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Shirley JD, Nauta KM, Gillingham JR, Diwakar S, Carlson EE. kinact / KI Value Determination for Penicillin-Binding Proteins in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592586. [PMID: 38746240 PMCID: PMC11092749 DOI: 10.1101/2024.05.05.592586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC 50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant k inact / K I is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, k inact / K I values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell k inact / K I assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro k inact / K I data and show a comparable relationship to previously established IC 50 values. These results support the validity of our in vivo k inact / K I method as a means of obtaining a full picture of β-lactam potency for a suite of PBPs. Abstract Figure
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2
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [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: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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3
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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4
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Moussa SH, Shapiro AB, McLeod SM, Iyer R, Carter NM, Tsai YK, Siu LK, Miller AA. Molecular drivers of resistance to sulbactam-durlobactam in contemporary clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2023; 67:e0066523. [PMID: 37843305 PMCID: PMC10648852 DOI: 10.1128/aac.00665-23] [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] [Received: 05/19/2023] [Accepted: 08/07/2023] [Indexed: 10/17/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex (ABC) causes severe infections that are difficult to treat due to pre-existing antibiotic resistance. Sulbactam-durlobactam (SUL-DUR) is a targeted β-lactam/β-lactamase inhibitor combination antibiotic designed to treat serious infections caused by Acinetobacter, including multidrug- and carbapenem-resistant strains. In a recent global surveillance study of 5,032 ABC clinical isolates collected from 2016 to 2021, less than 2% of ABC isolates had SUL-DUR MIC values >4 µg/mL. Molecular characterization of these isolates confirmed the primary drivers of resistance are metallo-β-lactamases or penicillin-binding protein 3 (PBP3) mutations, as previously described. In addition, this study shows that certain common PBP3 variants, such as A515V, are insufficient to confer sulbactam resistance and that the efflux of durlobactam by AdeIJK is likely to play a role in a subset of strains.
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Affiliation(s)
- Samir H. Moussa
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Adam B. Shapiro
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Sarah M. McLeod
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Ramkumar Iyer
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Nicole M. Carter
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
| | - Yu-Kuo Tsai
- Kemyth Biotech Co., Ltd., Taipei City, Taiwan
| | | | - Alita A. Miller
- Innoviva Specialty Therapeutics Inc., an affiliate of Entasis Therapeutics Inc., Waltham, Massachusetts, USA
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5
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López-Argüello S, Montaner M, Sayed ARM, Oliver A, Bulitta JB, Moya B. Penicillin-Binding Protein 5/6 Acting as a Decoy Target in Pseudomonas aeruginosa Identified by Whole-Cell Receptor Binding and Quantitative Systems Pharmacology. Antimicrob Agents Chemother 2023; 67:e0160322. [PMID: 37199612 PMCID: PMC10269149 DOI: 10.1128/aac.01603-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/23/2023] [Indexed: 05/19/2023] Open
Abstract
The β-lactam antibiotics have been successfully used for decades to combat susceptible Pseudomonas aeruginosa, which has a notoriously difficult to penetrate outer membrane (OM). However, there is a dearth of data on target site penetration and covalent binding of penicillin-binding proteins (PBP) for β-lactams and β-lactamase inhibitors in intact bacteria. We aimed to determine the time course of PBP binding in intact and lysed cells and estimate the target site penetration and PBP access for 15 compounds in P. aeruginosa PAO1. All β-lactams (at 2 × MIC) considerably bound PBPs 1 to 4 in lysed bacteria. However, PBP binding in intact bacteria was substantially attenuated for slow but not for rapid penetrating β-lactams. Imipenem yielded 1.5 ± 0.11 log10 killing at 1h compared to <0.5 log10 killing for all other drugs. Relative to imipenem, the rate of net influx and PBP access was ~ 2-fold slower for doripenem and meropenem, 7.6-fold for avibactam, 14-fold for ceftazidime, 45-fold for cefepime, 50-fold for sulbactam, 72-fold for ertapenem, ~ 249-fold for piperacillin and aztreonam, 358-fold for tazobactam, ~547-fold for carbenicillin and ticarcillin, and 1,019-fold for cefoxitin. At 2 × MIC, the extent of PBP5/6 binding was highly correlated (r2 = 0.96) with the rate of net influx and PBP access, suggesting that PBP5/6 acted as a decoy target that should be avoided by slowly penetrating, future β-lactams. This first comprehensive assessment of the time course of PBP binding in intact and lysed P. aeruginosa explained why only imipenem killed rapidly. The developed novel covalent binding assay in intact bacteria accounts for all expressed resistance mechanisms.
