1
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Alonso-García I, Vázquez-Ucha JC, Martínez-Guitián M, Lasarte-Monterrubio C, Rodríguez-Pallares S, Camacho-Zamora P, Rumbo-Feal S, Aja-Macaya P, González-Pinto L, Outeda-García M, Maceiras R, Guijarro-Sánchez P, Muíño-Andrade MJ, Fernández-González A, Oviaño M, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. Interplay between OXA-10 β-Lactamase Production and Low Outer-Membrane Permeability in Carbapenem Resistance in Enterobacterales. Antibiotics (Basel) 2023; 12:999. [PMID: 37370318 DOI: 10.3390/antibiotics12060999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The OXA-10 class D β-lactamase has been reported to contribute to carbapenem resistance in non-fermenting Gram-negative bacilli; however, its contribution to carbapenem resistance in Enterobacterales is unknown. In this work, minimum inhibitory concentrations (MICs), whole genome sequencing (WGS), cloning experiments, kinetic assays, molecular modelling studies, and biochemical assays for carbapenemase detection were performed to determine the impact of OXA-10 production on carbapenem resistance in two XDR clinical isolates of Escherichia coli with the carbapenem resistance phenotype (ertapenem resistance). WGS identified the two clinical isolates as belonging to ST57 in close genomic proximity to each other. Additionally, the presence of the blaOXA-10 gene was identified in both isolates, as well as relevant mutations in the genes coding for the OmpC and OmpF porins. Cloning of blaOXA-10 in an E. coli HB4 (OmpC and OmpF-deficient) demonstrated the important contribution of OXA-10 to increased carbapenem MICs when associated with porin deficiency. Kinetic analysis showed that OXA-10 has low carbapenem-hydrolysing activity, but molecular models revealed interactions of this β-lactamase with the carbapenems. OXA-10 was not detected with biochemical tests used in clinical laboratories. In conclusion, the β-lactamase OXA-10 limits the activity of carbapenems in Enterobacterales when combined with low permeability and should be monitored in the future.
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Affiliation(s)
- Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Martínez-Guitián
- NANOBIOFAR, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Campus Vida Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, Universidade da Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Salud Rodríguez-Pallares
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Camacho-Zamora
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Aja-Macaya
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Lucía González-Pinto
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Michelle Outeda-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - María José Muíño-Andrade
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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2
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In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity. Int J Mol Sci 2023; 24:ijms24065120. [PMID: 36982188 PMCID: PMC10049026 DOI: 10.3390/ijms24065120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).
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3
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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4
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Reidl CT, Mascarenhas R, Mohammad TSH, Lutz MR, Thomas PW, Fast W, Liu D, Becker DP. Cyclobutanone Inhibitor of Cobalt-Functionalized Metallo-γ-Lactonase AiiA with Cyclobutanone Ring Opening in the Active Site. ACS OMEGA 2021; 6:13567-13578. [PMID: 34095651 PMCID: PMC8173579 DOI: 10.1021/acsomega.0c06348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
An α-amido cyclobutanone possessing a C10 hydrocarbon tail was designed as a potential transition-state mimetic for the quorum-quenching metallo-γ-lactonase autoinducer inactivator A (AiiA) with the support of in-house modeling techniques and found to be a competitive inhibitor of dicobalt(II) AiiA with an inhibition constant of K i = 0.007 ± 0.002 mM. The catalytic mechanism of AiiA was further explored using our product-based transition-state modeling (PBTSM) computational approach, providing substrate-intermediate models arising during enzyme turnover and further insight into substrate-enzyme interactions governing native substrate catalysis. These interactions were targeted in the docking of cyclobutanone hydrates into the active site of AiiA. The X-ray crystal structure of dicobalt(II) AiiA cocrystallized with this cyclobutanone inhibitor unexpectedly revealed an N-(2-oxocyclobutyl)decanamide ring-opened acyclic product bound to the enzyme active site (PDB 7L5F). The C10 alkyl chain and its interaction with the hydrophobic phenylalanine clamp region of AiiA adjacent to the active site enabled atomic placement of the ligand atoms, including the C10 alkyl chain. A mechanistic hypothesis for the ring opening is proposed involving a radical-mediated process.
