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Wan X, Skurnik M. Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets. Methods Mol Biol 2024; 2793:237-256. [PMID: 38526734 DOI: 10.1007/978-1-0716-3798-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation. Moreover, steps are provided to predict protein-protein interactions and visualizing these using PyMOL. The culmination of these methods equips researchers with an effective pipeline to identify and analyze toxHPUFs and their potential targets, laying the groundwork for future experimental confirmations.
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Affiliation(s)
- Xing Wan
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Renard S, Versluys S, Taillier T, Dubarry N, Leroi-Geissler C, Rey A, Cornaire E, Sordello S, Carry JCB, Angouillant-Boniface O, Gouyon T, Thompson F, Lebourg G, Certal V, Balazs L, Arranz E, Doerflinger G, Bretin F, Gervat V, Brohan E, Kraft V, Boulenc X, Ducelier C, Bacqué E, Couturier C. Optimization of the Antibacterial Spectrum and the Developability Profile of the Novel-Class Natural Product Corramycin. J Med Chem 2023; 66:16869-16887. [PMID: 38088830 DOI: 10.1021/acs.jmedchem.3c01564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Corramycin 1 is a novel zwitterionic antibacterial peptide isolated from a culture of the myxobacterium Corallococcus coralloides. Though Corramycin displayed a narrow spectrum and modest MICs against sensitive bacteria, its ADMET and physchem profile as well as its high tolerability in mice along with an outstanding in vivo efficacy in an Escherichia coli septicemia mouse model were promising and prompted us to embark on an optimization program aiming at enlarging the spectrum and at increasing the antibacterial activities by modulating membrane permeability. Scanning the peptidic moiety by the Ala-scan strategy followed by key stabilization and introduction of groups such as a primary amine or siderophore allowed us to enlarge the spectrum and increase the overall developability profile. The optimized Corramycin 28 showed an improved mouse IV PK and a broader spectrum with high potency against key Gram-negative bacteria that translated into excellent efficacy in several in vivo mouse infection models.
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Affiliation(s)
| | | | - Thomas Taillier
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | | | | | - Astrid Rey
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | - Emilie Cornaire
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | | | | | | | - Thierry Gouyon
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | | | - Gilles Lebourg
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Victor Certal
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Laszlo Balazs
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Esther Arranz
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | | | | | - Vincent Gervat
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Eric Brohan
- Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine 94403, France
| | - Volker Kraft
- Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, Frankfurt am Main 65926, Germany
| | | | - Cécile Ducelier
- Sanofi, 1 Avenue Pierre Brossolette, Chilly-Mazarin 91385, France
| | - Eric Bacqué
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
| | - Cédric Couturier
- Evotec, 1541, Avenue Marcel Mérieux, Marcy L'Etoile 69280, France
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Lang M, Carvalho A, Baharoglu Z, Mazel D. Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules. Microbiol Mol Biol Rev 2023; 87:e0003622. [PMID: 38047635 PMCID: PMC10732077 DOI: 10.1128/mmbr.00036-22] [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: 12/05/2023] Open
Abstract
SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.
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Affiliation(s)
- Manon Lang
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - André Carvalho
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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Gerstmans H, Duyvejonck L, Vázquez R, Staes I, Borloo J, Abdelkader K, Leroy J, Cremelie E, Gutiérrez D, Tamés-Caunedo H, Ruas-Madiedo P, Rodríguez A, Aertsen A, Lammertyn J, Lavigne R, Briers Y. Distinct mode of action of a highly stable, engineered phage lysin killing Gram-negative bacteria. Microbiol Spectr 2023; 11:e0181323. [PMID: 37971248 PMCID: PMC10714810 DOI: 10.1128/spectrum.01813-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Engineered lysins are considered as highly promising alternatives for antibiotics. Our previous screening study using VersaTile technology identified 1D10 as a possible lead compound with activity against Acinetobacter baumannii strains under elevated human serum concentrations. In this manuscript, we reveal an unexpected mode of action and exceptional thermoresistance for lysin 1D10. Our findings shed new light on the development of engineered lysins, providing valuable insights for future research in this field.
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Affiliation(s)
- Hans Gerstmans
- Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Lisa Duyvejonck
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Roberto Vázquez
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Ines Staes
- Department of Microbial and Molecular Systems, Leuven, Belgium
| | | | - Karim Abdelkader
- Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Microbiology and Immunology, Beni-Suef University, Beni-Suef, Egypt
| | - Jeroen Leroy
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Emma Cremelie
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Diana Gutiérrez
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Héctor Tamés-Caunedo
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Ana Rodríguez
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Leuven, Belgium
| | | | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Yves Briers
- Department of Biotechnology, Ghent University, Ghent, Belgium
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Gargvanshi S, Heravi G, Ayon NJ, Gutheil WG. Screening the NCI diversity set V for anti-MRSA activity: cefoxitin synergy and LC-MS/MS confirmation of folate/thymidine biosynthesis inhibition. Microbiol Spectr 2023; 11:e0054123. [PMID: 37888993 PMCID: PMC10715016 DOI: 10.1128/spectrum.00541-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE New antibacterial agents are urgently needed to counter increasingly resistant bacteria. One approach to this problem is library screening for new antibacterial agents. Library screening efforts can be improved by increasing the information content of the screening effort. In this study, we screened the National Cancer Institute diversity set V against methicillin-resistant Staphylococcus aureus (MRSA) with several enhancements. One of these is to screen the library before and after microsomal metabolism as means to identify potential active metabolites. A second enhancement is to screen the library in the absence and presence of sub-minimum inhibitory concentration levels of another antibiotic, such as cefoxitin in this study. This identified four agents with synergistic activity with cefoxitin out of 16 agents with good MRSA activity alone. Finally, active agents from this effort were counter-screened in the presence of thymidine, which quickly identified three folate/thymidine biosynthesis inhibitors, and also screened for bactericidal vs bacteriostatic activity.
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Affiliation(s)
- Shivani Gargvanshi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Gioia Heravi
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Navid J. Ayon
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - William G. Gutheil
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
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56
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Chan WJ, Urandur S, Li H, Goudar VS. Recent advances in copper sulfide nanoparticles for phototherapy of bacterial infections and cancer. Nanomedicine (Lond) 2023; 18:2185-2204. [PMID: 38116732 DOI: 10.2217/nnm-2023-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Copper sulfide nanoparticles (CuS NPs) have attracted growing interest in biomedical research due to their remarkable properties, such as their high photothermal and thermodynamic capabilities, which are ideal for anticancer and antibacterial applications. This comprehensive review focuses on the current state of antitumor and antibacterial applications of CuS NPs. The initial section provides an overview of the various approaches to synthesizing CuS NPs, highlighting the size, shape and composition of CuS NPs fabricated using different methods. In this review, the mechanisms underlying the antitumor and antibacterial activities of CuS NPs in medical applications are discussed and the clinical challenges associated with the use of CuS NPs are also addressed.
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Affiliation(s)
- Wei-Jen Chan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sandeep Urandur
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Huatian Li
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Sharma C, Verma M, Abidi SMS, Shukla AK, Acharya A. Functional fluorescent nanomaterials for the detection, diagnosis and control of bacterial infection and biofilm formation: Insight towards mechanistic aspects and advanced applications. Colloids Surf B Biointerfaces 2023; 232:113583. [PMID: 37844474 DOI: 10.1016/j.colsurfb.2023.113583] [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: 07/26/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
Infectious diseases resulting from the high pathogenic potential of several bacteria possesses a major threat to human health and safety. Traditional methods used for screening of these microorganisms face major issues with respect to detection time, selectivity and specificity which may delay treatment for critically ill patients past the optimal time. Thus, a convincing and essential need exists to upgrade the existing methodologies for the fast detection of bacteria. In this context, increasing number of newly emerging nanomaterials (NMs) have been discovered for their effective use and applications in the area of diagnosis in bacterial infections. Recently, functional fluorescent nanomaterials (FNMs) are extensively explored in the field of biomedical research, particularly in developing new diagnostic tools, nanosensors, specific imaging modalities and targeted drug delivery systems for bacterial infection. It is interesting to note that organic fluorophores and fluorescent proteins have played vital role for imaging and sensing technologies for long, however, off lately fluorescent nanomaterials are increasingly replacing these due to the latter's unprecedented fluorescence brightness, stability in the biological environment, high quantum yield along with high sensitivity due to enhanced surface property etc. Again, taking advantage of their photo-excitation property, these can also be used for either photothermal and photodynamic therapy to eradicate bacterial infection and biofilm formation. Here, in this review, we have paid particular attention on summarizing literature reports on FNMs which includes studies detailing fluorescence-based bacterial detection methodologies, antibacterial and antibiofilm applications of the same. It is expected that the present review will attract the attention of the researchers working in this field to develop new engineered FNMs for the comprehensive diagnosis and treatment of bacterial infection and biofilm formation.
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Affiliation(s)
- Chandni Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Mohini Verma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Syed M S Abidi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Ashish K Shukla
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, H.P. 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Cebrián R, Lucas R, Fernández-Cantos MV, Slot K, Peñalver P, Martínez-García M, Párraga-Leo A, de Paz MV, García F, Kuipers OP, Morales JC. Synthesis and antimicrobial activity of aminoalkyl resveratrol derivatives inspired by cationic peptides. J Enzyme Inhib Med Chem 2023; 38:267-281. [PMID: 36600674 PMCID: PMC9828810 DOI: 10.1080/14756366.2022.2146685] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial resistance is a global concern, far from being resolved. The need of new drugs against new targets is imminent. In this work, we present a family of aminoalkyl resveratrol derivatives with antibacterial activity inspired by the properties of cationic amphipathic antimicrobial peptides. Surprisingly, the newly designed molecules display modest activity against aerobically growing bacteria but show surprisingly good antimicrobial activity against anaerobic bacteria (Gram-negative and Gram-positive) suggesting specificity towards this bacterial group. Preliminary studies into the action mechanism suggest that activity takes place at the membrane level, while no cross-resistance with traditional antibiotics is observed. Actually, some good synergistic relations with existing antibiotics were found against Gram-negative pathogens. However, some cytotoxicity was observed, despite their low haemolytic activity. Our results show the importance of the balance between positively charged moieties and hydrophobicity to improve antimicrobial activity, setting the stage for the design of new drugs based on these molecules.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands,Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs. GRANADA, University Hospital Clínico San Cecilio, Granada, Spain,CONTACT Rubén Cebrián University Hospital San Cecilio,Clinical Microbiology Department, Av. de la Innovación s/n, 18061, Granada, Spain
| | - Ricardo Lucas
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - María Victoria Fernández-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Koen Slot
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Pablo Peñalver
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Armilla, Granada, Spain
| | - Marta Martínez-García
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Antonio Párraga-Leo
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - María Violante de Paz
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - Federico García
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs. GRANADA, University Hospital Clínico San Cecilio, Granada, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands,Oscar P. Kuipers University of Groningen, Faculty of Science and Engineering, Department of Genetics, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Armilla, Granada, Spain,Juan Carlos Morales Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento 17, Armilla, 18016Granada, Spain
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Qi G, Tang Y, Shi L, Zhuang J, Liu X, Liu B. Capsule Shedding and Membrane Binding Enhanced Photodynamic Killing of Gram-Negative Bacteria by a Unimolecular Conjugated Polyelectrolyte. NANO LETTERS 2023; 23:10374-10382. [PMID: 37921703 DOI: 10.1021/acs.nanolett.3c02965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The development of new antimicrobial agents to treat infections caused by Gram-negative bacteria is of paramount importance due to increased antibiotic resistance worldwide. Herein, we show that a water-soluble porphyrin-cored hyperbranched conjugated polyelectrolyte (PorHP) exhibits high photodynamic bactericidal activity against the Gram-negative bacteria tested, including a multidrug-resistant (MDR) pathogen, while demonstrating low cytotoxicity toward mammalian cells. Comprehensive analyses reveal that the antimicrobial activity of PorHP proceeds via a multimodal mechanism by effective bacterial capsule shedding, strong bacterial outer membrane binding, and singlet oxygen generation. Through this multimodal antimicrobial mechanism, PorHP displays significant performance for Gram-negative bacteria with >99.9% photodynamic killing efficacy. Overall, PorHP shows great potential as an antimicrobial agent in fighting the growing threat of Gram-negative bacteria.
