. Microbial biosurfactants are abundantly found in bacterial species, predominantly Bacillus spp. and Pseudomonas spp. The chemical structures of biosurfactants involve the complexation of lipids with carbohydrates (glycolipoproteins and glycolipids), peptides (lipopeptides), and phosphates (phospholipids). Lipopeptides, in particular, have been the subject of extensive research due to their versatile properties, including emulsifying, antimicrobial, anticancer, and anti-inflammatory properties. This review provides an update on research progress in the classification of surfactants. Furthermore, it explores various bacterial biosurfactants and their functionalities, along with their advantages over synthetic surfactants. Finally, the potential applications of these biosurfactants in many industries and insights into future research directions are discussed.
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Affiliation(s)
- Salome Dini
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand; (S.D.); (A.E.-D.A.B.)
| | - Alaa El-Din A. Bekhit
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand; (S.D.); (A.E.-D.A.B.)
| | - Shahin Roohinejad
- Research and Development Division, Zoom Essence Inc., 1131 Victory Place, Hebron, KY 41048, USA (J.M.V.)
| | - Jim M. Vale
- Research and Development Division, Zoom Essence Inc., 1131 Victory Place, Hebron, KY 41048, USA (J.M.V.)
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand; (S.D.); (A.E.-D.A.B.)
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7
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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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8
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Smith IP, Pedebos C, Khalid S. Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics. J Phys Chem B 2024; 128:2717-2733. [PMID: 38457439 PMCID: PMC10961723 DOI: 10.1021/acs.jpcb.3c07985] [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: 12/06/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes encapsulate the aqueous periplasm, which contains the cell wall. Little is known about the mechanisms via which antimicrobial peptides move through the periplasm from the outer membrane to their site of action, the inner membrane. We utilize all-atom molecular dynamics to study two antimicrobial peptides, polymyxins B1 and E, within models of the E. coli periplasm crowded to different extents. In a simple chemical environment, both PMB1 and PME bind irreversibly to the cell wall. The presence of specific macromolecules leads to competition with the polymyxins for cell wall interaction sites, resulting in polymyxin dissociation from the cell wall. Chemical complexity also impacts interactions between polymyxins and Braun's lipoprotein; thus, the interaction modes of lipoprotein antibiotics within the periplasm are dependent upon the nature of the other species present.
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Affiliation(s)
- Iain P.
S. Smith
- School of
Chemistry, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Conrado Pedebos
- Programa
de Pós-Graduação em Biociências (PPGBio), Universidade Federal de Ciências da Saúde
de Porto Alegre—UFCSPA, Porto Alegre 90050-170, Brazil
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| | - Syma Khalid
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
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9
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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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10
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Mitchell ME, Gatzeva-Topalova PZ, Bargmann AD, Sammakia T, Sousa MC. Targeting the Conformational Change in ArnA Dehydrogenase for Selective Inhibition of Polymyxin Resistance. Biochemistry 2023; 62:2216-2227. [PMID: 37410993 PMCID: PMC10914316 DOI: 10.1021/acs.biochem.3c00227] [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] [Indexed: 07/08/2023]
Abstract
Polymyxins are important last resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative pathogens. However, pathogens have acquired resistance to polymyxins through a pathway that modifies lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N). Inhibition of this pathway is, therefore, a desirable strategy to combat polymyxin resistance. The first pathway-specific reaction is an NAD+-dependent oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcA) catalyzed by the dehydrogenase domain of ArnA (ArnA_DH). We present the crystal structure of Salmonella enterica serovar typhimurium ArnA in complex with UDP-GlcA showing that binding of the sugar nucleotide is sufficient to trigger a conformational change conserved in bacterial ArnA_DHs but absent in its human homologs, as confirmed by structure and sequence analysis. Ligand binding assays show that the conformational change is essential for NAD+ binding and catalysis. Enzyme activity and binding assays show that (i) UDP-GlcA analogs lacking the 6' carboxylic acid bind the enzyme but fail to trigger the conformational change, resulting in poor inhibition, and (ii) the uridine monophosphate moiety of the substrate provides most of the ligand binding energy. Mutation of asparagine 492 to alanine (N492A) disrupts the ability of ArnA_DH to undergo the conformational change while retaining substrate binding, suggesting that N492 is involved in sensing the 6' carboxylate in the substrate. These results identify the UDP-GlcA-induced conformational change in ArnA_DH as an essential mechanistic step in bacterial enzymes, providing a platform for selective inhibition.
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Affiliation(s)
- Megan E. Mitchell
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
| | | | - Austin D. Bargmann
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
| | - Tarek Sammakia
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
| | - Marcelo C. Sousa
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309
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11
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Zhang J, Ouyang X, Zhang F, Li B, Chang L, Yang P, Mao W, Gou S, Zhang Y, Liu H, Yao J, Ni J. Structure-Activity Relationship Study of Antimicrobial Peptide PE2 Delivered Novel Linear Derivatives with Potential of Eradicating Biofilms and Low Incidence of Drug Resistance. J Med Chem 2023. [PMID: 37368962 DOI: 10.1021/acs.jmedchem.3c00181] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The ongoing emergence of antibiotic-resistant pathogens had been dramatically stimulating and accelerating the need for new drugs. PE2 is a kind of cyclic lipopeptide with broad-spectrum antimicrobial activity. Herein, its structure-activity relationship was systematically investigated by employing 4 cyclic analogues and 23 linear analogues for the first time. The screened linear analogues 26 and 27 bearing different fatty acyls at N-termini and a Tyr residue at the 9th position had superior potency compared to the cyclic analogues and showed equivalent antimicrobial activity compared with PE2. Notably, 26 and 27 exhibited significant ability against multidrug-resistant bacteria, favorable resistance to protease, excellent performance against biofilm, low drug resistance, and high effectiveness against the mice pneumonia model. The antibacterial mechanisms of PE2 and linear derivatives 26 and 27 were also preliminarily explored in this study. As described above, 26 and 27 are promising antimicrobial candidates for the treatment of infections associated with drug-resistant bacteria.
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Affiliation(s)
- Jingying Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xu Ouyang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Fangyan Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Beibei Li
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Linlin Chang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Ping Yang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Wenbo Mao
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Sanhu Gou
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yun Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hui Liu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
| | - Jia Yao
- The First Hospital of Lanzhou University, Lanzhou 730000, P. R. China
| | - Jingman Ni
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Institute of Pharmaceutics, School of Pharmacy, and Research Unit of Peptide Science, Chinese Academy of Medical Sciences, 2019RU066, Lanzhou University, Lanzhou 730000, P. R. China
- Chinese Academy of Medical Sciences, Peking Union Medical College, Institute of Materia Medica, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China
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12
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Fux AC, Casonato Melo C, Michelini S, Swartzwelter BJ, Neusch A, Italiani P, Himly M. Heterogeneity of Lipopolysaccharide as Source of Variability in Bioassays and LPS-Binding Proteins as Remedy. Int J Mol Sci 2023; 24:ijms24098395. [PMID: 37176105 PMCID: PMC10179214 DOI: 10.3390/ijms24098395] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Lipopolysaccharide (LPS), also referred to as endotoxin, is the major component of Gram-negative bacteria's outer cell wall. It is one of the main types of pathogen-associated molecular patterns (PAMPs) that are known to elicit severe immune reactions in the event of a pathogen trespassing the epithelial barrier and reaching the bloodstream. Associated symptoms include fever and septic shock, which in severe cases, might even lead to death. Thus, the detection of LPS in medical devices and injectable pharmaceuticals is of utmost importance. However, the term LPS does not describe one single molecule but a diverse class of molecules sharing one common feature: their characteristic chemical structure. Each bacterial species has its own pool of LPS molecules varying in their chemical composition and enabling the aggregation into different supramolecular structures upon release from the bacterial cell wall. As this heterogeneity has consequences for bioassays, we aim to examine the great variability of LPS molecules and their potential to form various supramolecular structures. Furthermore, we describe current LPS quantification methods and the LPS-dependent inflammatory pathway and show how LPS heterogeneity can affect them. With the intent of overcoming these challenges and moving towards a universal approach for targeting LPS, we review current studies concerning LPS-specific binders. Finally, we give perspectives for LPS research and the use of LPS-binding molecules.