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Affiliation(s)
- Cory T. Reidl
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Romila Mascarenhas
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Thahani S. Habeeb Mohammad
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Marlon R. Lutz
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Pei W. Thomas
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Walter Fast
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dali Liu
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Daniel P. Becker
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
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5
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Affiliation(s)
- Sina Witzel
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - A. Stephen K. Hashmi
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jin Xie
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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6
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Salvio R, Placidi S, Bella M. Benzazetidines and Related Compounds: Synthesis and Potential. Chemistry 2020; 26:10157-10174. [DOI: 10.1002/chem.201905668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/24/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche Università “Tor Vergata” Via della Ricerca Scientifica, 1 00133 Roma Italy
- ISB—CNR Sezione Meccanismi di Reazione Università La Sapienza 00185 Roma Italy
| | - Simone Placidi
- Dipartimento di Chimica Sapienza Università di Roma P.le Aldo Moro 5 00185 Roma Italy
| | - Marco Bella
- Dipartimento di Chimica Sapienza Università di Roma P.le Aldo Moro 5 00185 Roma Italy
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7
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Si X, Zhang L, Wu Z, Rudolph M, Asiri AM, Hashmi ASK. Visible Light-Induced α-C(sp 3)-H Acetalization of Saturated Heterocycles Catalyzed by a Dimeric Gold Complex. Org Lett 2020; 22:5844-5849. [PMID: 32678618 DOI: 10.1021/acs.orglett.0c01924] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Saturated heterocyclic acetals are useful fragments in organic synthesis and other fields. Herein, C(sp3)-H dehydrogenative cross-couplings of ethers, tetrahydrothiophenes, and pyrrolidines were achieved under visible light irradiation by using iodobenzene and an in situ-formed gold complex. The broad functional group compatibility and substrate scope indicate that our strategy is a promising way to synthesize acetal analogues. The method was successfully applied in late-stage modifications of bioactive molecules. Gram scale syntheses and mechanistic studies are also presented.
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Affiliation(s)
- Xiaojia Si
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Lumin Zhang
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Zuozuo Wu
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Matthias Rudolph
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - A Stephen K Hashmi
- Organisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany.,Chemistry Department, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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8
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Laws M, Shaaban A, Rahman KM. Antibiotic resistance breakers: current approaches and future directions. FEMS Microbiol Rev 2020; 43:490-516. [PMID: 31150547 PMCID: PMC6736374 DOI: 10.1093/femsre/fuz014] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022] Open
Abstract
Infections of antibiotic-resistant pathogens pose an ever-increasing threat to mankind. The investigation of novel approaches for tackling the antimicrobial resistance crisis must be part of any global response to this problem if an untimely reversion to the pre-penicillin era of medicine is to be avoided. One such promising avenue of research involves so-called antibiotic resistance breakers (ARBs), capable of re-sensitising resistant bacteria to antibiotics. Although some ARBs have previously been employed in the clinical setting, such as the β-lactam inhibitors, we posit that the broader field of ARB research can yet yield a greater diversity of more effective therapeutic agents than have been previously achieved. This review introduces the area of ARB research, summarises the current state of ARB development with emphasis on the various major classes of ARBs currently being investigated and their modes of action, and offers a perspective on the future direction of the field.
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Affiliation(s)
- Mark Laws
- Institute of Pharmaceutical Sciences, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH
| | - Ali Shaaban
- Institute of Pharmaceutical Sciences, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Sciences, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH
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9
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Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism. Biomolecules 2020; 10:biom10060854. [PMID: 32503337 PMCID: PMC7356002 DOI: 10.3390/biom10060854] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
β-Lactam antibiotics are the most widely prescribed antibacterial drugs due to their low toxicity and broad spectrum. Their action is counteracted by different resistance mechanisms developed by bacteria. Among them, the most common strategy is the expression of β-lactamases, enzymes that hydrolyze the amide bond present in all β-lactam compounds. There are several inhibitors against serine-β-lactamases (SBLs). Metallo-β-lactamases (MBLs) are Zn(II)-dependent enzymes able to hydrolyze most β-lactam antibiotics, and no clinically useful inhibitors against them have yet been approved. Despite their large structural diversity, MBLs have a common catalytic mechanism with similar reaction species. Here, we describe a number of MBL inhibitors that mimic different species formed during the hydrolysis process: substrate, transition state, intermediate, or product. Recent advances in the development of boron-based and thiol-based inhibitors are discussed in the light of the mechanism of MBLs. We also discuss the use of chelators as a possible strategy, since Zn(II) ions are essential for substrate binding and catalysis.