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Affiliation(s)
- Guobin Qi
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
| | - Yufu Tang
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
| | - Leilei Shi
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - Jiahao Zhuang
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
| | - Xianglong Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
- Institute for Functional Intelligent Materials, National University of Singapore (Singapore), Blk S9, Level 9, 4 Science Drive 2, Singapore 117544
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Nardulli P, Ballini A, Zamparella M, De Vito D. The Role of Stakeholders' Understandings in Emerging Antimicrobial Resistance: A One Health Approach. Microorganisms 2023; 11:2797. [PMID: 38004808 PMCID: PMC10673085 DOI: 10.3390/microorganisms11112797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The increasing misuse of antibiotics in human and veterinary medicine and in agroecosystems and the consequent selective pressure of resistant strains lead to multidrug resistance (AMR), an expanding global phenomenon. Indeed, this phenomenon represents a major public health target with significant clinical implications related to increased morbidity and mortality and prolonged hospital stays. The current presence of microorganisms multi-resistant to antibiotics isolated in patients is a problem because of the additional burden of disease it places on the most fragile patients and the difficulty of finding effective therapies. In recent decades, international organizations like the World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC) have played significant roles in addressing the issue of AMR. The ECDC estimates that in the European Union alone, antibiotic resistance causes 33,000 deaths and approximately 880,000 cases of disability each year. The epidemiological impact of AMR inevitably also has direct economic consequences related not only to the loss of life but also to a reduction in the number of days worked, increased use of healthcare resources for diagnostic procedures and the use of second-line antibiotics when available. In 2015, the WHO, recognising AMR as a complex problem that can only be addressed by coordinated multi-sectoral interventions, promoted the One Health approach that considers human, animal, and environmental health in an integrated manner. In this review, the authors try to address why a collaboration of all stakeholders involved in AMR growth and management is necessary in order to achieve optimal health for people, animals, plants, and the environment, highlighting that AMR is a growing threat to human and animal health, food safety and security, economic prosperity, and ecosystems worldwide.
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Affiliation(s)
- Patrizia Nardulli
- S.C. Farmacia e UMACA IRCCS Istituto Tumori “Giovanni Paolo II”, Viale O. Flacco 65, 70124 Bari, Italy;
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | | | - Danila De Vito
- Department of Translational Biomedicine and Neuroscience, Medical School, University Aldo Moro of Bari, 70124 Bari, Italy;
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Yang P, Yang J, Long H, Huang K, Ji L, Lin H, Jiang X, Wang AK, Tian G, Ning K. MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality. IMETA 2023; 2:e131. [PMID: 38868224 PMCID: PMC10989818 DOI: 10.1002/imt2.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 06/14/2024]
Abstract
The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow. Data processing module: Uploaded data is processed to generate taxonomical distribution and functional composition results. Metagenome-wide association studies module (MWAS): Various methods, including biomarker analysis, PCA, co-occurrence networks, and sample classification, are employed using metadata. Data search module: Users can query nucleotide sequences to retrieve information in the MicroEXPERT database. Data visualization module: Visualization tools are used to illustrate the metagenome analysis results.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
- Institute of Medical GenomicsBiomedical Sciences College, Shandong First Medical UniversityJinanShandongChina
| | - Jialiang Yang
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
- Department of SciencesAcademician Workstation, Changsha Medical UniversityChangshaChina
| | - Haixia Long
- Department of Information Science TechnologyHainan Normal UniversityHaikouChina
| | - Kaimei Huang
- Department of MathematicsZhejiang Normal UniversityJinhuaChina
| | - Lei Ji
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Hanyang Lin
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | - Xiuli Jiang
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | | | - Geng Tian
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
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Fatima A, Ibrahim M, Naseer A, Pervez A, Asad M, Shah AA, Hasan F, Alonazi WB, Ferheen I, Khan S. Identification, Genome Sequencing, and Characterizations of Helicobacter pylori Sourced from Pakistan. Microorganisms 2023; 11:2658. [PMID: 38004670 PMCID: PMC10673187 DOI: 10.3390/microorganisms11112658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
The stomach's colonization by Helicobacter pylori (H. pylori) results in gastritis, ulcers, and stomach cancer. Frequently, pain is treated with medication, but resistant H. pylori infections are not. Therefore, it is important to find pharmacological targets and improved treatments for resistant H. pylori strains. The aim of the current study was sampling, identification, drug susceptibility testing following genome sequencing and comparative genome-wide analysis of selected H. pylori strains from Pakistan with three representative strains for virulence and drug-resistant characteristics. Based on culture, biochemistry, and molecular biology, 84 strains of H. pylori were identified, which made up 47% of the enrolled cases. Among all H. pylori strains, the highest resistance was reported for metronidazole with 82 H. pylori strains (98%), followed by clarithromycin with 62 resistant strains (74%). Among metronidazole-resistant strains, 38 strains (46%) were also resistant to clarithromycin, contributing 61% of clarithromycin resistant cases. Two strains, HPA1 and HPA2, isolated from 'gastritis' and 'gastric ulcer' patients, respectively, were further processed for WGS. The draft genome sequences of H. pylori strains HPA1 and HPA2 encode 1.66 Mbp and 1.67 Mbp genome size, 24 and 4 contiguous DNA sequences, and 1650 and 1625 coding sequences, respectively. Both the genomes showed greater than 90% similarity with the reference strain H. pylori ATCC 43504/PMSS1. The antibiotic-resistant genes were identified among all the strains with overall similarity above 95%, with minor differences in the sequence similarity. Using the virulent gene data obtained from the Virulence Factor Database, 75 to 85 virulent genes were identified in the five genome assemblies with various key genes such as cytolethal distending toxin (cdt), type IV secretion system, cag PAI, plasticity region, cell-motility- and flagellar-associated genes, neutrophil-activating protein (HP-NAP), T4SS effector cytotoxin-associated gene A (cagA), and urease-associated genes ureA and ureB, etc. Sequence similarity between the virulence factors found in this study and reference genes was at least 90%. In summary, the results of our study showed the relationship between clinical results and specific H. pylori strains' (HPA1 and HPA2) genetics such as antibiotic resistance and specific virulence factors. These findings provide valued understanding of the epidemiology of H. pylori-associated diseases. Moreover, identification and genomics analysis have provided insights into the epidemiology, genetic diversity, pathogenicity, and potential drug resistance genes of H. pylori strains, offering a foundation for developing more targeted and effective medical interventions, including anti-virulent medications.
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Affiliation(s)
- Anees Fatima
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
- Department of Microbiology, Faculty of Health & Biological Sciences, Abbottabad University of Science & Technology, Abbottabad 22500, Pakistan
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad (CUI), Sahiwal Campus, Sahiwal 55000, Pakistan (M.A.)
| | - Adil Naseer
- Department of Gastroenterology, Ayub Medical College, Main Mansehra Road, Abbottabad 22020, Pakistan;
| | - Arshid Pervez
- Department of Environmental Sciences, COMSATS University Islamabad (CUI), Abbottabad Campus, University Road, Tobe Camp, Abbottabad 22010, Pakistan;
| | - Muhammad Asad
- Department of Biosciences, COMSATS University Islamabad (CUI), Sahiwal Campus, Sahiwal 55000, Pakistan (M.A.)
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
| | - Fariha Hasan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
| | - Wadi B. Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11587, Saudi Arabia;
| | - Ifra Ferheen
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
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63
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Kim D, Lee J, Shyaka C, Kwak JH, Pai H, Rho M, Ciufolini MA, Han M, Park JH, Kim YR, Jung S, Jang AR, Kim E, Lee JY, Lee H, Son YJ, Hwang HJ. Identification of Micrococcin P2-Derivatives as Antibiotic Candidates against Two Gram-Positive Pathogens. J Med Chem 2023; 66:14263-14277. [PMID: 37796116 DOI: 10.1021/acs.jmedchem.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Thiopeptides exhibit potent antimicrobial activity against Gram-positive pathogens by inhibiting bacterial protein synthesis. Micrococcins are among the structurally simpler thiopeptides, but they have not been exploited in detail. This research involved a computational simulation of micrococcin P2 (MP2) docking in parallel with the structure-activity relationship (SAR) studied. The incorporation of particular nitrogen heterocycles in the side chain of MP2 enhances the antimicrobial activity. Micrococcin analogues 6c and 6d thus proved to be more effective against impetigo and C. difficile infection (CDI), respectively, as compared to current first-line treatments. Compound 6c also showed a shorter treatment period than that of a first-line treatment for impetigo. This may be attributed to its ability to downregulate pro-inflammatory cytokines. Compound 6d had no observed recurrence for C. difficile and exerted a minimal impact on the beneficial gut microbiome. Their pharmacokinetic properties and low toxicity profile make these compounds ideal candidates for the treatment of impetigo and CDI and validate their involvement in preclinical development.
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Affiliation(s)
- Dahyun Kim
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Jusuk Lee
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Clovis Shyaka
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Jin-Hwan Kwak
- School of Life Science, Handong Global University, 558 Handong Ro, Heunghae-Eup, Buk-Gu, Pohang 37554, Republic of Korea
- Office of the President, Sunlin University, 30, 36 Chogok-gil, Heunghae-Eup, Buk-Gu, Pohang 37560, Republic of Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, Hanyang University College of Medicine, 232 Wangsimri Ro, Seongdong-Gu, Seoul 04763, Republic of Korea
| | - Mina Rho
- Department of Computer Science, Hanyang University, 222 Wangsimri Ro, Seongdong-Gu, Seoul 04763, Republic of Korea
| | - Marco A Ciufolini
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6K 1Z1, Canada
| | - Minwoo Han
- New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Jong-Hwan Park
- Laboratory Animal Medicine, College of Veterinary Medicine and Animal Medical Institute, Chonnam National University, 77 Yongbong-ro, Buk-Gu, Gwangju 61186, Republic of Korea
- Nodcure Inc., 77 Yongbong-ro, Buk-Gu, Gwangju 61186, Republic of Korea
| | - Young-Rok Kim
- School of Life Science, Handong Global University, 558 Handong Ro, Heunghae-Eup, Buk-Gu, Pohang 37554, Republic of Korea
| | - Sungji Jung
- School of Life Science, Handong Global University, 558 Handong Ro, Heunghae-Eup, Buk-Gu, Pohang 37554, Republic of Korea
| | - Ah-Ra Jang
- Nodcure Inc., 77 Yongbong-ro, Buk-Gu, Gwangju 61186, Republic of Korea
| | - Eunjung Kim
- School of Life Science, Handong Global University, 558 Handong Ro, Heunghae-Eup, Buk-Gu, Pohang 37554, Republic of Korea
| | - Jee-Young Lee
- New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Hakyeong Lee
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Young-Jin Son
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
| | - Hee-Jong Hwang
- A&J Science Co., Ltd., 80 Chumbok Ro, Dong Gu, Daegu 41061, Republic of Korea
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64
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Wang W, Gu L, Wang J, Hu X, Wei B, Zhang H, Wang H, Chen J. Recent Advances in Polypeptide Antibiotics Derived from Marine Microorganisms. Mar Drugs 2023; 21:547. [PMID: 37888482 PMCID: PMC10608164 DOI: 10.3390/md21100547] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
In the post-antibiotic era, the rapid development of antibiotic resistance and the shortage of available antibiotics are triggering a new health-care crisis. The discovery of novel and potent antibiotics to extend the antibiotic pipeline is urgent. Small-molecule antimicrobial peptides have a wide variety of antimicrobial spectra and multiple innovative antimicrobial mechanisms due to their rich structural diversity. Consequently, they have become a new research hotspot and are considered to be promising candidates for next-generation antibiotics. Therefore, we have compiled a collection of small-molecule antimicrobial peptides derived from marine microorganisms from the last fifteen years to show the recent advances in this field. We categorize these compounds into three classes-cyclic oligopeptides, cyclic depsipeptides, and cyclic lipopeptides-according to their structural features, and present their sources, structures, and antimicrobial spectrums, with a discussion of the structure activity relationships and mechanisms of action of some compounds.
