1
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Glen KA, Lamont IL. Penicillin-binding protein 3 sequence variations reduce susceptibility of Pseudomonas aeruginosa to β-lactams but inhibit cell division. J Antimicrob Chemother 2024:dkae203. [PMID: 39001778 DOI: 10.1093/jac/dkae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/03/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND β-lactam antibiotics, which inhibit penicillin-binding protein 3 (PBP3) that is required for cell division, play a key role in treating P. aeruginosa infections. Some sequence variations in PBP3 have been associated with β-lactam resistance but the effects of variations on antibiotic susceptibility and on cell division have not been quantified. Antibiotic efflux can also reduce susceptibility. OBJECTIVES To quantify the effects of PBP3 variations on β-lactam susceptibility and cell morphology in P. aeruginosa. METHODS Nineteen PBP3 variants were expressed from a plasmid in the reference strain P. aeruginosa PAO1 and genome engineering was used to construct five mutants expressing PBP3 variants from the chromosome. The effects of the variations on β-lactam minimum inhibitory concentration (MIC) and cell morphology were measured. RESULTS Some PBP3 variations reduced susceptibility to a variety of β-lactam antibiotics including meropenem, ceftazidime, cefepime and ticarcillin with different variations affecting different antibiotics. None of the tested variations reduced susceptibility to imipenem or piperacillin. Antibiotic susceptibility was further reduced when PBP3 variants were expressed in mutant bacteria overexpressing the MexAB-OprM efflux pump, with some variations conferring clinical levels of resistance. Some PBP3 variations, and sub-MIC levels of β-lactams, reduced bacterial growth rates and inhibited cell division, causing elongated cells. CONCLUSIONS PBP3 variations in P. aeruginosa can increase the MIC of multiple β-lactam antibiotics, although not imipenem or piperacillin. PBP3 variations, or the presence of sub-lethal levels of β-lactams, result in elongated cells indicating that variations reduce the activity of PBP3 and may reduce bacterial fitness.
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Affiliation(s)
- Karl A Glen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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2
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Joshi T, Vijayakumar S, Ghosh S, Mathpal S, Ramaiah S, Anbarasu A. Identifying Novel Therapeutics for the Resistant Mutant "F533L" in PBP3 of Pseudomonas aeruginosa Using ML Techniques. ACS OMEGA 2024; 9:28046-28060. [PMID: 38973840 PMCID: PMC11223260 DOI: 10.1021/acsomega.4c00929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a highly infectious and antibiotic-resistant bacterium, which causes acute and chronic nosocomial infections. P. aeruginosa exhibits multidrug resistance due to the emergence of resistant mutants. The bacterium takes advantage of intrinsic and acquired resistance mechanisms to resist almost every antibiotic. To overcome the drug-resistance problem, there is a need to develop effective drugs against antibiotic-resistant mutants. Therefore, in this study, we selected the F533L mutation in PBP3 (penicillin-binding protein 3) because of its important role in β-lactam recognition. To target this mutation, we screened 147 antibacterial compounds from PubChem through a machine-learning model developed based on the decision stump algorithm with 75.75% accuracy and filtered out 55 compounds. Subsequently, out of 55 compounds, 47 compounds were filtered based on their drug-like activity. These 47 compounds were subjected to virtual screening to obtain binding affinity compounds. The binding affinity range of all 47 compounds was -11.3 to -4.6 kcal mol-1. The top 10 compounds were examined according to their binding with the mutation point. A molecular dynamic simulation of the top 8 compounds was conducted to understand the stability of the compounds containing the mutated PBP3. Out of 8 compounds, 3 compounds, namely, macozinone, antibacterial agent 71, and antibacterial agent 123, showed good stability and were validated by RMSD, RMSF, and binding-free analysis. The findings of this study revealed promising antibacterial compounds against the F533L mutant PBP3. Furthermore, developments in these compounds may pave the way for novel therapeutic interventions.
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Affiliation(s)
- Tushar Joshi
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Santhiya Vijayakumar
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Integrative Biology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Soumyadip Ghosh
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Shalini Mathpal
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical
and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- Department
of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
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3
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Fram B, Su Y, Truebridge I, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler MA, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nat Commun 2024; 15:5141. [PMID: 38902262 PMCID: PMC11190266 DOI: 10.1038/s41467-024-49119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely necessitates numerous primary sequence changes, and novel methods are needed to accurately predict combinations of mutations that maintain or enhance function. Models of sequence co-variation (e.g., EVcouplings), which leverage extensive information about various protein properties and activities from homologous protein sequences, have proven effective for many applications including structure determination and mutation effect prediction. We apply EVcouplings to computationally design variants of the model protein TEM-1 β-lactamase. Nearly all the 14 experimentally characterized designs were functional, including one with 84 mutations from the nearest natural homolog. The designs also had large increases in thermostability, increased activity on multiple substrates, and nearly identical structure to the wild type enzyme. This study highlights the efficacy of evolutionary models in guiding large sequence alterations to generate functional diversity for protein design applications.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Apriori Bio, Cambridge, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael A Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Dyno Therapeutics, 343 Arsenal Street, Watertown, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas P Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Jamoussi B, Al-Sharif MNM, Gzara L, Organji H, Almeelbi TB, Chakroun R, Al-Mur BA, Al Makishah NHM, Madkour MHF, Aloufi FA, Halawani RF. Hybrid Zinc Phthalocyanine/PVDF-HFP System for Reducing Biofouling in Water Desalination: DFT Theoretical and MolDock Investigations. Polymers (Basel) 2024; 16:1738. [PMID: 38932087 PMCID: PMC11207365 DOI: 10.3390/polym16121738] [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: 05/28/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Fouling and biofouling remain significant challenges in seawater desalination plants. One practical approach to address these issues is to develop anti-biofouling membranes. Therefore, novel hybrid zinc phthalocyanine/polyvinylidene fluoride-co-hexafluoropropylene (Zn(4-PPOx)4Pc/PVDF-HFP) membranes were prepared by electrospinning to evaluate their properties against biofouling. The hybrid nanofiber membrane was characterized by atomic force microscopy (AFM), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, and contact angle measurements. The theoretical calculations of PVDF-HFP, Zn(4-PPOx)4Pc), and Zn(4-PPOx)4Pc/PVDF-HFP nanofibers were performed using a hybrid functional RB3LYP and the 6-31 G (d,p) basis set, employing Gaussian 09. DFT calculations illustrated that the calculated physical and electronic parameters ensured the feasibility of the interaction of PVDF-HFP with Zn(4-PPOx)4Pc via a halogen-hydrogen bond, resulting in a highly stable and remarkably reactive structure. Moreover, molecular electrostatic potential (MEP) maps were drawn to identify the reactive regions of the Zn(4-PPOx)4Pc and PVDF-HFP/Zn(4-PPOx)4Pc nanofibers. Molecular docking analysis revealed that Zn(4-PPOx)4Pc has highest binding affinity (-8.56 kcal/mol) with protein from S. aureus (1N67) mainly with ten amino acids (ASP405, LYS374, GLU446, ASN406, ALA441, TYR372, LYS371, TYR448, LYS374, and ALA442). These findings highlight the promising potential of Zn(4-PPOx) 4Pc/PVDF-HFP nanocomposite membranes in improving the efficiency of water desalination by reducing biofouling and providing antibacterial properties.
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Affiliation(s)
- Bassem Jamoussi
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Mohhamed Naif M. Al-Sharif
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Lassaad Gzara
- Center of Excellence in Desalination Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (L.G.); (H.O.)
| | - Hussam Organji
- Center of Excellence in Desalination Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (L.G.); (H.O.)
| | - Talal B. Almeelbi
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Radhouane Chakroun
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Bandar A. Al-Mur
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Naief H. M. Al Makishah
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Mohamed H. F. Madkour
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Fahed A. Aloufi
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
| | - Riyadh F. Halawani
- Department of Environment, Faculty of Environmental Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.N.M.A.-S.); (T.B.A.); (R.C.); (B.A.A.-M.); (N.H.M.A.M.); (M.H.F.M.); (F.A.A.); (R.F.H.)
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5
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Bon CG, Grigg JC, Lee J, Robb CS, Caveney NA, Eltis LD, Strynadka NCJ. Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. J Struct Biol 2024; 216:108086. [PMID: 38527711 DOI: 10.1016/j.jsb.2024.108086] [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: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.
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Affiliation(s)
- Christopher G Bon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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6
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Liu F, Kou Q, Li H, Cao Y, Chen M, Meng X, Zhang Y, Wang T, Wang H, Zhang D, Yang Y. Discovery of YFJ-36: Design, Synthesis, and Antibacterial Activities of Catechol-Conjugated β-Lactams against Gram-Negative Bacteria. J Med Chem 2024; 67:6705-6725. [PMID: 38596897 DOI: 10.1021/acs.jmedchem.4c00265] [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: 04/11/2024]
Abstract
Cefiderocol is the first approved catechol-conjugated cephalosporin against multidrug-resistant Gram-negative bacteria, while its application was limited by poor chemical stability associated with the pyrrolidinium linker, moderate potency against Klebsiella pneumoniae and Acinetobacter baumannii, intricate procedures for salt preparation, and potential hypersensitivity. To address these issues, a series of novel catechol-conjugated derivatives were designed, synthesized, and evaluated. Extensive structure-activity relationships and structure-metabolism relationships (SMR) were conducted, leading to the discovery of a promising compound 86b (Code no. YFJ-36) with a new thioether linker. 86b exhibited superior and broad-spectrum in vitro antibacterial activity, especially against A. baumannii and K. pneumoniae, compared with cefiderocol. Potent in vivo efficacy was observed in a murine systemic infection model. Furthermore, the physicochemical stability of 86b in fluid medium at pH 6-8 was enhanced. 86b also reduced potential the risk of allergy owing to the quaternary ammonium linker. The improved properties of 86b supported its further research and development.