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10
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Chen C, Sun LY, Gao H, Kang PW, Li JQ, Zhen JB, Yang KW. Identification of Cisplatin and Palladium(II) Complexes as Potent Metallo-β-lactamase Inhibitors for Targeting Carbapenem-Resistant Enterobacteriaceae. ACS Infect Dis 2020; 6:975-985. [PMID: 32119777 DOI: 10.1021/acsinfecdis.9b00385] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The emergence and prevalence of carbapenem-resistant bacterial infection have seriously threatened the clinical use of almost all β-lactam antibacterials. The development of effective metallo-β-lactamase (MβL) inhibitors to restore the existing antibiotics efficacy is an ideal alternative. Although several types of serine-β-lactamase inhibitors have been successfully developed and used in clinical settings, MβL inhibitors are not clinically available to date. Herein, we identified that cisplatin and Pd(II) complexes are potent broad-spectrum inhibitors of the B1 and B2 subclasses of MβLs and effectively revived Meropenem efficacy against MβL-expressing bacteria in vitro. Enzyme kinetics, thermodynamics, inductively coupled plasma atomic emission spectrometry (ICP-AES), matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), and site-directed mutation assays revealed that these metal complexes irreversibly inhibited NDM-1 through a novel inhibition mode involving binding to Cys208 and displacing one Zn(II) ion of the enzyme with one Pt(II) containing two NH3's or one Pd(II) ion. Importantly, the combination therapy of Meropenem and metal complexes significantly suppressed the development of higher-level resistance in bacteria producing NDM-1, also effectively reduced the bacterial burden in liver and spleen of mice infected by carbapenem-resistant Enterobacteriaceae producing NDM-1. These findings will offer potential lead compounds for the further development of clinically useful inhibitors targeting MβLs.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Peng-Wei Kang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, 1 Xuefu Avenue, Xi’an, Shaanxi 710127, P. R. China
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11
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Sadhukhan S, Santhi J, Baire B. The α,α‐Dihalocarbonyl Building Blocks: An Avenue for New Reaction Development in Organic Synthesis. Chemistry 2020; 26:7145-7175. [DOI: 10.1002/chem.201905475] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/08/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Santu Sadhukhan
- Department of ChemistryIndian Institute of Technology Madras Chennai 600036 India
| | - Jampani Santhi
- Department of ChemistryIndian Institute of Technology Madras Chennai 600036 India
| | - Beeraiah Baire
- Department of ChemistryIndian Institute of Technology Madras Chennai 600036 India
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12
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Habeeb Mohammad TS, Reidl CT, Zeller M, Becker DP. Synthesis of a protected 2-aminocyclobutanone as a modular transition state synthon for medicinal chemistry. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Yan Y, Li G, Li G. Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Med Res Rev 2020; 40:1558-1592. [PMID: 32100311 DOI: 10.1002/med.21665] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Yu‐Hang Yan
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Gen Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Guo‐Bo Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
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14
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Pemberton OA, Jaishankar P, Akhtar A, Adams JL, Shaw LN, Renslo AR, Chen Y. Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J Med Chem 2019; 62:8480-8496. [PMID: 31483651 DOI: 10.1021/acs.jmedchem.9b00728] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gram-negative pathogens expressing serine β-lactamases (SBLs) and metallo-β-lactamases (MBLs), especially those with carbapenemase activity, threaten the clinical utility of almost all β-lactam antibiotics. Here we describe the discovery of a heteroaryl phosphonate scaffold that exhibits noncovalent cross-class inhibition of representative carbapenemases, specifically the SBL KPC-2 and the MBLs NDM-1 and VIM-2. The most potent lead, compound 16, exhibited low nM to low μM inhibition of KPC-2, NDM-1, and VIM-2. Compound 16 potentiated imipenem efficacy against resistant clinical and laboratory bacterial strains expressing carbapenemases while showing some cytotoxicity toward human HEK293T cells only at concentrations above 100 μg/mL. Complex structures with KPC-2, NDM-1, and VIM-2 demonstrate how these inhibitors achieve high binding affinity to both enzyme classes. These findings provide a structurally and mechanistically new scaffold for drug discovery targeting multidrug resistant Gram-negative pathogens and more generally highlight the active site features of carbapenemases that can be leveraged for lead discovery.
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Affiliation(s)
- Orville A Pemberton
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Afroza Akhtar
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Jessie L Adams
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Yu Chen
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
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15
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The assemblage of covalent and metal binding dual functional scaffold for cross-class metallo-β-lactamases inhibition. Future Med Chem 2019; 11:2381-2394. [PMID: 31544522 DOI: 10.4155/fmc-2019-0008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: The discovery and development of novel broad-spectrum MβLs inhibitors are urgent to overcome antibiotic resistance mediated by MβLs. Methods & results: Herein, the synthesized 21 compounds exhibited potent inhibition to the clinically important MβLs (NDM-1, IMP-1 and ImiS) and effectively restored the antibacterial efficacy of cefazolin and imipenem against Escherichia coli harboring MβLs. 5b was first identified to be dual functional broad-spectrum MβLs inhibitor through assemblage of covalent and metal binding scaffold, which irreversibly inhibited B1, B2 MβLs via forming a Se–S covalent bond, and competitively inhibited B3 MβLs by coordinating the metals at active site. Conclusion: The designed compounds can serve as potent broad-spectrum MβLs inhibitors and combat MβLs-producing ‘superbug’ in combination with β-lactams.