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Affiliation(s)
| | | | | | | | | | | | - Hong Wang
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianwei Chen
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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65
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Podoll JD, Rosen E, Wang W, Gao Y, Zhang J, Wang X. A small-molecule membrane fluidizer re-sensitizes methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics. Antimicrob Agents Chemother 2023; 67:e0005123. [PMID: 37681969 PMCID: PMC10583677 DOI: 10.1128/aac.00051-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
Novel antibacterial agents and strategies are urgently needed to fight against the ongoing global antibiotic resistance problem. While natural products remain the main source in antibiotic discovery, synthetic antibacterials provide an attractive alternative and may evade the ancient antibiotic resistance. Herein, we report a small molecule that re-sensitizes methicillin-resistant Staphylococcus aureus to β-lactam antibiotics with extremely low potential for resistance development. It belongs to a new class of broad-spectrum antibacterials, trypyricins, which share similar structural characteristics and mechanism of action to the cationic antimicrobial peptides. Mechanistic studies indicated that trypyricins fluidize and disrupt bacterial cytoplasmic membrane. These results suggested that trypyricins represent a promising new class of antibacterials and may be further developed as antibiotic adjuvants to fight against resistant bacteria in the clinic.
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Affiliation(s)
| | - Emma Rosen
- Recreo Pharmaceuticals Inc, Yale Circle, Boulder, Colorado, USA
| | - Wei Wang
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
| | - Yuefeng Gao
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
| | - Jing Zhang
- Recreo Pharmaceuticals Inc, Yale Circle, Boulder, Colorado, USA
| | - Xiang Wang
- Department of Chemistry, University of Colorado, Boulder, Colorado, USA
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66
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Shi T, Cui Y, Yuan H, Qi R, Yu Y. Burgeoning Single-Atom Nanozymes for Efficient Bacterial Elimination. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2760. [PMID: 37887911 PMCID: PMC10609188 DOI: 10.3390/nano13202760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
To fight against antibacterial-resistant bacteria-induced infections, the development of highly efficient antibacterial agents with a low risk of inducing resistance is exceedingly urgent. Nanozymes can rapidly kill bacteria with high efficiency by generating reactive oxygen species via enzyme-mimetic catalytic reactions, making them promising alternatives to antibiotics for antibacterial applications. However, insufficient catalytic activity greatly limits the development of nanozymes to eliminate bacterial infection. By increasing atom utilization to the maximum, single-atom nanozymes (SAzymes) with an atomical dispersion of active metal sites manifest superior enzyme-like activities and have achieved great results in antibacterial applications in recent years. In this review, the latest advances in antibacterial SAzymes are summarized, with specific attention to the action mechanism involved in antibacterial applications covering wound disinfection, osteomyelitis treatment, and marine antibiofouling. The remaining challenges and further perspectives of SAzymes for practical antibacterial applications are also discussed.
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Affiliation(s)
- Tongyu Shi
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China; (T.S.); (Y.C.); (H.Y.)
| | - Yuanyuan Cui
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China; (T.S.); (Y.C.); (H.Y.)
| | - Huanxiang Yuan
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China; (T.S.); (Y.C.); (H.Y.)
| | - Ruilian Qi
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China; (T.S.); (Y.C.); (H.Y.)
| | - Yu Yu
- School of Science, Beijing Jiaotong University, Beijing 100044, China
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67
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Lennard PR, Hiemstra PS, Nibbering PH. Complementary Activities of Host Defence Peptides and Antibiotics in Combating Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2023; 12:1518. [PMID: 37887219 PMCID: PMC10604037 DOI: 10.3390/antibiotics12101518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Due to their ability to eliminate antimicrobial resistant (AMR) bacteria and to modulate the immune response, host defence peptides (HDPs) hold great promise for the clinical treatment of bacterial infections. Whereas monotherapy with HDPs is not likely to become an effective first-line treatment, combinations of such peptides with antibiotics can potentially provide a path to future therapies for AMR infections. Therefore, we critically reviewed the recent literature regarding the antibacterial activity of combinations of HDPs and antibiotics against AMR bacteria and the approaches taken in these studies. Of the 86 studies compiled, 56 featured a formal assessment of synergy between agents. Of the combinations assessed, synergistic and additive interactions between HDPs and antibiotics amounted to 84.9% of the records, while indifferent and antagonistic interactions accounted for 15.1%. Penicillin, aminoglycoside, fluoro/quinolone, and glycopeptide antibiotic classes were the most frequently documented as interacting with HDPs, and Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecium were the most reported bacterial species. Few studies formally evaluated the effects of combinations of HDPs and antibiotics on bacteria, and even fewer assessed such combinations against bacteria within biofilms, in animal models, or in advanced tissue infection models. Despite the biases of the current literature, the studies suggest that effective combinations of HDPs and antibiotics hold promise for the future treatment of infections caused by AMR bacteria.
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Affiliation(s)
- Patrick R. Lennard
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
- Institute of Immunology and Infection, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FE, UK
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Centre, Leiden 2333, The Netherlands
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden 2333, The Netherlands;
| | - Pieter S. Hiemstra
- PulmoScience Lab, Department of Pulmonology, Leiden University Medical Centre, Leiden 2333, The Netherlands
| | - Peter H. Nibbering
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden 2333, The Netherlands;
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Podolnikova NP, Lishko VK, Roberson R, Koh Z, Derkach D, Richardson D, Sheller M, Ugarova TP. Platelet factor 4 improves survival in a murine model of antibiotic-susceptible and methicillin-resistant Staphylococcus aureus peritonitis. Front Cell Infect Microbiol 2023; 13:1217103. [PMID: 37868353 PMCID: PMC10585365 DOI: 10.3389/fcimb.2023.1217103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/13/2023] [Indexed: 10/24/2023] Open
Abstract
The complement receptor CR3, also known as integrin Mac-1 (CD11b/CD18), is one of the major phagocytic receptors on the surface of neutrophils and macrophages. We previously demonstrated that in its protein ligands, Mac-1 binds sequences enriched in basic and hydrophobic residues and strongly disfavors negatively charged sequences. The avoidance by Mac-1 of negatively charged surfaces suggests that the bacterial wall and bacterial capsule possessing net negative electrostatic charge may repel Mac-1 and that the cationic Mac-1 ligands can overcome this evasion by acting as opsonins. Indeed, we previously showed that opsonization of Gram-negative Escherichia coli with several cationic peptides, including PF4 (Platelet Factor 4), strongly augmented phagocytosis by macrophages. Here, we investigated the effect of recombinant PF4 (rPF4) on phagocytosis of Gram-positive Staphylococcus aureus in vitro and examined its impact in a mouse model of S. aureus peritonitis. Characterization of the interaction of rPF4 with nonencapsulated and encapsulated S. aureus showed that rPF4 localizes on the bacterial surface, thus making it available for Mac-1. Furthermore, rPF4 did not have direct bactericidal and bacteriostatic activity and was not toxic to host cells. rPF4 enhanced phagocytosis of S. aureus bioparticles by various primary and cultured Mac-1-expressing leukocytes by several folds. It also increased phagocytosis of live nonencapsulated and encapsulated bacteria. Notably, the augmentation of phagocytosis by rPF4 did not compromise the intracellular killing of S. aureus by macrophages. Using a murine S. aureus peritonitis model, we showed that treatment of infected mice with rPF4 caused a significant increase in the clearance of antibiotic-susceptible S. aureus and its methicillin-resistant (MRSA) variant and markedly improved survival. These findings indicate that rPF4 binding to the bacterial surface circumvents its antiphagocytic properties, improving host defense against antibiotic-susceptible and antibiotic-resistant bacteria.
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Affiliation(s)
| | - Valeryi K. Lishko
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Robert Roberson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zhiqian Koh
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | | | | | - Michael Sheller
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Tatiana P. Ugarova
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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69
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Peng B, Li H, Peng XX. Call for next-generation drugs that remove the uptake barrier to combat antibiotic resistance. Drug Discov Today 2023; 28:103753. [PMID: 37640151 DOI: 10.1016/j.drudis.2023.103753] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/15/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Existing antibacterial agents can be categorized into two generations, but bacterial insensitivity towards both of these generations poses a serious public health challenge worldwide. Thus, novel approaches and/or novel antibacterials are urgently needed to maintain a concentration of antibacterials that is lethal to bacteria that are resistant to existing antibiotic treatments. Metabolite(s)-based adjuvants that promote antibiotic uptake and enhance antibiotic efficacy are an effective strategy that is unlikely to develop resistance. Thus, we propose a metabolite(s)-based approach, in which metabolites and antibacterials are combined, as a promising strategy for the development of next-generation agents to combat a variety of antibiotic-resistant pathogens.
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Affiliation(s)
- Bo Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, People's Republic of China
| | - Hui Li
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, People's Republic of China
| | - Xuan-Xian Peng
- State Key Laboratory of Bio-Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, University City, Guangzhou 510006, People's Republic of China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, People's Republic of China.
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70
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Huang Y, Chen Y, Lu Z, Yu B, Zou L, Song X, Han H, Jin Q, Ji J. Facile Synthesis of Self-Targeted Zn 2+ -Gallic acid Nanoflowers for Specific Adhesion and Elimination of Gram-Positive Bacteria. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302578. [PMID: 37376855 DOI: 10.1002/smll.202302578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Transition metal ions are served as disinfectant thousand years ago. However, the in vivo antibacterial application of metal ions is strongly restricted due to its high affinity with proteins and lack of appropriate bacterial targeting method. Herein, for the first time, Zn2+ -gallic acid nanoflowers (ZGNFs) are synthesized by a facile one-pot method without additional stabilizing agents. ZGNFs are stable in aqueous solution while can be easily decomposed in acidic environments. Besides, ZGNFs can specifically adhere onto Gram-positive bacteria, which is mediated by the interaction of quinone from ZGNFs and amino groups from teichoic acid of Gram-positive bacteria. ZGNFs exhibit high bactericidal effect toward various Gram-positive bacteria in multiple environments, which can be ascribed to the in situ Zn2+ release on bacterial surface. Transcriptome studies reveal that ZGNFs can disorder basic metabolic processes of Methicillin-resistant Staphylococcus aureus (MRSA). Moreover, in a MRSA-induced keratitis model, ZGNFs exhibit long-term retention in the infected corneal site and prominent MRSA elimination efficacy due to the self-targeting ability. This research not only reports an innovative method to prepare metal-polyphenol nanoparticles, but also provides a novel nanoplatform for targeted delivery of Zn2+ in combating Gram-positive bacterial infections.