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Affiliation(s)
- Fangjun Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Qunhuan Kou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Hongyuan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yangzhi Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Meng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Xin Meng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinyong Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Ting Wang
- Department of Microbiology, Sichuan Primed Bio-Tech Group Co., Ltd., Chengdu, Sichuan Province 610041, P. R. China
| | - Hui Wang
- China Pharmaceutical University, Jiangsu 211198, China
| | - Dan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
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7
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Oliver A, Rojo-Molinero E, Arca-Suarez J, Beşli Y, Bogaerts P, Cantón R, Cimen C, Croughs PD, Denis O, Giske CG, Graells T, Daniel Huang TD, Iorga BI, Karatuna O, Kocsis B, Kronenberg A, López-Causapé C, Malhotra-Kumar S, Martínez LM, Mazzariol A, Meyer S, Naas T, Notermans DW, Oteo-Iglesias J, Pedersen T, Pirš M, Poeta P, Poirel L, Pournaras S, Sundsfjord A, Szabó D, Tambić-Andrašević A, Vatcheva-Dobrevska R, Vitkauskienė A, Jeannot K. Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group. Clin Microbiol Infect 2024; 30:469-480. [PMID: 38160753 DOI: 10.1016/j.cmi.2023.12.026] [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: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
SCOPE Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum β-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved β-lactams and β-lactam/β-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles. METHODS To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members. QUESTIONS ADDRESSED IN THE POSITION PAPER To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on β-lactams, (b) the susceptibility profiles associated with the most relevant β-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms. IMPLICATION The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.
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Affiliation(s)
- Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Estrella Rojo-Molinero
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Arca-Suarez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Yeşim Beşli
- Department of Medical Microbiology, Amerikan Hastanesi, Istanbul, Turkey
| | - Pierre Bogaerts
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Rafael Cantón
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany; Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter D Croughs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Olivier Denis
- Department of Microbiology, CHU Namur Site-Godinne, Université Catholique de Louvain, Yvoir, Belgium; Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Tíscar Graells
- Department of Neurobiology, Care Sciences and Society (NVS), Division of Family Medicine and Primary Care, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Te-Din Daniel Huang
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Bogdan I Iorga
- CNRS, Institut de Chimie des Substances Naturelles, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Béla Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Andreas Kronenberg
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Luis Martínez Martínez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Annarita Mazzariol
- Microbiology and Virology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Sylvain Meyer
- INSERM UMR 1092 and Université of Limoges, Limoges, France
| | - Thierry Naas
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France; Équipe INSERM ReSIST, Faculté de Médecine, Université Paris-Saclay, Paris, France
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mateja Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Patricia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Portugal; Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; University of Trás-os-Montes and Alto Douro, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland; University of Fribourg, Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
| | - Spyros Pournaras
- Laboratory of Clinical Microbiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dora Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary; Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Arjana Tambić-Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Zagreb, Croatia; School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Astra Vitkauskienė
- Department of Laboratory Medicine, Faculty of Medicine, Medical Academy, Lithuanian University of Health Science, Kaunas, Lithuania
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement UMR 6249, CNRS, Université Franche-Comté, Besançon, France
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8
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Weng C, Tan YLK, Koh WG, Ang WH. Harnessing Transition Metal Scaffolds for Targeted Antibacterial Therapy. Angew Chem Int Ed Engl 2023; 62:e202310040. [PMID: 37621226 DOI: 10.1002/anie.202310040] [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: 07/14/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 08/26/2023]
Abstract
Antimicrobial resistance, caused by persistent adaptation and growing resistance of pathogenic bacteria to overprescribed antibiotics, poses one of the most serious and urgent threats to global public health. The limited pipeline of experimental antibiotics in development further exacerbates this looming crisis and new drugs with alternative modes of action are needed to tackle evolving pathogenic adaptation. Transition metal complexes can replenish this diminishing stockpile of drug candidates by providing compounds with unique properties that are not easily accessible using pure organic scaffolds. We spotlight four emerging strategies to harness these unique properties to develop new targeted antibacterial agents.
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Affiliation(s)
- Cheng Weng
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | | | - Wayne Gareth Koh
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
- NUS Graduate School of Integrative Sciences and Engineering, 28 Medical Drive, Singapore, 117456, Singapore
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9
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Guru A, Taviti AC, Sethy M, Ray S, Dixit A, Beuria TK. The cell division protein ZapE is targeted by the antibiotic aztreonam to induce cell filamentation in Escherichia coli. FEBS Lett 2023; 597:2931-2945. [PMID: 37857499 DOI: 10.1002/1873-3468.14759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023]
Abstract
Bacterial division is mediated by a protein complex called the Z-ring, and Z-ring associated protein E (ZapE) is a Z-ring-associated protein that acts as its negative regulator. In the present study, we show that treatment of Escherichia coli with the antibiotic aztreonam stabilized the Z-ring, induced filamentation, and reduced viability, with similar phenotypes being observed in ZapE deletion strains. Aztreonam treatment decreased ZapE expression, and the overexpression of ZapE rescued filamentous morphology significantly and viability partially. However, overexpression of filamentous temperature sensitive I (FtsI), a known target of aztreonam, could not rescue the filamentation. Interestingly, overexpression of ZapE and FtsI together was able to rescue both filamentous morphology and cell viability. Using in silico and biochemical analyses, we show that aztreonam directly interacts with ZapE. Our study suggests that the inhibitory effects of aztreonam in E. coli could be mediated by targeting ZapE.
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Affiliation(s)
- Ankeeta Guru
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | | | - Madhusmita Sethy
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Srusti Ray
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Anshuman Dixit
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Tushar Kant Beuria
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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10
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Bertonha AF, Silva CCL, Shirakawa KT, Trindade DM, Dessen A. Penicillin-binding protein (PBP) inhibitor development: A 10-year chemical perspective. Exp Biol Med (Maywood) 2023; 248:1657-1670. [PMID: 38030964 PMCID: PMC10723023 DOI: 10.1177/15353702231208407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Bacterial cell wall formation is essential for cellular survival and morphogenesis. The peptidoglycan (PG), a heteropolymer that surrounds the bacterial membrane, is a key component of the cell wall, and its multistep biosynthetic process is an attractive antibacterial development target. Penicillin-binding proteins (PBPs) are responsible for cross-linking PG stem peptides, and their central role in bacterial cell wall synthesis has made them the target of successful antibiotics, including β-lactams, that have been used worldwide for decades. Following the discovery of penicillin, several other compounds with antibiotic activity have been discovered and, since then, have saved millions of lives. However, since pathogens inevitably become resistant to antibiotics, the search for new active compounds is continuous. The present review highlights the ongoing development of inhibitors acting mainly in the transpeptidase domain of PBPs with potential therapeutic applications for the development of new antibiotic agents. Both the critical aspects of the strategy, design, and structure-activity relationships (SAR) are discussed, covering the main published articles over the last 10 years. Some of the molecules described display activities against main bacterial pathogens and could open avenues toward the development of new, efficient antibacterial drugs.
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Affiliation(s)
- Ariane F Bertonha
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Caio C L Silva
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Karina T Shirakawa
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, Brazil
| | - Daniel M Trindade
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
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11
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Kothari A, Kherdekar R, Mago V, Uniyal M, Mamgain G, Kalia RB, Kumar S, Jain N, Pandey A, Omar BJ. Age of Antibiotic Resistance in MDR/XDR Clinical Pathogen of Pseudomonas aeruginosa. Pharmaceuticals (Basel) 2023; 16:1230. [PMID: 37765038 PMCID: PMC10534605 DOI: 10.3390/ph16091230] [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: 07/08/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance in Pseudomonas aeruginosa remains one of the most challenging phenomena of everyday medical science. The universal spread of high-risk clones of multidrug-resistant/extensively drug-resistant (MDR/XDR) clinical P. aeruginosa has become a public health threat. The P. aeruginosa bacteria exhibits remarkable genome plasticity that utilizes highly acquired and intrinsic resistance mechanisms to counter most antibiotic challenges. In addition, the adaptive antibiotic resistance of P. aeruginosa, including biofilm-mediated resistance and the formation of multidrug-tolerant persisted cells, are accountable for recalcitrance and relapse of infections. We highlighted the AMR mechanism considering the most common pathogen P. aeruginosa, its clinical impact, epidemiology, and save our souls (SOS)-mediated resistance. We further discussed the current therapeutic options against MDR/XDR P. aeruginosa infections, and described those treatment options in clinical practice. Finally, other therapeutic strategies, such as bacteriophage-based therapy and antimicrobial peptides, were described with clinical relevance.