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Affiliation(s)
- Alexandra C Fux
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
- Chemical Biology Department, R&D Reagents, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Cristiane Casonato Melo
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
- Chemical Biology Department, R&D Reagents, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Sara Michelini
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Benjamin J Swartzwelter
- Department of Microbiology, Immunology, and Pathology, 1601 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - Andreas Neusch
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Paola Italiani
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche (CNR), Via P. Castellino 111, 80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Naples, Italy
| | - Martin Himly
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
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13
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Han X, Cui AL, Yang HX, Wu L, Wei R, Liu Q, Li ZR, Hu HY. Polymyxin-based fluorescent probes to combat Gram-negative antimicrobial resistance. Talanta 2023; 260:124576. [PMID: 37148689 DOI: 10.1016/j.talanta.2023.124576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Reliable diagnostic approaches especially those targeting critical Gram-negative bacteria are urgently needed for the prevention of antimicrobial resistance. Polymyxin B (PMB) which specifically targets the outer membrane of Gram-negative bacteria is the last-line antibiotic against life-threatening multidrug-resistant Gram-negative bacteria. However, increasing number of studies have reported the spread of PMB-resistant strains. With the aim to specifically detect Gram-negative bacteria and potentially reduce the irrational use of antibiotics, we herein rationally designed two Gram-negative bacteria specific fluorescent probes based on our previous activity-toxicity optimization of PMB. The in vitro probe PMS-Dns showed fast and selective labeling of Gram-negative pathogens in complex biological cultures. Subsequently, we constructed the caged in vivo fluorescent probe PMS-Cy-NO2 by conjugating bacterial nitroreductase (NTR)-activatable positive charged hydrophobic near-infrared (NIR) fluorophore with polymyxin scaffold. Significantly, PMS-Cy-NO2 exhibited excellent Gram-negative bacterial detection capability with the differentiation between Gram-positive and Gram-negative in a mouse skin infection model.
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Affiliation(s)
- Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - A-Long Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - He-Xian Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Lingling Wu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Rao Wei
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qian Liu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Zhuo-Rong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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14
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Romano K, Hung D. Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119407. [PMID: 36543281 PMCID: PMC9922520 DOI: 10.1016/j.bbamcr.2022.119407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.
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Affiliation(s)
- K.P. Romano
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - D.T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,Corresponding author at: The Broad Institute of MIT and Harvard, Cambridge, MA, USA. (D.T. Hung)
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15
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Cai X, Orsi M, Capecchi A, Köhler T, van Delden C, Javor S, Reymond JL. An intrinsically disordered antimicrobial peptide dendrimer from stereorandomized virtual screening. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101161. [PMID: 36632208 PMCID: PMC9780108 DOI: 10.1016/j.xcrp.2022.101161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Membrane-disruptive amphiphilic antimicrobial peptides behave as intrinsically disordered proteins by being unordered in water and becoming α-helical in contact with biological membranes. We recently discovered that synthesizing the α-helical antimicrobial peptide dendrimer L-T25 ((KL)8(KKL)4(KLL)2 KKLL) using racemic amino acids to form stereorandomized sr-T25, an analytically pure mixture of all possible diastereoisomers of L-T25, preserved antibacterial activity but abolished hemolysis and cytotoxicity, pointing to an intrinsically disordered antibacterial conformation and an α-helical cytotoxic conformation. In this study, to identify non-toxic intrinsically disordered homochiral antimicrobial peptide dendrimers (AMPDs), we surveyed sixty-three sr-analogs of sr-T25 selected by virtual screening. One of the analogs, sr-X18 ((KL)8(KLK)4(KLL)2 KLLL), lost antibacterial activity as L-enantiomer and became hemolytic due to α-helical folding. By contrast, the L- and D-enantiomers of sr-X22 ((KL)8(KL)4(KKLL)2 KLKK) were equally antibacterial, non-hemolytic, and non-toxic, implying an intrinsically disordered bioactive conformation. Screening stereorandomized libraries may be generally useful to identify or optimize intrinsically disordered bioactive peptides.
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Affiliation(s)
- Xingguang Cai
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Markus Orsi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Alice Capecchi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Sacha Javor
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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16
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Wang Y, Wu P, Liu F, Chen J, Xue J, Qin Y, Chen F, Wang S, Ji L. Design, synthesis, and biological evaluation of membrane-active honokiol derivatives as potent antibacterial agents. Eur J Med Chem 2022; 240:114593. [PMID: 35820350 DOI: 10.1016/j.ejmech.2022.114593] [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: 04/17/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 11/19/2022]
Abstract
Infections caused by drug-resistant bacteria have emerged to be one of the greatest threats to global public health, and new antimicrobial agents with novel mechanisms of action hence are in an urgent need to combat bacterial resistance. Herein, we reported the design, synthesis, and antibacterial evaluation of novel honokiol derivatives as mimics of antimicrobial peptides (AMPs). These mimics showed potent antimicrobial properties against Gram-positive bacteria. Among them, the most promising compound 13b exhibited excellent antibacterial activity, rapid bactericidal properties, avoidance of antibiotic resistance, and weak hemolytic and cytotoxic activities. In addition, compound 13b not only inhibited the biofilm formation but also destroy the preformed biofilm. Mechanism studies further revealed that compound 13b killed bacteria rapidly by interrupting the bacterial membrane. More intriguingly, compound 13b exhibited potent in vivo antibacterial efficacy in a mouse septicemia model induced by Staphylococcus aureus ATCC43300. These results highlight the potential of 13b to be used as therapeutic agents.
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Affiliation(s)
- Yinhu Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China.
| | - Ping Wu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Fangquan Liu
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Junjie Chen
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Jie Xue
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Yinhui Qin
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Fang Chen
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Shuo Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China.
| | - Lusha Ji
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China.
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17
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Blair JMA, Zeth K, Bavro VN, Sancho-Vaello E. The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Rev 2022; 46:6617596. [PMID: 35749576 PMCID: PMC9629497 DOI: 10.1093/femsre/fuac032] [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: 12/16/2021] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.
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Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Enea Sancho-Vaello
- Corresponding author. College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. E-mail:
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18
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A synthetic lipopeptide targeting top-priority multidrug-resistant Gram-negative pathogens. Nat Commun 2022; 13:1625. [PMID: 35338128 PMCID: PMC8956739 DOI: 10.1038/s41467-022-29234-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 03/07/2022] [Indexed: 11/08/2022] Open
Abstract
The emergence of multidrug-resistant (MDR) Gram-negative pathogens is an urgent global medical challenge. The old polymyxin lipopeptide antibiotics (polymyxin B and colistin) are often the only therapeutic option due to resistance to all other classes of antibiotics and the lean antibiotic drug development pipeline. However, polymyxin B and colistin suffer from major issues in safety (dose-limiting nephrotoxicity, acute toxicity), pharmacokinetics (poor exposure in the lungs) and efficacy (negligible activity against pulmonary infections) that have severely limited their clinical utility. Here we employ chemical biology to systematically optimize multiple non-conserved positions in the polymyxin scaffold, and successfully disconnect the therapeutic efficacy from the toxicity to develop a new synthetic lipopeptide, structurally and pharmacologically distinct from polymyxin B and colistin. This resulted in the clinical candidate F365 (QPX9003) with superior safety and efficacy against lung infections caused by top-priority MDR pathogens Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae. Polymyxins are often the last therapeutic option for multidrug-resistant (MDR) bacteria, but have suboptimal safety and efficacy. Here the authors report the discovery and development of a synthetic lipopeptide with an improved safety and efficacy against top-priority MDR Gram-negative pathogens.
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19
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Sun Y, Deng Z, Jiang X, Yuan B, Yang K. Interactions between polymyxin B and various bacterial membrane mimics: A molecular dynamics study. Colloids Surf B Biointerfaces 2021; 211:112288. [PMID: 34942463 DOI: 10.1016/j.colsurfb.2021.112288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/21/2021] [Accepted: 12/11/2021] [Indexed: 11/17/2022]
Abstract
Polymyxin B (PMB) is clinically used as a last-line therapy against life-threatening Gram-negative "superbugs". However, thorough understanding of the membrane actions of PMB at a molecular level is still lacking. In this work, a variety of bacterial membrane mimics with varying lipid compositions were built, and their interactions with PMB were systematically investigated using coarse-grained molecular dynamics simulation. PMB demonstrated characteristic preference to specific lipid species during its interaction with different membrane systems, such as the rough mutant lipipolysacchrides (Re LPS) preference in an outer membrane (OM) or the cardiolipin and POPG affinity in an inner membrane (IM). As a result of the lipid-specific actions, complicated membrane interaction states of PMB were observed, including adsorption on the OM surface. In contrast, for the IM or a mutative OM containing "impurity lipids" like POPE, POPG or lipid A, it could insert into the membrane via its acyl chain. Such actions of PMB influence the structure and lipid mobility of the membrane. In particular, the OM-bound PMB breaks the synchronous movement of Re LPS molecules in the outer leaflet and makes them diffuse more randomly, while its insertion into IM blocks the phospholipid diffusion and makes the membrane more homogeneous in the trajectory space. Our results provide insight into the action mechanism of PMB at a membrane level and a foundation for developing novel and safer polymyxin strategies for better clinical use.