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Affiliation(s)
- Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yongcheng Chen
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhouyu Lu
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Bo Yu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Lingyun Zou
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xiaohui Song
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Haijie Han
- Eye Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Qiao Jin
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, P. R. China
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71
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Skrzyniarz K, Kuc-Ciepluch D, Lasak M, Arabski M, Sanchez-Nieves J, Ciepluch K. Dendritic systems for bacterial outer membrane disruption as a method of overcoming bacterial multidrug resistance. Biomater Sci 2023; 11:6421-6435. [PMID: 37605901 DOI: 10.1039/d3bm01255g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The alarming rise of multi-drug resistant microorganisms has increased the need for new approaches through the development of innovative agents that are capable of attaching to the outer layers of bacteria and causing permanent damage by penetrating the bacterial outer membrane. The permeability (disruption) of the outer membrane of Gram-negative bacteria is now considered to be one of the main ways to overcome multidrug resistance in bacteria. Natural and synthetic permeabilizers such as AMPs and dendritic systems seem promising. However, due to their advantages in terms of biocompatibility, antimicrobial capacity, and wide possibilities for modification and synthesis, highly branched polymers and dendritic systems have gained much more interest in recent years. Various forms of arrangement, and structure of the skeleton, give dendritic systems versatile applications, especially the possibility of attaching other ligands to their surface. This review will focus on the mechanisms used by different types of dendritic polymers, and their complexes with macromolecules to enhance their antimicrobial effect, and to permeabilize the bacterial outer membrane. In addition, future challenges and potential prospects are illustrated in the hope of accelerating the advancement of nanomedicine in the fight against resistant pathogens.
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Affiliation(s)
- Kinga Skrzyniarz
- Division of Medical Biology, Jan Kochanowski University, Kielce, Poland.
| | | | - Magdalena Lasak
- Division of Medical Biology, Jan Kochanowski University, Kielce, Poland.
| | - Michał Arabski
- Division of Medical Biology, Jan Kochanowski University, Kielce, Poland.
| | - Javier Sanchez-Nieves
- Dpto. de Química Orgánica y Química Inorgánica, Universidad de Alcalá (UAH), Campus Universitario, E-28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química "Andrés M. del Río" (IQAR, UAH), Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
- Institute for Health Research Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Karol Ciepluch
- Division of Medical Biology, Jan Kochanowski University, Kielce, Poland.
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Yu T, Chong LC, Nantasenamat C, Anuwongcharoen N, Piacham T. Machine learning approaches to study the structure-activity relationships of LpxC inhibitors. EXCLI JOURNAL 2023; 22:975-991. [PMID: 38023567 PMCID: PMC10630528 DOI: 10.17179/excli2023-6356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/01/2023] [Indexed: 12/01/2023]
Abstract
Antimicrobial resistance (AMR) has emerged as one of the global threats to human health in the 21st century. Drug discovery of inhibitors against novel targets rather than conventional bacterial targets has been considered an inevitable strategy for the growing threat of AMR infections. In this study, we applied quantitative structure-activity relationship (QSAR) modeling to the LpxC inhibitors to predict the inhibitory activity. In addition, we performed various cheminformatics analysis consisting of the exploration of the chemical space, identification of chemotypes, performing structure-activity landscape and activity cliffs as well as construction of the Structure-Activity Similarity (SAS) map. We built a total of 24 QSAR classification models using PubChem and MACCS fingerprint with 12 various machine learning algorithms. The best model with PubChem fingerprint is the Extremely Gradient Boost model (accuracy on the training set: 0.937; accuracy on the 10-fold cross-validation set: 0.795; accuracy on the test set: 0.799). Furthermore, it was found that the best model using the MACCS fingerprint was the Random Forest model (accuracy on the training set: 0.955; accuracy on the 10-fold cross-validation set: 0.803; accuracy on the test set: 0.785). In addition, we have identified eight consensus activity cliff generators that are highly informative for further SAR investigations. It is hoped that findings presented herein can provide guidance for further lead optimization of LpxC inhibitors.
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Affiliation(s)
- Tianshi Yu
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Türkiye
| | - Chanin Nantasenamat
- Streamlit Open Source, Snowflake Inc., San Mateo, California 94402, United States
| | - Nuttapat Anuwongcharoen
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Theeraphon Piacham
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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73
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Podolnikova NP, Lishko VK, Roberson R, Koh Z, Derkach D, Richardson D, Sheller M, Ugarova TP. PLATELET FACTOR 4 (PF4) IMPROVES SURVIVAL IN A MURINE MODEL OF ANTIBIOTIC-SUSCEPTIBLE AND METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS PERITONITIS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554865. [PMID: 37662328 PMCID: PMC10473751 DOI: 10.1101/2023.08.25.554865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The complement receptor CR3, also known as integrin Mac-1 (CD11b/CD18), is one of the major phagocytic receptors on the surface of neutrophils and macrophages. We previously demonstrated that in its protein ligands, Mac-1 binds sequences enriched in basic and hydrophobic residues and strongly disfavors negatively charged sequences. The avoidance by Mac-1 of negatively charged surfaces suggests that the bacterial wall and bacterial capsule possessing net negative electrostatic charge may repel Mac-1 and that the cationic Mac-1 ligands can overcome this evasion by acting as opsonins. Indeed, we previously showed that opsonization of Gram-negative Escherichia coli with several cationic peptides, including PF4 (Platelet Factor 4), strongly augmented phagocytosis by macrophages. Here, we investigated the effect of recombinant PF4 (rPF4) on phagocytosis of Gram-positive Staphylococcus aureus in vitro and examined its impact in a mouse model of S. aureus peritonitis. Characterization of the interaction of rPF4 with nonencapsulated and encapsulated S. aureus showed that rPF4 localizes on the bacterial surface, thus making it available for Mac-1. Furthermore, rPF4 did not have direct bactericidal and bacteriostatic activity and was not toxic to host cells. rPF4 enhanced phagocytosis of S. aureus bioparticles by various primary and cultured Mac-1-expressing leukocytes by several folds. It also increased phagocytosis of live nonencapsulated and encapsulated bacteria. Notably, the augmentation of phagocytosis by rPF4 did not compromise the intracellular killing of S. aureus by macrophages. Using a murine S. aureus peritonitis model, we showed that treatment of infected mice with rPF4 caused a significant increase in the clearance of antibiotic-susceptible S. aureus and its methicillin-resistant (MRSA) variant and markedly improved survival. These findings indicate that rPF4 binding to the bacterial surface circumvents its antiphagocytic properties, improving host defense against antibiotic-susceptible and antibiotic-resistant bacteria.
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Affiliation(s)
| | | | - Robert Roberson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Zhqian Koh
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | | | | | - Michael Sheller
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
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74
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Medellín-Luna MF, Hernández-López H, Castañeda-Delgado JE, Martinez-Gutierrez F, Lara-Ramírez E, Espinoza-Rodríguez JJ, García-Cruz S, Portales-Pérez DP, Cervantes-Villagrana AR. Fluoroquinolone Analogs, SAR Analysis, and the Antimicrobial Evaluation of 7-Benzimidazol-1-yl-fluoroquinolone in In Vitro, In Silico, and In Vivo Models. Molecules 2023; 28:6018. [PMID: 37630269 PMCID: PMC10458221 DOI: 10.3390/molecules28166018] [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: 07/14/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Structure-activity relationship (SAR) studies allow the evaluation of the relationship between structural chemical changes and biological activity. Fluoroquinolones have chemical characteristics that allow their structure to be modified and new analogs with different therapeutic properties to be generated. The objective of this research is to identify and select the C-7 heterocycle fluoroquinolone analog (FQH 1-5) with antibacterial activity similar to the reference fluoroquinolone through in vitro, in silico, and in vivo evaluations. First, SAR analysis was conducted on the FQH 1-5, using an in vitro antimicrobial sensibility model in order to select the best compound. Then, an in silico model mechanism of action analysis was carried out by molecular docking. The non-bacterial cell cytotoxicity was evaluated, and finally, the antimicrobial potential was determined by an in vivo model of topical infection in mice. The results showed antimicrobial differences between the FQH 1-5 and Gram-positive and Gram-negative bacteria, identifying the 7-benzimidazol-1-yl-fluoroquinolone (FQH-2) as the most active against S. aureus. Suggesting the same mechanism of action as the other fluoroquinolones; no cytotoxic effects on non-bacterial cells were found. FQH-2 was demonstrated to decrease the amount of bacteria in infected wound tissue.
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Affiliation(s)
- Mitzzy Fátima Medellín-Luna
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas 98000, Mexico
| | - Hiram Hernández-López
- Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Julio Enrique Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas 98000, Mexico
- Investigadores por México, CONAHCYT, Consejo Nacional de Humanidades, Ciencias y Tecnologias, Ciudad de México 03940, Mexico
| | - Fidel Martinez-Gutierrez
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Centro de Investigación en Ciencias de la Salud y Biomedicina, UASLP, Sierra Leona No. 550, Lomas, San Luis Potosí 28210, Mexico
| | - Edgar Lara-Ramírez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reyonsa 88710, Mexico
| | | | - Salvador García-Cruz
- Departamento de Cirugía Experimental e Investigación Quirúrgica y Bioterio, “Claude Bernard”, Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico
| | - Diana Patricia Portales-Pérez
- Ciencias Farmacobiológicas, Facultad de Ciencias Químicas, Universidad Autónoma de San Luís Potosí, San Luis Potosí 78210, Mexico; (M.F.M.-L.)
- Centro de Investigación en Ciencias de la Salud y Biomedicina, UASLP, Sierra Leona No. 550, Lomas, San Luis Potosí 28210, Mexico
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75
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Butler MS, Henderson IR, Capon RJ, Blaskovich MAT. Antibiotics in the clinical pipeline as of December 2022. J Antibiot (Tokyo) 2023; 76:431-473. [PMID: 37291465 PMCID: PMC10248350 DOI: 10.1038/s41429-023-00629-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
The need for new antibacterial drugs to treat the increasing global prevalence of drug-resistant bacterial infections has clearly attracted global attention, with a range of existing and upcoming funding, policy, and legislative initiatives designed to revive antibacterial R&D. It is essential to assess whether these programs are having any real-world impact and this review continues our systematic analyses that began in 2011. Direct-acting antibacterials (47), non-traditional small molecule antibacterials (5), and β-lactam/β-lactamase inhibitor combinations (10) under clinical development as of December 2022 are described, as are the three antibacterial drugs launched since 2020. Encouragingly, the increased number of early-stage clinical candidates observed in the 2019 review increased in 2022, although the number of first-time drug approvals from 2020 to 2022 was disappointingly low. It will be critical to monitor how many Phase-I and -II candidates move into Phase-III and beyond in the next few years. There was also an enhanced presence of novel antibacterial pharmacophores in early-stage trials, and at least 18 of the 26 phase-I candidates were targeted to treat Gram-negative bacteria infections. Despite the promising early-stage antibacterial pipeline, it is essential to maintain funding for antibacterial R&D and to ensure that plans to address late-stage pipeline issues succeed.
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Affiliation(s)
- Mark S Butler
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, 4072, Australia.
| | - Ian R Henderson
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, 4072, Australia
| | - Robert J Capon
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, 4072, Australia
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, 4072, Australia.