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Affiliation(s)
- Ashish Kothari
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Radhika Kherdekar
- Department of Dentistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Vishal Mago
- Department of Burn and Plastic Surgery, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Madhur Uniyal
- Department of Trauma Surgery, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Garima Mamgain
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Roop Bhushan Kalia
- Department of Orthopaedics, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Sandeep Kumar
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA 30912, USA;
| | - Neeraj Jain
- Department of Medical Oncology, All India Institute of Medical Sciences, Rishikesh 249203, India
- Division of Cancer Biology, Central Drug Research Institute, Lucknow 226031, India
| | - Atul Pandey
- Department of Entomology, University of Kentucky, Lexington, KY 40503, USA
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh 249203, India;
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12
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Zhu Y, Kang Y, Zhang H, Yu W, Zhang G, Zhang J, Kang W, Duan S, Xu Y, Yang Q. Emergence of ST463 exoU-Positive, Imipenem-Nonsusceptible Pseudomonas aeruginosa Isolates in China. Microbiol Spectr 2023; 11:e0010523. [PMID: 37314344 PMCID: PMC10434062 DOI: 10.1128/spectrum.00105-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
This study investigated the resistance mechanisms and the distribution and proportions of virulence genes, including exoU, in 182 imipenem-nonsusceptible Pseudomonas aeruginosa (INS-PA) strains collected from China in 2019. There was no obvious prevalent sequence type or concentrated evolutionary multilocus sequence typing (MLST) type on the INS-PA phylogenetic tree in China. All of the INS-PA isolates harbored β-lactamases with/without other antimicrobial mechanisms, such as gross disruption of oprD and overexpression of efflux genes. Compared with exoU-negative isolates, exoU-positive isolates (25.3%, 46/182) presented higher virulence in A549 cell cytotoxicity assays. The southeast region of China had the highest proportion (52.2%, 24/46) of exoU-positive strains. The most frequent exoU-positive strains belonged to sequence type 463 (ST463) (23.9%, 11/46) and presented multiple resistance mechanisms and higher virulence in the Galleria mellonella infection model. The complex resistance mechanisms in INS-PA and the emergence of ST463 exoU-positive, multidrug-resistant P. aeruginosa strains in southeast China indicated a challenge that might lead to clinical treatment failure and higher mortality. IMPORTANCE This study investigates the resistance mechanisms and distribution and proportions of virulence genes of imipenem-nonsusceptible Pseudomonas aeruginosa (INS-PA) isolates in China in 2019. Harboring PDC and OXA-50-like genes is discovered as the most prevalent resistance mechanism in INS-PA, and the virulence of exoU-positive INS-PA isolates was significantly higher than that of exoU-negative INS-PA isolates. There was an emergence of ST463 exoU-positive INS-PA isolates in Zhejiang, China, most of which presented multidrug resistance and hypervirulence.
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Affiliation(s)
- Ying Zhu
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Kang
- MRL Global Medical Affairs, MSD China, Shanghai, China
| | - Hui Zhang
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Yu
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ge Zhang
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjia Zhang
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Kang
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Simeng Duan
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Clinical Laboratory Department, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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13
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Simner PJ, Bergman Y, Conzemius R, Jacobs E, Tekle T, Beisken S, Tamma PD. An NDM-Producing Escherichia coli Clinical Isolate Exhibiting Resistance to Cefiderocol and the Combination of Ceftazidime-Avibactam and Aztreonam: Another Step Toward Pan-β-Lactam Resistance. Open Forum Infect Dis 2023; 10:ofad276. [PMID: 37416757 PMCID: PMC10319620 DOI: 10.1093/ofid/ofad276] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/15/2023] [Indexed: 07/08/2023] Open
Abstract
Background Cefiderocol and ceftazidime-avibactam plus aztreonam (CZA-ATM) are preferred treatment regimens for New Delhi metallo-β-lactamase (NDM)-producing infections. Methods We report the case of a US patient who traveled to India to receive a renal transplant. He subsequently experienced pyelonephritis by an NDM-producing Escherichia coli. Broth microdilution and the broth disk elution method indicated resistance to all β-lactams, including cefiderocol and CZA-ATM. Whole-genome sequencing investigations were undertaken to identify resistance mechanisms. Results An E. coli isolate belonging to sequence type (ST) 167 containing a blaNDM-5 gene was identified on a plasmid of the IncFIA/IncFIB/IncFIC replicon groups. When compared with the genome of another ST167 E. coli clinical isolate containing blaNDM-5 and exhibiting susceptibility to cefiderocol and CZA-ATM, a 12-base pair insertion in ftsI, translating to a 4-amino acid duplication in PBP3, was identified. Moreover, a blaCMY-59 gene was harbored on an IncI-γ replicon type, and frameshift mutations were identified in the cirA iron transport gene. Conclusions This is the first clinical case of a US patient harboring an NDM-producing isolate exhibiting resistance to all available β-lactam agents. The isolate's unexpected resistance to cefiderocol and CZA-ATM was likely due to a combination of (1) a modified PBP3 (increased MICs to both regimens), (2) truncated iron-binding protein (increased cefiderocol MIC), and (3) a blaCMY gene (reduced CZA-ATM activity). E. coli ST167 clinical isolates harboring blaNDM-5 genes are a recognized international high-risk clone. When coupled with the additional mechanisms identified in our patient's isolate, which is not uncommon for this high-risk clone, pan-β-lactam resistance may occur.
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Affiliation(s)
- Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Emily Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tsigereda Tekle
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Pranita D Tamma
- Correspondence: Pranita D. Tamma, MD, MHS, Johns Hopkins University School of Medicine, 200 N. Wolfe Street, Room 3149, Baltimore, MD 21287 ()
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14
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Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
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Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
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15
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Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539914. [PMID: 37214973 PMCID: PMC10197589 DOI: 10.1101/2023.05.09.539914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam J. Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B. Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- current address: Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nicholas P. Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
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16
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Käshammer L, van den Ent F, Jeffery M, Jean NL, Hale VL, Löwe J. Cryo-EM structure of the bacterial divisome core complex and antibiotic target FtsWIQBL. Nat Microbiol 2023:10.1038/s41564-023-01368-0. [PMID: 37127704 DOI: 10.1038/s41564-023-01368-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
In most bacteria, cell division relies on the synthesis of new cell wall material by the multiprotein divisome complex. Thus, at the core of the divisome are the transglycosylase FtsW, which synthesises peptidoglycan strands from its substrate Lipid II, and the transpeptidase FtsI that cross-links these strands to form a mesh, shaping and protecting the bacterial cell. The FtsQ-FtsB-FtsL trimeric complex interacts with the FtsWI complex and is involved in regulating its enzymatic activities; however, the structure of this pentameric complex is unknown. Here, we present the cryogenic electron microscopy structure of the FtsWIQBL complex from Pseudomonas aeruginosa at 3.7 Å resolution. Our work reveals intricate structural details, including an extended coiled coil formed by FtsL and FtsB and the periplasmic interaction site between FtsL and FtsI. Our structure explains the consequences of previously reported mutations and we postulate a possible activation mechanism involving a large conformational change in the periplasmic domain. As FtsWIQBL is central to the divisome, our structure is foundational for the design of future experiments elucidating the precise mechanism of bacterial cell division, an important antibiotic target.
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Affiliation(s)
- Lisa Käshammer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Magnus Jeffery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolas L Jean
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Victoria L Hale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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17
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Zhang Q, Song B, Xu Y, Yang Y, Ji J, Cao W, Lu J, Ding J, Cao H, Chu B, Hong J, Wang H, He Y. In vivo bioluminescence imaging of natural bacteria within deep tissues via ATP-binding cassette sugar transporter. Nat Commun 2023; 14:2331. [PMID: 37087540 PMCID: PMC10122673 DOI: 10.1038/s41467-023-37827-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/03/2023] [Indexed: 04/24/2023] Open
Abstract
Most existing bioluminescence imaging methods can only visualize the location of engineered bacteria in vivo, generally precluding the imaging of natural bacteria. Herein, we leverage bacteria-specific ATP-binding cassette sugar transporters to internalize luciferase and luciferin by hitchhiking them on the unique carbon source of bacteria. Typically, the synthesized bioluminescent probes are made of glucose polymer (GP), luciferase, Cy5 and ICG-modified silicon nanoparticles and their substrates are made of GP and D-luciferin-modified silicon nanoparticles. Compared with bacteria with mutations in transporters, which hardly internalize the probes in vitro (i.e., ~2% of uptake rate), various bacteria could robustly engulf the probes with a high uptake rate of around 50%. Notably, the developed strategy enables ex vivo bioluminescence imaging of human vitreous containing ten species of pathogens collected from patients with bacterial endophthalmitis. By using this platform, we further differentiate bacterial and non-bacterial nephritis and colitis in mice, while their chemiluminescent counterparts are unable to distinguish them.
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Affiliation(s)
- Qian Zhang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Bin Song
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Yanan Xu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Yunmin Yang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Jian Ji
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Wenjun Cao
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China
| | - Jianping Lu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Jiali Ding
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Haiting Cao
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Binbin Chu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, China.
| | - Houyu Wang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China.
| | - Yao He
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China.
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18
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Liu M, Chu B, Sun R, Ding J, Ye H, Yang Y, Wu Y, Shi H, Song B, He Y, Wang H, Hong J. Antisense Oligonucleotides Selectively Enter Human-Derived Antibiotic-Resistant Bacteria through Bacterial-Specific ATP-Binding Cassette Sugar Transporter. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300477. [PMID: 37002615 DOI: 10.1002/adma.202300477] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Current vehicles used to deliver antisense oligonucleotides (ASOs) cannot distinguish between bacterial and mammalian cells, greatly hindering the preclinical or clinical treatment of bacterial infections, especially those caused by antibiotic-resistant bacteria. Herein, bacteria-specific ATP-binding cassette (ABC) sugar transporters are leveraged to selectively internalize ASOs by hitchhiking them on α (1-4)-glucosidically linked glucose polymers. Compared with their cell-penetrating peptide counterparts, which are non-specifically engulfed by mammalian and bacterial cells, the presented therapeutics consisting of glucose polymer and antisense peptide nucleic-acid-modified nanoparticles are selectively internalized into the human-derived multidrug-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus, and they display a much higher uptake rate (i.e., 51.6%). The developed strategy allows specific and efficient killing of nearly 100% of the antibiotic-resistant bacteria. Its significant curative efficacy against bacterial keratitis and endophthalmitis is also shown. This strategy will expand the focus of antisense technology to include bacterial cells other than mammalian cells.