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Affiliation(s)
- Yuliang Sun
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Zhixiong Deng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, Shandong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China.
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, Jiangsu, China.
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20
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Weerakoon D, Petrov K, Pedebos C, Khalid S. Polymyxin B1 within the E. coli cell envelope: insights from molecular dynamics simulations. Biophys Rev 2021; 13:1061-1070. [PMID: 35047090 PMCID: PMC8724489 DOI: 10.1007/s12551-021-00869-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/22/2021] [Indexed: 11/25/2022] Open
Abstract
Polymyxins are used as last-resort antibiotics, where other treatments have been ineffectual due to antibiotic resistance. However, resistance to polymyxins has also been now reported, therefore it is instructive to characterise at the molecular level, the mechanisms of action of polymyxins. Here we review insights into these mechanisms from molecular dynamics simulations and discuss the utility of simulations as a complementary technique to experimental methodologies.
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Affiliation(s)
| | - Kamen Petrov
- Hertford College, University of Oxford, Oxford, OX1 3BW UK
| | - Conrado Pedebos
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
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21
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Goode A, Yeh V, Bonev BB. Interactions of polymyxin B with lipopolysaccharide-containing membranes. Faraday Discuss 2021; 232:317-329. [PMID: 34550139 PMCID: PMC8704168 DOI: 10.1039/d1fd00036e] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial resistance to antibiotics constantly remodels the battlefront between infections and antibiotic therapy. Polymyxin B, a cationic peptide with an anti-Gram-negative spectrum of activity is re-entering use as a last resort measure and as an adjuvant. We use fluorescence dequenching to investigate the role of the rough chemotype bacterial lipopolysaccharide from E. coli BL21 as a molecular facilitator of membrane disruption by LPS. The minimal polymyxin B/lipid ratio required for leakage onset increased from 5.9 × 10−4 to 1.9 × 10−7 in the presence of rLPS. We confirm polymyxin B activity against E. coli BL21 by the agar diffusion method and determined a MIC of 291 μg ml−1. Changes in lipid membrane stability and dynamics in response to polymyxin and the role of LPS are investigated by 31P NMR and high resolution 31P MAS NMR relaxation is used to monitor selective molecular interactions between polymyxin B and rLPS within bilayer lipid membranes. We observe a strong facilitating effect from rLPS on the membrane lytic properties of polymyxin B and a specific, pyrophosphate-mediated process of molecular recognition of LPS by polymyxin B. Polymyxin B uses bacterial LPS as docking receptor to cross the outer membrane.![]()
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Affiliation(s)
- Alice Goode
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Vivien Yeh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Boyan B Bonev
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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22
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Manzo G, Gianfanti F, Hind CK, Allison L, Clarke M, Hohenbichler J, Limantoro I, Martin B, Do Carmo Silva P, Ferguson PM, Hodgson-Casson AC, Fleck RA, Sutton JM, Phoenix DA, Mason AJ. Impacts of Metabolism and Organic Acids on Cell Wall Composition and Pseudomonas aeruginosa Susceptibility to Membrane Active Antimicrobials. ACS Infect Dis 2021; 7:2310-2323. [PMID: 34329558 DOI: 10.1021/acsinfecdis.1c00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reliable antimicrobial susceptibility testing is essential in informing both clinical antibiotic therapy decisions and the development of new antibiotics. Mammalian cell culture media have been proposed as an alternative to bacteriological media, potentially representing some critical aspects of the infection environment more accurately. Here, we use a combination of NMR metabolomics and electron microscopy to investigate the response of Escherichia coli and Pseudomonas aeruginosa to growth in differing rich media to determine whether and how this determines metabolic strategies, the composition of the cell wall, and consequently susceptibility to membrane active antimicrobials including colistin and tobramycin. The NMR metabolomic approach is first validated by characterizing the expected E. coli acid stress response to fermentation and the accompanying changes in the cell wall composition, when cultured in glucose rich mammalian cell culture media. Glucose is not a major carbon source for P. aeruginosa but is associated with a response to osmotic stress and a modest increase in colistin tolerance. Growth of P. aeruginosa in a range of bacteriological media is supported by consumption of formate, an important electron donor in anaerobic respiration. In mammalian cell culture media, however, the overall metabolic strategy of P. aeruginosa is instead dependent on consumption of glutamine and lactate. Formate doping of mammalian cell culture media does not alter the overall metabolic strategy but is associated with polyamine catabolism, remodelling of both inner and outer membranes, and a modest sensitization of P. aeruginosa PAO1 to colistin. Further, in a panel of P. aeruginosa isolates an increase between 2- and 3-fold in sensitivity to tobramycin is achieved through doping with other organic acids, notably propionate which also similarly enhances the activity of colistin. Organic acids are therefore capable of nonspecifically influencing the potency of membrane active antimicrobials.
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Affiliation(s)
- Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Federico Gianfanti
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Charlotte K. Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Leanne Allison
- Centre for Ultrastructural Imaging, Guy’s Campus, King’s College London, London SE1 1UL, United Kingdom
| | - Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Julia Hohenbichler
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Ilene Limantoro
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Bethany Martin
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Phoebe Do Carmo Silva
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - Philip M. Ferguson
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Alice C. Hodgson-Casson
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Roland A. Fleck
- Centre for Ultrastructural Imaging, Guy’s Campus, King’s College London, London SE1 1UL, United Kingdom
| | - J. Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG United Kingdom
| | - David A. Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London SE1 0AA, United Kingdom
| | - A. James Mason
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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23
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Khoshbayan A, Shariati A, Shahmoradi S, Baseri Z, Mozafari H, Darban-Sarokhalil D. Prevalence and molecular mechanisms of colistin resistance in Acinetobacter baumannii clinical isolates in Tehran, Iran. Acta Microbiol Immunol Hung 2021. [PMID: 34370684 DOI: 10.1556/030.2021.01420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/28/2021] [Indexed: 01/02/2023]
Abstract
Colistin is one of the last remaining active antibiotics against multidrug resistant Gram-negative bacteria. However, several recent studies reported colistin-resistant (ColR) Acinetobacter baumannii from different countries. In the current study, we investigated molecular mechanisms involved in colistin resistance in A. baumannii isolates from different clinical samples.A total of 110 clinical A. baumannii isolates were collected from two hospitals in Tehran. Minimum inhibitory concentrations (MICs) were determined by broth microdilution according to the Clinical and Laboratory Standards Institute. For the ColR isolates, mutation was detected in pmrA, pmrB, lpxA, lpxC, and lpxD genes using the polymerase chain reaction (PCR) and sequencing. Moreover, the relative expression of the pmrC gene was calculated using quantitative reverse transcription PCR. Three colistin resistant isolates were identified with MIC between 8 and 16 μg/mL and were resistant to all the tested antimicrobial agents. All the three isolates had a mutation in the pmrB, pmrA, lpxA, lpxD, and lpxC genes. Moreover, the overexpression of pmrC gene was observed in all isolates. Our results showed that the upregulation of the PmrAB two component system was the primary mechanism linked to colistin resistance among the studied colistin resistant A. baumannii isolates.
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Affiliation(s)
- Amin Khoshbayan
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samane Shahmoradi
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohre Baseri
- 2Department of Pathology and Laboratory Medicine, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Haniyeh Mozafari
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- 1Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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24
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Elias R, Duarte A, Perdigão J. A Molecular Perspective on Colistin and Klebsiella pneumoniae: Mode of Action, Resistance Genetics, and Phenotypic Susceptibility. Diagnostics (Basel) 2021; 11:1165. [PMID: 34202395 PMCID: PMC8305994 DOI: 10.3390/diagnostics11071165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/26/2022] Open
Abstract
Klebsiella pneumoniae is a rod-shaped, encapsulated, Gram-negative bacteria associated with multiple nosocomial infections. Multidrug-resistant (MDR) K. pneumoniae strains have been increasing and the therapeutic options are increasingly limited. Colistin is a long-used, polycationic, heptapeptide that has regained attention due to its activity against Gram-negative bacteria, including the MDR K. pneumoniae strains. However, this antibiotic has a complex mode of action that is still under research along with numerous side-effects. The acquisition of colistin resistance is mainly associated with alteration of lipid A net charge through the addition of cationic groups synthesized by the gene products of a multi-genic regulatory network. Besides mutations in these chromosomal genes, colistin resistance can also be achieved through the acquisition of plasmid-encoded genes. Nevertheless, the diversity of molecular markers for colistin resistance along with some adverse colistin properties compromises the reliability of colistin-resistance monitorization methods. The present review is focused on the colistin action and molecular resistance mechanisms, along with specific limitations on drug susceptibility testing for K. pneumoniae.