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76
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Bekale LA, Sharma D, Bacacao B, Chen J, Santa Maria PL. Eradication of Bacterial Persister Cells By Leveraging Their Low Metabolic Activity Using Adenosine Triphosphate Coated Gold Nanoclusters. NANO TODAY 2023; 51:101895. [PMID: 37575958 PMCID: PMC10421611 DOI: 10.1016/j.nantod.2023.101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Bacteria first develop tolerance after antibiotic exposure; later genetic resistance emerges through the population of tolerant bacteria. Bacterial persister cells are the multidrug-tolerant subpopulation within an isogenic bacteria culture that maintains genetic susceptibility to antibiotics. Because of this link between antibiotic tolerance and resistance and the rise of antibiotic resistance, there is a pressing need to develop treatments to eradicate persister cells. Current anti persister cell strategies are based on the paradigm of "awakening" them from their low metabolic state before attempting eradication with traditional antibiotics. Herein, we demonstrate that the low metabolic activity of persister cells can be exploited for eradication over their metabolically active counterparts. We engineered gold nanoclusters coated with adenosine triphosphate (AuNC@ATP) as a benchmark nanocluster that kills persister cells over exponential growth bacterial cells and prove the feasibility of this new concept. Finally, using AuNC@ATP as a new research tool, we demonstrated that it is possible to prevent the emergence of antibiotic-resistant superbugs with an anti-persister compound. Eradicating persister cells with AuNC@ATP in an isogenic culture of bacteria stops the emergence of superbug bacteria mediated by the sub-lethal dose of conventional antibiotics. Our findings lay the groundwork for developing novel nano-antibiotics targeting persister cells, which promise to prevent the emergence of superbugs and prolong the lifespan of currently available antibiotics.
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Affiliation(s)
- Laurent A. Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Devesh Sharma
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Jing Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Peter L. Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
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77
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Wu J, Xu C, Ye Z, Chen H, Wang Y, Yang K, Yuan B. Transition between Different Diffusion Modes of Individual Lipids during the Membrane-Specific Action of As-CATH4 Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301713. [PMID: 37093200 DOI: 10.1002/smll.202301713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/02/2023] [Indexed: 05/03/2023]
Abstract
The cell membrane permeabilization ability of immune defense antimicrobial peptides (AMPs) is widely applied in biomedicine. Although the mechanisms of peptide-membrane interactions have been widely investigated, analyses at the molecular level are still lacking. Herein, the membrane-specific action of a native AMP, As-CATH4, is investigated using a single-lipid tracking method in combination with live cell and model membrane assays conducted at different scales. The peptide-membrane interaction process is characterized by analyzing single-lipid diffusion behaviors. As-CATH4 exhibits potent antimicrobial activity through bacterial membrane permeabilization, with moderate cytotoxicity against mammalian cells. In-plane diffusion analyses of individual lipids show that the lipid molecules exhibit non-Gaussian and heterogeneous diffusion behaviors in both pristine and peptide-treated membranes, which can be decomposed into two Gaussian subgroups corresponding to normal- and slow-diffusive lipids. Assessment of the temporal evolution of these two diffusion modes of lipids reveal that the peptide action states of As-CATH4 include surface binding, transmembrane defect formation, and dynamic equilibrium. The action mechanisms of As-CATH4 at varying concentrations and against different membranes are distinguished. This work resolves the simultaneous mixed diffusion mechanisms of single lipids in biomimetic cell membranes, especially during dynamic membrane permeabilization by AMPs.
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Affiliation(s)
- Jinfeng Wu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Cheng Xu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Zifan Ye
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Haibo Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
| | - Yipeng Wang
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, 215006, P. R. China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, P. R. China
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78
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Alanko I, Sandberg R, Brockmann E, de Haas CJC, van Strijp JAG, Lamminmäki U, Salo‐Ahen OMH. Isolation and functional analysis of phage-displayed antibody fragments targeting the staphylococcal superantigen-like proteins. Microbiologyopen 2023; 12:e1371. [PMID: 37642487 PMCID: PMC10350561 DOI: 10.1002/mbo3.1371] [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: 02/08/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 08/31/2023] Open
Abstract
Staphylococcus aureus produces numerous virulence factors that manipulate the immune system, helping the bacteria avoid phagocytosis. In this study, we are investigating three immune evasion molecules called the staphylococcal superantigen-like proteins 1, 5, and 10 (SSL1, SSL5, and SSL10). All three SSLs inhibit vital host immune processes and contribute to S. aureus immune evasion. This study aimed to identify single-chain variable fragment (scFvs) antibodies from synthetic antibody phage libraries, which can recognize either of the three SSLs and could block the interaction between the SSLs and their respective human targets. The antibodies were isolated after three rounds of panning against SSL1, SSL5, and SSL10, and their ability to bind to the SSLs was studied using a time-resolved fluorescence-based immunoassay. We successfully obtained altogether 44 unique clones displaying binding activity to either SSL1, SSL5, or SSL10. The capability of the SSL-recognizing scFvs to inhibit the SSLs' function was tested in an MMP9 enzymatic activity assay, a P-selectin glycoprotein ligand 1 competitive binding assay, and an IgG1-mediated phagocytosis assay. We could show that one scFv was able to inhibit SSL1 and maintain MMP9 activity in a concentration-dependent manner. Finally, the structure of this inhibiting scFv was modeled and used to create putative scFv-SSL1-complex models by protein-protein docking. The complex models were subjected to a 100-ns molecular dynamics simulation to assess the possible binding mode of the antibody.
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Affiliation(s)
- Ida Alanko
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
| | - Rebecca Sandberg
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
| | | | - Carla J. C. de Haas
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Jos A. G. van Strijp
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Urpo Lamminmäki
- Department of Life TechnologiesUniversity of TurkuTurkuFinland
| | - Outi M. H. Salo‐Ahen
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
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79
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Ioannou P, Baliou S, Kofteridis DP. Antimicrobial Peptides in Infectious Diseases and Beyond-A Narrative Review. Life (Basel) 2023; 13:1651. [PMID: 37629508 PMCID: PMC10455936 DOI: 10.3390/life13081651] [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: 07/17/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Despite recent medical research and clinical practice developments, the development of antimicrobial resistance (AMR) significantly limits therapeutics for infectious diseases. Thus, novel treatments for infectious diseases, especially in this era of increasing AMR, are urgently needed. There is ongoing research on non-classical therapies for infectious diseases utilizing alternative antimicrobial mechanisms to fight pathogens, such as bacteriophages or antimicrobial peptides (AMPs). AMPs are evolutionarily conserved molecules naturally produced by several organisms, such as plants, insects, marine organisms, and mammals, aiming to protect the host by fighting pathogenic microorganisms. There is ongoing research regarding developing AMPs for clinical use in infectious diseases. Moreover, AMPs have several other non-medical applications in the food industry, such as preservatives, animal husbandry, plant protection, and aquaculture. This review focuses on AMPs, their origins, biology, structure, mechanisms of action, non-medical applications, and clinical applications in infectious diseases.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Stella Baliou
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Diamantis P. Kofteridis
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
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80
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Sui B, Wang X, Zhao T, Zhen J, Ren H, Liu W, Zhang X, Zhang C. Design, Screening, and Characterization of Engineered Phage Endolysins with Extracellular Antibacterial Activity against Gram-Negative Bacteria. Appl Environ Microbiol 2023; 89:e0058123. [PMID: 37338346 PMCID: PMC10370328 DOI: 10.1128/aem.00581-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Phage-encoded endolysins are emerging antibacterial agents based on their ability to efficiently degrade peptidoglycan on Gram-positive bacteria, but the envelope characteristics of Gram-negative bacteria limit their application. Engineering modifications of endolysins can improve the optimization of their penetrative and antibacterial properties. This study constructed a screening platform to screen for engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular antibacterial activity against Escherichia coli. An oligonucleotide of 20 repeated NNK codons was inserted upstream of the endolysin gene Bp7e to construct a chimeric endolysin library in the pColdTF vector. The chimeric Art-Bp7e proteins were expressed by transforming the plasmid library into E. coli BL21 and released by chloroform fumigation, and the protein activities were evaluated by the spotting method and the colony-counting method to screen for promising proteins. Sequence analysis showed that all screened proteins with extracellular activities had a chimeric peptide with a positive charge and an α-helical structure. Also, a representative protein, Art-Bp7e6, was further characterized. It exhibited broad antibacterial activity against E. coli (7/21), Salmonella enterica serovar Enteritidis (4/10), Pseudomonas aeruginosa (3/10), and even Staphylococcus aureus (1/10). In the transmembrane process, the chimeric peptide of Art-Bp7e6 depolarized the host cell envelope, increased the permeability of the cell, and facilitated the movement of Art-Bp7e6 across the envelope to hydrolyze the peptidoglycan. In conclusion, the screening platform successfully screened for chimeric endolysins with extracellular antibacterial activities against Gram-negative bacteria, which provides methodological support for the further screening of engineered endolysins with high extracellular activities against Gram-negative bacteria. Also, the established platform showed broad application prospects and can be used to screen various proteins. IMPORTANCE The presence of the envelope in Gram-negative bacteria limits the use of phage endolysins, and engineering endolysins is an efficient way to optimize their penetrative and antibacterial properties. We built a platform for endolysin engineering and screening. A random peptide was fused with the phage endolysin Bp7e to construct a chimeric endolysin library, and engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular activity against Gram-negative bacteria were successfully screened from the library. The purposeful Art-Bp7e had a chimeric peptide with an abundant positive charge and an α-helical structure, which led Bp7e to acquire the ability for the extracellular lysis of Gram-negative bacteria and showed a broad lysis spectrum. The platform provides a huge library capacity without the limitations of reported proteins or peptides. It can be utilized for the further screening of optimal endolysins against Gram-negative bacteria as well as for the screening of additional proteins with specific modifications.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinrui Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tianyi Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jianyu Zhen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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81
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El-Sayed SM, Ahmed SA, Gulia K, Lenhard JR, Hassan AHE, Farahat AA. Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1040. [PMID: 37513951 PMCID: PMC10384254 DOI: 10.3390/ph16071040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.
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Affiliation(s)
- Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - Samar A Ahmed
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Justin R Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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Sterle M, Durcik M, Stevenson CEM, Henderson SR, Szili PE, Czikkely M, Lawson DM, Maxwell A, Cahard D, Kikelj D, Zidar N, Pal C, Mašič LP, Ilaš J, Tomašič T, Cotman AE, Zega A. Exploring the 5-Substituted 2-Aminobenzothiazole-Based DNA Gyrase B Inhibitors Active against ESKAPE Pathogens. ACS OMEGA 2023; 8:24387-24395. [PMID: 37457471 PMCID: PMC10339456 DOI: 10.1021/acsomega.3c01930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
We present a new series of 2-aminobenzothiazole-based DNA gyrase B inhibitors with promising activity against ESKAPE bacterial pathogens. Based on the binding information extracted from the cocrystal structure of DNA gyrase B inhibitor A, in complex with Escherichia coli GyrB24, we expanded the chemical space of the benzothiazole-based series to the C5 position of the benzothiazole ring. In particular, compound E showed low nanomolar inhibition of DNA gyrase (IC50 < 10 nM) and broad-spectrum antibacterial activity against pathogens belonging to the ESKAPE group, with the minimum inhibitory concentration < 0.03 μg/mL for most Gram-positive strains and 4-16 μg/mL against Gram-negative E. coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. To understand the binding mode of the synthesized inhibitors, a combination of docking calculations, molecular dynamics (MD) simulations, and MD-derived structure-based pharmacophore modeling was performed. The computational analysis has revealed that the substitution at position C5 can be used to modify the physicochemical properties and antibacterial spectrum and enhance the inhibitory potency of the compounds. Additionally, a discussion of challenges associated with the synthesis of 5-substituted 2-aminobenzothiazoles is presented.
