1
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Price S, Que EL. Probing metalloenzyme dynamics in living systems: Contemporary advances in fluorescence imaging tools and applications. Curr Opin Chem Biol 2024; 81:102475. [PMID: 38852500 DOI: 10.1016/j.cbpa.2024.102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024]
Abstract
Metalloenzymes are essential to cellular function, and their overexpression or enhanced activation are potential therapeutic targets. However, the study of metalloenzymes in vitro presents various challenges, leading many to develop tools to study them in their native cellular environment. Small-molecule fluorescence probes are commonly used to monitor metalloenzyme function, activity, and distribution in situ. These include probes that are activity-based (fluorescence is mediated by enzyme activity) or binding-based (fluorescence is mediated by interactions with the enzyme upon binding its metal cofactor). We discuss recent innovations that overcome key design challenges, such as the rapid diffusion of activity-based probes, the difficulty of probing redox-active enzymes, the selectivity of binding-based probes, and the poor penetration depth of fluorescence, and describe novel applications of these tools.
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Affiliation(s)
- Sky Price
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Emily L Que
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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2
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Azman AA, Muhd Noor ND, Leow ATC, Mohd Noor SA, Mohamad Ali MS. Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi. Int J Biol Macromol 2024; 271:132395. [PMID: 38761915 DOI: 10.1016/j.ijbiomac.2024.132395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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3
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Cheng Z, Aitha M, Thomas CA, Sturgill A, Fairweather M, Hu A, Bethel CR, Rivera DD, Dranchak P, Thomas PW, Li H, Feng Q, Tao K, Song M, Sun N, Wang S, Silwal SB, Page RC, Fast W, Bonomo RA, Weese M, Martinez W, Inglese J, Crowder MW. Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase. J Chem Inf Model 2024; 64:3977-3991. [PMID: 38727192 PMCID: PMC11129921 DOI: 10.1021/acs.jcim.3c02015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
The worldwide spread of the metallo-β-lactamases (MBL), especially New Delhi metallo-β-lactamase-1 (NDM-1), is threatening the efficacy of β-lactams, which are the most potent and prescribed class of antibiotics in the clinic. Currently, FDA-approved MBL inhibitors are lacking in the clinic even though many strategies have been used in inhibitor development, including quantitative high-throughput screening (qHTS), fragment-based drug discovery (FBDD), and molecular docking. Herein, a machine learning-based prediction tool is described, which was generated using results from HTS of a large chemical library and previously published inhibition data. The prediction tool was then used for virtual screening of the NIH Genesis library, which was subsequently screened using qHTS. A novel MBL inhibitor was identified and shown to lower minimum inhibitory concentrations (MICs) of Meropenem for a panel of E. coli and K. pneumoniae clinical isolates expressing NDM-1. The mechanism of inhibition of this novel scaffold was probed utilizing equilibrium dialyses with metal analyses, native state electrospray ionization mass spectrometry, UV-vis spectrophotometry, and molecular docking. The uncovered inhibitor, compound 72922413, was shown to be 9-hydroxy-3-[(5-hydroxy-1-oxa-9-azaspiro[5.5]undec-9-yl)carbonyl]-4H-pyrido[1,2-a]pyrimidin-4-one.
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Affiliation(s)
- Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Mahesh Aitha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Aidan Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Mitch Fairweather
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Amy Hu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Dann D. Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Pei W. Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Han Li
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Qi Feng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Kaicheng Tao
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Minshuai Song
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Na Sun
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Shuo Wang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walt Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH 44106, USA
| | - Maria Weese
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Waldyn Martinez
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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4
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Chung SF, Tam SY, Wong WT, So PK, Cheong WL, Mak CW, Lee LMY, Chan PH, Wong KY, Leung YC. Fluorescently Modified NDM-1: A Versatile Drug Sensor for Rapid In Vitro β-Lactam Antibiotic and Inhibitor Screening. ACS OMEGA 2024; 9:9161-9169. [PMID: 38434906 PMCID: PMC10906033 DOI: 10.1021/acsomega.3c08117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 03/05/2024]
Abstract
We successfully developed a fluorescent drug sensor from clinically relevant New Delhi metallo-β-lactamase-1 (NDM-1). The F70 residue was chosen to be replaced with a cysteine for conjugation with thiol-reactive fluorescein-5-maleimide to form fluorescent F70Cf, where "f" refers to fluorescein-5-maleimide. Our proteolytic studies of unlabeled F70C and labeled F70Cf monitored by electrospray ionization-mass spectrometry (ESI-MS) revealed that fluorescein-5-maleimide was specifically linked to C70 in 1:1 mole ratio (F70C:fluorophore). Our drug sensor (F70Cf) can detect the β-lactam antibiotics cefotaxime and cephalothin by giving stronger fluorescence in the initial binding phase and then declining fluorescence signals as a result of the hydrolysis of the antibiotics into acid products. F70Cf can also detect non-β-lactam inhibitors (e.g., l-captopril, d-captopril, dl-thiorphan, and thanatin). In all cases, F70Cf exhibits stronger fluorescence due to inhibitor binding and subsequently sustained fluorescence signals in a later stage. Native ESI-MS results show that F70Cf can bind to all four inhibitors. Moreover, our drug sensor is compatible with a high-throughput microplate reader and has the capability to perform in vitro drug screening.
