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Jiao F, Bao Y, Li M, Zhang Y, Zhang F, Wang P, Tao J, Tong HHY, Guo J. Unraveling the mechanism of ceftaroline-induced allosteric regulation in penicillin-binding protein 2a: insights for novel antibiotic development against methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0089523. [PMID: 37971241 PMCID: PMC10720500 DOI: 10.1128/aac.00895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) acquires high-level resistance against β-lactam antibiotics by expressing penicillin-binding protein 2a (PBP2a). PBP2a is a cell wall-synthesizing protein whose closed active site exhibits a reduced binding affinity toward β-lactam antibiotics. Ceftaroline (CFT), a fifth-generation cephalosporin, can effectively inhibit the PBP2a activity by binding to an allosteric site to trigger the active site opening, allowing a second CFT to access the active site. However, the essential mechanism behind the allosteric behavior of PBP2a remains unclear. Herein, computational simulations are employed to elucidate how CFT allosterically regulates the conformation and dynamics of the active site of PBP2a. While CFT stabilizes the allosteric domain surrounding it, it simultaneously enhances the dynamics of the catalytic domain. Specifically, the study successfully captured the opening process of the active pocket in the allosteric CFT-bound systems and discovered that CFT alters the potential signal-propagating pathways from the allosteric site to the active site. These findings reveal the implied mechanism of the CFT-mediated allostery in PBP2a and provide new insights into dual-site drug design or combination therapy against MRSA targeting PBP2a.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H. Y. Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
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2
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Baran A, Kwiatkowska A, Potocki L. Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race. Int J Mol Sci 2023; 24:ijms24065777. [PMID: 36982857 PMCID: PMC10056106 DOI: 10.3390/ijms24065777] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.
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Affiliation(s)
- Aleksandra Baran
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
| | - Aleksandra Kwiatkowska
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszów, ul. Towarnickiego 3, 35-959 Rzeszów, Poland
| | - Leszek Potocki
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
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3
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Wu RA, Feng J, Yue M, Liu D, Ding T. Overuse of food-grade disinfectants threatens a global spread of antimicrobial-resistant bacteria. Crit Rev Food Sci Nutr 2023; 64:6870-6879. [PMID: 36756870 DOI: 10.1080/10408398.2023.2176814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Food-grade disinfectants are extensively used for microbial decontamination of food processing equipment. In recent years, food-grade disinfectants have been increasingly used. However, the overuse of disinfectants causes another major issue, which is the emergence and spread of antimicrobial-resistant bacteria on a global scale. As the ongoing pandemic takes global attention, bacterial infections with antibiotic resistance are another ongoing pandemic that often goes unnoticed and will be the next real threat to humankind. Here, the effects of food-grade disinfectant overuse on the global emergence and spread of antimicrobial-resistant bacteria were reviewed. It was found that longtime exposure to the most common food-grade disinfectants promoted resistance to clinically important antibiotics in pathogenic bacteria, namely cross-resistance. Currently, the use of disinfectants is largely unregulated. The mechanisms of cross-resistance are regulated by intrinsic molecular mechanisms including efflux pumps, DNA repair system, modification of the molecular target, and metabolic adaptation. Cross-resistance can also be acquired by mobile genetic elements. Long-term exposure to disinfectants has an impact on the dissemination of antimicrobial resistance in soil, plants, animals, water, and human gut environments.
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Affiliation(s)
- Ricardo A Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jinsong Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Min Yue
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
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4
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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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5
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Salleh MZ, Banga Singh KK, Deris ZZ. Structural Insights into Substrate Binding and Antibiotic Inhibition of Enterobacterial Penicillin-Binding Protein 6. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071022. [PMID: 35888109 PMCID: PMC9320039 DOI: 10.3390/life12071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/03/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
Abstract
Shigella sonnei remains the second most common cause of shigellosis in young children and is now increasingly dominant across developing countries. The global emergence of drug resistance has become a main burden in the treatment of S. sonnei infections and β-lactam antibiotics, such as pivmecillinam and ceftriaxone, are recommended to be used as second-line treatment. They work by inhibiting the biosynthesis of the peptidoglycan layer of bacterial cell walls, in which the final transpeptidation step is facilitated by penicillin-binding proteins (PBPs). In this study, using protein homology modelling, we modelled the structure of PBP6 from S. sonnei and comprehensively examined the molecular interactions between PBP6 and its pentapeptide substrate and two antibiotic inhibitors. The docked complex of S. sonnei PBP6 with pentapeptides showed that the substrate bound to the active site groove of the DD-carboxypeptidase domain, via hydrogen bonding interactions with the residues S79, V80, Q101, G144, D146 and R240, in close proximity to the catalytic nucleophile S36 for the nucleophilic attack. Two residues, R240 and T208, were found to be important in ligand recognition and binding, where they formed strong hydrogen bonds with the substrate and β-lactams, respectively. Our results provide valuable information on the molecular interactions essential for ligand recognition and catalysis by PBP6. Understanding these interactions will be helpful in the development of effective drugs to treat S. sonnei infections.