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Affiliation(s)
- Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Aida Duarte
- Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Monte da Caparica, 2829-511 Almada, Portugal
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
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25
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Aronica PGA, Reid LM, Desai N, Li J, Fox SJ, Yadahalli S, Essex JW, Verma CS. Computational Methods and Tools in Antimicrobial Peptide Research. J Chem Inf Model 2021; 61:3172-3196. [PMID: 34165973 DOI: 10.1021/acs.jcim.1c00175] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that has increased the number of diseases and infections that risk going untreated. There is an urgent need to develop alternative strategies and treatments to address this issue. One class of molecules that is attracting significant interest is that of antimicrobial peptides (AMPs). Their design and development has been aided considerably by the applications of molecular models, and we review these here. These methods include the use of tools to explore the relationships between their structures, dynamics, and functions and the increasing application of machine learning and molecular dynamics simulations. This review compiles resources such as AMP databases, AMP-related web servers, and commonly used techniques, together aimed at aiding researchers in the area toward complementing experimental studies with computational approaches.
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Affiliation(s)
- Pietro G A Aronica
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Lauren M Reid
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ.,MedChemica Ltd, Alderley Park, Macclesfield, Cheshire, U.K. SK10 4TG
| | - Nirali Desai
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Division of Biological and Life Sciences, Ahmedabad University, Central Campus, Ahmedabad, Gujarat, India 380009
| | - Jianguo Li
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Singapore Eye Research Institute, 20 College Road Discovery Tower, Singapore 169856
| | - Stephen J Fox
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Shilpa Yadahalli
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield Southampton, Hampshire, U.K. SO17 1BJ
| | - Chandra S Verma
- Bioinformatics Institute at A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, 637551 Singapore
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26
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Colistin Resistance in Aeromonas spp. Int J Mol Sci 2021; 22:ijms22115974. [PMID: 34205867 PMCID: PMC8199210 DOI: 10.3390/ijms22115974] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/22/2022] Open
Abstract
The increase in the use of antimicrobials such as colistin for the treatment of infectious diseases has led to the appearance of Aeromonas strains resistant to this drug. However, resistance to colistin not only occurs in the clinical area but has also been determined in Aeromonas isolates from the environment or animals, which has been determined by the detection of mcr genes that confer a resistance mechanism to colistin. The variants mcr-1, mcr-3, and mcr-5 have been detected in the genus Aeromonas in animal, environmental, and human fluids samples. In this article, an overview of the resistance to colistin in Aeromonas is shown, as well as the generalities of this molecule and the recommended methods to determine colistin resistance to be used in some of the genus Aeromonas.
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27
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Investigating the action of the microalgal pigment marennine on Vibrio splendidus by in vivo 2H and 31P solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183642. [PMID: 34000261 DOI: 10.1016/j.bbamem.2021.183642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/21/2022]
Abstract
This work investigates the potential probiotic effect of marennine - a natural pigment produced by the diatom Haslea ostrearia - on Vibrio splendidus. These marine bacteria are often considered a threat for aquaculture; therefore, chemical antibiotics can be required to reduce bacterial outbreaks. In vivo2H solid-state NMR was used to probe the effects of marennine on the bacterial membrane in the exponential and stationary phases. Comparisons were made with polymyxin B (PxB) - an antibiotic used in aquaculture and known to interact with Gram(-) bacteria membranes. We also investigated the effect of marennine using 31P solid-state NMR on model membranes. Our results show that marennine has little effect on phospholipid headgroups dynamics, but reduces the acyl chain fluidity. Our data suggest that the two antimicrobial agents perturb V. splendidus membranes through different mechanisms. While PxB would alter the bacterial outer and inner membranes, marennine would act through a membrane stiffening mechanism, without affecting the bilayer integrity. Our study proposes this microalgal pigment, which is harmless for humans, as a potential treatment against vibriosis.
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28
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Lin L, Du Y, Song J, Wang W, Yang C. Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut. Acc Chem Res 2021; 54:2076-2087. [PMID: 33856204 DOI: 10.1021/acs.accounts.1c00068] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As a newly discovered organ, gut microbiota has been extensively studied in the last two decades, with their highly diverse and fundamental roles in the physiology of many organs and systems of the host being gradually revealed. However, most of the current research heavily relies on DNA sequencing-based methodologies. To truly understand the complex physiological and pathological functions demonstrated by commensal and pathogenic gut bacteria, we need more powerful methods and tools, among which imaging strategies suitable for approaching this ecosystem in different settings are one of the most desirable. Although the phrase gut "dark matter" is often used in referring to the unculturability of many gut bacteria, it is also applicable to describing the formidable difficulties in visualizing these microbes in the intestines. To develop suitable and versatile chemical and biological tools for imaging bacteria in the gut, great efforts have been devoted in the past several years.In this Account, we highlight the recent progress made by our group and other laboratories in the development of visualization strategies for commensal microbiota and pathogenic bacteria in the gut. First, we summarize our efforts toward the development of derivatized antibiotic staining probes that directly bind to specific bacterial surface structures for selective labeling of different groups of gut bacteria. Next, metabolic labeling-based imaging strategies, using unnatural amino acids, unnatural sugars, and stable isotopes, for imaging gut bacteria on various scales and in different settings are discussed in detail. We then introduce nucleic acid staining-based bacterial imaging, using either general nucleic acid-binding reagents or selective-labeling techniques (e.g., fluorescence in situ hybridization) to meet the diverse needs in gut microbiota research. This classical imaging strategy has witnessed a renaissance owing to a series of new technical advancements. Furthermore, despite the notorious difficulties of performing genetic manipulations in many commensal gut bacteria, great effort has been made recently in engineering gut bacteria with reporters like fluorescent proteins and acoustic response proteins.Our perspectives on the current limitations of the chemical tools and strategies and the future directions for improvement are also presented. We hope that this Account can offer valuable references to spark new ideas and invite new efforts to help decipher the complex biological and chemical interactions between commensal microbiota and pathogenic bacteria and the hosts.
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Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yahui Du
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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29
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Surur AS, Sun D. Macrocycle-Antibiotic Hybrids: A Path to Clinical Candidates. Front Chem 2021; 9:659845. [PMID: 33996753 PMCID: PMC8120311 DOI: 10.3389/fchem.2021.659845] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022] Open
Abstract
The tale of abate in antibiotics continued defense mechanisms that chaperone the rise of drug-defying superbugs—on the other hand, the astray in antibacterial drug discovery and development. Our salvation lies in circumventing the genesis of resistance. Considering the competitive advantages of antibacterial chemotherapeutic agents equipped with multiple warheads against resistance, the development of hybrids has rejuvenated. The adoption of antibiotic hybrid paradigm to macrocycles has advanced novel chemical entities to clinical trials. The multi-targeted TD-1792, for instance, retained potent antibacterial activities against multiple strains that are resistant to its constituent, vancomycin. Moreover, the antibiotic conjugation of rifamycins has provided hybrid clinical candidates with desirable efficacy and safety profiles. In 2020, the U.S. FDA has granted an orphan drug designation to TNP-2092, a conjugate of rifamycin and fluoroquinolone, for the treatment of prosthetic joint infections. DSTA4637S is a pioneer antibacterial agent under clinical development and represents a novel class of bacterial therapy, that is, antibody–antibiotic conjugates. DSTA4637S is effective against the notorious persistent S. aureus bacteremia, a revelation of the abracadabra potential of antibiotic hybrid approaches.
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Affiliation(s)
- Abdrrahman Shemsu Surur
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
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30
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Li J, Guan D, Chen F, Shi W, Lan L, Huang W. Total and Semisyntheses of Polymyxin Analogues with 2-Thr or 10-Thr Modifications to Decipher the Structure-Activity Relationship and Improve the Antibacterial Activity. J Med Chem 2021; 64:5746-5765. [PMID: 33909428 DOI: 10.1021/acs.jmedchem.0c02217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we report the total and semisyntheses of a series of polymyxin analogues with 2-Thr and 10-Thr modifications to reveal the structure-activity relationship (SAR), which has not been fully elucidated previously. We employed two total-synthetic strategies to facilitate the diversified replacements on 2-Thr or 10-Thr, respectively. Moreover, semisynthetic approaches were utilized to achieve selective esterification of 2-Thr or dual esterification of both 2- and 10-Thr. Based on the results of in vitro antibacterial assays, SAR analysis implicated that the replacement of 2-/10-Thr with amino acids carrying hydrophobic side chains can maintain the activity against Pseudomonas aeruginosa but had varied effects on other tested Gram-negative bacteria. The aminoacetyl esterification on 2-/10-Thr achieved excellent antibacterial activity, and the compound 76 exhibited 2-8-fold higher activity against different strains and lower toxicity toward the HK-2 cell line. This work explored the SAR of polymyxin 2-/10-Thr and provided a promising strategy for the development of novel polymyxin derivatives.