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16
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Cesta DJ, Somersan Karakaya S, Saito K, Javidnia PE, Roberts J, Ling Y, Gold BS, Lopez Quezada L, Zhang D, Abramyan TM, Kireev DB, Aubé J, Scarry SM. Synthesis and Antibacterial Evaluation of Cephalosporin Isosteres. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Drew J. Cesta
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599 USA
| | - Selin Somersan Karakaya
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Kohta Saito
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Prisca E. Javidnia
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Julia Roberts
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Yan Ling
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Ben S. Gold
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Landys Lopez Quezada
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - David Zhang
- Department of Microbiology and Immunology and Department of Medicine Weill Cornell Medicine New York, NY 10065 USA
| | - Tigran M. Abramyan
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599 USA
| | - Dmitri B. Kireev
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599 USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599 USA
| | - Sarah M. Scarry
- Division of Chemical Biology and Medicinal Chemistry UNC Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill, NC 27599 USA
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17
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Torelli NJ, Akhtar A, DeFrees K, Jaishankar P, Pemberton OA, Zhang X, Johnson C, Renslo AR, Chen Y. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. ACS Infect Dis 2019; 5:1013-1021. [PMID: 30942078 DOI: 10.1021/acsinfecdis.9b00052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Serine and metallo-carbapenemases are a serious health concern due to their capability to hydrolyze nearly all β-lactam antibiotics. However, the molecular basis for their unique broad-spectrum substrate profile is poorly understood, particularly for serine carbapenemases, such as KPC-2. Using substrates and newly identified small molecules, we compared the ligand binding properties of KPC-2 with the noncarbapenemase CTX-M-14, both of which are Class A β-lactamases with highly similar active sites. Notably, compared to CTX-M-14, KPC-2 was more potently inhibited by hydrolyzed β-lactam products (product inhibition), as well as by a series of novel tetrazole-based inhibitors selected from molecular docking against CTX-M-14. Together with complex crystal structures, these data suggest that the KPC-2 active site has an enhanced ability to form favorable interactions with substrates and small molecule ligands due to its increased hydrophobicity and flexibility. Such properties are even more pronounced in metallo-carbapenemases, such as NDM-1, which was also inhibited by some of the novel tetrazole compounds, including one displaying comparable low μM affinities against both KPC-2 and NDM-1. Our results suggest that carbapenemase activity confers an evolutionary advantage on producers via a broad β-lactam substrate scope but also a mechanistic Achilles' heel that can be exploited for new inhibitor discovery. The complex structures demonstrate, for the first time, how noncovalent inhibitors can be engineered to simultaneously target both serine and metallo-carbapenemases. Despite the relatively modest activity of the current compounds, these studies also demonstrate that hydrolyzed products and tetrazole-based chemotypes can provide valuable starting points for broad-spectrum inhibitor discovery against carbapenemases.
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Affiliation(s)
- Nicholas J. Torelli
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Kyle DeFrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Cody Johnson
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
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18
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Thomas PW, Cammarata M, Brodbelt JS, Monzingo AF, Pratt RF, Fast W. A Lysine-Targeted Affinity Label for Serine-β-Lactamase Also Covalently Modifies New Delhi Metallo-β-lactamase-1 (NDM-1). Biochemistry 2019; 58:2834-2843. [PMID: 31145588 DOI: 10.1021/acs.biochem.9b00393] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The divergent sequences, protein structures, and catalytic mechanisms of serine- and metallo-β-lactamases hamper the development of wide-spectrum β-lactamase inhibitors that can block both types of enzymes. The O-aryloxycarbonyl hydroxamate inactivators of Enterobacter cloacae P99 class C serine-β-lactamase are unusual covalent inhibitors in that they target both active-site Ser and Lys residues, resulting in a cross-link consisting of only two atoms. Many clinically relevant metallo-β-lactamases have an analogous active-site Lys residue used to bind β-lactam substrates, suggesting a common site to target with covalent inhibitors. Here, we demonstrate that an O-aryloxycarbonyl hydroxamate inactivator of serine-β-lactamases can also serve as a classical affinity label for New Delhi metallo-β-lactamase-1 (NDM-1). Rapid dilution assays, site-directed mutagenesis, and global kinetic fitting are used to map covalent modification at Lys211 and determine KI (140 μM) and kinact (0.045 min-1) values. Mass spectrometry of the intact protein and the use of ultraviolet photodissociation for extensive fragmentation confirm stoichiometric covalent labeling that occurs specifically at Lys211. A 2.0 Å resolution X-ray crystal structure of inactivated NDM-1 reveals that the covalent adduct is bound at the substrate-binding site but is not directly coordinated to the active-site zinc cluster. These results indicate that Lys-targeted affinity labels might be a successful strategy for developing compounds that can inactivate both serine- and metallo-β-lactamases.