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6
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Xu Y, Chen H, Xu S, Liu J, Chen Y, Gui L, Li H, Li R, Yuan Z, Li B. β-Lactamase-Responsive Probe for Efficient Photodynamic Therapy of Drug-Resistant Bacterial Infection. ACS Sens 2022; 7:1361-1371. [PMID: 35442628 DOI: 10.1021/acssensors.1c02485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several photosensitizers have recently been proposed as novel approaches against β-lactamase-producing drug-resistant bacteria. However, these reported photosensitizers are rarely used for accurate recognition of drug-resistant bacteria. To tackle this challenge, the structurally modified photosensitizer CySG-2 based on a lipophilic cationic heptamethine indocyanine near-infrared (NIR) dye (IR-780) and an important synthesis intermediate of cephalosporin antibiotic (GCLE) not only achieved the accurate recognition of TEM-1 methicillin-resistant Staphylococcus aureus (MRSA) successfully but also achieved antimicrobial photodynamic therapy (aPDT) in animal models infected by drug-resistant bacteria. Accurate enzyme recognition and efficient photodynamic therapy capabilities allow CySG-2 to achieve one stone with two birds. In addition, CySG-2 could also promote the eradication of internalized MRSA by facilitating the autophagy process, which is synergistic with its capacity of inducing reactive oxygen species generation under NIR laser irradiation for aPDT. Collectively, it is an effective multifunctional photosensitizer with the potential ability to guide the optimal use of different antibiotics and apply them in clinical treatment.
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Affiliation(s)
- Yue Xu
- Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Haiyan Chen
- Cancer Systems Imaging Department, The University of Texas MD Anderson Cancer Center, 1881 East Road, 3SCR4.3600, Houston, Texas 77054, United States
| | - Shufen Xu
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Ji Liu
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Yang Chen
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Lijuan Gui
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Hua Li
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Ruixi Li
- Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang 550004, China
| | - Zhenwei Yuan
- Department of Biomedical Engineering, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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7
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Ahmad N, Dugad S, Chauhan V, Ahmed S, Sharma K, Kachhap S, Zaidi R, Bishai WR, Lamichhane G, Kumar P. Allosteric cooperation in ß-lactam binding to a non-classical transpeptidase. eLife 2022; 11:73055. [PMID: 35475970 PMCID: PMC9094749 DOI: 10.7554/elife.73055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
L,D-transpeptidase function predominates in atypical 3®3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis. Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or ß-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by ß-lactams. Here we report identification of an allosteric site at a distance of 21 Å from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second ß-lactam molecule and influences binding at the catalytic site. We provide evidence that two ß-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual ß-lactam binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis./em>.
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Affiliation(s)
- Nazia Ahmad
- Department of Biochemistry, Jamia Hamdard University, Delhi, India
| | - Sanmati Dugad
- Department of Infectious Diseases, Johns Hopkins University, Baltimore, United States
| | - Varsha Chauhan
- Department of Infectious Diseases, Johns Hopkins University, Baltimore, United States
| | - Shubbir Ahmed
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute, Faridabad, India
| | - Kunal Sharma
- Department of Biochemistry, Jamia Hamdard University, Delhi, India
| | - Sangita Kachhap
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek, Poland
| | - Rana Zaidi
- Department of Biochemistry, Jamia Hamdard University, Delhi, India
| | - William R Bishai
- Department of Infectious Diseases, Johns Hopkins University, Baltimore, United States
| | - Gyanu Lamichhane
- Department of Infectious Diseases, Johns Hopkins University, Baltimore, United States
| | - Pankaj Kumar
- Medicine, Johns Hopkins University, Baltimore, United States
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8
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Grams RJ, Hsu KL. Reactive chemistry for covalent probe and therapeutic development. Trends Pharmacol Sci 2022; 43:249-262. [PMID: 34998611 PMCID: PMC8840975 DOI: 10.1016/j.tips.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.