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Affiliation(s)
- Jian Li
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Dongliang Guan
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Feifei Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiwei Shi
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lefu Lan
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 310024, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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31
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Synchrotron-based X-ray fluorescence microscopy reveals accumulation of polymyxins in single human alveolar epithelial cells. Antimicrob Agents Chemother 2021; 65:AAC.02314-20. [PMID: 33649114 PMCID: PMC8092916 DOI: 10.1128/aac.02314-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Intravenous administration of the last-line polymyxins results in poor drug exposure in the lungs and potential nephrotoxicity; while inhalation therapy offers better pharmacokinetics/pharmacodynamics for pulmonary infections by delivering the antibiotic to the infection site directly. However, polymyxin inhalation therapy has not been optimized and adverse effects can occur. This study aimed to quantitatively determine the intracellular accumulation and distribution of polymyxins in single human alveolar epithelial A549 cells. Cells were treated with an iodine-labeled polymyxin probe FADDI-096 (5.0 and 10.0 μM) for 1, 4, and 24 h. Concentrations of FADDI-096 in single A549 cells were determined by synchrotron-based X-ray fluorescence microscopy. Concentration- and time-dependent accumulation of FADDI-096 within A549 cells was observed. The intracellular concentrations (mean ± SEM, n ≥ 189) of FADDI-096 were 1.58 ± 0.11, 2.25 ± 0.10, and 2.46 ± 0.07 mM following 1, 4 and 24 h of treatment at 10 μM, respectively. The corresponding intracellular concentrations following the treatment at 5 μM were 0.05 ± 0.01, 0.24 ± 0.04, and 0.25 ± 0.02 mM (n ≥ 189). FADDI-096 was mainly localized throughout the cytoplasm and nuclear region over 24 h. The intracellular zinc concentration increased in a concentration- and time-dependent manner. This is the first study to quantitatively map the accumulation of polymyxins in human alveolar epithelial cells and provides crucial insights for deciphering the mechanisms of their pulmonary toxicity. Importantly, our results may shed light on the optimization of inhaled polymyxins in patients and the development of new-generation safer polymyxins.
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Abstract
Antibiotic resistance is a major global health challenge and, worryingly, several key Gram negative pathogens can become resistant to most currently available antibiotics. Polymyxins have been revived as a last-line therapeutic option for the treatment of infections caused by multidrug-resistant Gram negative bacteria, in particular Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacterales. Polymyxins were first discovered in the late 1940s but were abandoned soon after their approval in the late 1950s as a result of toxicities (e.g., nephrotoxicity) and the availability of "safer" antibiotics approved at that time. Therefore, knowledge on polymyxins had been scarce until recently, when enormous efforts have been made by several research teams around the world to elucidate the chemical, microbiological, pharmacokinetic/pharmacodynamic, and toxicological properties of polymyxins. One of the major achievements is the development of the first scientifically based dosage regimens for colistin that are crucial to ensure its safe and effective use in patients. Although the guideline has not been developed for polymyxin B, a large clinical trial is currently being conducted to optimize its clinical use. Importantly, several novel, safer polymyxin-like lipopeptides are developed to overcome the nephrotoxicity, poor efficacy against pulmonary infections, and narrow therapeutic windows of the currently used polymyxin B and colistin. This review discusses the latest achievements on polymyxins and highlights the major challenges ahead in optimizing their clinical use and discovering new-generation polymyxins. To save lives from the deadly infections caused by Gram negative "superbugs," every effort must be made to improve the clinical utility of the last-line polymyxins. SIGNIFICANCE STATEMENT: Antimicrobial resistance poses a significant threat to global health. The increasing prevalence of multidrug-resistant (MDR) bacterial infections has been highlighted by leading global health organizations and authorities. Polymyxins are a last-line defense against difficult-to-treat MDR Gram negative pathogens. Unfortunately, the pharmacological information on polymyxins was very limited until recently. This review provides a comprehensive overview on the major achievements and challenges in polymyxin pharmacology and clinical use and how the recent findings have been employed to improve clinical practice worldwide.
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Affiliation(s)
- Sue C Nang
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Mohammad A K Azad
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Tony Velkov
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Qi Tony Zhou
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
| | - Jian Li
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia (S.C.N., M.A.K.A., J.L.); Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia (T.V.); and Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana (Q.T.Z.)
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33
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Jiang L, Zhu Y, Luan P, Xu J, Ru G, Fu JG, Sang N, Xiong Y, He Y, Lin GQ, Wang J, Zhang J, Li R. Bacteria -Anchoring Hybrid Liposome Capable of Absorbing Multiple Toxins for Antivirulence Therapy of Escherichia coli Infection. ACS NANO 2021; 15:4173-4185. [PMID: 33606516 DOI: 10.1021/acsnano.0c04800] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antivirulence therapy by cell membrane coated nanoparticles has shown promise against bacterial infections. However, current approaches remain unsatisfactory when facing Escherichia coli (E. coli) infections, since the E. coli secretes multiple bacterial toxins including endotoxins and exotoxins that are challenging to eliminate simultaneously. What is worse, the absorptive scavengers normally rely on random contact of the diffuse toxins, which is not efficient. For the current cell membrane coated platform, the single type of cell membrane cannot fully meet the detoxing requirement facing multiple toxins. To address these problems, a polymyxin B (PMB)-modified, red blood cell (RBC)-mimetic hybrid liposome (P-RL) was developed. The P-RL was fabricated succinctly through fusion of PMB-modified lipids and the RBC membranes. By the strong interaction between PMB and the E. coli membrane, P-RL could attach and anchor to the E. coli; attributed to the fused RBC membrane and modified PMB, the P-RL could then efficiently neutralize both endotoxins and exotoxins from the toxin fountainhead. In vitro and in vivo results demonstrated the P-RL had a significant anchoring effect to E. coli. Moreover, compared with the existing RBC vesicles or PMB-modified liposomes, P-RL exhibited a superior therapeutic effect against RBC hemolysis, macrophage activation, and a mixed-toxin infection in mice. Potently, P-RL could inhibit E. coli O157:H7-induced skin damage, intestinal infection, and mouse death. Overall, the P-RL could potentially improve the detoxing efficiency and markedly expand the detoxification spectrum of current antivirulence systems, which provides different insights into drug-resistant E. coli treatment.
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Affiliation(s)
- Lixian Jiang
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuying Zhu
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Pengwei Luan
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiazhen Xu
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ge Ru
- NMPA Key Laboratory for Monitoring and Evaluation of Cosmetics, Shanghai Institute for Food and Drug Control, Shanghai 201203, China
| | - Jian-Guo Fu
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Nina Sang
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yang Xiong
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Yuwei He
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Guo-Qiang Lin
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianxin Wang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jiange Zhang
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ruixiang Li
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 311402, China
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
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Siriwardena T, Gan BH, Köhler T, van Delden C, Javor S, Reymond JL. Stereorandomization as a Method to Probe Peptide Bioactivity. ACS CENTRAL SCIENCE 2021; 7:126-134. [PMID: 33532575 PMCID: PMC7845017 DOI: 10.1021/acscentsci.0c01135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 06/01/2023]
Abstract
Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (sr) peptides, containing up to billions of different stereoisomers, as well-defined single HPLC peaks, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane-disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane-disruptive, and antibiofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogues of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane-disruptive and lipopolysaccharide-neutralizing activity, pointing to the existence of additional targets.
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Affiliation(s)
- Thissa
N. Siriwardena
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Sacha Javor
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Metier C, Dow J, Wootton H, Lynham S, Wren B, Wagner GK. Profiling of Haemophilus influenzae strain R2866 with carbohydrate-based covalent probes. Org Biomol Chem 2021; 19:476-485. [PMID: 33355321 DOI: 10.1039/d0ob01971b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the application of four covalent probes based on anomerically pure d-galactosamine and d-glucosamine scaffolds for the profiling of Haemophilus influenzae strain R2866. The probes have been used successfully for the labelling of target proteins not only in cell lysates, but also in intact cells. Differences in the labelling patterns between lysates and intact cells indicate that the probes can penetrate into the periplasm, but not the cytoplasm of H. influenzae. Analysis of selected target proteins by LC-MS/MS suggests predominant labelling of nucleotide-binding proteins, including several known antibacterial drug targets. Our protocols will aid the identification of molecular determinants of bacterial pathogenicity in Haemophilus influenzae and other bacterial pathogens.
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Affiliation(s)
- Camille Metier
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Jennifer Dow
- London School of Hygiene and Tropical Medicine, Department of Infection Biology, Keppel Street, London, WC1E, 7HT, UK
| | - Hayley Wootton
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Brendan Wren
- London School of Hygiene and Tropical Medicine, Department of Infection Biology, Keppel Street, London, WC1E, 7HT, UK
| | - Gerd K Wagner
- Queen's University Belfast, School of Pharmacy, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK.