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Affiliation(s)
- Maša Sterle
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Martina Durcik
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Clare E. M. Stevenson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
| | - Sara R. Henderson
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Petra Eva Szili
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - Marton Czikkely
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - David M. Lawson
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
| | - Anthony Maxwell
- Department
of Biochemistry and Metabolism, John Innes
Centre, Norwich Research Park, Norwich NR4 7UH, U.K.
| | - Dominique Cahard
- CNRS
UMR 6014 COBRA, Normandie Université, Mont Saint Aignan 76821, France
| | - Danijel Kikelj
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Nace Zidar
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Csaba Pal
- Synthetic
and Systems Biology Unit, Biological Research Centre, Institute of Biochemistry, Szeged H-6726, Hungary
| | - Lucija Peterlin Mašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Janez Ilaš
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Tihomir Tomašič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Andrej Emanuel Cotman
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
| | - Anamarija Zega
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana 1000, Slovenia
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83
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Bhowmick J, Nag M, Ghosh P, Rajmani RS, Chatterjee R, Karmakar K, Chandra K, Chatterjee J, Chakravortty D, Varadarajan R. A CcdB toxin-derived peptide acts as a broad-spectrum antibacterial therapeutic in infected mice. EMBO Rep 2023; 24:e55338. [PMID: 37166011 PMCID: PMC10328072 DOI: 10.15252/embr.202255338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
The bacterial toxin CcdB (Controller of Cell death or division B) targets DNA Gyrase, an essential bacterial topoisomerase, which is also the molecular target for fluoroquinolones. Here, we present a short cell-penetrating 24-mer peptide, CP1-WT, derived from the Gyrase-binding region of CcdB and examine its effect on growth of Escherichia coli, Salmonella Typhimurium, Staphylococcus aureus and a carbapenem- and tigecycline-resistant strain of Acinetobacter baumannii in both axenic cultures and mouse models of infection. The CP1-WT peptide shows significant improvement over ciprofloxacin in terms of its in vivo therapeutic efficacy in treating established infections of S. Typhimurium, S. aureus and A. baumannii. The molecular mechanism likely involves inhibition of Gyrase or Topoisomerase IV, depending on the strain used. The study validates the CcdB binding site on bacterial DNA Gyrase as a viable and alternative target to the fluoroquinolone binding site.
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Grants
- Department of Biotechnology, Ministry of Science and Technology, India - Indian Institute of Science (DBT-IISc) partnership program
- BT/COE/34/SP15219/2015 Department of Biotechnology, Ministry of Science and Technology, India
- DT.20/11/2015 Department of Biotechnology, Ministry of Science and Technology, India
- Department of Science and Technology, Ministry of Science and Technology, India (DST FIST)
- Ministry of Education, India (MHRD)
- University Grants Commission, Ministry of Education, India (UGC Centre for Advanced Studies)
- Department of Biotechnology, Ministry of Science and Technology, India
- Ministry of Education, India (MHRD)
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Affiliation(s)
- Jayantika Bhowmick
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Manish Nag
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Pritha Ghosh
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Raju S Rajmani
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Ritika Chatterjee
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kapudeep Karmakar
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Kasturi Chandra
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
| | - Jayanta Chatterjee
- Molecular Biophysics Unit (MBU)Indian Institute of ScienceBangaloreIndia
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell BiologyIndian Institute of ScienceBangaloreIndia
- School of BiologyIndian Institute of Science Education and Research Thiruvananthapuram (IISER TVM)ThiruvananthapuramIndia
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84
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Elek CKA, Brown TL, Le Viet T, Evans R, Baker DJ, Telatin A, Tiwari SK, Al-Khanaq H, Thilliez G, Kingsley RA, Hall LJ, Webber MA, Adriaenssens EM. A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses. Microb Genom 2023; 9:mgen001065. [PMID: 37463032 PMCID: PMC10438801 DOI: 10.1099/mgen.0.001065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.
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Affiliation(s)
- Claire K. A. Elek
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Teagan L. Brown
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - David J. Baker
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Sumeet K. Tiwari
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Gaëtan Thilliez
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL—Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark A. Webber
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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85
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Freezman IM, Parthasarathy A, Miranda RR, Watts LM, Hudson AO. Chromatographic isolation of potentially novel antibiotic compounds produced by Yimella sp. RIT 621. BMC Res Notes 2023; 16:114. [PMID: 37349752 DOI: 10.1186/s13104-023-06393-0] [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: 12/14/2022] [Accepted: 06/16/2023] [Indexed: 06/24/2023] Open
Abstract
OBJECTIVE Antibiotic resistant infections have become a global health crisis causing 1.2 million deaths worldwide in 2019 [1]. In a previous study, we identified a bacterium from a rare genus, Yimella, and found in an initial antibiotic screening that they produce broad-spectrum bactericidal compounds [2]. Herein, we focus on the characterization of these potential novel antimicrobial compounds produced by Yimella sp. RIT 621. RESULTS We used solid-phase extraction and C18 reverse-phase chromatography to isolate the antibiotic-active compounds found in organic extracts from liquid cultures of Yimella sp. RIT 621. We tracked the antimicrobial activity by testing the extracts in disc diffusion inhibitory assays and observed its increase after each purification stage.
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Affiliation(s)
- Ian M Freezman
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Dr, 14623, Rochester, NY, USA
| | | | - Renata Rezende Miranda
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Dr, 14623, Rochester, NY, USA
| | - Lizabeth M Watts
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Dr, 14623, Rochester, NY, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Dr, 14623, Rochester, NY, USA.
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86
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Song F, Sheng J, Tan J, Xie H, Wang X, Guo W. Characterization of an Enterococcus faecalis bacteriophage SFQ1 as a potential therapeutic agent. Front Microbiol 2023; 14:1210319. [PMID: 37426023 PMCID: PMC10324664 DOI: 10.3389/fmicb.2023.1210319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus faecalis is a well-established resident of the human gastrointestinal tract and is also a major cause of human infections. Unfortunately, therapeutic options for E. faecalis infections remain limited, particularly with the emergence of vancomycin-resistant strains in hospital settings. Consequently, there has been a renewed interest in phage therapy as an alternative to antibiotics. In this study, we have isolated a bacteriophage, vB_EfaS-SFQ1, from hospital sewage, which effectively infects E. faecalis strain EFS01. Phage SFQ1 is a siphovirus and exhibits a relatively broad host range. Furthermore, it has a short latent period of approximately 10 min and a large burst size of about 110 PFU/cell at a multiplicity of infection (MOI) of 0.01, and it could effectively disrupt the biofilms formed by E. faecalis. Thus, this study provides a detailed characterization of E. faecalis phage SFQ1, which has great potential for treating E. faecalis infections.
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Affiliation(s)
- Fuqiang Song
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Jun Sheng
- Department of Orthopaedics, The General Hospital of Western Theater Command, Chengdu, China
| | - Jishan Tan
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Huajie Xie
- Department of Medical Laboratory, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaoyu Wang
- Department of Clinical Pharmacy, The General Hospital of Western Theater Command, Chengdu, China
| | - Wenqiong Guo
- School of Nursing, Chengdu Medical College, Chengdu, China
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87
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Li X, Song Y, Chen X, Yin J, Wang P, Huang H, Yin H. Single-cell microfluidics enabled dynamic evaluation of drug combinations on antibiotic resistance bacteria. Talanta 2023; 265:124814. [PMID: 37343360 DOI: 10.1016/j.talanta.2023.124814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023]
Abstract
The rapid spread of antibiotic resistance has become a significant threat to global health, yet the development of new antibiotics is outpaced by emerging new resistance. To treat multidrug-resistant bacteria and prolong the lifetime of existing antibiotics, a productive strategy is to use combinations of antibiotics and/or adjuvants. However, evaluating drug combinations is primarily based on end-point checkerboard measurements, which provide limited information to study the mechanism of action and the discrepancies in the clinical outcomes. Here, single-cell microfluidics is used for rapid evaluation of the efficacy and mode of action of antibiotic combinations within 3 h. Focusing on multidrug-resistant Acinetobacter baumannii, the combination between berberine hydrochloride (BBH, as an adjuvant) and carbapenems (meropenem, MEM) or β-lactam antibiotic is evaluated. Real-time tracking of individual cells to programmable delivered antibiotics reveals multiple phenotypes (i.e., susceptible, resistant, and persistent cells) with fidelity. Our study discovers that BBH facilitates the accumulation of antibiotics within cells, indicating synergistic effects (FICI = 0.5). For example, the combination of 256 mg/L BBH and 16 mg/L MEM has a similar killing effect (i.e., the inhibition rates >90%) as the MIC of MEM (64 mg/L). Importantly, the synergistic effect of a combination can diminish if the bacteria are pre-stressed with any single drug. Such information is vital for understanding the underlying mechanisms of combinational treatments. Overall, our platform provides a promising approach to evaluate the dynamic and heterogenous response of a bacterial population to antibiotics, which will facilitate new drug discovery and reduce emerging antibiotic resistance.
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Affiliation(s)
- Xiaobo Li
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China; James Watt School of Engineering, University of Glasgow, G12 8LT, UK
| | - Yanqing Song
- James Watt School of Engineering, University of Glasgow, G12 8LT, UK
| | - Xiuzhao Chen
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Jianan Yin
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Ping Wang
- Tianjin Modern Innovative TCM Technology Co. Ltd., 300392, China
| | - He Huang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China.
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, G12 8LT, UK.
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88
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Vasiliev G, Kubo AL, Vija H, Kahru A, Bondar D, Karpichev Y, Bondarenko O. Synergistic antibacterial effect of copper and silver nanoparticles and their mechanism of action. Sci Rep 2023; 13:9202. [PMID: 37280318 DOI: 10.1038/s41598-023-36460-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/04/2023] [Indexed: 06/08/2023] Open
Abstract
Bacterial infections are one of the leading causes of death worldwide. In the case of topical bacterial infections such as wound infections, silver (Ag) has historically been one of the most widely used antibacterials. However, scientific publications have demonstrated the adverse effects of silver on human cells, ecotoxicity and insufficient antibacterial effect for the complete elimination of bacterial infections. The use of Ag in the form of nanoparticles (NPs, 1-100 nm) allows to control the release of antibacterial Ag ions but is still not sufficient to eliminate infection and avoid cytotoxicity. In this study, we tested the potency of differently functionalized copper oxide (CuO) NPs to enhance the antibacterial properties of Ag NPs. The antibacterial effect of the mixture of CuO NPs (CuO, CuO-NH2 and CuO-COOH NPs) with Ag NPs (uncoated and coated) was studied. CuO and Ag NP combinations were more efficient than Cu or Ag (NPs) alone against a wide range of bacteria, including antibiotic-resistant strains such as gram-negative Escherichia coli and Pseudomonas aeruginosa as well as gram-positive Staphylococcus aureus, Enterococcus faecalis and Streptococcus dysgalactiae. We showed that positively charged CuO NPs enhanced the antibacterial effect of Ag NPs up to 6 times. Notably, compared to the synergy of CuO and Ag NPs, the synergy of respective metal ions was low, suggesting that NP surface is required for the enhanced antibacterial effect. We also studied the mechanisms of synergy and showed that the production of Cu+ ions, faster dissolution of Ag+ from Ag NPs and lower binding of Ag+ by proteins of the incubation media in the presence of Cu2+ were the main mechanisms of the synergy. In summary, CuO and Ag NP combinations allowed increasing the antibacterial effect up to 6 times. Thus, using CuO and Ag NP combinations enables to retain excellent antibacterial effects due to Ag and synergy and enhances beneficial effects, since Cu is a vital microelement for human cells. Thus, we suggest using combinations of Ag and CuO NPs in antibacterial materials, such as wound care products, to increase the antibacterial effect of Ag, improve safety and prevent and cure topical bacterial infections.