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Affiliation(s)
- Mingzhu Liu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Binbin Chu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Rong Sun
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiali Ding
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Han Ye
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
| | - Yunmin Yang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yuqi Wu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Haoliang Shi
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Bin Song
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yao He
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Houyu Wang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
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19
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Frei A, Verderosa AD, Elliott AG, Zuegg J, Blaskovich MAT. Metals to combat antimicrobial resistance. Nat Rev Chem 2023; 7:202-224. [PMID: 37117903 PMCID: PMC9907218 DOI: 10.1038/s41570-023-00463-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2023] [Indexed: 02/10/2023]
Abstract
Bacteria, similar to most organisms, have a love-hate relationship with metals: a specific metal may be essential for survival yet toxic in certain forms and concentrations. Metal ions have a long history of antimicrobial activity and have received increasing attention in recent years owing to the rise of antimicrobial resistance. The search for antibacterial agents now encompasses metal ions, nanoparticles and metal complexes with antimicrobial activity ('metalloantibiotics'). Although yet to be advanced to the clinic, metalloantibiotics are a vast and underexplored group of compounds that could lead to a much-needed new class of antibiotics. This Review summarizes recent developments in this growing field, focusing on advances in the development of metalloantibiotics, in particular, those for which the mechanism of action has been investigated. We also provide an overview of alternative uses of metal complexes to combat bacterial infections, including antimicrobial photodynamic therapy and radionuclide diagnosis of bacterial infections.
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Affiliation(s)
- Angelo Frei
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Anthony D Verderosa
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alysha G Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A T Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
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20
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Karlowsky JA, Hackel MA, Wise MG, Six DA, Uehara T, Daigle DM, Cusick SM, Pevear DC, Moeck G, Sahm DF. In Vitro Activity of Cefepime-Taniborbactam and Comparators against Clinical Isolates of Gram-Negative Bacilli from 2018 to 2020: Results from the Global Evaluation of Antimicrobial Resistance via Surveillance (GEARS) Program. Antimicrob Agents Chemother 2023; 67:e0128122. [PMID: 36541767 PMCID: PMC9872668 DOI: 10.1128/aac.01281-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Taniborbactam is a novel cyclic boronate β-lactamase inhibitor in clinical development in combination with cefepime. We assessed the in vitro activity of cefepime-taniborbactam and comparators against a 2018-2020 collection of Enterobacterales (n = 13,731) and Pseudomonas aeruginosa (n = 4,619) isolates cultured from infected patients attending hospitals in 56 countries. MICs were determined by CLSI broth microdilution. Taniborbactam was tested at a fixed concentration of 4 μg/mL. Isolates with cefepime-taniborbactam MICs of ≥16 μg/mL underwent whole-genome sequencing. β-lactamase genes were identified in meropenem-resistant isolates by PCR/Sanger sequencing. Against Enterobacterales, taniborbactam reduced the cefepime MIC90 value by >64-fold (from >16 to 0.25 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 99.7% of all Enterobacterales isolates; >97% of isolates with multidrug-resistant (MDR) and ceftolozane-tazobactam-resistant phenotypes; ≥90% of isolates with meropenem-resistant, difficult-to-treat-resistant (DTR), meropenem-vaborbactam-resistant, and ceftazidime-avibactam-resistant phenotypes; 100% of VIM-positive, AmpC-positive, and KPC-positive isolates; 98.7% of extended-spectrum β-lactamase (ESBL)-positive; 98.8% of OXA-48-like-positive; and 84.6% of NDM-positive isolates. Against P. aeruginosa, taniborbactam reduced the cefepime MIC90 value by 4-fold (from 32 to 8 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 97.4% of all P. aeruginosa isolates; ≥85% of isolates with meropenem-resistant, MDR, and meropenem-vaborbactam-resistant phenotypes; >75% of isolates with DTR, ceftazidime-avibactam-resistant, and ceftolozane-tazobactam-resistant phenotypes; and 87.4% of VIM-positive isolates. Multiple potential mechanisms, including carriage of IMP, certain alterations in PBP3, permeability (porin) defects, and possibly, upregulation of efflux were present in most isolates with cefepime-taniborbactam MICs of ≥16 μg/mL. We conclude that cefepime-taniborbactam exhibited potent in vitro activity against Enterobacterales and P. aeruginosa and inhibited most carbapenem-resistant isolates, including those carrying serine carbapenemases or NDM/VIM metallo-β-lactamases (MBLs).
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Affiliation(s)
- James A. Karlowsky
- IHMA, Schaumburg, Illinois, USA
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - David A. Six
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
| | | | | | | | | | - Greg Moeck
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
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21
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Peukert C, Gasser V, Orth T, Fritsch S, Normant V, Cunrath O, Schalk IJ, Brönstrup M. Trojan Horse Siderophore Conjugates Induce Pseudomonas aeruginosa Suicide and Qualify the TonB Protein as a Novel Antibiotic Target. J Med Chem 2023; 66:553-576. [PMID: 36548006 PMCID: PMC9841981 DOI: 10.1021/acs.jmedchem.2c01489] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 12/24/2022]
Abstract
Rising infection rates with multidrug-resistant pathogens calls for antibiotics with novel modes of action. Herein, we identify the inner membrane protein TonB, a motor of active uptake in Gram-negative bacteria, as a novel target in antimicrobial therapy. The interaction of the TonB box of outer membrane transporters with TonB is crucial for the internalization of essential metabolites. We designed TonB box peptides and coupled them with synthetic siderophores in order to facilitate their uptake into bacteria in up to 32 synthetic steps. Three conjugates repressed the growth of Pseudomonas aeruginosa cells unable to produce their own siderophores, with minimal inhibitory concentrations between 0.1 and 0.5 μM. The transporters mediating uptake of these compounds were identified as PfeA and PirA. The study illustrates a variant of cellular suicide where a transporter imports its own inhibitor and demonstrates that artificial siderophores can import cargo with molecular weights up to 4 kDa.
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Affiliation(s)
- Carsten Peukert
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Véronique Gasser
- CNRS, University
of Strasbourg, UMR7242, ESBS, Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Till Orth
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Sarah Fritsch
- CNRS, University
of Strasbourg, UMR7242, ESBS, Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Vincent Normant
- CNRS, University
of Strasbourg, UMR7242, ESBS, Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Olivier Cunrath
- CNRS, University
of Strasbourg, UMR7242, ESBS, Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Isabelle J. Schalk
- CNRS, University
of Strasbourg, UMR7242, ESBS, Boulevard Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Mark Brönstrup
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- German
Center for Infection Research (DZIF), Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Center for
Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
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22
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Almeida MC, da Costa PM, Sousa E, Resende DISP. Emerging Target-Directed Approaches for the Treatment and Diagnosis of Microbial Infections. J Med Chem 2023; 66:32-70. [PMID: 36586133 DOI: 10.1021/acs.jmedchem.2c01212] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
With the rising levels of drug resistance, developing efficient antimicrobial therapies has become a priority. A promising strategy is the conjugation of antibiotics with relevant moieties that can potentiate their activity by target-directing. The conjugation of siderophores with antibiotics allows them to act as Trojan horses by hijacking the microorganisms' highly developed iron transport systems and using them to carry the antibiotic into the cell. Through the analysis of relevant examples of the past decade, this Perspective aims to reveal the potential of siderophore-antibiotic Trojan horses for the treatment of infections and the role of siderophores in diagnostic techniques. Other conjugated molecules will be the subject of discussion, namely those involving vitamin B12, carbohydrates, and amino acids, as well as conjugated compounds targeting protein degradation and β-lactamase activated prodrugs.
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Affiliation(s)
- Mariana C Almeida
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Paulo M da Costa
- CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Diana I S P Resende
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.,CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
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23
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Kiss-Szemán AJ, Takács L, Orgován Z, Stráner P, Jákli I, Schlosser G, Masiulis S, Harmat V, Menyhárd DK, Perczel A. A carbapenem antibiotic inhibiting a mammalian serine protease: structure of the acylaminoacyl peptidase-meropenem complex. Chem Sci 2022; 13:14264-14276. [PMID: 36545146 PMCID: PMC9749117 DOI: 10.1039/d2sc05520a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022] Open
Abstract
The structure of porcine AAP (pAAP) in a covalently bound complex with meropenem was determined by cryo-EM to 2.1 Å resolution, showing the mammalian serine-protease inhibited by a carbapenem antibiotic. AAP is a modulator of the ubiquitin-proteasome degradation system and the site of a drug-drug interaction between the widely used antipsychotic, valproate and carbapenems. The active form of pAAP - a toroidal tetramer - binds four meropenem molecules covalently linked to the catalytic Ser587 of the serine-protease triad, in an acyl-enzyme state. AAP is hindered from fully processing the antibiotic by the displacement and protonation of His707 of the catalytic triad. We show that AAP is made susceptible to the association by its unusually sheltered active pockets and flexible catalytic triads, while the carbapenems possess sufficiently small substituents on their β-lactam rings to fit into the shallow substrate-specificity pocket of the enzyme.