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Affiliation(s)
| | | | | | | | - R F Pratt
- Department of Chemistry , Wesleyan University , Middletown , Connecticut 06459 , United States
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19
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Qiu L, Wen Z, Li Y, Tian K, Deng Y, Shen B, Duan Y, Huang Y. Stereoselective functionalization of platensimycin and platencin by sulfa-Michael/aldol reactions. Org Biomol Chem 2019; 17:4261-4272. [PMID: 30816397 DOI: 10.1039/c9ob00324j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bioinspired sulfa-Michael/aldol cascade reactions have been developed for the semisynthesis of sulfur-containing heterocyclic derivatives of platensimycin and platencin, with three newly formed contiguous stereogenic centers. Density functional theory calculations revealed the mechanism for the stereochemistry control. This method was used in a synthesis of a platensimycin thiophene analogue with potent antibacterial activities against Staphylococcus aureus.
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Affiliation(s)
- Lin Qiu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, China.
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20
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 437] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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21
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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22
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Verdino A, Zollo F, De Rosa M, Soriente A, Hernández-Martínez MÁ, Marabotti A. Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases. BMC STRUCTURAL BIOLOGY 2018; 18:13. [PMID: 30286754 PMCID: PMC6389238 DOI: 10.1186/s12900-018-0092-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/20/2018] [Indexed: 11/30/2022]
Abstract
Background One of the main concerns of the modern medicine is the frightening spread of antimicrobial resistance caused mainly by the misuse of antibiotics. The researchers worldwide are actively involved in the search for new classes of antibiotics, and for the modification of known molecules in order to face this threatening problem. We have applied a computational approach to predict the interactions between a new cephalosporin derivative containing an additional β-lactam ring with different substituents, and several serine β-lactamases representative of the different classes of this family of enzymes. Results The results of the simulations, performed by using a covalent docking approach, has shown that this compound, although able to bind the selected β-lactamases, has a different predicted binding score for the two β-lactam rings, suggesting that one of them could be more resistant to the attack of these enzymes and stay available to perform its bactericidal activity. Conclusions The detailed analysis of the complexes obtained by these simulations suggests possible hints to modulate the affinity of this compound towards these enzymes, in order to develop new derivatives with improved features to escape to degradation. Electronic supplementary material The online version of this article (10.1186/s12900-018-0092-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Verdino
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Felicia Zollo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Margherita De Rosa
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Annunziata Soriente
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | | | - Anna Marabotti
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
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23
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Somboro AM, Osei Sekyere J, Amoako DG, Essack SY, Bester LA. Diversity and Proliferation of Metallo-β-Lactamases: a Clarion Call for Clinically Effective Metallo-β-Lactamase Inhibitors. Appl Environ Microbiol 2018; 84:e00698-18. [PMID: 30006399 PMCID: PMC6121990 DOI: 10.1128/aem.00698-18] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The worldwide proliferation of life-threatening metallo-β-lactamase (MBL)-producing Gram-negative bacteria is a serious concern to public health. MBLs are compromising the therapeutic efficacies of β-lactams, particularly carbapenems, which are last-resort antibiotics indicated for various multidrug-resistant bacterial infections. Inhibition of enzymes mediating antibiotic resistance in bacteria is one of the major promising means for overcoming bacterial resistance. Compounds having potential MBL-inhibitory activity have been reported, but none are currently under clinical trials. The need for developing safe and efficient MBL inhibitors (MBLIs) is obvious, particularly with the continuous spread of MBLs worldwide. In this review, the emergence and escalation of MBLs in Gram-negative bacteria are discussed. The relationships between different class B β-lactamases identified up to 2017 are represented by a phylogenetic tree and summarized. In addition, approved and/or clinical-phase serine β-lactamase inhibitors are recapitulated to reflect the successful advances made in developing class A β-lactamase inhibitors. Reported MBLIs, their inhibitory properties, and their purported modes of inhibition are delineated. Insights into structural variations of MBLs and the challenges involved in developing potent MBLIs are also elucidated and discussed. Currently, natural products and MBL-resistant β-lactam analogues are the most promising agents that can become clinically efficient MBLIs. A deeper comprehension of the mechanisms of action and activity spectra of the various MBLs and their inhibitors will serve as a bedrock for further investigations that can result in clinically useful MBLIs to curb this global menace.
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Affiliation(s)
- Anou M Somboro
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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24
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Abboud MI, Kosmopoulou M, Krismanich AP, Johnson JW, Hinchliffe P, Brem J, Claridge TDW, Spencer J, Schofield CJ, Dmitrienko GI. Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis. Chemistry 2018; 24:5734-5737. [PMID: 29250863 PMCID: PMC5947706 DOI: 10.1002/chem.201705886] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 01/25/2023]
Abstract
The most important resistance mechanism to β-lactam antibiotics involves hydrolysis by two β-lactamase categories: the nucleophilic serine and the metallo-β-lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19 F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13 C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition-state and/or intermediate analogues as inhibitors of all β-lactamase classes.