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Affiliation(s)
- Silvia López-Argüello
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Maria Montaner
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Alaa RM. Sayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Department of Chemistry, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Jürgen B. Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Bartolome Moya
- 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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6
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Shirley JD, Nauta KM, Carlson EE. Live-Cell Profiling of Penicillin-Binding Protein Inhibitors in Escherichia coli MG1655. ACS Infect Dis 2022; 8:1241-1252. [PMID: 35763562 PMCID: PMC10040144 DOI: 10.1021/acsinfecdis.2c00004] [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] [Indexed: 11/28/2022]
Abstract
Penicillin-binding proteins (PBPs) make up an essential class of bacterial enzymes that carry out the final steps of peptidoglycan synthesis and regulate the recycling of this polymeric structure. PBPs are an excellent drug target and have been the most clinically relevant antibacterial target since the 1940s with the introduction of β-lactams. Despite this, a large gap in knowledge remains regarding the individual function and regulation of each PBP homologue in most bacteria. This can be attributed to a lack of chemical tools and methods that enable the study of individual PBPs in an activity-dependent manner and in their native environment. The development of such methods in Gram-negative bacteria has been particularly challenging due to the presence of an outer membrane and numerous resistance mechanisms. To address this, we have developed an optimized live-cell assay for screening inhibitors of the PBPs in Escherichia coli MG1655. We utilized EDTA to permeabilize Gram-negative cells, enabling increased penetration of our readout probe, Bocillin-FL, and subsequent analysis of PBP-inhibition profiles. To identify scaffolds for future development of PBP-selective activity-based probes, we screened ten β-lactams, one diazabicyclooctane, and one monobactam for their PBP-selectivity profiles in E. coli MG1655. These results demonstrate the utility of our assay for the screening of inhibitors in live, non-hypersusceptible Gram-negative organisms.
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Affiliation(s)
- Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Kelsie M Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States.,Department of Pharmacology, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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7
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Rational design of a new antibiotic class for drug-resistant infections. Nature 2021; 597:698-702. [PMID: 34526714 DOI: 10.1038/s41586-021-03899-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 08/11/2021] [Indexed: 11/08/2022]
Abstract
The development of new antibiotics to treat infections caused by drug-resistant Gram-negative pathogens is of paramount importance as antibiotic resistance continues to increase worldwide1. Here we describe a strategy for the rational design of diazabicyclooctane inhibitors of penicillin-binding proteins from Gram-negative bacteria to overcome multiple mechanisms of resistance, including β-lactamase enzymes, stringent response and outer membrane permeation. Diazabicyclooctane inhibitors retain activity in the presence of β-lactamases, the primary resistance mechanism associated with β-lactam therapy in Gram-negative bacteria2,3. Although the target spectrum of an initial lead was successfully re-engineered to gain in vivo efficacy, its ability to permeate across bacterial outer membranes was insufficient for further development. Notably, the features that enhanced target potency were found to preclude compound uptake. An improved optimization strategy leveraged porin permeation properties concomitant with biochemical potency in the lead-optimization stage. This resulted in ETX0462, which has potent in vitro and in vivo activity against Pseudomonas aeruginosa plus all other Gram-negative ESKAPE pathogens, Stenotrophomonas maltophilia and biothreat pathogens. These attributes, along with a favourable preclinical safety profile, hold promise for the successful clinical development of the first novel Gram-negative chemotype to treat life-threatening antibiotic-resistant infections in more than 25 years.