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36
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Gan BH, Cai X, Javor S, Köhler T, Reymond JL. Synergistic Effect of Propidium Iodide and Small Molecule Antibiotics with the Antimicrobial Peptide Dendrimer G3KL against Gram-Negative Bacteria. Molecules 2020; 25:E5643. [PMID: 33266085 PMCID: PMC7730455 DOI: 10.3390/molecules25235643] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/22/2022] Open
Abstract
There is an urgent need to develop new antibiotics against multidrug-resistant bacteria. Many antimicrobial peptides (AMPs) are active against such bacteria and often act by destabilizing membranes, a mechanism that can also be used to permeabilize bacteria to other antibiotics, resulting in synergistic effects. We recently showed that G3KL, an AMP with a multibranched dendritic topology of the peptide chain, permeabilizes the inner and outer membranes of Gram-negative bacteria including multidrug-resistant strains, leading to efficient bacterial killing. Here, we show that permeabilization of the outer and inner membranes of Pseudomonas aeruginosa by G3KL, initially detected using the DNA-binding fluorogenic dye propidium iodide (PI), also leads to a synergistic effect between G3KL and PI in this bacterium. We also identify a synergistic effect between G3KL and six different antibiotics against the Gram-negative Klebsiella pneumoniae, against which G3KL is inactive.
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Affiliation(s)
- Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Xingguang Cai
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland;
- Service of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
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Ryu JS, Im SH, Kang YK, Kim YS, Chung HJ. Ultra-fast and universal detection of Gram-negative bacteria in complex samples based on colistin derivatives. Biomater Sci 2020; 8:2111-2119. [PMID: 31967117 DOI: 10.1039/c9bm01926j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gram-negative bacteria are a significant cause of infections acquired in both hospital and community settings, resulting in a high mortality rate worldwide. Currently, a Gram-negative infection is diagnosed by symptom evaluation and is treated with empiric antibiotics which target both Gram-negative and Gram-positive bacteria. A rapid and simple diagnostic method would enable immediate and targeted treatment, while dramatically reducing antibiotic overuse. Herein, we introduce a method utilizing a fluorescent derivative of colistin (COL-FL), that can directly label the Gram-negative cell wall of live bacteria and universally detect the targets within 10 min. By using the COL-FL assay, we achieved the differential labeling of various Gram-negative pathogens related to hospital-acquired infections, which could be subsequently detected via spectrofluorometry and microscopy. Further, we determined that our method can be used for complex samples, such as combinations of multiple bacterial types; bacteria in the presence of mammalian cells; and bacteria with serum components. This assay can be integrated into a simple diagnostic platform for rapid screening tests and the stratification of Gram-negative bacterial infections in the clinic.
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Affiliation(s)
- Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
| | - San Hae Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yoo Kyung Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea. and Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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Neubauer D, Jaśkiewicz M, Sikorska E, Bartoszewska S, Bauer M, Kapusta M, Narajczyk M, Kamysz W. Effect of Disulfide Cyclization of Ultrashort Cationic Lipopeptides on Antimicrobial Activity and Cytotoxicity. Int J Mol Sci 2020; 21:E7208. [PMID: 33003569 PMCID: PMC7582905 DOI: 10.3390/ijms21197208] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Ultrashort cationic lipopeptides (USCLs) are considered to be a promising class of antimicrobials with high activity against a broad-spectrum of microorganisms. However, the majority of these compounds are characterized by significant toxicity toward human cells, which hinders their potential application. To overcome those limitations, several approaches have been advanced. One of these is disulfide cyclization that has been shown to improve drug-like characteristics of peptides. In this article the effect of disulfide cyclization of the polar head of N-palmitoylated USCLs on in vitro biological activity has been studied. Lipopeptides used in this study consisted of three or four basic amino acids (lysine and arginine) and cystine in a cyclic peptide. In general, disulfide cyclization of the lipopeptides resulted in peptides with reduced cytotoxicity. Disulfide-cyclized USCLs exhibited improved selectivity between Candida sp., Gram-positive strains and normal cells in contrast to their linear counterparts. Interactions between selected USCLs and membranes were studied by molecular dynamics simulations using a coarse-grained force field. Moreover, membrane permeabilization properties and kinetics were examined. Fluorescence and transmission electron microscopy revealed damage to Candida cell membrane and organelles. Concluding, USCLs are strong membrane disruptors and disulfide cyclization of polar head can have a beneficial effect on its in vitro selectivity between Candida sp. and normal human cells.
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Affiliation(s)
- Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
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Ayoub Moubareck C. Polymyxins and Bacterial Membranes: A Review of Antibacterial Activity and Mechanisms of Resistance. MEMBRANES 2020; 10:membranes10080181. [PMID: 32784516 PMCID: PMC7463838 DOI: 10.3390/membranes10080181] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022]
Abstract
Following their initial discovery in the 1940s, polymyxin antibiotics fell into disfavor due to their potential clinical toxicity, especially nephrotoxicity. However, the dry antibiotic development pipeline, together with the rising global prevalence of infections caused by multidrug-resistant (MDR) Gram-negative bacteria have both rejuvenated clinical interest in these polypeptide antibiotics. Parallel to the revival of their use, investigations into the mechanisms of action and resistance to polymyxins have intensified. With an initial known effect on biological membranes, research has uncovered the detailed molecular and chemical interactions that polymyxins have with Gram-negative outer membranes and lipopolysaccharide structure. In addition, genetic and epidemiological studies have revealed the basis of resistance to these agents. Nowadays, resistance to polymyxins in MDR Gram-negative pathogens is well elucidated, with chromosomal as well as plasmid-encoded, transferrable pathways. The aims of the current review are to highlight the important chemical, microbiological, and pharmacological properties of polymyxins, to discuss their mechanistic effects on bacterial membranes, and to revise the current knowledge about Gram-negative acquired resistance to these agents. Finally, recent research, directed towards new perspectives for improving these old agents utilized in the 21st century, to combat drug-resistant pathogens, is summarized.
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40
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Yang DH, Liu S, Cao L, Zheng YD, Huang JF, Ge R, He QY, Sun X. Quantitative secretome analysis of polymyxin B resistance in Escherichia coli. Biochem Biophys Res Commun 2020; 530:307-313. [PMID: 32828304 DOI: 10.1016/j.bbrc.2020.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 02/02/2023]
Abstract
Bacterial resistance has become a serious threat to human health. In particular, the gradual development of resistance to polymyxins, the last line of defense for human infections, is a major issue. Secreted proteins contribute to the interactions between bacteria and the environment. In this study, we compared the secretomes of polymyxin B-sensitive and -resistant Escherichia coli strains by data-independent acquisition mass spectrometry. In total, 87 differentially expressed secreted proteins were identified in polymyxin B-resistant E. coli compared to the sensitive strain. A GO enrichment analysis indicated that the differentially expressed proteins were involved in biological processes, including bacterial-type flagellum-dependent cell motility, ion transport, carbohydrate derivative biosynthetic process, cellular response to stimulus, organelle organization, and cell wall organization or biogenesis. The differentially expressed secreted proteins in polymyxin B-resistant bacteria were enriched for multiple pathways, suggesting that the resistance phenotype depends on complex regulatory mechanisms. A potential biomarker or drug target (YebV) was found in polymyxin B-resistant E. coli. This work clarifies the secretome changes associated with the acquisition of polymyxin resistance and may contribute to drug development.