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Affiliation(s)
- R. Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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9
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Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem 2021; 12:1623-1639. [PMID: 34778765 PMCID: PMC8528271 DOI: 10.1039/d1md00200g] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/25/2021] [Indexed: 12/24/2022] Open
Abstract
The β-lactams are the most widely used antibacterial agents worldwide. These antibiotics, a group that includes the penicillins and cephalosporins, are covalent inhibitors that target bacterial penicillin-binding proteins and disrupt peptidoglycan synthesis. Bacteria can achieve resistance to β-lactams in several ways, including the production of serine β-lactamase enzymes. While β-lactams also covalently interact with serine β-lactamases, these enzymes are capable of deacylating this complex, treating the antibiotic as a substrate. In this tutorial-style review, we provide an overview of the β-lactam antibiotics, focusing on their covalent interactions with their target proteins and resistance mechanisms. We begin by describing the structurally diverse range of β-lactam antibiotics and β-lactamase inhibitors that are currently used as therapeutics. Then, we introduce the penicillin-binding proteins, describing their functions and structures, and highlighting their interactions with β-lactam antibiotics. We next describe the classes of serine β-lactamases, exploring some of the mechanisms by which they achieve the ability to degrade β-lactams. Finally, we introduce the l,d-transpeptidases, a group of bacterial enzymes involved in peptidoglycan synthesis which are also targeted by β-lactam antibiotics. Although resistance mechanisms are now prevalent for all antibiotics in this class, past successes in antibiotic development have at least delayed this onset of resistance. The β-lactams continue to be an essential tool for the treatment of infectious disease, and recent advances (e.g., β-lactamase inhibitor development) will continue to support their future use.
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Affiliation(s)
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University Kingston ON K7L 3N6 Canada
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10
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Zheng M, Lin H, Zhang W, Tang S, Liu D, Cai J. Poly(l-ornithine)-Grafted Zinc Phthalocyanines as Dual-Functional Antimicrobial Agents with Intrinsic Membrane Damage and Photothermal Ablation Capacity. ACS Infect Dis 2021; 7:2917-2929. [PMID: 34570483 DOI: 10.1021/acsinfecdis.1c00392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Multifunctional antimicrobial peptides that combine the intrinsic microbicidal property of cationic polypeptide chains and additional antibacterial strategy hold promising applications for the treatment of infections caused by antibiotic-resistant bacteria, especially "superbugs". In the present study, star-shaped copolymers ZnPc-g-PLO with a zinc phthalocyanine (ZnPc) core and four poly(l-ornithine) (PLO) arms were designed, synthesized, and evaluated as dual-functional antimicrobial agents, that is, intrinsic membrane damage and photothermal ablation capacity. In an aqueous solution, amphiphilic ZnPc-g-PLO molecules self-assemble into nanosized polymeric micelles with an aggregated ZnPc core and star-shaped PLO periphery, where the ZnPc core exhibits appreciable aggregation-induced photothermal conversion efficiency. In the absence of laser irradiation, ZnPc-g-PLO micelles display potent and broad-spectrum antibacterial activities via physical bacterial membrane disruption as a result of the high cationic charge density of the star-shaped PLO. Upon laser irradiation, significant improvement in bactericidal potency was realized due to the efficacious photothermal sterilization from the ZnPc core. Notably, ZnPc-g-PLO micelles did not induce drug-resistance upon subinhibitory passages. In summary, dual-functional ZnPc-g-PLO copolymers can serve as promising antibacterial agents for the treatment of infectious diseases caused by antibiotic-resistant bacteria.