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8
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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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9
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Discovery of Pyrrolidine-2,3-diones as Novel Inhibitors of P. aeruginosa PBP3. Antibiotics (Basel) 2021; 10:antibiotics10050529. [PMID: 34064358 PMCID: PMC8147781 DOI: 10.3390/antibiotics10050529] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/01/2022] Open
Abstract
The alarming threat of the spread of multidrug resistant bacteria currently leaves clinicians with very limited options to combat infections, especially those from Gram-negative bacteria. Hence, innovative strategies to deliver the next generation of antibacterials are urgently needed. Penicillin binding proteins (PBPs) are proven targets inhibited by β-lactam antibiotics. To discover novel, non-β-lactam inhibitors against PBP3 of Pseudomonas aeruginosa, we optimised a fluorescence assay based on a well-known thioester artificial substrate and performed a target screening using a focused protease-targeted library of 2455 compounds, which led to the identification of pyrrolidine-2,3-dione as a potential scaffold to inhibit the PBP3 target. Further chemical optimisation using a one-pot three-component reaction protocol delivered compounds with excellent target inhibition, initial antibacterial activities against P. aeruginosa and no apparent cytotoxicity. Our investigation revealed the key structural features; for instance, 3-hydroxyl group (R2) and a heteroaryl group (R1) appended to the N-pyrroldine-2,3-dione via methylene linker required for target inhibition. Overall, the discovery of the pyrrolidine-2,3-dione class of inhibitors of PBP3 brings opportunities to target multidrug-resistant bacterial strains and calls for further optimisation to improve antibacterial activity against P. aeruginosa.
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10
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Lang Y, Shah NR, Tao X, Reeve SM, Zhou J, Moya B, Sayed ARM, Dharuman S, Oyer JL, Copik AJ, Fleischer BA, Shin E, Werkman C, Basso KB, Lucas DD, Sutaria DS, Mégroz M, Kim TH, Loudon-Hossler V, Wright A, Jimenez-Nieves RH, Wallace MJ, Cadet KC, Jiao Y, Boyce JD, LoVullo ED, Schweizer HP, Bonomo RA, Bharatham N, Tsuji BT, Landersdorfer CB, Norris MH, Shin BS, Louie A, Balasubramanian V, Lee RE, Drusano GL, Bulitta JB. Combating Multidrug-Resistant Bacteria by Integrating a Novel Target Site Penetration and Receptor Binding Assay Platform Into Translational Modeling. Clin Pharmacol Ther 2021; 109:1000-1020. [PMID: 33576025 PMCID: PMC10662281 DOI: 10.1002/cpt.2205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/26/2022]
Abstract
Multidrug-resistant bacteria are causing a serious global health crisis. A dramatic decline in antibiotic discovery and development investment by pharmaceutical industry over the last decades has slowed the adoption of new technologies. It is imperative that we create new mechanistic insights based on latest technologies, and use translational strategies to optimize patient therapy. Although drug development has relied on minimal inhibitory concentration testing and established in vitro and mouse infection models, the limited understanding of outer membrane permeability in Gram-negative bacteria presents major challenges. Our team has developed a platform using the latest technologies to characterize target site penetration and receptor binding in intact bacteria that inform translational modeling and guide new discovery. Enhanced assays can quantify the outer membrane permeability of β-lactam antibiotics and β-lactamase inhibitors using multiplex liquid chromatography tandem mass spectrometry. While β-lactam antibiotics are known to bind to multiple different penicillin-binding proteins (PBPs), their binding profiles are almost always studied in lysed bacteria. Novel assays for PBP binding in the periplasm of intact bacteria were developed and proteins identified via proteomics. To characterize bacterial morphology changes in response to PBP binding, high-throughput flow cytometry and time-lapse confocal microscopy with fluorescent probes provide unprecedented mechanistic insights. Moreover, novel assays to quantify cytosolic receptor binding and intracellular drug concentrations inform target site occupancy. These mechanistic data are integrated by quantitative and systems pharmacology modeling to maximize bacterial killing and minimize resistance in in vitro and mouse infection models. This translational approach holds promise to identify antibiotic combination dosing strategies for patients with serious infections.