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Affiliation(s)
- Dong-Hong Yang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Shiqin Liu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Linlin Cao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yun-Dan Zheng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Jian-Fang Huang
- Guangdong Province Key Laboratory of Molecule Immunology and Antibody Engineering, Jinan University, Guangzhou, 510632, China
| | - Ruiguang Ge
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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41
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Pi H, Nguyen HT, Venter H, Boileau AR, Woolford L, Garg S, Page SW, Russell CC, Baker JR, McCluskey A, O'Donovan LA, Trott DJ, Ogunniyi AD. In vitro Activity of Robenidine Analog NCL195 in Combination With Outer Membrane Permeabilizers Against Gram-Negative Bacterial Pathogens and Impact on Systemic Gram-Positive Bacterial Infection in Mice. Front Microbiol 2020; 11:1556. [PMID: 32849325 PMCID: PMC7417630 DOI: 10.3389/fmicb.2020.01556] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
Multidrug-resistant (MDR) pathogens, particularly the ESKAPE group (Enterococcus faecalis/faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and Enterobacter spp.), have become a public health threat worldwide. Development of new antimicrobial classes and the use of drugs in combination are potential strategies to treat MDR ESKAPE pathogen infections and promote optimal antimicrobial stewardship. Here, the in vitro antimicrobial activity of robenidine analog NCL195 alone or in combination with different concentrations of three outer membrane permeabilizers [ethylenediaminetetraacetic acid (EDTA), polymyxin B nonapeptide (PMBN), and polymyxin B (PMB)] was further evaluated against clinical isolates and reference strains of key Gram-negative bacteria. NCL195 alone was bactericidal against Neisseria meningitidis and Neisseria gonorrhoeae (MIC/MBC = 32 μg/mL) and demonstrated synergistic activity against P. aeruginosa, E. coli, K. pneumoniae, and Enterobacter spp. strains in the presence of subinhibitory concentrations of EDTA, PMBN, or PMB. The additive and/or synergistic effects of NCL195 in combination with EDTA, PMBN, or PMB are promising developments for a new chemical class scaffold to treat Gram-negative infections. Tokuyasu cryo ultramicrotomy was used to visualize the effect of NCL195 on bioluminescent S. aureus membrane morphology. Additionally, NCL195’s favorable pharmacokinetic and pharmacodynamic profile was further explored in in vivo safety studies in mice and preliminary efficacy studies against Gram-positive bacteria. Mice administered two doses of NCL195 (50 mg/kg) by the intraperitoneal (IP) route 4 h apart showed no adverse clinical effects and no observable histological effects in major organs. In bioluminescent Streptococcus pneumoniae and S. aureus murine sepsis challenge models, mice that received two 50 mg/kg doses of NCL195 4 or 6 h apart exhibited significantly reduced bacterial loads and longer survival times than untreated mice. However, further medicinal chemistry and pharmaceutical development to improve potency, solubility, and selectivity is required before efficacy testing in Gram-negative infection models.
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Affiliation(s)
- Hongfei Pi
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Hang Thi Nguyen
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.,Department of Pharmacology, Toxicology, Internal Medicine and Diagnostics, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Alexandra R Boileau
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Sanjay Garg
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | | | - Cecilia C Russell
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Jennifer R Baker
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Lisa A O'Donovan
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food & Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Abiodun D Ogunniyi
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
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Zhu Y, Lu J, Han M, Jiang X, Azad MAK, Patil NA, Lin Y, Zhao J, Hu Y, Yu HH, Chen K, Boyce JD, Dunstan RA, Lithgow T, Barlow CK, Li W, Schneider‐Futschik EK, Wang J, Gong B, Sommer B, Creek DJ, Fu J, Wang L, Schreiber F, Velkov T, Li J. Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000704. [PMID: 32775156 PMCID: PMC7403960 DOI: 10.1002/advs.202000704] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/28/2020] [Indexed: 05/13/2023]
Abstract
Multidrug-resistant Acinetobacter baumannii is a top-priority pathogen globally and polymyxins are a last-line therapy. Polymyxin dependence in A. baumannii (i.e., nonculturable on agar without polymyxins) is a unique and highly-resistant phenotype with a significant potential to cause treatment failure in patients. The present study discovers that a polymyxin-dependent A. baumannii strain possesses mutations in both lpxC (lipopolysaccharide biosynthesis) and katG (reactive oxygen species scavenging) genes. Correlative multiomics analyses show a significantly remodeled cell envelope and remarkably abundant phosphatidylglycerol in the outer membrane (OM). Molecular dynamics simulations and quantitative membrane lipidomics reveal that polymyxin-dependent growth emerges only when the lipopolysaccharide-deficient OM distinctively remodels with ≥ 35% phosphatidylglycerol, and with "patch" binding on the OM by the rigid polymyxin molecules containing strong intramolecular hydrogen bonding. Rather than damaging the OM, polymyxins bind to the phosphatidylglycerol-rich OM and strengthen the membrane integrity, thereby protecting bacteria from external reactive oxygen species. Dependent growth is observed exclusively with polymyxin analogues, indicating a critical role of the specific amino acid sequence of polymyxins in forming unique structures for patch-binding to bacterial OM. Polymyxin dependence is a novel antibiotic resistance mechanism and the current findings highlight the risk of 'invisible' polymyxin-dependent isolates in the evolution of resistance.
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Affiliation(s)
- Yan Zhu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jing Lu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mei‐Ling Han
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Xukai Jiang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Mohammad A. K. Azad
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Nitin A. Patil
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yu‐Wei Lin
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Jinxin Zhao
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Yang Hu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Heidi H. Yu
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Ke Chen
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - John D. Boyce
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Rhys A. Dunstan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Trevor Lithgow
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | | | - Weifeng Li
- School of Physics and State Key Laboratory of Crystal MaterialsShandong UniversityJinan250100China
| | | | - Jiping Wang
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
| | - Bin Gong
- School of Computer Science and TechnologyShandong UniversityJinan250100China
| | - Bjorn Sommer
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Darren J. Creek
- Drug Delivery, Disposition and DynamicsMonash Institute of Pharmaceutical SciencesMonash UniversityMelbourne3052Australia
| | - Jing Fu
- Department of Mechanical and Aerospace EngineeringMonash UniversityMelbourne3800Australia
| | - Lushan Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdao CampusQingdao266237China
| | - Falk Schreiber
- Department of Computer and Information ScienceUniversity of KonstanzKonstanz78457Germany
| | - Tony Velkov
- Department of Pharmacology and TherapeuticsUniversity of MelbourneMelbourne3010Australia
| | - Jian Li
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityMelbourne3800Australia
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43
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DAPTOMYCIN, its membrane-active mechanism vs. that of other antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183395. [PMID: 32526177 DOI: 10.1016/j.bbamem.2020.183395] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/04/2020] [Accepted: 06/07/2020] [Indexed: 11/23/2022]
Abstract
Over 3000 membrane-active antimicrobial peptides (AMPs) have been discovered, but only three of them have been approved by the U.S. Food and Drug Administration (FDA) for therapeutic applications, i.e., gramicidin, daptomycin and colistin. Of the three approved AMPs, daptomycin is a last-line-of-defense antibiotic for treating Gram-positive infections. However its use has already created bacterial resistance. To search for its substitutes that might counter the resistance, we need to understand its molecular mechanism. The mode of action of daptomycin appears to be causing bacterial membrane depolarization through ion leakage. Daptomycin forms a unique complex with calcium ions and phosphatidylglycerol molecules in membrane at a specific stoichiometric ratio: Dap2Ca3PG2. How does this complex promote ion conduction across the membrane? We hope that biophysics of peptide-membrane interaction can answer this question. This review summarizes the biophysical works that have been done on membrane-active AMPs to understand their mechanisms of action, including gramicidin, daptomycin, and underdeveloped pore-forming AMPs. The analysis suggests that daptomycin forms transient ionophores in the target membranes. We discuss questions that remain to be answered.
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44
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Wang KC, Huang CH, Chang PR, Huang MT, Fang SB. Role of wzxE in Salmonella Typhimurium lipopolysaccharide biosynthesis and interleukin-8 secretion regulation in human intestinal epithelial cells. Microbiol Res 2020; 238:126502. [PMID: 32535400 DOI: 10.1016/j.micres.2020.126502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
Abstract
In Salmonella Typhimurium (S. Typhimurium), lipopolysaccharide (LPS) anchored on the bacterial outer membrane is a major immune stimulus that can broadly activate immune cells and induce innate immune responses. wzxE is involved in bacterial LPS biosynthesis but has rarely been reported in Salmonella; wzxE encodes a flipase that can flip the precursor of LPS across the membrane into the periplasm space. Our preliminary data showed that the wzxE transposon mutant of S. Typhimurium could not significantly adhere to and invade into HEp-2 cells, but the mechanism remains unknown. In this study, we infected human LS174T, Caco-2, HeLa, and THP-1 cells with the wild-type S. Typhimurium strain SL1344, its wzxE mutant, and its complemented strain. wzxE depletion significantly attenuated bacterial adhesion and internalization in the four cell types. In addition, the postinfectious production of interleukin-8 (IL-8) was significantly decreased in the Caco-2 cells infected with the wzxE mutant. Bacterial LPS stained with polymyxin B probe also exhibited a reduced signal in the wzxE mutant. The silver staining of purified LPS demonstrated a significant reduction of the O-antigen (OAg) chain in the wzxE mutant. To confirm the role of OAg in the wzxE mutant during infection, we treated the HT-29 cells with the S. Typhimurium strain SL1344, its wzxE mutant, and their purified LPS, which revealed significantly decreased IL-8 secretion in the HT-29 cells treated with purified LPS from the wzxE mutant and with the wzxE mutant. In conclusion, wzxE mediates LPS biosynthesis and plays a major role in bacterial pathogenesis by regulating OAg flipping.