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Affiliation(s)
- Maochao Zheng
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
- Department of Pharmacy, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310022, China
| | - Huanchang Lin
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Wancong Zhang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
- Plastic Surgery Institute of Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
- Plastic Surgery Institute of Shantou University Medical College, 69 Dongxiabei Road, Shantou 515041, China
| | - Daojun Liu
- Department of Pharmacy, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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11
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Zandi TA, Townsend CA. Competing off-loading mechanisms of meropenem from an l,d-transpeptidase reduce antibiotic effectiveness. Proc Natl Acad Sci U S A 2021; 118:e2008610118. [PMID: 34187885 PMCID: PMC8271661 DOI: 10.1073/pnas.2008610118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The carbapenem family of β-lactam antibiotics displays a remarkably broad spectrum of bactericidal activity, exemplified by meropenem's phase II clinical trial success in patients with pulmonary tuberculosis, a devastating disease for which β-lactam drugs historically have been notoriously ineffective. The discovery and validation of l,d-transpeptidases (Ldts) as critical drug targets of bacterial cell-wall biosynthesis, which are only potently inhibited by the carbapenem and penem structural classes, gave an enzymological basis for the effectiveness of the first antitubercular β-lactams. Decades of study have delineated mechanisms of β-lactam inhibition of their canonical targets, the penicillin-binding proteins; however, open questions remain regarding the mechanisms of Ldt inhibition that underlie programs in drug design, particularly the optimization of kinetic behavior and potency. We have investigated critical features of mycobacterial Ldt inhibition and demonstrate here that the covalent inhibitor meropenem undergoes both reversible reaction and nonhydrolytic off-loading reactions from the cysteine transpeptidase LdtMt2 through a high-energy thioester adduct. Next-generation carbapenem optimization strategies should minimize adduct loss from unproductive mechanisms of Ldt adducts that reduce effective drug concentration.
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Affiliation(s)
- Trevor A Zandi
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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12
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Saidjalolov S, Edoo Z, Fonvielle M, Mayer L, Iannazzo L, Arthur M, Etheve-Quelquejeu M, Braud E. Synthesis of Carbapenems Containing Peptidoglycan Mimetics and Inhibition of the Cross-Linking Activity of a Transpeptidase of l,d Specificity. Chemistry 2021; 27:3542-3551. [PMID: 33336443 DOI: 10.1002/chem.202004831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Indexed: 11/07/2022]
Abstract
The carbapenem class of β-lactams has been optimized against Gram-negative bacteria producing extended-spectrum β-lactamases by introducing substituents at position C2. Carbapenems are currently investigated for the treatment of tuberculosis as these drugs are potent covalent inhibitors of l,d-transpeptidases involved in mycobacterial cell wall assembly. The optimization of carbapenems for inactivation of these unusual targets is sought herein by exploiting the nucleophilicity of the C8 hydroxyl group to introduce chemical diversity. As β-lactams are structure analogs of peptidoglycan precursors, the substituents were chosen to increase similarity between the drug and the substrate. Fourteen peptido-carbapenems were efficiently synthesized. They were more effective than the reference drug, meropenem, owing to the positive impact of a phenethylthio substituent introduced at position C2 but the peptidomimetics added at position C8 did not further improve the activity. Thus, position C8 can be modified to modulate the pharmacokinetic properties of highly efficient carbapenems.
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Affiliation(s)
- Saidbakhrom Saidjalolov
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Zainab Edoo
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Louis Mayer
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
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13
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Naha A, Kumar Miryala S, Debroy R, Ramaiah S, Anbarasu A. Elucidating the multi-drug resistance mechanism of Enterococcus faecalis V583: A gene interaction network analysis. Gene 2020; 748:144704. [DOI: 10.1016/j.gene.2020.144704] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
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14
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J. Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J. Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C. Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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15
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Ferraz R, Silva D, Dias AR, Dias V, Santos MM, Pinheiro L, Prudêncio C, Noronha JP, Petrovski Ž, Branco LC. Synthesis and Antibacterial Activity of Ionic Liquids and Organic Salts Based on Penicillin G and Amoxicillin hydrolysate Derivatives against Resistant Bacteria. Pharmaceutics 2020; 12:pharmaceutics12030221. [PMID: 32131540 PMCID: PMC7150922 DOI: 10.3390/pharmaceutics12030221] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/21/2022] Open
Abstract
The preparation and characterization of ionic liquids and organic salts (OSILs) that contain anionic penicillin G [secoPen] and amoxicillin [seco-Amx] hydrolysate derivatives and their in vitro antibacterial activity against sensitive and resistant Escherichia coli and Staphylococcus aureus strains is reported. Eleven hydrolyzed β-lactam-OSILs were obtained after precipitation in moderate-to-high yields via the neutralization of the basic ammonia buffer of antibiotics with different cation hydroxide salts. The obtained minimum inhibitory concentration (MIC) data of the prepared compounds showed a relative decrease of the inhibitory concentrations (RDIC) in the order of 100 in the case of [C2OHMIM][seco-Pen] against sensitive S. aureus ATCC25923 and, most strikingly, higher than 1000 with [C16Pyr][seco-Amx] against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. These outstanding in vitro results showcase that a straightforward transformation of standard antibiotics into hydrolyzed organic salts can dramatically change the pharmaceutical activity of a drug, including giving rise to potent formulations of antibiotics against deadly bacteria strains.