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Affiliation(s)
- Grigory Vasiliev
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia
- Nanordica Medical OÜ, Vana-Lõuna tn 39a-7, 10134, Tallinn, Harjumaa, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Anna-Liisa Kubo
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia
- Nanordica Medical OÜ, Vana-Lõuna tn 39a-7, 10134, Tallinn, Harjumaa, Estonia
| | - Heiki Vija
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia
| | - Anne Kahru
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia
- Estonian Academy of Sciences, Kohtu 6, 10130, Tallinn, Estonia
| | - Denys Bondar
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Yevgen Karpichev
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Olesja Bondarenko
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia.
- Nanordica Medical OÜ, Vana-Lõuna tn 39a-7, 10134, Tallinn, Harjumaa, Estonia.
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89
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Ioannou P, Baliou S, Samonis G. Bacteriophages in Infectious Diseases and Beyond-A Narrative Review. Antibiotics (Basel) 2023; 12:1012. [PMID: 37370331 DOI: 10.3390/antibiotics12061012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of antibiotics has revolutionized medicine and has changed medical practice, enabling successful fighting of infection. However, quickly after the start of the antibiotic era, therapeutics for infectious diseases started having limitations due to the development of antimicrobial resistance. Since the antibiotic pipeline has largely slowed down, with few new compounds being produced in the last decades and with most of them belonging to already-existing classes, the discovery of new ways to treat pathogens that are resistant to antibiotics is becoming an urgent need. To that end, bacteriophages (phages), which are already used in some countries in agriculture, aquaculture, food safety, and wastewater plant treatments, could be also used in clinical practice against bacterial pathogens. Their discovery one century ago was followed by some clinical studies that showed optimistic results that were limited, however, by some notable obstacles. However, the rise of antibiotics during the next decades left phage research in an inactive status. In the last decades, new studies on phages have shown encouraging results in animals. Hence, further studies in humans are needed to confirm their potential for effective and safe treatment in cases where there are few or no other viable therapeutic options. This study reviews the biology and applications of phages for medical and non-medical uses in a narrative manner.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine Department, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Stella Baliou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George Samonis
- School of Medicine, University of Crete, 71003 Heraklion, Greece
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90
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Draveny M, Rose C, Pinet A, Ferrié L, Figadère B, Brunel JM, Masi M. Scope and Limitations of Exploiting the Ability of the Chemosensitizer NV716 to Enhance the Activity of Tetracycline Derivatives against Pseudomonas aeruginosa. Molecules 2023; 28:molecules28114262. [PMID: 37298737 DOI: 10.3390/molecules28114262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The spread of antibiotic resistance is an urgent threat to global health that requires new therapeutic approaches. Treatments for pathogenic Gram-negative bacteria are particularly challenging to identify due to the robust OM permeability barrier in these organisms. One strategy is to use antibiotic adjuvants, a class of drugs that have no significant antibacterial activity on their own but can act synergistically with certain antibiotics. Previous studies described the discovery and development of polyaminoisoprenyl molecules as antibiotic adjuvants with an OM effect. In particular, the compound NV716 has been shown to sensitize Pseudomonas aeruginosa to tetracycline antibiotics such as doxycycline. Here, we sought to explore the disruption of OM to sensitize P. aeruginosa to otherwise inactive antimicrobials using a series of tetracycline derivatives in the presence of NV716. We found that OM disruption expands the hydrophobicity threshold consistent with antibacterial activity to include hydrophobic molecules, thereby altering permeation rules in Gram-negative bacteria.
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Affiliation(s)
- Margot Draveny
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
| | - Clémence Rose
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Alexis Pinet
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Laurent Ferrié
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Bruno Figadère
- BioCIS, Bâtiment H. Moissan, Université Paris-Saclay, CNRS, 91400 Orsay, France
| | - Jean-Michel Brunel
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Muriel Masi
- MCT, INSERM U1261, UMR_MD1, Aix-Marseille Univ. & IRBA SSA, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
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91
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Huang Y, Wang Z, Liu Z, Huan Q, Liu Y, Li R, Wang M, Xiao X. Gigantol restores the sensitivity of mcr carrying multidrug-resistant bacteria to colistin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 117:154886. [PMID: 37269755 DOI: 10.1016/j.phymed.2023.154886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/27/2023] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND The emergence and wide spread of plasmid-mediated colistin resistance gene (mcr-1) and its mutants have immensely limited the efficacy of colistin in treating multidrug-resistant (MDR) Gram-negative bacterial infections. The development of synergistic combinations of antibiotics with a natural product that coped with the resistance of MDR bacteria was an economic strategy to restore antibiotics activity. Herein, we investigated gigantol, a bibenzyl phytocompound, for restoring in vitro and in vivo, the sensitivity of mcr-positive bacteria to colistin. METHODS The synergistic activity of gigantol and colistin against multidrug-resistant Enterobacterales was studied via checkerboard assay and time-killing curve. Subsequently, the transcription and protein expression levels of mcr-1 gene were determined by RT-PCR and Western blots. The interaction of gigantol and MCR-1 was simulated via molecular docking and verified via site-directed mutagenesis of MCR-1. Hemolytic activity and cytotoxicity assay were used to evaluate the safety of gigantol. Finally, the in vivo synergistic effect was evaluated via two animal infection models. RESULTS Gigantol restored the activity of colistin against mcr-positive bacteria E.coli B2 (MIC from 4 μg/ml to 0.25 μg/ml), Salmonella 15E343 (MIC from 8 μg/ml to 1 μg/ml), K. pneumoniae 19-2-1 (MIC from 32 μg/ml to 2 μg/ml) carrying mcr-1, mcr-3, mcr-8, respectively. Mechanistic studies revealed that gigantol down-regulated the expression of genes involved in LPS-modification, reduced the MCR-1 products and inhibited the activity of MCR-1 by binding to amino acid residues Tyr287 and Pro481 in its D-glucose-binding pocket. Safety evaluation showed that the addition of gigantol relieves the hemolysis caused by colistin. Compared with monotherapy, the combination of gigantol and colistin significantly improved the survival rate of Gallgallella mellonella larvae and mice infected by E.coli B2. Moreover, there was a considerable decrease in the bacterial load present in the viscera of mice. CONCLUSION Our results confirmed that gigantol was a potential colistin adjuvant, and could be used to tackle multi-drug resistant Gram-negative pathogen infections combined with colistin.
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Affiliation(s)
- Yanhu Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Quanmin Huan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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92
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Heithoff DM, Barnes V L, Mahan SP, Fried JC, Fitzgibbons LN, House JK, Mahan MJ. Re-evaluation of FDA-approved antibiotics with increased diagnostic accuracy for assessment of antimicrobial resistance. Cell Rep Med 2023; 4:101023. [PMID: 37116500 PMCID: PMC10213814 DOI: 10.1016/j.xcrm.2023.101023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/16/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
Accurate assessment of antibiotic susceptibility is critical for treatment of antimicrobial resistant (AMR) infections. Here, we examine whether antimicrobial susceptibility testing in media more physiologically representative of in vivo conditions improves prediction of clinical outcome relative to standard bacteriologic medium. This analysis reveals that ∼15% of minimum inhibitory concentration (MIC) values obtained in physiologic media predicted a change in susceptibility that crossed a clinical breakpoint used to categorize patient isolates as susceptible or resistant. The activities of antibiotics having discrepant results in different media were evaluated in murine sepsis models. Testing in cell culture medium improves the accuracy by which MIC assays predict in vivo efficacy. This analysis identifies several antibiotics for treatment of AMR infections that standard testing failed to identify and those that are ineffective despite indicated use by standard testing. Methods with increased diagnostic accuracy mitigate the AMR crisis via utilizing existing agents and optimizing drug discovery.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Lucien Barnes V
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - John K House
- Faculty of Science, School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia.
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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93
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Barman S, Mukherjee S, Jolly L, Troiano C, Grottesi A, Basak D, Calligari P, Bhattacharjee B, Bocchinfuso G, Stella L, Haldar J. Isoamphipathic antibacterial molecules regulating activity and toxicity through positional isomerism. Chem Sci 2023; 14:4845-4856. [PMID: 37181778 PMCID: PMC10171078 DOI: 10.1039/d2sc06065e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Peptidomimetic antimicrobials exhibit a selective interaction with bacterial cells over mammalian cells once they have achieved an optimum amphiphilic balance (hydrophobicity/hydrophilicity) in the molecular architecture. To date, hydrophobicity and cationic charge have been considered the crucial parameters to attain such amphiphilic balance. However, optimization of these properties is not enough to circumvent unwanted toxicity towards mammalian cells. Hence, herein, we report new isoamphipathic antibacterial molecules (IAMs: 1-3) where positional isomerism was introduced as one of the guiding factors for molecular design. This class of molecules displayed good (MIC = 1-8 μg mL-1 or μM) to moderate [MIC = 32-64 μg mL-1 (32.2-64.4 μM)] antibacterial activity against multiple Gram-positive and Gram-negative bacteria. Positional isomerism showed a strong influence on regulating antibacterial activity and toxicity for ortho [IAM-1: MIC = 1-32 μg mL-1 (1-32.2 μM), HC50 = 650 μg mL-1 (654.6 μM)], meta [IAM-2: MIC = 1-16 μg mL-1 (1-16.1 μM), HC50 = 98 μg mL-1 (98.7 μM)] and para [IAM-3: MIC = 1-16 μg mL-1 (1-16.1 μM), HC50 = 160 μg mL-1 (161.1 μM)] isomers. Co-culture studies and investigation of membrane dynamics indicated that ortho isomer, IAM-1 exerted more selective activity towards bacterial over mammalian membranes, compared to meta and para isomers. Furthermore, the mechanism of action of the lead molecule (IAM-1) has been characterized through detailed molecular dynamics simulations. In addition, the lead molecule displayed substantial efficacy against dormant bacteria and mature biofilms, unlike conventional antibiotics. Importantly, IAM-1 exhibited moderate in vivo activity against MRSA wound infection in a murine model with no detectable dermal toxicity. Altogether, the report explored the design and development of isoamphipathic antibacterial molecules to establish the role of positional isomerism in achieving selective and potential antibacterial agents.
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Affiliation(s)
- Swagatam Barman
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
| | - Sudip Mukherjee
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
| | - Logia Jolly
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
| | - Cassandra Troiano
- Department of Chemical Science and Technologies, University of Rome Tor Vergata via della Ricerca Scientifica, 1 00133 Rome Italy
| | | | - Debajyoti Basak
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata via della Ricerca Scientifica, 1 00133 Rome Italy
| | - Brinta Bhattacharjee
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata via della Ricerca Scientifica, 1 00133 Rome Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata via della Ricerca Scientifica, 1 00133 Rome Italy
| | - Jayanta Haldar
- Antibacterial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore 560064 India
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94
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Leonard C, Crabb N, Glover D, Cooper S, Bouvy J, Wobbe M, Perkins M. Can the UK 'Netflix' Payment Model Boost the Antibacterial Pipeline? APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2023; 21:365-372. [PMID: 36646872 PMCID: PMC9842493 DOI: 10.1007/s40258-022-00786-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/18/2022] [Indexed: 05/03/2023]
Abstract
The silent pandemic of antimicrobial resistance (AMR) is a global issue needing prompt attention. A comprehensive one-health approach across human and animal health, agriculture and the environment is needed to solve this, addressing overuse of antibacterials, and of course, optimising measures for preventing and controlling infection. We also need a robust pipeline of new antibacterials. However, the current pipeline is inadequate and several companies with new antibacterials have gone bankrupt due to low sales, leading to a 'broken market'. To address this, the UK has completed a project using novel approaches to value assessment and reimbursement for two antibacterials. The new funding arrangements for these products commenced on 1st July 2022, delinking reimbursement from volume of sales; a so-called 'pull incentive', with payments based on the added value to the whole-health and social-care system, not just to individual patients. This article describes how the project was devised, developed, and progressed. The learning from this work might help other countries to adopt or adapt the approach to fit with their national systems, and collectively achieve a global incentive to reinvigorate the antibacterial pipeline.