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Affiliation(s)
- Anna J. Kiss-Szemán
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary
| | - Luca Takács
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Pál Stráner
- ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Imre Jákli
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Gitta Schlosser
- ELKH-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Eötvös Loránd UniversityBudapestHungary
| | - Simonas Masiulis
- Materials and Structural Analysis Division, Thermo Fisher ScientificEindhovenThe Netherlands
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd UniversityPázmány Péter sétány 1/ABudapestHungary,ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research NetworkBudapestHungary+36-1-372-2500/1653+36-1-372-2500/6547
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24
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Sacco MD, Wang S, Adapa SR, Zhang X, Lewandowski EM, Gongora MV, Keramisanou D, Atlas ZD, Townsend JA, Gatdula JR, Morgan RT, Hammond LR, Marty MT, Wang J, Eswara PJ, Gelis I, Jiang RHY, Sun X, Chen Y. A unique class of Zn 2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Nat Commun 2022; 13:4370. [PMID: 35902581 PMCID: PMC9334274 DOI: 10.1038/s41467-022-32086-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.
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Affiliation(s)
- Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Shaohui Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Eric M Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Maura V Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | | | - Zachary D Atlas
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA
| | - Julia A Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jean R Gatdula
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Ryan T Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Lauren R Hammond
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prahathees J Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Rays H Y Jiang
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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Bové M, Coenye T. The anti-virulence activity of the non-mevalonate pathway inhibitor FR900098 towards Burkholderia cenocepacia is maintained during experimental evolution. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35358034 DOI: 10.1099/mic.0.001170] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Burkholderia cenocepacia infections are difficult to treat and there is an urgent need for alternative (combination) treatments. The use of anti-virulence therapies in combination with antibiotics is a possible strategy to increase the antimicrobial susceptibility of the pathogen and to slow down the development of resistance. In the present study we evaluated the β-lactam and colistin-potentiating activity, and anti-virulence effect of the non-mevalonate pathway inhibitor FR900098 against B. cenocepacia in various in vitro and in vivo models. In addition, we evaluated whether repeated exposure to FR900098 alone or when combined with ceftazidime leads to increased resistance. FR900098 potentiated the activity of colistin and several β-lactam antibiotics (aztreonam, cefepime, cefotaxime, ceftazidime, mecillinam and piperacillin) but not of imipenem and meropenem. When used alone or in combination with ceftazidime, FR900098 increased the survival of infected Galleria mellonella and Caenorhabditis elegans. Furthermore, combining ceftazidime with FR900098 resulted in a significant inhibition of the biofilm formation of B. cenocepacia. Repeated exposure to FR900098 in the C. elegans infection model did not lead to decreased activity, and the susceptibility of the evolved B. cenocepacia HI2424 lineages to ceftazidime, FR900098 and the combination of both remained unchanged. In conclusion, FR900098 reduces B. cenocepacia virulence and potentiates ceftazidime in an in vivo C. elegans model, and this activity is not lost during the experimental evolution experiment carried out in the present study.
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Affiliation(s)
- Mona Bové
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
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Structural Characterization of the D179N and D179Y Variants of KPC-2 β-Lactamase: Ω-Loop Destabilization as a Mechanism of Resistance to Ceftazidime-Avibactam. Antimicrob Agents Chemother 2022; 66:e0241421. [PMID: 35341315 DOI: 10.1128/aac.02414-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemases (KPC-2 and KPC-3) present a global clinical threat, as these β-lactamases confer resistance to carbapenems and oxyimino-cephalosporins. Recent clinically identified KPC variants with substitutions at Ambler position D179, located in the Ω loop, are resistant to the β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam, but susceptible to meropenem-vaborbactam. To gain insights into ceftazidime-avibactam resistance conferred by D179N/Y variants of KPC-2, crystal structures of these variants were determined. The D179N KPC-2 structure revealed that the change of the carboxyl to an amide moiety at position 179 disrupted the salt bridge with R164 present in wild-type KPC-2. Additional interactions were disrupted in the Ω loop, causing a decrease in the melting temperature. Shifts originating from N179 were also transmitted toward the active site, including ∼1-Å shifts of the deacylation water and interacting residue N170. The structure of the D179Y KPC-2 β-lactamase revealed more drastic changes, as this variant exhibited disorder of the Ω loop, with other flanking regions also being disordered. We postulate that the KPC-2 variants can accommodate ceftazidime because the Ω loop is displaced in D179Y or can be more readily displaced in D179N KPC-2. To understand why the β-lactamase inhibitor vaborbactam is less affected by the D179 variants than avibactam, we determined the crystal structure of D179N KPC-2 in complex with vaborbactam, which revealed wild-type KPC-2-like vaborbactam-active site interactions. Overall, the structural results regarding KPC-2 D179 variants revealed various degrees of destabilization of the Ω loop that contribute to ceftazidime-avibactam resistance, possible substrate-assisted catalysis of ceftazidime, and meropenem and meropenem-vaborbactam susceptibility.
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Antimicrobial Treatment Options for Difficult-to-Treat Resistant Gram-Negative Bacteria Causing Cystitis, Pyelonephritis, and Prostatitis: A Narrative Review. Drugs 2022; 82:407-438. [PMID: 35286622 PMCID: PMC9057390 DOI: 10.1007/s40265-022-01676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 02/06/2023]
Abstract
Urinary tract infections, including cystitis, acute pyelonephritis, and prostatitis, are among the most common diagnoses prompting antibiotic prescribing. The rise in antimicrobial resistance over the past decades has led to the increasing challenge of urinary tract infections because of multidrug-resistant and "difficult-to-treat resistance" among Gram-negative bacteria. Recent advances in pharmacotherapy and medical microbiology are modernizing how these urinary tract infections are treated. Advances in pharmacotherapy have included not only the development and approval of novel antibiotics, such as ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam, ceftolozane/tazobactam, cefiderocol, plazomicin, and glycylcyclines, but also the re-examination of the potential role of legacy antibiotics, including older aminoglycosides and tetracyclines. Recent advances in medical microbiology allow phenotypic and molecular mechanism of resistance testing, and thus antibiotic prescribing can be tailored to the mechanism of resistance in the infecting pathogen. Here, we provide a narrative review on the clinical and pre-clinical studies of drugs that can be used for difficult-to-treat resistant Gram-negative bacteria, with a particular focus on data relevant to the urinary tract. We also offer a pragmatic framework for antibiotic selection when encountering urinary tract infections due to difficult-to-treat resistant Gram-negative bacteria based on the organism and its mechanism of resistance.
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Galvão JLFM, Rosa LLS, Diniz Neto H, Silva DDF, Nóbrega JR, Cordeiro LV, Figueiredo PTRD, Andrade Júnior FPD, Oliveira Filho AAD, Lima EDO. Antibacterial effect of isoeugenol against Pseudomonas aeruginosa. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902022e20075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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29
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β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects. Pathogens 2021; 10:pathogens10121638. [PMID: 34959593 PMCID: PMC8706265 DOI: 10.3390/pathogens10121638] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen, causing a wide range of acute and chronic infections. β-lactam antibiotics including penicillins, carbapenems, monobactams, and cephalosporins play a key role in the treatment of P. aeruginosa infections. However, a significant number of isolates of these bacteria are resistant to β-lactams, complicating treatment of infections and leading to worse outcomes for patients. In this review, we summarize studies demonstrating the health and economic impacts associated with β-lactam-resistant P. aeruginosa. We then describe how β-lactams bind to and inhibit P. aeruginosa penicillin-binding proteins that are required for synthesis and remodelling of peptidoglycan. Resistance to β-lactams is multifactorial and can involve changes to a key target protein, penicillin-binding protein 3, that is essential for cell division; reduced uptake or increased efflux of β-lactams; degradation of β-lactam antibiotics by increased expression or altered substrate specificity of an AmpC β-lactamase, or by the acquisition of β-lactamases through horizontal gene transfer; and changes to biofilm formation and metabolism. The current understanding of these mechanisms is discussed. Lastly, important knowledge gaps are identified, and possible strategies for enhancing the effectiveness of β-lactam antibiotics in treating P. aeruginosa infections are considered.
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Kumar V, Viviani SL, Ismail J, Agarwal S, Bonomo RA, van den Akker F. Structural analysis of the boronic acid β-lactamase inhibitor vaborbactam binding to Pseudomonas aeruginosa penicillin-binding protein 3. PLoS One 2021; 16:e0258359. [PMID: 34653211 PMCID: PMC8519428 DOI: 10.1371/journal.pone.0258359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial resistance (AMR) mediated by β-lactamases is the major and leading cause of resistance to penicillins and cephalosporins among Gram-negative bacteria. β-Lactamases, periplasmic enzymes that are widely distributed in the bacterial world, protect penicillin-binding proteins (PBPs), the major cell wall synthesizing enzymes, from inactivation by β-lactam antibiotics. Developing novel PBP inhibitors with a non-β-lactam scaffold could potentially evade this resistance mechanism. Based on the structural similarities between the evolutionary related serine β-lactamases and PBPs, we investigated whether the potent β-lactamase inhibitor, vaborbactam, could also form an acyl-enzyme complex with Pseudomonas aeruginosa PBP3. We found that this cyclic boronate, vaborbactam, inhibited PBP3 (IC50 of 262 μM), and its binding to PBP3 increased the protein thermal stability by about 2°C. Crystallographic analysis of the PBP3:vaborbactam complex reveals that vaborbactam forms a covalent bond with the catalytic S294. The amide moiety of vaborbactam hydrogen bonds with N351 and the backbone oxygen of T487. The carboxyl group of vaborbactam hydrogen bonds with T487, S485, and S349. The thiophene ring and cyclic boronate ring of vaborbactam form hydrophobic interactions, including with V333 and Y503. The active site of the vaborbactam-bound PBP3 harbors the often observed ligand-induced formation of the aromatic wall and hydrophobic bridge, yet the residues involved in this wall and bridge display much higher temperature factors compared to PBP3 structures bound to high-affinity β-lactams. These insights could form the basis for developing more potent novel cyclic boronate-based PBP inhibitors to inhibit these targets and overcome β-lactamases-mediated resistance mechanisms.