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Affiliation(s)
- Ke-Chuan Wang
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Chih-Hung Huang
- Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan.
| | - Pei-Ru Chang
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Ming-Te Huang
- Department of Surgery, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan; Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Shiuh-Bin Fang
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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45
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Qiao Y, Geng H, Jiang N, Zhu X, Li C, Cai Q. Polymyxin B–modified upconversion nanoparticles for selective detection of Gram-negative bacteria such as Escherichia coli. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820911266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Upconversion nanoparticles, Yb,Tm,Fe-doped NaYF4 nanoparticles, are synthesized and modified with polymyxin B for the selective detection of Gram-negative bacteria. Polymyxin B, a cyclic cationic antimicrobial peptide which can specifically bind to the lipopolysaccharides of cell wall of Gram-negative bacteria, such as Escherichia coli, is used to target and bind Gram-negative bacteria. The bacteria are then quantified by measuring the fluorescence intensity of the upconversion nanoparticle–bacteria complexes at 801 nm under 980 nm excitation. A limit of detection of 36 CFU/mL is achieved in the detection of Escherichia coli, and Escherichia coli in soybean milk is successfully detected. The limited autofluorescence and photobleaching properties of the upconversion nanoparticles make the proposed method useful for in vivo fluorescence imaging of Gram-negative bacteria.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Hongchao Geng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Ning Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Xingqi Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Chenyi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
| | - Qingyun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, P.R. China
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Swarbrick JD, Karas JA, Li J, Velkov T. Structure of micelle bound cationic peptides by NMR spectroscopy using a lanthanide shift reagent. Chem Commun (Camb) 2020; 56:2897-2900. [PMID: 32037418 DOI: 10.1039/c9cc09207b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
[Tm(DPA)3]3- was used to generate multiple, paramagnetic nuclear Overhauser effect NMR spectra of cationic peptides when weakly bound to a lipopolysaccharide micelle. Increased spectral resolution combined with a marked increase in the number of distance restraints yielded high resolution structures of polymyxin and MSI-594 in the liposaccharide bound state.
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Affiliation(s)
- James D Swarbrick
- Department of Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Gan BH, Siriwardena TN, Javor S, Darbre T, Reymond JL. Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL. ACS Infect Dis 2019; 5:2164-2173. [PMID: 31618574 DOI: 10.1021/acsinfecdis.9b00299] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We recently discovered that peptide dendrimers such as G3KL ((KL)8(KKL)4(KKL)2KKL, K = branching l-lysine) exert strong activity against Gram-negative bacteria including Pseudomonas aeruginosa, Acinetobacter baumannii, and Escherichia coli. Herein, we report a detailed mechanistic study using fluorescence labeled analogs bearing fluorescein (G3KL-Fluo) or dansyl (G3KL-Dansyl), which show a similar bioactivity profile as G3KL. Imaging bacterial killing by super-resolution stimulated emission depletion (STED) microscopy, time-lapse imaging, and transmission electron microscopy (TEM) reveals that the dendrimer localizes at the bacterial membrane, induces membrane depolarization and permeabilization, and destroys the outer leaflet and the inner membrane. G3KL accumulates in bacteria against which it is active; however, it only weakly penetrates into eukaryotic cells without inducing significant toxicity. G3KL furthermore binds to lipopolysaccharide (LPS) and inhibits the LPS induced release of TNF-α by macrophages, similarly to polymyxin B. Taken together, these experiments show that G3KL behaves as a potent membrane disruptive antimicrobial peptide.
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Affiliation(s)
- Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thissa N. Siriwardena
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Mutations in pmrB Confer Cross-Resistance between the LptD Inhibitor POL7080 and Colistin in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.00511-19. [PMID: 31235628 PMCID: PMC6709506 DOI: 10.1128/aac.00511-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Pseudomonas aeruginosa is a major bacterial pathogen associated with a rising prevalence of antibiotic resistance. We evaluated the resistance mechanisms of P. aeruginosa against POL7080, a species-specific, first-in-class antibiotic in clinical trials that targets the lipopolysaccharide transport protein LptD. We isolated a series of POL7080-resistant strains with mutations in the two-component sensor gene pmrB. Pseudomonas aeruginosa is a major bacterial pathogen associated with a rising prevalence of antibiotic resistance. We evaluated the resistance mechanisms of P. aeruginosa against POL7080, a species-specific, first-in-class antibiotic in clinical trials that targets the lipopolysaccharide transport protein LptD. We isolated a series of POL7080-resistant strains with mutations in the two-component sensor gene pmrB. Transcriptomic and confocal microscopy studies support a resistance mechanism shared with colistin, involving lipopolysaccharide modifications that mitigate antibiotic cell surface binding.
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Madhumanchi S, Suedee R, Nakpheng T, Tinpun K, Temboot P, Srichana T. Binding interactions of bacterial lipopolysaccharides to polymyxin B in an amphiphilic carrier 'sodium deoxycholate sulfate'. Colloids Surf B Biointerfaces 2019; 182:110374. [PMID: 31330430 DOI: 10.1016/j.colsurfb.2019.110374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/19/2022]
Abstract
This work presents the outcomes of a comparative study of molecular interactions of polymyxin B (PMB) and F12 and F13 formulations in the mole ratios of 1:2 and 1:3 of PMB:sodium deoxycholate sulfate (SDCS), respectively, and a commercial PMB formulation (CPMB) with lipopolysaccharides (LPS). Several spectroscopic and interfacial studies were performed to obtain LPS-peptide interactions at a molecular level. The fluorescence titrimetry method revealed that the F12 formulation (325 nM) exhibited a lower number of binding sites to the LPS compared to CPMB and F13 as well as PMB alone (537 nM). Similarly, in the presence of LPS, the F12 formulation (88 nm) exhibited smaller particle sizes in the dynamic light scattering study compared to PMB (116 nm), CPMB, and the F13 formulation. An interfacial study and circular dichroism spectroscopy revealed PMB and CPMB insertion into the LPS micelles to destabilize and disrupt the LPS membrane, whereas the F12 and F13 formulations may induce pseudo-aggregation. The NMR and IR studies showed that the presence of SDCS, the hydrophobicity of PMB increased by hydrogen bonding and electrostatic interactions and formed stabilized PMB-SDCS micelles. The PMB-SDCS formulation is likely to release PMB for easy penetration into the lipid membrane and cause disruption of the complex LPS micelles. Furthermore, the PMB-SDCS formulations neutralized and detoxified the LPS micelles with minimal toxicity to normal kidney tubular cells as well as an immortalised kidney cell line. The antimicrobial properties of PMBloaded SDCS nanomicelles were effective against a resistant strain of Pseudomonas aeruginosa.
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Affiliation(s)
- Sreenu Madhumanchi
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand; Molecular Recognition Materials Research Unit, Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Roongnapa Suedee
- Molecular Recognition Materials Research Unit, Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Titpawan Nakpheng
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Kittiya Tinpun
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Pornvichai Temboot
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Teerapol Srichana
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
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50
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Domalaon R, Ammeter D, Brizuela M, Gorityala BK, Zhanel GG, Schweizer F. Repurposed Antimicrobial Combination Therapy: Tobramycin-Ciprofloxacin Hybrid Augments Activity of the Anticancer Drug Mitomycin C Against Multidrug-Resistant Gram-Negative Bacteria. Front Microbiol 2019; 10:1556. [PMID: 31354660 PMCID: PMC6636613 DOI: 10.3389/fmicb.2019.01556] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023] Open
Abstract
The lack of therapeutic options to treat infections caused by multidrug-resistant (MDR) pathogens, especially Gram-negative bacteria, is apparent. Therefore, it is imperative to develop new strategies to address the problem of antimicrobial resistance. Repurposing non-antibiotic commercial drugs for antimicrobial therapy presents a viable option. We screened six anticancer drugs for their potential use in antimicrobial therapy. Here, we provide in vitro evidence that suggests feasibility to repurpose the anticancer drug mitomycin C against MDR Gram-negative bacteria. We also demonstrated that mitomycin C, etoposide and doxorubicin were affected by drug efflux in Pseudomonas aeruginosa. In combination with a tobramycin-ciprofloxacin antibiotic hybrid (TOB-CIP), the antibacterial activity of mitomycin C was enhanced against MDR clinical isolates of P. aeruginosa, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae. In fact, 4 μg/mL (3 μM) TOB-CIP reduced the minimum inhibitory concentration of mitomycin C to ≤1 μg/mL against MDR Gram-negative bacteria, except A. baumannii. We showed that synergy was inherent to TOB-CIP and that neither tobramycin nor ciprofloxacin individually synergized with mitomycin C. Our finding supports identifying adjuvant partners for mitomycin C, such as TOB-CIP, to enhance suitability for antimicrobial therapy.
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Affiliation(s)
- Ronald Domalaon
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Derek Ammeter
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Marc Brizuela
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | | | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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