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Affiliation(s)
- Yinzhi Lang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Nirav R. Shah
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Jansen R&D, Johnson & Johnson, Spring House, Pennsylvania, USA
| | - Xun Tao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Stephanie M. Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jieqiang Zhou
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Bartolome Moya
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Alaa R. M. Sayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Department of Chemistry, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremiah L. Oyer
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Alicja J. Copik
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Brett A. Fleischer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Eunjeong Shin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Carolin Werkman
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Kari B. Basso
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Deanna Deveson Lucas
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Dhruvitkumar S. Sutaria
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
- Present address: Genentech USA,Inc., South San Francisco, California, USA
| | - Marianne Mégroz
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tae Hwan Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, Korea
| | - Victoria Loudon-Hossler
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Amy Wright
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Rossie H. Jimenez-Nieves
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keisha C. Cadet
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - Yuanyuan Jiao
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
| | - John D. Boyce
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Eric D. LoVullo
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P. Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Robert A. Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Nagakumar Bharatham
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Brian T. Tsuji
- Laboratory for Antimicrobial Pharmacodynamics, University at Buffalo, Buffalo, New York, USA
| | - Cornelia B. Landersdorfer
- Drug Delivery, Disposition, and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael H. Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography and the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Beom Soo Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Arnold Louie
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Venkataraman Balasubramanian
- BUGWORKS Research India Pvt. Ltd., Centre for Cellular & Molecular Platforms, National Centre for Biological Sciences, Bengaluru, Karnataka, India
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - George L. Drusano
- Institute for Therapeutic Innovation, College of Medicine, University of Florida, Orlando, Florida, USA
| | - Jürgen B. Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, Florida, USA
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11
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Miao L, Liu W, Qiao Q, Li X, Xu Z. Fluorescent antibiotics for real-time tracking of pathogenic bacteria. J Pharm Anal 2020; 10:444-451. [PMID: 33133728 PMCID: PMC7591806 DOI: 10.1016/j.jpha.2020.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023] Open
Abstract
The harm of pathogenic bacteria to humans has promoted extensive research on physiological processes of pathogens, such as the mechanism of bacterial infection, antibiotic mode of action, and bacterial antimicrobial resistance. Most of these processes can be better investigated by timely tracking of fluorophore-derived antibiotics in living cells. In this paper, we will review the recent development of fluorescent antibiotics featuring the conjugation with various fluorophores, and focus on their applications in fluorescent imaging and real-time detection for various physiological processes of bacteria in vivo. Profiles of Fluorophores-derived Antibiotics in Development. Discussing the influence on antibiotic activity after conjugating fluorophore. Fluorescent Tracking to better understand physiological processes of Pathogenic bacteria. Live-Cell imaging to investigate bacteria in their native environment.
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Affiliation(s)
- Lu Miao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Weiwei Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaolian Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116012, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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12
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Keshri V, Chabrière E, Pinault L, Colson P, Diene SM, Rolain JM, Raoult D, Pontarotti P. Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases. Int J Mol Sci 2020; 21:E6260. [PMID: 32872436 PMCID: PMC7504333 DOI: 10.3390/ijms21176260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/17/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
The probability of the evolution of a character depends on two factors: the probability of moving from one character state to another character state and the probability of the new character state fixation. The more the evolution of a character is probable, the more the convergent evolution will be witnessed, and consequently, convergent evolution could mean that the convergent character evolution results as a combination of these two factors. We investigated this phenomenon by studying the convergent evolution of biochemical functions. For the investigation we used the case of β-lactamases. β-lactamases hydrolyze β-lactams, which are antimicrobials able to block the DD-peptidases involved in bacterial cell wall synthesis. β-lactamase activity is present in two different superfamilies: the metallo-β-lactamase and the serine β-lactamase. The mechanism used to hydrolyze the β-lactam is different for the two superfamilies. We named this kind of evolution an allo-convergent evolution. We further showed that the β-lactamase activity evolved several times within each superfamily, a convergent evolution type that we named iso-convergent evolution. Both types of convergent evolution can be explained by the two evolutionary mechanisms discussed above. The probability of moving from one state to another is explained by the promiscuous β-lactamase activity present in the ancestral sequences of each superfamily, while the probability of fixation is explained in part by positive selection, as the organisms having β-lactamase activity allows them to resist organisms that secrete β-lactams. Indeed, an organism that has a mutation that increases the β-lactamase activity will be selected, as the organisms having this activity will have an advantage over the others.