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Affiliation(s)
- Martine I. Abboud
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Magda Kosmopoulou
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Anthony P. Krismanich
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Jarrod W. Johnson
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Philip Hinchliffe
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Jürgen Brem
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | | | - Gary I. Dmitrienko
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
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25
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Search for non-lactam inhibitors of mtb β-lactamase led to its open shape in apo state: new concept for antibiotic design. Sci Rep 2017; 7:6204. [PMID: 28740144 PMCID: PMC5524718 DOI: 10.1038/s41598-017-06023-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/06/2017] [Indexed: 01/14/2023] Open
Abstract
Mtb β-lactamase (BlaC) is extremely efficient in hydrolyzing ß-lactam antibiotics which renders/leads to protection and/or resistance to this bug. There is a compelling need to develop new non-lactam inhibitors which can bind and inhibit BlaC, but cannot be hydrolyzed, thus neutralizing this survival mechanism of Mtb. Using the crystal structure of BlaC we screened 750000 purchasable compounds from ZINC Database for their theoretical affinity to the enzyme’s active site. 32 of the best hits of the compounds having tetra-, tri- and thiadi-azole moiety were tested in vitro, and 4 efficiently inhibited the enzymatic activity of recombinant BlaC. Characterization of the shape of BlaC−/+ inhibitors by small angle X-ray scattering (SAXS) brought forth that BlaC adopts: (1) an open shape (radius of gyration of 2.3 nm compared to 1.9 nm of crystal structures) in solution; (2) closed shape similar to observed crystal structure(s) in presence of effective inhibitor; and (3) a closed shape which opens up when a hydrolysable inhibitor is present in solution. New BlaC inhibitors were: 1-(4-(pyridin-3-yl)-thiazol-2-ylamino)-2-(7,8,9-triaza-bicyclo[4.3.0]nona-1(6),2,4,8-tetraen-7-yl)-ethanone; 8-butyl-3-((5-(pyridin-2-yl)-4H-1,2,4-triazol-3-ylamino)-formyl)-8-aza-bicyclo[4.3.0]nona-1(6),2,4-triene-7,9-dione; 1-(3-((5-(5-bromo-thiophen-2-yl)-1,3,4-oxadiazol-2-yl)-methoxy)-phenyl)-1H-1,2,3,4-tetraazole; and 1-(2,3-dimethyl-phenylamino)-2-(2-(1-(2-methoxy-5-methyl-phenyl)-1H-1,2,3,4-tetraazol-5-ylsulfanyl)-acetylamino)-ethanone. The open-close shape of BlaC questions the physiological significance of the closed shape known for BlaC−/+ inhibitors and paves new path for structure aided design of novel inhibitors.
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Abstract
The global overuse of antibiotics has led to the emergence of drug-resistant pathogenic bacteria. Bacteria can combat β-lactams by expressing β-lactamases. Inhibitors of one class of β-lactamase, the serine-β-lactamases, are used clinically to prevent degradation of β-lactam antibiotics. However, a second class of β-lactamase, the metallo-β-lactamases (MBLs), function by a different mechanism to serine-β-lactamases and no inhibitors of MBLs have progressed to be used in the clinic. Bacteria that express MBLs are an increasingly important threat to human health. This review outlines various approaches taken to discover MBL inhibitors, with an emphasis on the different chemical classes of inhibitors. Recent progress, particularly new screening methods and the rational design of potent MBL inhibitors are discussed.
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Devi P, Rutledge PJ. Cyclobutanone Analogues of β-Lactam Antibiotics: β-Lactamase Inhibitors with Untapped Potential? Chembiochem 2017; 18:338-351. [PMID: 27992105 DOI: 10.1002/cbic.201600529] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 11/11/2022]
Abstract
β-Lactam antibiotics have been used for many years to treat bacterial infections. However the effective treatment of an increasing range of microbial infections is threatened by bacterial resistance to β-lactams: the prolonged, widespread (and at times reckless) use of these drugs has spawned widespread resistance, which renders them ineffective against many bacterial strains. The cyclobutanone ring system is isosteric with β-lactam: in cyclobutanone analogues, the eponymous cyclic amide is replaced with an all-carbon ring, the amide N is substituted by a tertiary C-H α to a ketone. Cyclobutanone analogues of various β-lactam antibiotics have been investigated over the last 35 years, initially as prospective antibiotics in their own right and inhibitors of the β-lactamase enzymes that impart resistance to β-lactams. More recently they have been tested as inhibitors of other serine proteases and as mechanistic probes of β-lactam biosynthesis. Cyclobutanone analogues of the penam ring system are the first reversible inhibitors with moderate activity against all classes of β-lactamase; other compounds from this family inhibit Streptomyces R61 dd-carboxypeptidase/transpeptidase, human neutrophil elastase and porcine pancreatic elastase. But has their potential as enzyme inhibitors been fully exploited? Challenges in synthesising diversely functionalised cyclobutanone derivatives mean that only a limited number have been made (with limited structural diversity) and evaluated. This review surveys the different synthetic approaches that have been taken to these compounds, the investigations made to evaluate their biological activity and prospects for future developments in this area.