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Affiliation(s)
- Ricardo Ferraz
- Ciências Químicas e das Biomoléculas (CQB) e Centro de Investigação em Saúde e Ambiente (CISA), Escola Superior de Saúde do Instituto Politécnico do Porto, 4400-330 Porto, Portugal; (A.R.D.); (V.D.); (C.P.)
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Correspondence: (R.F.); (Ž.P.); (L.C.B.)
| | - Dário Silva
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
| | - Ana Rita Dias
- Ciências Químicas e das Biomoléculas (CQB) e Centro de Investigação em Saúde e Ambiente (CISA), Escola Superior de Saúde do Instituto Politécnico do Porto, 4400-330 Porto, Portugal; (A.R.D.); (V.D.); (C.P.)
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Vitorino Dias
- Ciências Químicas e das Biomoléculas (CQB) e Centro de Investigação em Saúde e Ambiente (CISA), Escola Superior de Saúde do Instituto Politécnico do Porto, 4400-330 Porto, Portugal; (A.R.D.); (V.D.); (C.P.)
| | - Miguel M. Santos
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
| | - Luís Pinheiro
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
| | - Cristina Prudêncio
- Ciências Químicas e das Biomoléculas (CQB) e Centro de Investigação em Saúde e Ambiente (CISA), Escola Superior de Saúde do Instituto Politécnico do Porto, 4400-330 Porto, Portugal; (A.R.D.); (V.D.); (C.P.)
- i3S, Instituto de Inovação e Investigação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - João Paulo Noronha
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
| | - Željko Petrovski
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
- Correspondence: (R.F.); (Ž.P.); (L.C.B.)
| | - Luís C. Branco
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (D.S.); (M.M.S.); (L.P.); (J.P.N.)
- Correspondence: (R.F.); (Ž.P.); (L.C.B.)
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16
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Dražić T, Kopf S, Corridan J, Leuthold MM, Bertoša B, Klein CD. Peptide-β-lactam Inhibitors of Dengue and West Nile Virus NS2B-NS3 Protease Display Two Distinct Binding Modes. J Med Chem 2019; 63:140-156. [DOI: 10.1021/acs.jmedchem.9b00759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Sara Kopf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - James Corridan
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Mila M. Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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17
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Sharma N, Singh V, Pandey AK, Mishra BN, Kulsoom M, Dasgupta N, Khan S, El-Enshasy HA, Haque S. Preparation and Evaluation of the ZnO NP-Ampicillin/Sulbactam Nanoantibiotic: Optimization of Formulation Variables Using RSM Coupled GA Method and Antibacterial Activities. Biomolecules 2019; 9:E764. [PMID: 31766572 PMCID: PMC6995637 DOI: 10.3390/biom9120764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/10/2019] [Accepted: 11/17/2019] [Indexed: 12/18/2022] Open
Abstract
Nanoparticles (NPs) possessing antibacterial activity represent an effective way of overcoming bacterial resistance. In the present work, we report a novel formulation of a nanoantibiotic formed using Ampicillin/sulbactam (Ams) and a zinc oxide nanoparticle (ZnO NP). 'ZnO NP-Ams' nanoantibiotic formulation is optimized using response surface methodology coupled genetic algorithm approach. The optimized formulation of nanoantibiotic (ZnO NP: 49.9 μg/mL; Ams: 33.6 μg/mL; incubation time: 27 h) demonstrated 15% enhanced activity compared to the unoptimized formulation against K. pneumoniae. The reactive oxygen species (ROS) generation was directly proportional to the interaction time of nanoantibiotic and K. pneumoniae after the initial lag phase of ~18 h as evident from 2'-7'-Dichlorodihydrofluorescein diacetate assay. A low minimum inhibitory concentration (6.25 μg/mL) of nanoantibiotic formulation reveals that even a low concentration of nanoantibiotic can prove to be effective against K. pneumoniae. The importance of nanoantibiotic formulation is also evident by the fact that the 100 μg/mL of Ams and 25 µg of ZnO NP was required individually to inhibit the growth of K. pneumonia, whereas only 6.25 μg/mL of optimized nanoantibiotic formulation (ZnO NP and Ams in the ratio of 49.9: 33.6 in μg/mL and conjugation time of 27 h) was needed for the same.