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Affiliation(s)
- Vivek Keshri
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Eric Chabrière
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Lucile Pinault
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Philippe Colson
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Seydina M Diene
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Jean-Marc Rolain
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Didier Raoult
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
| | - Pierre Pontarotti
- Aix-Marseille Univ IRD, APHM, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (V.K.); (E.C.); (L.P.); (P.C.); (S.M.D.); (J.-M.R.); (D.R.)
- SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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13
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Cochrane SA, Lohans CT. Breaking down the cell wall: Strategies for antibiotic discovery targeting bacterial transpeptidases. Eur J Med Chem 2020; 194:112262. [PMID: 32248005 DOI: 10.1016/j.ejmech.2020.112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
Abstract
The enzymes involved in bacterial cell wall synthesis are established antibiotic targets, and continue to be a central focus for antibiotic development. Bacterial penicillin-binding proteins (and, in some bacteria, l,d-transpeptidases) form essential peptide cross-links in the cell wall. Although the β-lactam class of antibiotics target these enzymes, bacterial resistance threatens their clinical use, and there is an urgent unmet need for new antibiotics. However, the search for new antibiotics targeting the bacterial cell wall is hindered by a number of obstacles associated with screening the enzymes involved in peptidoglycan synthesis. This review describes recent approaches for measuring the activity and inhibition of penicillin-binding proteins and l,d-transpeptidases, highlighting strategies that are poised to serve as valuable tools for high-throughput screening of transpeptidase inhibitors, supporting the development of new antibiotics.
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Affiliation(s)
- Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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14
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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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15
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Shapiro AB, Comita-Prevoir J, Sylvester M. 5-Carboxytetramethylrhodamine-Ampicillin Fluorescence Anisotropy-Based Assay of Escherichia coli Penicillin-Binding Protein 2 Transpeptidase Inhibition. ACS Infect Dis 2019; 5:863-872. [PMID: 30848883 DOI: 10.1021/acsinfecdis.8b00351] [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: 12/17/2022]
Abstract
The high-molecular mass penicillin-binding proteins (PBPs) are the essential targets of the β-lactam classes of antibacterial drugs. In the Gram-negative pathogen Escherichia coli, these include PBP1a, PBP1b, PBP2, and PBP3. Techniques that enable facile measurement of the potency of inhibition of these targets are valuable for understanding structure-activity relationships in programs aimed at discovering new antibiotics to combat drug-resistant infections. Continuous fluorescence anisotropy-based assays for inhibition of soluble constructs of PBP1a, PBP2, and PBP3 from the serious Gram-negative bacterial pathogens Pseudomonas aeruginosa and Acinetobacter baumannii and PBP3 from E. coli using the fluorescent phenoxypenicillin analogue BOCILLIN FL have been described previously, but this technique was not useful for PBP2 from E. coli due to a lack of change in fluorescence anisotropy or intensity upon reaction. Here, we report that a fluorescent analogue of ampicillin, 5-carboxytetramethylrhodamine-ampicillin (5-TAMRA-ampicillin), was useful as the indicator in a continuous fluorescence anisotropy-based kinetic assay for inhibition of a soluble construct of PBP2 from E. coli. The assay enables measurement of the bimolecular rate constant for inhibition kinact /Ki. This measurement was made for representative drugs from four classes of β-lactams and for the diazabicyclooctenone ETX2514. 5-TAMRA-ampicillin was also useful in a fluorescence anisotropy-based assay for P. aeruginosa PBP2 and in fluorescence intensity-based assays with PBP1a and PBP3 from P. aeruginosa and A. baumannii and PBP3 from E. coli.