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Affiliation(s)
- Prarthana Devi
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
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Chang S, Holmes M, Mowat J, Meanwell M, Britton R. α‐Arylation and Ring Expansion of Annulated Cyclobutanones: Stereoselective Synthesis of Functionalized Tetralones. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608449] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stanley Chang
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Michael Holmes
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Jeffrey Mowat
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Michael Meanwell
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Robert Britton
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
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29
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Chang S, Holmes M, Mowat J, Meanwell M, Britton R. α‐Arylation and Ring Expansion of Annulated Cyclobutanones: Stereoselective Synthesis of Functionalized Tetralones. Angew Chem Int Ed Engl 2016; 56:748-752. [DOI: 10.1002/anie.201608449] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/24/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Stanley Chang
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Michael Holmes
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Jeffrey Mowat
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Michael Meanwell
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Robert Britton
- Department of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
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Avci FG, Altinisik FE, Vardar Ulu D, Ozkirimli Olmez E, Sariyar Akbulut B. An evolutionarily conserved allosteric site modulates beta-lactamase activity. J Enzyme Inhib Med Chem 2016; 31:33-40. [PMID: 27353461 DOI: 10.1080/14756366.2016.1201813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Declining efficiency of antibiotic-inhibitor combinatorial therapies in treating beta-lactamase mediated resistance necessitates novel inhibitor development. Allosteric inhibition offers an alternative to conventional drugs that target the conserved active site. Here, we show that the evolutionarily conserved PWP triad located at the N-terminus of the H10 helix directly interacts with the allosteric site in TEM-1 beta-lactamase and regulates its activity. While point mutations in the PWP triad preserve the overall secondary structures around the allosteric site, they result in a more open and dynamic global structure with decreased chemical stability and increased aggregation propensity. These mutant enzymes with a less compact hydrophobic core around the allosteric site displayed significant activity loss. Detailed sequence and structure conservation analyses revealed that the PWP triad is an evolutionarily conserved motif unique to class A beta-lactamases aligning its allosteric site and hence is an effective potential target for enzyme regulation and selective drug design.
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Affiliation(s)
- Fatma Gizem Avci
- a Department of Bioengineering , Marmara University , İstanbul , Turkey
| | | | - Didem Vardar Ulu
- b Department of Chemistry , Boston University , Boston , MA , USA , and
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31
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Brindisi M, Brogi S, Giovani S, Gemma S, Lamponi S, De Luca F, Novellino E, Campiani G, Docquier JD, Butini S. Targeting clinically-relevant metallo-β-lactamases: from high-throughput docking to broad-spectrum inhibitors. J Enzyme Inhib Med Chem 2016; 31:98-109. [DOI: 10.3109/14756366.2016.1172575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Margherita Brindisi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | - Simone Brogi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | - Simone Giovani
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | - Sandra Gemma
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | - Stefania Lamponi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | - Filomena De Luca
- Department of Medical Biotechnology, University of Siena, Siena, Italy, and
| | - Ettore Novellino
- Department of Pharmacy, University of Napoli Federico II, Napoli, Italy
| | - Giuseppe Campiani
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
| | | | - Stefania Butini
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, Siena, Italy,
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy,
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32
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Zhang YL, Yang KW, Zhou YJ, LaCuran AE, Oelschlaeger P, Crowder MW. Diaryl-Substituted Azolylthioacetamides: Inhibitor Discovery of New Delhi Metallo-β-Lactamase-1 (NDM-1). ChemMedChem 2014; 9:2445-8. [DOI: 10.1002/cmdc.201402249] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 11/09/2022]
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33
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Abstract
The β-lactam antibiotics are essential for the treatment of a wide range of human bacterial diseases. However, a class of zinc-dependent hydrolases known as the metallo-β-lactamase (MBL) can confer bacteria with extended spectrum β-lactam resistance. To date, there are no clinically approved MBL inhibitors, making these enzymes a serious threat to human health. In this review, a structural approach is taken to outline some of the more promising MBL inhibitors and shed light on how the resistance conferred by this emerging class of enzymes may be circumvented in the future.