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Affiliation(s)
- Nidhi Sharma
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Asheesh Kumar Pandey
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Maria Kulsoom
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Nandita Dasgupta
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Sitapur Road, Lucknow-226021, Uttar Pradesh, India; (N.S.); (V.S.); (A.K.P.); (B.N.M.); (M.K.); (N.D.)
| | - Saif Khan
- Department of Basic Sciences, College of Dental Sciences, University of Ha’il, Ha’il-2440, Saudi Arabia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Johor, Malaysia
- City of Scientific Research and Technological Applications, New Burg Al Arab, Alexandria 21934, Egypt
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
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18
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Triboulet S, Edoo Z, Compain F, Ourghanlian C, Dupuis A, Dubée V, Sutterlin L, Atze H, Etheve-Quelquejeu M, Hugonnet JE, Arthur M. Tryptophan Fluorescence Quenching in β-Lactam-Interacting Proteins Is Modulated by the Structure of Intermediates and Final Products of the Acylation Reaction. ACS Infect Dis 2019; 5:1169-1176. [PMID: 31056908 DOI: 10.1021/acsinfecdis.9b00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In most bacteria, β-lactam antibiotics inhibit the last cross-linking step of peptidoglycan synthesis by acylation of the active-site Ser of d,d-transpeptidases belonging to the penicillin-binding protein (PBP) family. In mycobacteria, cross-linking is mainly ensured by l,d-transpeptidases (LDTs), which are promising targets for the development of β-lactam-based therapies for multidrug-resistant tuberculosis. For this purpose, fluorescence spectroscopy is used to investigate the efficacy of LDT inactivation by β-lactams but the basis for fluorescence quenching during enzyme acylation remains unknown. In contrast to what has been reported for PBPs, we show here using a model l,d-transpeptidase (Ldtfm) that fluorescence quenching of Trp residues does not depend upon direct hydrophobic interaction between Trp residues and β-lactams. Rather, Trp fluorescence was quenched by the drug covalently bound to the active-site Cys residue of Ldtfm. Fluorescence quenching was not quantitatively determined by the size of the drug and was not specific of the thioester link connecting the β-lactam carbonyl to the catalytic Cys as quenching was also observed for acylation of the active-site Ser of β-lactamase BlaC from M. tuberculosis. Fluorescence quenching was extensive for reaction intermediates containing an amine anion and for acylenzymes containing an imine stabilized by mesomeric effect, but not for acylenzymes containing a protonated β-lactam nitrogen. Together, these results indicate that the extent of fluorescence quenching is determined by the status of the β-lactam nitrogen. Thus, fluorescence kinetics can provide information not only on the efficacy of enzyme inactivation but also on the structure of the covalent adducts responsible for enzyme inactivation.
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Affiliation(s)
- Sebastien Triboulet
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Fabrice Compain
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
- Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 20 rue Leblanc, F-75015 Paris, France
| | - Clément Ourghanlian
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Adrian Dupuis
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Vincent Dubée
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Laetitia Sutterlin
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Heiner Atze
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005 France
- CNRS UMR 8601, 45 rue des Saints-Pères, Paris, F-75006 France
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 15 rue de l’Ecole de Médecine, F-75006 Paris, France
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19
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Ibeji CU, Lawal MM, Tolufashe GF, Govender T, Naicker T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study. Chemphyschem 2019; 20:1126-1134. [PMID: 30969480 DOI: 10.1002/cphc.201900173] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/13/2019] [Indexed: 11/06/2022]
Abstract
β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C-N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a-2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C-N), which is why the six-membered ring lactams C-N bond are more rigid than those with five-membered ring lactams. The calculated ΔG# values from the acylation reaction of the lactams (involving the S-H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C-N cleavage in the five-membered ring lactams especially in the 1-2 derivatives (17.58 kcal mol-1 ). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.