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Affiliation(s)
- Sai-Fung Chung
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Suet-Ying Tam
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Wai-Ting Wong
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Pui-Kin So
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Wing-Lam Cheong
- Department
of Science, School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, Hong Kong
| | - Chun-Wing Mak
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Leo Man-Yuen Lee
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Pak-Ho Chan
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
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5
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Wang Q, Sun Y, Zhao S, Bai C, Cong Z, Dong Y, Wang T. Metallo-β-lactamases immobilized by magnetic zeolitic imidazolate frameworks-8 for degradation of β-lactam antibiotics in an aqueous environment. RSC Adv 2023; 13:34884-34890. [PMID: 38035241 PMCID: PMC10687608 DOI: 10.1039/d3ra05973a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023] Open
Abstract
Residual antibiotics in nature are an important cause of antimicrobial drug resistance, and how to deal with residual β-lactam antibiotics in aqueous environments has become an urgent issue. In this work, magnetic zeolitic imidazolate frameworks-8 (ZIF-8) for immobilizing metallo-β-lactamases (MBLs), or Fe3O4@ZIF-8@MBLs, were successfully synthesized using the one-pot method in aqueous solution. The morphology and chemical structure of Fe3O4@ZIF-8@MBLs were characterized by scanning electron microscopy, energy dispersive spectra, X-ray diffraction, infrared spectra, physical adsorption, and zeta potential. Further, the degradation performance of Fe3O4@ZIF-8@MBLs for β-lactam antibiotics (penicillin G, cefoperazone, meropenem) in an aqueous environment was investigated by UV-visible absorption spectrophotometry. The results indicated that Fe3O4@ZIF-8@MBLs, compared to control ZIF-8, exhibited superior degradation ability, excellent reusability, and better stability under several harsh conditions. The strategy of combining ZIF-8 and MBLs to form magnetic porous polymers may be suitable for removing β-lactam antibiotics from an aqueous environment. This work provided an original insight into future studies on the degradation of β-lactam antibiotics employing MBLs immobilized by magnetic metal-organic frameworks.
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Affiliation(s)
- Quanfang Wang
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an 710061 China
| | - Yuefeng Sun
- School of Pharmacy, Xi'an Medical College Xi'an 710021 China
| | - Shidi Zhao
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an 710061 China
| | - Chuqi Bai
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an 710061 China
| | - Zhiwei Cong
- School of Mechanical Engineering, Xi'an Jiaotong University Xi'an 710049 China
| | - Yalin Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an 710061 China
| | - Taotao Wang
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an 710061 China
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6
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Thomas CA, Cheng Z, Bethel CR, Hujer AM, Sturgill AM, Onuoha K, Page RC, Bonomo RA, Crowder MW. The directed evolution of NDM-1. Antimicrob Agents Chemother 2023; 67:e0071423. [PMID: 37874296 PMCID: PMC10649027 DOI: 10.1128/aac.00714-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/10/2023] [Indexed: 10/25/2023] Open
Abstract
β-Lactam antibiotics are among the most frequently prescribed therapeutic agents. A common mechanism of resistance toward β-lactam antibiotics is the production of β-lactamases. These enzymes are capable of hydrolyzing the β-lactam bond, rendering the drug inactive. Among the four described classes, the metallo- β-lactamases (MBLs, class B) employ one or two zinc ions in the active site for catalysis. One of the three most clinically relevant MBLs is New Delhi Metallo- β-Lactamase (NDM-1). The current study sought to investigate the in vitro protein evolution of NDM-1 β-lactamase using error-prone polymerase chain reaction. Evaluation revealed that variants were not found to confer higher levels of resistance toward meropenem based on amino acid substitutions. Thus, we postulate that increases in transcription or changes in zinc transport may be clinically more relevant to meropenem resistance than amino acid substitutions.