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Affiliation(s)
- Vijay Kumar
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Samantha L. Viviani
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeeda Ismail
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Shreya Agarwal
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert A. Bonomo
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
- Louis Stokes Cleveland Veteran’s Affairs Medical Center Research Service, Cleveland, Ohio, United States of America
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio, United States of America
- VA Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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Newman H, Krajnc A, Bellini D, Eyermann CJ, Boyle GA, Paterson NG, McAuley KE, Lesniak R, Gangar M, von Delft F, Brem J, Chibale K, Schofield CJ, Dowson CG. High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes. J Med Chem 2021; 64:11379-11394. [PMID: 34337941 PMCID: PMC9282634 DOI: 10.1021/acs.jmedchem.1c00717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effectiveness of β-lactam antibiotics is increasingly compromised by β-lactamases. Boron-containing inhibitors are potent serine-β-lactamase inhibitors, but the interactions of boron-based compounds with the penicillin-binding protein (PBP) β-lactam targets have not been extensively studied. We used high-throughput X-ray crystallography to explore reactions of a boron-containing fragment set with the Pseudomonas aeruginosa PBP3 (PaPBP3). Multiple crystal structures reveal that boronic acids react with PBPs to give tricovalently linked complexes bonded to Ser294, Ser349, and Lys484 of PaPBP3; benzoxaboroles react with PaPBP3 via reaction with two nucleophilic serines (Ser294 and Ser349) to give dicovalently linked complexes; and vaborbactam reacts to give a monocovalently linked complex. Modifications of the benzoxaborole scaffold resulted in a moderately potent inhibition of PaPBP3, though no antibacterial activity was observed. Overall, the results further evidence the potential for the development of new classes of boron-based antibiotics, which are not compromised by β-lactamase-driven resistance.
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Affiliation(s)
- Hector Newman
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Alen Krajnc
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Dom Bellini
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Charles J. Eyermann
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Grant A. Boyle
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Neil G. Paterson
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Katherine E. McAuley
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Robert Lesniak
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Mukesh Gangar
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Frank von Delft
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Structural
Genomics Consortium (SGC), University of
Oxford, Oxford, U.K.
- Department
of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, Didcot OX11 0FA, U.K.
| | - Jürgen Brem
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch 7701, South Africa
| | - Christopher J. Schofield
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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32
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Freischem S, Grimm I, López-Pérez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergräber OH. Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Biomolecules 2021; 11:biom11071057. [PMID: 34356681 PMCID: PMC8301747 DOI: 10.3390/biom11071057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/05/2023] Open
Abstract
Novel antimicrobial strategies are urgently required because of the rising threat of multi drug resistant bacterial strains and the infections caused by them. Among the available target structures, the so-called penicillin binding proteins are of particular interest, owing to their good accessibility in the periplasmic space, and the lack of homologous proteins in humans, reducing the risk of side effects of potential drugs. In this report, we focus on the interaction of the innovative β-lactam antibiotic AIC499 with penicillin binding protein 3 (PBP3) from Escherichia coli and Pseudomonas aeruginosa. This recently developed monobactam displays broad antimicrobial activity, against Gram-negative strains, and improved resistance to most classes of β-lactamases. By analyzing crystal structures of the respective complexes, we were able to explore the binding mode of AIC499 to its target proteins. In addition, the apo structures determined for PBP3, from P. aeruginosa and the catalytic transpeptidase domain of the E. coli orthologue, provide new insights into the dynamics of these proteins and the impact of drug binding.
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Affiliation(s)
- Stefan Freischem
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Immanuel Grimm
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Arancha López-Pérez
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Type NE2 4AX, UK
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Burkhard Klenke
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Cuong Vuong
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Andrew J. Dingley
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Correspondence:
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A γ-lactam siderophore antibiotic effective against multidrug-resistant Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter spp. Eur J Med Chem 2021; 220:113436. [PMID: 33933754 DOI: 10.1016/j.ejmech.2021.113436] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Serious infections caused by multidrug-resistant (MDR) organisms (Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii) present a critical need for innovative drug development. Herein, we describe the preclinical evaluation of YU253911, 2, a novel γ-lactam siderophore antibiotic with potent antimicrobial activity against MDR Gram-negative pathogens. Penicillin-binding protein (PBP) 3 was shown to be a target of 2 using a binding assay with purified P. aeruginosa PBP3. The specific binding interactions with P. aeruginosa were further characterized with a high-resolution (2.0 Å) X-ray structure of the compound's acylation product in P. aeruginosa PBP3. Compound 2 was shown to have a concentration >1 μg/ml at the 6 h time point when administered intravenously or subcutaneously in mice. Employing a meropenem resistant strain of P. aeruginosa, 2 was shown to have dose-dependent efficacy at 50 and 100 mg/kg q6h dosing in a mouse thigh infection model. Lastly, we showed that a novel γ-lactam and β-lactamase inhibitor (BLI) combination can effectively lower minimum inhibitory concentrations (MICs) against carbapenem resistant Acinetobacter spp. that demonstrated decreased susceptibility to 2 alone.
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Yoon EJ, Jeong SH. Mobile Carbapenemase Genes in Pseudomonas aeruginosa. Front Microbiol 2021; 12:614058. [PMID: 33679638 PMCID: PMC7930500 DOI: 10.3389/fmicb.2021.614058] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Structural Characterization of Diazabicyclooctane β-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. mBio 2021; 12:mBio.03058-20. [PMID: 33593978 PMCID: PMC8545096 DOI: 10.1128/mbio.03058-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant (MDR) pathogens pose a significant public health threat. A major mechanism of resistance expressed by MDR pathogens is β-lactamase-mediated degradation of β-lactam antibiotics. The diazabicyclooctane (DBO) compounds zidebactam and WCK 5153, recognized as β-lactam “enhancers” due to inhibition of Pseudomonas aeruginosa penicillin-binding protein 2 (PBP2), are also class A and C β-lactamase inhibitors. To structurally probe their mode of PBP2 inhibition as well as investigate why P. aeruginosa PBP2 is less susceptible to inhibition by β-lactam antibiotics compared to the Escherichia coli PBP2, we determined the crystal structure of P. aeruginosa PBP2 in complex with WCK 5153. WCK 5153 forms an inhibitory covalent bond with the catalytic S327 of PBP2. The structure suggests a significant role for the diacylhydrazide moiety of WCK 5153 in interacting with the aspartate in the S-X-N/D PBP motif. Modeling of zidebactam in the active site of PBP2 reveals a similar binding mode. Both DBOs increase the melting temperature of PBP2, affirming their stabilizing interactions. To aid in the design of DBOs that can inhibit multiple PBPs, the ability of three DBOs to interact with P. aeruginosa PBP3 was explored crystallographically. Even though the DBOs show covalent binding to PBP3, they destabilized PBP3. Overall, the studies provide insights into zidebactam and WCK 5153 inhibition of PBP2 compared to their inhibition of PBP3 and the evolutionarily related KPC-2 β-lactamase. These molecular insights into the dual-target DBOs advance our knowledge regarding further DBO optimization efforts to develop novel potent β-lactamase-resistant, non-β-lactam PBP inhibitors.
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De Rosa M, Verdino A, Soriente A, Marabotti A. The Odd Couple(s): An Overview of Beta-Lactam Antibiotics Bearing More Than One Pharmacophoric Group. Int J Mol Sci 2021; 22:ijms22020617. [PMID: 33435500 PMCID: PMC7826672 DOI: 10.3390/ijms22020617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 01/15/2023] Open
Abstract
β-lactam antibiotics are among the most important and widely used antimicrobials worldwide and are comprised of a large family of compounds, obtained by chemical modifications of the common scaffolds. Usually these modifications include the addition of active groups, but less frequently, molecules were synthesized in which either two β-lactam rings were joined to create a single bifunctional compound, or the azetidinone ring was joined to another antibiotic scaffold or another molecule with a different activity, in order to create a molecule bearing two different pharmacophoric functions. In this review, we report some examples of these derivatives, highlighting their biological properties and discussing how this strategy can lead to the development of innovative antibiotics that can represent either novel weapons against the rampant increase of antimicrobial resistance, or molecules with a broader spectrum of action.
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Affiliation(s)
- Margherita De Rosa
- Correspondence: (M.D.R.); (A.M.); Tel.: +39-089-969553 (M.D.R.); +39-089-969583 (A.M.)
| | | | | | - Anna Marabotti
- Correspondence: (M.D.R.); (A.M.); Tel.: +39-089-969553 (M.D.R.); +39-089-969583 (A.M.)
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37
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Cordeiro L, Diniz-Neto H, Figueiredo P, Souza H, Sousa A, Andrade-Júnior F, Melo T, Ferreira E, Oliveira R, Athayde-Filho P, Barbosa-Filho J, Oliveira-Filho A, Lima E. Potential of 2-Chloro- N-(4-fluoro-3-nitrophenyl)acetamide Against Klebsiella pneumoniae and In Vitro Toxicity Analysis. Molecules 2020; 25:molecules25173959. [PMID: 32877986 PMCID: PMC7504751 DOI: 10.3390/molecules25173959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae causes a wide range of community and nosocomial infections. The high capacity of this pathogen to acquire resistance drugs makes it necessary to develop therapeutic alternatives, discovering new antibacterial molecules. Acetamides are molecules that have several biological activities. However, there are no reports on the activity of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide. Based on this, this study aimed to investigate the in vitro antibacterial activity of this molecule on K. pneumoniae, evaluating whether the presence of the chloro atom improves this effect. Then, analyzing its antibacterial action more thoroughly, as well as its cytotoxic and pharmacokinetic profile, in order to contribute to future studies for the viability of a new antibacterial drug. It was shown that the substance has good potential against K. pneumoniae and the chloro atom is responsible for improving this activity, stabilizing the molecule in the target enzyme at the site. The substance possibly acts on penicillin-binding protein, promoting cell lysis. The analysis of cytotoxicity and mutagenicity shows favorable results for future in vivo toxicological tests to be carried out, with the aim of investigating the potential of this molecule. In addition, the substance showed an excellent pharmacokinetic profile, indicating good parameters for oral use.