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Affiliation(s)
- Adam B. Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Mark Sylvester
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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16
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Abstract
β-Lactamases, the major resistance determinant for β-lactam antibiotics in Gram-negative bacteria, are ancient enzymes whose origins can be traced back millions of years ago. These well-studied enzymes, currently numbering almost 2,800 unique proteins, initially emerged from environmental sources, most likely to protect a producing bacterium from attack by naturally occurring β-lactams. Their ancestors were presumably penicillin-binding proteins that share sequence homology with β-lactamases possessing an active-site serine. Metallo-β-lactamases also exist, with one or two catalytically functional zinc ions. Although penicillinases in Gram-positive bacteria were reported shortly after penicillin was introduced clinically, transmissible β-lactamases that could hydrolyze recently approved cephalosporins, monobactams, and carbapenems later became important in Gram-negative pathogens. Nomenclature is based on one of two major systems. Originally, functional classifications were used, based on substrate and inhibitor profiles. A later scheme classifies β-lactamases according to amino acid sequences, resulting in class A, B, C, and D enzymes. A more recent nomenclature combines the molecular and biochemical classifications into 17 functional groups that describe most β-lactamases. Some of the most problematic enzymes in the clinical community include extended-spectrum β-lactamases (ESBLs) and the serine and metallo-carbapenemases, all of which are at least partially addressed with new β-lactamase inhibitor combinations. New enzyme variants continue to be described, partly because of the ease of obtaining sequence data from whole-genome sequencing studies. Often, these new enzymes are devoid of any phenotypic descriptions, making it more difficult for clinicians and antibiotic researchers to address new challenges that may be posed by unusual β-lactamases.
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Affiliation(s)
- Karen Bush
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
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17
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Kim JS, Yamasaki R, Song S, Zhang W, Wood TK. Single cell observations show persister cells wake based on ribosome content. Environ Microbiol 2018. [PMID: 29528544 DOI: 10.1111/1462-2920.14093] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since persister cells survive antibiotic treatments through dormancy and resuscitate to reconstitute infections, it is imperative to determine the rate at which these cells revive. Using two sets of Escherichia coli persister cells, those arising after antibiotic treatment at low levels and those generated at high levels by ceasing transcription via rifampicin pretreatment (shown to be bona fide persisters through eight sets of experiments), we used microscopy of single cells to determine that the resuscitation of dormant persisters is heterogeneous and includes cells that grow immediately. In all, five phenotypes were found during the observation of persister cells when fresh nutrients were added: (i) immediate division, (ii) immediate elongation followed by division, (iii) immediate elongation but no division, (iv) delayed elongation/division and (v) no growth. In addition, once cell division begins, the growth rate is that of exponential cells. Critically, the greater the ribosome content, the faster the persister cells resuscitate.
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Affiliation(s)
- Jun-Seob Kim
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Weiwei Zhang
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
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18
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Fluorescent Antibiotics: New Research Tools to Fight Antibiotic Resistance. Trends Biotechnol 2018; 36:523-536. [PMID: 29478675 DOI: 10.1016/j.tibtech.2018.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/02/2023]
Abstract
Better understanding how multidrug-resistant (MDR) bacteria can evade current and novel antibiotics requires a better understanding of the chemical biology of antibiotic action. This necessitates using new tools and techniques to advance our knowledge of bacterial responses to antibiotics, ideally in live cells in real time, to selectively investigate bacterial growth, division, metabolism, and resistance in response to antibiotic challenge. In this review, we discuss the preparation and biological evaluation of fluorescent antibiotics, focussing on how these reporters and assay methods can help elucidate resistance mechanisms. We also examine the potential utility of such probes for real-time in vivo diagnosis of infections.
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19
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Frequency and Mechanism of Spontaneous Resistance to Sulbactam Combined with the Novel β-Lactamase Inhibitor ETX2514 in Clinical Isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2018; 62:AAC.01576-17. [PMID: 29133555 DOI: 10.1128/aac.01576-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/03/2017] [Indexed: 12/18/2022] Open
Abstract
The novel diazabicyclooctenone ETX2514 is a potent, broad-spectrum serine β-lactamase inhibitor that restores sulbactam activity against resistant Acinetobacter baumannii The frequency of spontaneous resistance to sulbactam-ETX2514 in clinical isolates was found to be 7.6 × 10-10 to <9.0 × 10-10 at 4× MIC and mapped to residues near the active site of penicillin binding protein 3 (PBP3). Purified mutant PBP3 proteins demonstrated reduced affinity for sulbactam. In a sulbactam-sensitive isolate, resistance also mapped to stringent response genes associated with resistance to PBP2 inhibitors, suggesting that in addition to β-lactamase inhibition, ETX2514 may enhance sulbactam activity in A. baumannii via inhibition of PBP2.