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34
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Drawz SM, Papp-Wallace KM, Bonomo RA. New β-lactamase inhibitors: a therapeutic renaissance in an MDR world. Antimicrob Agents Chemother 2013; 58:1835-46. [PMID: 24379206 PMCID: PMC4023773 DOI: 10.1128/aac.00826-13] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
As the incidence of Gram-negative bacterial infections for which few effective treatments remain increases, so does the contribution of drug-hydrolyzing β-lactamase enzymes to this serious clinical problem. This review highlights recent advances in β-lactamase inhibitors and focuses on agents with novel mechanisms of action against a wide range of enzymes. To this end, we review the β-lactamase inhibitors currently in clinical trials, select agents still in preclinical development, and older therapeutic approaches that are being revisited. Particular emphasis is placed on the activity of compounds at the forefront of the developmental pipeline, including the diazabicyclooctane inhibitors (avibactam and MK-7655) and the boronate RPX7009. With its novel reversible mechanism, avibactam stands to be the first new β-lactamase inhibitor brought into clinical use in the past 2 decades. Our discussion includes the importance of selecting the appropriate partner β-lactam and dosing regimens for these promising agents. This "renaissance" of β-lactamase inhibitors offers new hope in a world plagued by multidrug-resistant (MDR) Gram-negative bacteria.
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Affiliation(s)
- Sarah M. Drawz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
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35
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Faridoon, Ul Islam N. An Update on the Status of Potent Inhibitors of Metallo-β-Lactamases. Sci Pharm 2013; 81:309-27. [PMID: 23833706 PMCID: PMC3700068 DOI: 10.3797/scipharm.1302-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/28/2013] [Indexed: 11/22/2022] Open
Abstract
The production of metallo-β-lactamases is the most important strategy by which pathogenic bacteria become resistant to currently known β-lactam antibiotics. The emergence of these enzymes is particularly concerning for the future treatment of bacterial infections. There are no clinically available drugs capable of inhibiting any of the metallo-β-lactamases, so there is an urgent need to find such inhibitors. In this review, an up-to-date status of the inhibitors investigated for the inhibition of metallo-β-lactamases has been given so that this rich source of structural information of presently known metallo-β-lactamases could be helpful in generating a broad-spectrum potent inhibitor of metallo-β-lactamases.
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Affiliation(s)
- Faridoon
- Chemistry Department, Islamia College University, Peshawar-25120, Pakistan
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Filippova EV, Weston LA, Kuhn ML, Geissler B, Gehring AM, Armoush N, Adkins CT, Minasov G, Dubrovska I, Shuvalova L, Winsor JR, Lavis LD, Satchell KJF, Becker DP, Anderson WF, Johnson RJ. Large scale structural rearrangement of a serine hydrolase from Francisella tularensis facilitates catalysis. J Biol Chem 2013; 288:10522-35. [PMID: 23430251 DOI: 10.1074/jbc.m112.446625] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tularemia is a deadly, febrile disease caused by infection by the gram-negative bacterium, Francisella tularensis. Members of the ubiquitous serine hydrolase protein family are among current targets to treat diverse bacterial infections. Herein we present a structural and functional study of a novel bacterial carboxylesterase (FTT258) from F. tularensis, a homologue of human acyl protein thioesterase (hAPT1). The structure of FTT258 has been determined in multiple forms, and unexpectedly large conformational changes of a peripheral flexible loop occur in the presence of a mechanistic cyclobutanone ligand. The concomitant changes in this hydrophobic loop and the newly exposed hydrophobic substrate binding pocket suggest that the observed structural changes are essential to the biological function and catalytic activity of FTT258. Using diverse substrate libraries, site-directed mutagenesis, and liposome binding assays, we determined the importance of these structural changes to the catalytic activity and membrane binding activity of FTT258. Residues within the newly exposed hydrophobic binding pocket and within the peripheral flexible loop proved essential to the hydrolytic activity of FTT258, indicating that structural rearrangement is required for catalytic activity. Both FTT258 and hAPT1 also showed significant association with liposomes designed to mimic bacterial or human membranes, respectively, even though similar structural rearrangements for hAPT1 have not been reported. The necessity for acyl protein thioesterases to have maximal catalytic activity near the membrane surface suggests that these conformational changes in the protein may dually regulate catalytic activity and membrane association in bacterial and human homologues.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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37
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Chen J, Yu R, Shen B, Xu Y, Liu Y, Zheng H, Yao W. Docking-based 3D-QSAR modeling of the inhibitors of IMP metallo-β-lactamase. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0172-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2012; 65:455-78. [PMID: 21740228 DOI: 10.1146/annurev-micro-090110-102911] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
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Affiliation(s)
- Karen Bush
- Biology Department, Indiana University, Bloomington, Indiana 47401, USA.
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Borbulevych O, Kumarasiri M, Wilson B, Llarrull LI, Lee M, Hesek D, Shi Q, Peng J, Baker BM, Mobashery S. Lysine Nzeta-decarboxylation switch and activation of the beta-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus. J Biol Chem 2011; 286:31466-72. [PMID: 21775440 DOI: 10.1074/jbc.m111.252189] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of β-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N(ζ)-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N(ζ)-decarboxylation. This unique process, termed the lysine N(ζ)-decarboxylation switch, arrests the sensor domain in the activated ("on") state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.
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Affiliation(s)
- Oleg Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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