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Affiliation(s)
- Laísa Cordeiro
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
- Correspondence: ; Tel.: +55-83-3216-7347
| | - Hermes Diniz-Neto
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Pedro Figueiredo
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Helivaldo Souza
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - Aleson Sousa
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Francisco Andrade-Júnior
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Thamara Melo
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Elba Ferreira
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Rafael Oliveira
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - Petrônio Athayde-Filho
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Brazil; (H.S.); (R.O.); (P.A.-F.)
| | - José Barbosa-Filho
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
| | - Abrahão Oliveira-Filho
- Rural Health and Technology Center, Federal University of Campina Grande, 58708-110 Patos, Brazil;
| | - Edeltrudes Lima
- Department of Pharmaceutical Science, Health Sciences Center, Federal University of Paraíba, 58033-455 João Pessoa, Paraíba, Brazil; (H.D.-N.); (P.F.); (A.S.); (F.A.-J.); (T.M.); (E.F.); (J.B.-F.); (E.L.)
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38
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Goldberg JA, Nguyen H, Kumar V, Spencer EJ, Hoyer D, Marshall EK, Cmolik A, O'Shea M, Marshall SH, Hujer AM, Hujer KM, Rudin SD, Domitrovic TN, Bethel CR, Papp-Wallace KM, Logan LK, Perez F, Jacobs MR, van Duin D, Kreiswirth BM, Bonomo RA, Plummer MS, van den Akker F. A γ-Lactam Siderophore Antibiotic Effective against Multidrug-Resistant Gram-Negative Bacilli. J Med Chem 2020; 63:5990-6002. [PMID: 32420736 DOI: 10.1021/acs.jmedchem.0c00255] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Treatment of multidrug-resistant Gram-negative bacterial pathogens represents a critical clinical need. Here, we report a novel γ-lactam pyrazolidinone that targets penicillin-binding proteins (PBPs) and incorporates a siderophore moiety to facilitate uptake into the periplasm. The MIC values of γ-lactam YU253434, 1, are reported along with the finding that 1 is resistant to hydrolysis by all four classes of β-lactamases. The druglike characteristics and mouse PK data are described along with the X-ray crystal structure of 1 binding to its target PBP3.
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Affiliation(s)
- Joel A Goldberg
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Ha Nguyen
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Elizabeth J Spencer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Denton Hoyer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Emma K Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Anna Cmolik
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Margaret O'Shea
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Kristine M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - T Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Latania K Logan
- Department of Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, Illinois 60612, United States.,Cook County Health and Hospital Systems, Chicago, Illinois 60612, United States
| | - Federico Perez
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Michael R Jacobs
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Pathology, University Hospitals Cleveland Medical Center, Division of Clinical Microbiology, Cleveland, Ohio 44106, United States
| | - David van Duin
- University of North Carolina School of Medicine, Chapel Hill, North Carolina 27514, United States
| | - Barry M Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07601, United States
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.,Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Mark S Plummer
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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39
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Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase. Antimicrob Agents Chemother 2020; 64:AAC.00123-20. [PMID: 32205343 PMCID: PMC7269475 DOI: 10.1128/aac.00123-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022] Open
Abstract
Multidrug resistance among Gram-negative bacteria is a major global public health threat. Metallo-β-lactamases (MBLs) target the most widely used antibiotic class, the β-lactams, including the most recent generation of carbapenems. Interspecies spread renders these enzymes a serious clinical threat, and there are no clinically available inhibitors. We present the crystal structures of IMP-13, a structurally uncharacterized MBL from the Gram-negative bacterium Pseudomonas aeruginosa found in clinical outbreaks globally, and characterize the binding using solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The crystal structures of apo IMP-13 and IMP-13 bound to four clinically relevant carbapenem antibiotics (doripenem, ertapenem, imipenem, and meropenem) are presented. Active-site plasticity and the active-site loop, where a tryptophan residue stabilizes the antibiotic core scaffold, are essential to the substrate-binding mechanism. The conserved carbapenem scaffold plays the most significant role in IMP-13 binding, explaining the broad substrate specificity. The observed plasticity and substrate-locking mechanism provide opportunities for rational drug design of novel metallo-β-lactamase inhibitors, essential in the fight against antibiotic resistance.
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40
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Hypermutator Pseudomonas aeruginosa Exploits Multiple Genetic Pathways To Develop Multidrug Resistance during Long-Term Infections in the Airways of Cystic Fibrosis Patients. Antimicrob Agents Chemother 2020; 64:AAC.02142-19. [PMID: 32071060 DOI: 10.1128/aac.02142-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/20/2019] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa exploits intrinsic and acquired resistance mechanisms to resist almost every antibiotic used in chemotherapy. Antimicrobial resistance in P. aeruginosa isolates recovered from cystic fibrosis (CF) patients is further enhanced by the occurrence of hypermutator strains, a hallmark of chronic infections in CF patients. However, the within-patient genetic diversity of P. aeruginosa populations related to antibiotic resistance remains unexplored. Here, we show the evolution of the mutational resistome profile of a P. aeruginosa hypermutator lineage by performing longitudinal and transversal analyses of isolates collected from a CF patient throughout 20 years of chronic infection. Our results show the accumulation of thousands of mutations, with an overall evolutionary history characterized by purifying selection. However, mutations in antibiotic resistance genes appear to have been positively selected, driven by antibiotic treatment. Antibiotic resistance increased as infection progressed toward the establishment of a population constituted by genotypically diversified coexisting sublineages, all of which converged to multidrug resistance. These sublineages emerged by parallel evolution through distinct evolutionary pathways, which affected genes of the same functional categories. Interestingly, ampC and ftsI, encoding the β-lactamase and penicillin-binding protein 3, respectively, were found to be among the most frequently mutated genes. In fact, both genes were targeted by multiple independent mutational events, which led to a wide diversity of coexisting alleles underlying β-lactam resistance. Our findings indicate that hypermutators, apart from boosting antibiotic resistance evolution by simultaneously targeting several genes, favor the emergence of adaptive innovative alleles by clustering beneficial/compensatory mutations in the same gene, hence expanding P. aeruginosa strategies for persistence.
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41
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Structural Insights into Ceftobiprole Inhibition of Pseudomonas aeruginosa Penicillin-Binding Protein 3. Antimicrob Agents Chemother 2020; 64:AAC.00106-20. [PMID: 32152075 DOI: 10.1128/aac.00106-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/28/2020] [Indexed: 02/08/2023] Open
Abstract
Ceftobiprole is an advanced-generation broad-spectrum cephalosporin antibiotic with potent and rapid bactericidal activity against Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus, as well as susceptible Gram-negative pathogens, including Pseudomonas sp. pathogens. In the case of Pseudomonas aeruginosa, ceftobiprole acts by inhibiting P. aeruginosa penicillin-binding protein 3 (PBP3). Structural studies were pursued to elucidate the molecular details of this PBP inhibition. The crystal structure of the His-tagged PBP3-ceftobiprole complex revealed a covalent bond between the ligand and the catalytic residue S294. Ceftobiprole binding leads to large active site changes near binding sites for the pyrrolidinone and pyrrolidine rings. The S528 to L536 region adopts a conformation previously not observed in PBP3, including partial unwinding of the α11 helix. These molecular insights can lead to a deeper understanding of β-lactam-PBP interactions that result in major changes in protein structure, as well as suggesting how to fine-tune current inhibitors and to develop novel inhibitors of this PBP.
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42
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Cascioferro S, Parrino B, Carbone D, Schillaci D, Giovannetti E, Cirrincione G, Diana P. Thiazoles, Their Benzofused Systems, and Thiazolidinone Derivatives: Versatile and Promising Tools to Combat Antibiotic Resistance. J Med Chem 2020; 63:7923-7956. [PMID: 32208685 PMCID: PMC7997583 DOI: 10.1021/acs.jmedchem.9b01245] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Thiazoles,
their benzofused systems, and thiazolidinone derivatives
are widely recognized as nuclei of great value for obtaining molecules
with various biological activities, including analgesic, anti-inflammatory,
anti-HIV, antidiabetic, antitumor, and antimicrobial. In particular,
in the past decade, many compounds bearing these heterocycles have
been studied for their promising antibacterial properties due to their
action on different microbial targets. Here we assess the recent development
of this class of compounds to address mechanisms underlying antibiotic
resistance at both bacterial-cell and community levels (biofilms).
We also explore the SAR and the prospective clinical application of
thiazole and its benzofused derivatives, which act as inhibitors of
mechanisms underlying antibiotic resistance in the treatment of severe
drug-resistant infections. In addition, we examined all bacterial
targets involved in their antimicrobial activity reporting, when described,
their spontaneous frequencies of resistance.