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Affiliation(s)
- Colm Leonard
- National Institute for Health and Care Excellence, Level 1A, City Tower, Manchester, M1 4BT, UK.
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| | - Nick Crabb
- National Institute for Health and Care Excellence, Level 1A, City Tower, Manchester, M1 4BT, UK
| | - David Glover
- NHS England and NHS Improvement, Skipton House, 80 London Road, London, SE1 6LH, UK
| | - Sophie Cooper
- National Institute for Health and Care Excellence, Level 1A, City Tower, Manchester, M1 4BT, UK
| | - Jacoline Bouvy
- National Institute for Health and Care Excellence, Level 1A, City Tower, Manchester, M1 4BT, UK
| | - Milena Wobbe
- National Institute for Health and Care Excellence, Level 1A, City Tower, Manchester, M1 4BT, UK
| | - Mark Perkins
- NHS England and NHS Improvement, Skipton House, 80 London Road, London, SE1 6LH, UK
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95
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Marzaman ANF, Roska TP, Sartini S, Utami RN, Sulistiawati S, Enggi CK, Manggau MA, Rahman L, Shastri VP, Permana AD. Recent Advances in Pharmaceutical Approaches of Antimicrobial Agents for Selective Delivery in Various Administration Routes. Antibiotics (Basel) 2023; 12:antibiotics12050822. [PMID: 37237725 DOI: 10.3390/antibiotics12050822] [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: 03/06/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Globally, the increase of pathogenic bacteria with antibiotic-resistant characteristics has become a critical challenge in medical treatment. The misuse of conventional antibiotics to treat an infectious disease often results in increased resistance and a scarcity of effective antimicrobials to be used in the future against the organisms. Here, we discuss the rise of antimicrobial resistance (AMR) and the need to combat it through the discovery of new synthetic or naturally occurring antibacterial compounds, as well as insights into the application of various drug delivery approaches delivered via various routes compared to conventional delivery systems. AMR-related infectious diseases are also discussed, as is the efficiency of various delivery systems. Future considerations in developing highly effective antimicrobial delivery devices to address antibiotic resistance are also presented here, especially on the smart delivery system of antibiotics.
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Affiliation(s)
| | - Tri Puspita Roska
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Sartini Sartini
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Rifka Nurul Utami
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | | | | | | | - Latifah Rahman
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Venkatram Prasad Shastri
- Institute for Macromolecular Chemistry, Albert Ludwigs Universitat Freiburg, 79085 Freiburg, Germany
| | - Andi Dian Permana
- Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
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96
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Gannett C, Banks P, Chuong C, Weger-Lucarelli J, Mevers E, Lowell AN. Semisynthetic blasticidin S ester derivatives show enhanced antibiotic activity. RSC Med Chem 2023; 14:782-789. [PMID: 37122539 PMCID: PMC10131614 DOI: 10.1039/d2md00412g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/05/2023] [Indexed: 03/19/2023] Open
Abstract
A rich potential source of new antibiotics are undeveloped natural product cytotoxins, provided they can be derivatized to restrict their activity to bacteria. In this work, we describe modification of one such candidate, the broad-spectrum, translation termination inhibitor, blasticidin S. By semisynthetically modifying blasticidin S, we produced a series of ester derivatives of this highly polar, zwitterionic compound in a single step. These derivatives showed a marked increase in activity against Gram-positive bacteria and an increase in selectivity index for pathogenic bacteria over human cells. The results of this study suggest that semisynthetic derivatization of blasticidin S and other neglected natural product antimicrobials has the potential to increase their activity against and selectivity for bacteria, an approach that can be leveraged for the development of leads against antimicrobial resistant pathogens.
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Affiliation(s)
- Cole Gannett
- Department of Chemistry, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA (540) 231 5842
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
| | - Paige Banks
- Department of Chemistry, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA (540) 231 5842
| | - Christina Chuong
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
| | - Emily Mevers
- Department of Chemistry, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA (540) 231 5842
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
- Faculty of Health Sciences, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
| | - Andrew N Lowell
- Department of Chemistry, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA (540) 231 5842
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
- Faculty of Health Sciences, Virginia Polytechnic Institute and State University (Virginia Tech) Blacksburg VA 24061 USA
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97
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Xu Y, Wu Y, Hu Y, Xu M, Liu Y, Ding Y, Chen J, Huang X, Wen L, Li J, Zhu C. Bacteria-based multiplex system eradicates recurrent infections with drug-resistant bacteria via photothermal killing and protective immunity elicitation. Biomater Res 2023; 27:27. [PMID: 37024953 PMCID: PMC10080897 DOI: 10.1186/s40824-023-00363-0] [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: 12/09/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The high mortality associated with drug-resistant bacterial infections is an intractable clinical problem resulting from the low susceptibility of these bacteria to antibiotics and the high incidence of recurrent infections. METHODS Herein, a photosynthetic bacteria-based multiplex system (Rp@Al) composed of natural Rhodopseudomonas palustris (Rp) and Food and Drug Administration-approved aluminum (Al) adjuvant, was developed to combat drug-resistant bacterial infections and prevent their recurrence. We examined its photothermal performance and in vitro and in vivo antibacterial ability; revealed its protective immunomodulatory effect; verified its preventative effect on recurrent infections; and demonstrated the system's safety. RESULTS Rp@Al exhibits excellent photothermal properties with an effective elimination of methicillin-resistant Staphylococcus aureus (MRSA). In addition, Rp@Al enhances dendritic cell activation and further triggers a T helper 1 (TH1)/TH2 immune response, resulting in pathogen-specific immunological memory against recurrent MRSA infection. Upon second infection, Rp@Al-treated mice show significantly lower bacterial burden, faster abscess recovery, and higher survival under near-lethal infection doses than control mice. CONCLUSIONS This innovative multiplex system, with superior photothermal and immunomodulatory effects, presents great potential for the treatment and prevention of drug-resistant bacterial infections.
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Affiliation(s)
- Youcui Xu
- Medical Research Center, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Yi Wu
- Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yi Hu
- Center for Biomedical Imaging, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Mengran Xu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yanyan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Yuting Ding
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Jing Chen
- School of Life Sciences, Hefei Normal University, Hefei, 230601, Anhui, China
| | - Xiaowan Huang
- Medical Research Center, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
| | - Longping Wen
- Medical Research Center, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China.
| | - Chen Zhu
- Department of Orthopaedics, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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98
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Khalid K, Rox K. All Roads Lead to Rome: Enhancing the Probability of Target Attainment with Different Pharmacokinetic/Pharmacodynamic Modelling Approaches. Antibiotics (Basel) 2023; 12:antibiotics12040690. [PMID: 37107052 PMCID: PMC10135278 DOI: 10.3390/antibiotics12040690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
In light of rising antimicrobial resistance and a decreasing number of antibiotics with novel modes of action, it is of utmost importance to accelerate development of novel treatment options. One aspect of acceleration is to understand pharmacokinetics (PK) and pharmacodynamics (PD) of drugs and to assess the probability of target attainment (PTA). Several in vitro and in vivo methods are deployed to determine these parameters, such as time-kill-curves, hollow-fiber infection models or animal models. However, to date the use of in silico methods to predict PK/PD and PTA is increasing. Since there is not just one way to perform the in silico analysis, we embarked on reviewing for which indications and how PK and PK/PD models as well as PTA analysis has been used to contribute to the understanding of the PK and PD of a drug. Therefore, we examined four recent examples in more detail, namely ceftazidime-avibactam, omadacycline, gepotidacin and zoliflodacin as well as cefiderocol. Whereas the first two compound classes mainly relied on the ‘classical’ development path and PK/PD was only deployed after approval, cefiderocol highly profited from in silico techniques that led to its approval. Finally, this review shall highlight current developments and possibilities to accelerate drug development, especially for anti-infectives.
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Affiliation(s)
- Kashaf Khalid
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
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99
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Eller KA, Stamo DF, McCollum CR, Campos JK, Levy M, Nagpal P, Chatterjee A. Photoactivated antibiotics to treat intracellular infection of bacteria. NANOSCALE ADVANCES 2023; 5:1910-1918. [PMID: 36998655 PMCID: PMC10044578 DOI: 10.1039/d2na00378c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/08/2022] [Indexed: 06/19/2023]
Abstract
Antibiotic resistance combined with pathogen internalization leads to debilitating infections. Here we test novel superoxide producing, stimuli-activated quantum dots (QDs), to treat an intracellular infection of Salmonella enterica serovar Typhimurium in an osteoblast precursor cell line. These QDs are precisely tuned to reduce dissolved oxygen to superoxide and kill bacteria upon stimulation (e.g., light). We show QDs provide tunable clearance at various multiplicities of infection and limited host cell toxicity by modulating their concentration and stimuli intensity, proving the efficacy of superoxide producing QDs for intracellular infection treatment and establishing a framework for further testing in different infection models.
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Affiliation(s)
- Kristen A Eller
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
| | - Dana F Stamo
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
| | - Colleen R McCollum
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
| | - Jocelyn K Campos
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
| | - Max Levy
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
- Renewable and Sustainable Energy Institute, University of Colorado Boulder Boulder CO 80303 USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Colorado Technology Center Louisville CO 80027 USA
- Antimicrobial Regeneration Consortium Labs Louisville CO 80027 USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80303 USA
- Sachi Bioworks Inc., Colorado Technology Center Louisville CO 80027 USA
- Antimicrobial Regeneration Consortium Labs Louisville CO 80027 USA
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100
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Tököli A, Bodnár B, Bogár F, Paragi G, Hetényi A, Bartus É, Wéber E, Hegedüs Z, Szabó Z, Kecskeméti G, Szakonyi G, Martinek TA. Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design. Pharmaceutics 2023; 15:pharmaceutics15041032. [PMID: 37111518 PMCID: PMC10143822 DOI: 10.3390/pharmaceutics15041032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g., ExoI and RecO) is essential for designing high-affinity SSB mimetic inhibitors. Molecular dynamics simulations revealed the transient interactions of SSB-Ct with two hot spots on ExoI and RecO. The residual flexibility of the peptide-protein complexes allows adaptive molecular recognition. Scanning with non-canonical amino acids revealed that modifications at both termini of SSB-Ct could increase the affinity, supporting the two-hot-spot binding model. Combining unnatural amino acid substitutions on both segments of the peptide resulted in enthalpy-enhanced affinity, accompanied by enthalpy-entropy compensation, as determined by isothermal calorimetry. NMR data and molecular modeling confirmed the reduced flexibility of the improved affinity complexes. Our results highlight that the SSB-Ct mimetics bind to the DNA metabolizing targets through the hot spots, interacting with both of segments of the ligands.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Brigitta Bodnár
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Ferenc Bogár
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Gábor Paragi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- Institute of Physics, University of Pécs, H7624 Pécs, Hungary
- Department of Theoretical Physics, University of Szeged, H6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Zoltán Szabó
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gábor Kecskeméti
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged, H6720 Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, H6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), H6720 Szeged, Hungary
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