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Affiliation(s)
- Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.,Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Monsurat M Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
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Negative Impact of Carbapenem Methylation on the Reactivity of β-Lactams for Cysteine Acylation as Revealed by Quantum Calculations and Kinetic Analyses. Antimicrob Agents Chemother 2019; 63:AAC.02039-18. [PMID: 30718252 DOI: 10.1128/aac.02039-18] [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: 09/21/2018] [Accepted: 01/29/2019] [Indexed: 11/20/2022] Open
Abstract
The Enterococcus faecium l,d-transpeptidase (Ldtfm) mediates resistance to most β-lactam antibiotics in this bacterium by replacing classical peptidoglycan polymerases. The catalytic Cys of Ldtfm is rapidly acylated by β-lactams belonging to the carbapenem class but not by penams or cephems. We previously reported quantum calculations and kinetic analyses for Ldtfm and showed that the inactivation profile is not determined by differences in drug binding (KD [equilibrium dissociation constant] values in the 50 to 80 mM range). In this study, we analyzed the reaction of a Cys sulfhydryl with various β-lactams in the absence of the enzyme environment in order to compare the intrinsic reactivity of drugs belonging to the penam, cephem, and carbapenem classes. For this purpose, we synthesized cyclic Cys-Asn (cCys-Asn) to generate a soluble molecule with a sulfhydryl closely mimicking a cysteine in a polypeptide chain, thereby avoiding free reactive amino and carboxyl groups. Computational studies identified a thermodynamically favored pathway involving a concerted rupture of the β-lactam amide bond and formation of an amine anion. Energy barriers indicated that the drug reactivity was the highest for nonmethylated carbapenems, intermediate for methylated carbapenems and cephems, and the lowest for penams. Electron-withdrawing groups were key reactivity determinants by enabling delocalization of the negative charge of the amine anion. Acylation rates of cCys-Asn determined by spectrophotometry revealed the same order in the reactivity of β-lactams. We concluded that the rate of Ldtfm acylation is largely determined by the β-lactam reactivity with one exception, as the enzyme catalytic pocket fully compensated for the detrimental effect of carbapenem methylation.
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Copper inhibits peptidoglycan LD-transpeptidases suppressing β-lactam resistance due to bypass of penicillin-binding proteins. Proc Natl Acad Sci U S A 2018; 115:10786-10791. [PMID: 30275297 DOI: 10.1073/pnas.1809285115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The peptidoglycan (PG) layer stabilizes the bacterial cell envelope to maintain the integrity and shape of the cell. Penicillin-binding proteins (PBPs) synthesize essential 4-3 cross-links in PG and are inhibited by β-lactam antibiotics. Some clinical isolates and laboratory strains of Enterococcus faecium and Escherichia coli achieve high-level β-lactam resistance by utilizing β-lactam-insensitive LD-transpeptidases (LDTs) to produce exclusively 3-3 cross-links in PG, bypassing the PBPs. In E. coli, other LDTs covalently attach the lipoprotein Lpp to PG to stabilize the envelope and maintain the permeability barrier function of the outermembrane. Here we show that subminimal inhibitory concentration of copper chloride sensitizes E. coli cells to sodium dodecyl sulfate and impair survival upon LPS transport stress, indicating reduced cell envelope robustness. Cells grown in the presence of copper chloride lacked 3-3 cross-links in PG and displayed reduced covalent attachment of Braun's lipoprotein and reduced incorporation of a fluorescent d-amino acid, suggesting inhibition of LDTs. Copper dramatically decreased the minimal inhibitory concentration of ampicillin in E. coli and E. faecium strains with a resistance mechanism relying on LDTs and inhibited purified LDTs at submillimolar concentrations. Hence, our work reveals how copper affects bacterial cell envelope stability and counteracts LDT-mediated β-lactam resistance.
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