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Affiliation(s)
- Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Daniela Carbone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, DeBoelelaan 1117, 1081HV, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, via Giovannini 13, 56017 San Giuliano Terme, Pisa, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
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43
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Lu Z, Wang H, Zhang A, Liu X, Zhou W, Yang C, Guddat L, Yang H, Schofield CJ, Rao Z. Structures of Mycobacterium tuberculosis Penicillin-Binding Protein 3 in Complex with Five β-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol Pharmacol 2020; 97:287-294. [DOI: 10.1124/mol.119.118042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/14/2020] [Indexed: 11/22/2022] Open
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44
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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45
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Borisov DV, Veselovsky AV. [Ligand-receptor binding kinetics in drug design]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:42-53. [PMID: 32116225 DOI: 10.18097/pbmc20206601042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured <i>in vitro</i> at steady concentrations of the receptor and ligand, which are differed from <i>in vivo</i> environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.
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Affiliation(s)
- D V Borisov
- Institute of Biomedical Chemistry, Moscow, Russia
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46
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Influence of the α-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 β-Lactamase. Antimicrob Agents Chemother 2019; 64:AAC.01473-19. [PMID: 31685462 DOI: 10.1128/aac.01473-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/26/2022] Open
Abstract
The prevalence of multidrug-resistant Pseudomonas aeruginosa has led to the reexamination of older "forgotten" drugs, such as temocillin, for their ability to combat resistant microbes. Temocillin is the 6-α-methoxy analogue of ticarcillin, a carboxypenicillin with well-characterized antipseudomonal properties. The α-methoxy modification confers resistance to serine β-lactamases, yet temocillin is ineffective against P. aeruginosa growth. The origins of temocillin's inferior antibacterial properties against P. aeruginosa have remained relatively unexplored. Here, we analyze the reaction kinetics, protein stability, and binding conformations of temocillin and ticarcillin with penicillin-binding protein 3 (PBP3), an essential PBP in P. aeruginosa We show that the 6-α-methoxy group perturbs the stability of the PBP3 acyl-enzyme, which manifests in an elevated off-rate constant (k off) in biochemical assays comparing temocillin with ticarcillin. Complex crystal structures with PBP3 reveal similar binding modes of the two drugs but with important differences. Most notably, the 6-α-methoxy group disrupts a high-quality hydrogen bond with a conserved residue important for ligand binding while also being inserted into a crowded active site, possibly destabilizing the active site and enabling water molecule from bulk solvent to access and cleave the acyl-enzyme bond. This hypothesis is supported by the observation that the acyl-enzyme complex of temocillin has reduced thermal stability compared with ticarcillin. Furthermore, we explore temocillin's mechanism of β-lactamase inhibition with a high-resolution complex structure of CTX-M-14 class A serine β-lactamase. The results suggest that the α-methoxy group prevents hydrolysis by locking the compound into an unexpected conformation that impedes access of the catalytic water to the acyl-enzyme adduct.
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47
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Li ZW, Lu X, Wang YX, Hu XX, Fu HG, Gao LM, You XF, Tang S, Song DQ. Synthesis and antibacterial evaluation against resistant Gram-negative bacteria of monobactams bearing various substituents on oxime residue. Bioorg Chem 2019; 94:103487. [PMID: 31831161 DOI: 10.1016/j.bioorg.2019.103487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/30/2019] [Accepted: 11/27/2019] [Indexed: 01/21/2023]
Abstract
Based on the structural characteristics of aztreonam (AZN) and its target PBP3, a series of new monobactam derivatives bearing various substituents on oxime residue were prepared and evaluated for their antibacterial activities against susceptible and resistant Gram-negative bacteria. Among them, compounds 8p and 8r displayed moderate potency with MIC values of 0.125-32 μg/mL against most tested Gram-negative strains, comparable to AZN. Meanwhile, the combination of 8p and 8r with avibactam as a β-lactamases inhibitor, in a ratio of 1:16, showed a promising synergistic effect against both ESBLs- and NDM-1-producing K. pneumoniae, with significantly reduced MIC values up to 8-fold and >256-fold respectively. Furthermore, both of them demonstrated excellent safety profiles both in vitro and in vivo. The results provided powerful information for further structural optimization of monobactam antibiotics to fight β-lactamase-producing resistant Gram-negative bacteria.
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Affiliation(s)
- Zhi-Wen Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xi Lu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yan-Xiang Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xin-Xin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hai-Gen Fu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Li-Mei Gao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xue-Fu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Sheng Tang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Dan-Qing Song
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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48
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Page MGP. The Role of Iron and Siderophores in Infection, and the Development of Siderophore Antibiotics. Clin Infect Dis 2019; 69:S529-S537. [PMID: 31724044 PMCID: PMC6853763 DOI: 10.1093/cid/ciz825] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Iron is an essential nutrient for bacterial growth, replication, and metabolism. Humans store iron bound to various proteins such as hemoglobin, haptoglobin, transferrin, ferritin, and lactoferrin, limiting the availability of free iron for pathogenic bacteria. However, bacteria have developed various mechanisms to sequester or scavenge iron from the host environment. Iron can be taken up by means of active transport systems that consist of bacterial small molecule siderophores, outer membrane siderophore receptors, the TonB-ExbBD energy-transducing proteins coupling the outer and the inner membranes, and inner membrane transporters. Some bacteria also express outer membrane receptors for iron-binding proteins of the host and extract iron directly from these for uptake. Ultimately, iron is acquired and transported into the bacterial cytoplasm. The siderophores are small molecules produced and released by nearly all bacterial species and are classified according to the chemical nature of their iron-chelating group (ie, catechol, hydroxamate, α-hydroxyl-carboxylate, or mixed types). Siderophore-conjugated antibiotics that exploit such iron-transport systems are under development for the treatment of infections caused by gram-negative bacteria. Despite demonstrating high in vitro potency against pathogenic multidrug-resistant bacteria, further development of several candidates had stopped due to apparent adaptive resistance during exposure, lack of consistent in vivo efficacy, or emergence of side effects in the host. However, cefiderocol, with an optimized structure, has advanced and has been investigated in phase 1 to 3 clinical trials. This article discusses the mechanisms implicated in iron uptake and the challenges associated with the design and utilization of siderophore-mimicking antibiotics.
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Affiliation(s)
- Malcom G P Page
- Life Sciences and Chemistry, Jacobs University, Bremen gGmbh, Bremen, Germany
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El-Shorbagi AN, Chaudhary S. Monobactams: A Unique Natural Scaffold of Four-Membered Ring Skeleton, Recent Development to Clinically Overcome Infections by Multidrug- Resistant Microbes. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666190516113202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background:
Monobactam antibiotics have been testified to demonstrate significant antibacterial
activity especially the treatment of infections by superbug microbes. Recently, research has
been focused on the structural modifications, and new generation of this privileged natural scaffold.
Objective:
Efforts have been made to discover the structure-antibacterial relationship of monbactams
in order to avoid the aimless work involving the ongoing generated analogues. This review aims to
summarize the current knowledge and development of monobactams as a broad-spectrum antibacterial
scaffolds. The recent structural modifications that expand the activity, especially in the infections
by resistant-strains, combinational therapies and dosing, as well as the possibility of crosshypersensitivity/
reactivity/tolerability with penicillins and cephalosporins will also be summarized
and inferred. Different approaches will be covered with emphasis on chemical methods and Structure-
Activity Relationship (SAR), in addition to the proposed mechanisms of action. Clinical investigation
of monobactams tackling various aspects will not be missed in this review.
Conclusion:
The conclusion includes the novels approaches, that could be followed to design new
research projects and reduce the pitfalls in the future development of monobactams.
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Affiliation(s)
- Abdel Nasser El-Shorbagi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Sachin Chaudhary
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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Cabot G, Florit-Mendoza L, Sánchez-Diener I, Zamorano L, Oliver A. Deciphering β-lactamase-independent β-lactam resistance evolution trajectories in Pseudomonas aeruginosa. J Antimicrob Chemother 2019; 73:3322-3331. [PMID: 30189050 DOI: 10.1093/jac/dky364] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 08/13/2018] [Indexed: 11/14/2022] Open
Abstract
Background While resistance related to the expression of β-lactamases, such as AmpC from Pseudomonas aeruginosa, has been deeply studied, this work addresses the gap in the knowledge of other potential bacterial strategies to overcome the activity of β-lactams when β-lactamases are not expressed. Methods We analysed β-lactam resistance evolution trajectories in a WT strain and in isogenic mutants either lacking AmpC (AmpC mutant) or unable to express it (AmpG mutant), exposed to increasing concentrations of ceftazidime for 7 days in quintuplicate experiments. Characterization of evolved lineages included susceptibility profiles, whole-genome sequences, resistance mechanisms, fitness (competitive growth assays) and virulence (Caenorhabditis elegans model). Results Development of resistance was faster for the WT strain but, after 7 days, all strains reached clinical ceftazidime resistance levels. The main resistance mechanism in the WT strain was ampC overexpression, due to mutations in dacB and ampD or mpl. In contrast, ampC overexpression did not evolve in any of the AmpG lineages. Moreover, sequencing of the ΔAmpC and ΔAmpG evolved lineages revealed alternative resistance mutations (not seen in WT lineages) that included, in all cases, large (50-600 kb) deletions of specific chromosomal regions together with mutations leading to β-lactam target [ftsI (PBP3)] modification and/or the overexpression or structural modification of the efflux pump MexAB-OprM. Finally, evolved lineages from the AmpC and, especially, AmpG mutants showed a reduced fitness and virulence. Conclusions In addition to providing new insights into β-lactam resistance mechanisms and evolution, our findings should be helpful for guiding future strategies to combat P. aeruginosa infections.
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Affiliation(s)
- Gabriel Cabot
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Llorenç Florit-Mendoza
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Irina Sánchez-Diener
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Laura Zamorano
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
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