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20
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Durand-Réville TF, Guler S, Comita-Prevoir J, Chen B, Bifulco N, Huynh H, Lahiri S, Shapiro AB, McLeod SM, Carter NM, Moussa SH, Velez-Vega C, Olivier NB, McLaughlin R, Gao N, Thresher J, Palmer T, Andrews B, Giacobbe RA, Newman JV, Ehmann DE, de Jonge B, O'Donnell J, Mueller JP, Tommasi RA, Miller AA. ETX2514 is a broad-spectrum β-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii. Nat Microbiol 2017; 2:17104. [PMID: 28665414 DOI: 10.1038/nmicrobiol.2017.104] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022]
Abstract
Multidrug-resistant (MDR) bacterial infections are a serious threat to public health. Among the most alarming resistance trends is the rapid rise in the number and diversity of β-lactamases, enzymes that inactivate β-lactams, a class of antibiotics that has been a therapeutic mainstay for decades. Although several new β-lactamase inhibitors have been approved or are in clinical trials, their spectra of activity do not address MDR pathogens such as Acinetobacter baumannii. This report describes the rational design and characterization of expanded-spectrum serine β-lactamase inhibitors that potently inhibit clinically relevant class A, C and D β-lactamases and penicillin-binding proteins, resulting in intrinsic antibacterial activity against Enterobacteriaceae and restoration of β-lactam activity in a broad range of MDR Gram-negative pathogens. One of the most promising combinations is sulbactam-ETX2514, whose potent antibacterial activity, in vivo efficacy against MDR A. baumannii infections and promising preclinical safety demonstrate its potential to address this significant unmet medical need.
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Affiliation(s)
| | - Satenig Guler
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Brendan Chen
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Neil Bifulco
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Hoan Huynh
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Sushmita Lahiri
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Adam B Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Sarah M McLeod
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Nicole M Carter
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Samir H Moussa
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Camilo Velez-Vega
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Nelson B Olivier
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Ning Gao
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Jason Thresher
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Tiffany Palmer
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Beth Andrews
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Joseph V Newman
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - David E Ehmann
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - John O'Donnell
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - John P Mueller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Rubén A Tommasi
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Alita A Miller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
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21
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Steiner EM, Schneider G, Schnell R. Binding and processing of β‐lactam antibiotics by the transpeptidase Ldt
Mt2
from
Mycobacterium tuberculosis. FEBS J 2017; 284:725-741. [DOI: 10.1111/febs.14010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Eva Maria Steiner
- Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics Karolinska Institutet Stockholm Sweden
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22
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Calvez P, Breukink E, Roper DI, Dib M, Contreras-Martel C, Zapun A. Substitutions in PBP2b from β-Lactam-resistant Streptococcus pneumoniae Have Different Effects on Enzymatic Activity and Drug Reactivity. J Biol Chem 2017; 292:2854-2865. [PMID: 28062575 DOI: 10.1074/jbc.m116.764696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Pneumococcus resists β-lactams by expressing variants of its target enzymes, the penicillin-binding proteins (PBPs), with many amino acid substitutions. Up to 10% of the sequence can be modified. These altered PBPs have a much reduced reactivity with the drugs but retain their physiological activity of cross-linking the peptidoglycan, the major constituent of the bacterial cell wall. However, because β-lactams are chemical and structural mimics of the natural substrate, resistance mediated by altered PBPs raises the following paradox: how PBPs that react poorly with the drugs maintain a sufficient level of activity with the physiological substrate. This question is addressed for the first time in this study, which compares the peptidoglycan cross-linking activity of PBP2b from susceptible and resistant strains with their inhibition by different β-lactams. Unexpectedly, the enzymatic activity of the variants did not correlate with their antibiotic reactivity. This finding indicates that some of the numerous amino acid substitutions were selected to restore a viable level of enzymatic activity by a compensatory molecular mechanism.
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Affiliation(s)
- Philippe Calvez
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Eefjan Breukink
- the Department of Chemical Biology and Organic Chemistry, Institute of Biomembranes, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584 CH, The Netherlands, and
| | - David I Roper
- the School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mélanie Dib
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Carlos Contreras-Martel
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - André Zapun
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France,
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23
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Shapiro AB. Investigation of β-lactam antibacterial drugs, β-lactamases, and penicillin-binding proteins with fluorescence polarization and anisotropy: a review. Methods Appl Fluoresc 2016; 4:024002. [DOI: 10.1088/2050-6120/4/2/024002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Murphy-Benenato KE, Bhagunde PR, Chen A, Davis HE, Durand-Réville TF, Ehmann DE, Galullo V, Harris JJ, Hatoum-Mokdad H, Jahić H, Kim A, Manjunatha MR, Manyak EL, Mueller J, Patey S, Quiroga O, Rooney M, Sha L, Shapiro AB, Sylvester M, Tan B, Tsai AS, Uria-Nickelsen M, Wu Y, Zambrowski M, Zhao SX. Discovery of Efficacious Pseudomonas aeruginosa-Targeted Siderophore-Conjugated Monocarbams by Application of a Semi-mechanistic Pharmacokinetic/Pharmacodynamic Model. J Med Chem 2015; 58:2195-205. [DOI: 10.1021/jm501506f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - M. R. Manjunatha
- Infection
Innovative Medicines, AstraZeneca India Pvt. Ltd., Bellary Road, Bangalore 560024, India
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Molecular mechanisms of sulbactam antibacterial activity and resistance determinants in Acinetobacter baumannii. Antimicrob Agents Chemother 2015; 59:1680-9. [PMID: 25561334 DOI: 10.1128/aac.04808-14] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sulbactam is a class A β-lactamase inhibitor with intrinsic whole-cell activity against certain bacterial species, including Acinetobacter baumannii. The clinical use of sulbactam for A. baumannii infections is of interest due to increasing multidrug resistance in this pathogen. However, the molecular drivers of its antibacterial activity and resistance determinants have yet to be precisely defined. Here we show that the antibacterial activities of sulbactam vary widely across contemporary A. baumannii clinical isolates and are mediated through inhibition of the penicillin-binding proteins (PBPs) PBP1 and PBP3, with very low frequency of resistance; the rare pbp3 mutants with high levels of resistance to sulbactam are attenuated in fitness. These results support further investigation of the potential clinical utility of sulbactam.
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Fluorescence anisotropy-based measurement of Pseudomonas aeruginosa penicillin-binding protein 2 transpeptidase inhibitor acylation rate constants. Anal Biochem 2014; 463:15-22. [DOI: 10.1016/j.ab.2014.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 11/20/2022]
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June CM, Vaughan RM, Ulberg LS, Bonomo RA, Witucki LA, Leonard DA. A fluorescent carbapenem for structure function studies of penicillin-binding proteins, β-lactamases, and β-lactam sensors. Anal Biochem 2014; 463:70-4. [PMID: 25058926 DOI: 10.1016/j.ab.2014.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/12/2014] [Indexed: 11/29/2022]
Abstract
By reacting fluorescein isothiocyanate with meropenem, we have prepared a carbapenem-based fluorescent β-lactam. Fluorescein-meropenem binds both penicillin-binding proteins and β-lactam sensors and undergoes a typical acylation reaction in the active site of these proteins. The probe binds the class D carbapenemase OXA-24/40 with close to the same affinity as meropenem and undergoes a complete catalytic hydrolysis reaction. The visible light excitation and strong emission of fluorescein render this molecule a useful structure-function probe through its application in sodium dodecyl sulfate-polyacrylamide gel electrophoresis assays as well as solution-based kinetic anisotropy assays. Its classification as a carbapenem β-lactam and the position of its fluorescent modification render it a useful complement to other fluorescent β-lactams, most notably Bocillin FL. In this study, we show the utility of fluorescein-meropenem by using it to detect mutants of OXA-24/40 that arrest at the acyl-intermediate state with carbapenem substrates but maintain catalytic competency with penicillin substrates.
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Affiliation(s)
- Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Robert M Vaughan
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Lucas S Ulberg
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and Department of Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Laurie A Witucki
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA.
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