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Affiliation(s)
- Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aidan M. Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Kelechi Onuoha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Clinician Scientist Investigator, Ohio, Cleveland, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Jia Y, Schroeder B, Pfeifer Y, Fröhlich C, Deng L, Arkona C, Kuropka B, Sticht J, Ataka K, Bergemann S, Wolber G, Nitsche C, Mielke M, Leiros HKS, Werner G, Rademann J. Kinetics, Thermodynamics, and Structural Effects of Quinoline-2-Carboxylates, Zinc-Binding Inhibitors of New Delhi Metallo-β-lactamase-1 Re-sensitizing Multidrug-Resistant Bacteria for Carbapenems. J Med Chem 2023; 66:11761-11791. [PMID: 37585683 DOI: 10.1021/acs.jmedchem.3c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Carbapenem resistance mediated by metallo-β-lactamases (MBL) such as New Delhi metallo-β-lactamase-1 (NDM-1) has become a major factor threatening the efficacy of essential β-lactam antibiotics. Starting from hit fragment dipicolinic acid (DPA), 8-hydroxy- and 8-sulfonamido-quinoline-2-carboxylic acids were developed as inhibitors of NDM-1 with highly improved inhibitory activity and binding affinity. The most active compounds formed reversibly inactive ternary protein-inhibitor complexes with two zinc ions as proven by native protein mass spectrometry and bio-layer interferometry. Modification of the NDM-1 structure with remarkable entropic gain was shown by isothermal titration calorimetry and NMR spectroscopy of isotopically labeled protein. The best compounds were potent inhibitors of NDM-1 and other representative MBL with no or little inhibition of human zinc-binding enzymes. These inhibitors significantly reduced the minimum inhibitory concentrations (MIC) of meropenem for multidrug-resistant bacteria recombinantly expressing blaNDM-1 as well as for several multidrug-resistant clinical strains at concentrations non-toxic to human cells.
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Affiliation(s)
- Yuwen Jia
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Barbara Schroeder
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Christopher Fröhlich
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Lihua Deng
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Benno Kuropka
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Silke Bergemann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Martin Mielke
- Department of Infectious Diseases, Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Guido Werner
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
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8
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Sahoo S, Sahoo RK, Dixit S, Behera DU, Subudhi E. NDM-5-carrying Klebsiella pneumoniae ST437 belonging to high-risk clonal complex (CC11) from an urban river in eastern India. 3 Biotech 2023; 13:139. [PMID: 37124981 PMCID: PMC10133422 DOI: 10.1007/s13205-023-03556-5] [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: 11/29/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
In this study, we described the carbapenem bla NDM-5-carrying extensive drug-resistant (XDR) K. pneumoniae ST437 from an urban river water Kathajodi in Odisha, India. The presence of carbapenem and co-occurrence of other resistance determinants (bla NDM-5, bla CTX-M, bla SHV, and bla TEM), virulence factors (fimH, mrkD, entB, irp-1, and ybtS), and capsular serotype (K54) represent its pathogenic potential. The insertion sequence ISAba125 and the bleomycin resistance gene ble MBL at upstream and downstream, respectively, could play a significant role in the horizontal transmission of the bla NDM-5. Its biofilm formation ability contributes toward environmental protection and its survivability. MLST analysis assigned the isolate to ST437 and clonal lineage to ST11 (CC11) with a single locus variant. The ST437 K. pneumoniae, a global epidemic clone, has been reported in North America, Europe, and Asia. This work contributes in understanding of the mechanisms behind the spread of bla NDM-5 K. pneumoniae ST437 and demands extensive molecular surveillance of river and nearby hospitals for better community health. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03556-5.
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Affiliation(s)
- Saubhagini Sahoo
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to Be University), Kalinga Nagar, Ghatikia, Bhubaneswar, 751029 Odisha India
| | - Rajesh Kumar Sahoo
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to Be University), Kalinga Nagar, Ghatikia, Bhubaneswar, 751029 Odisha India
| | - Sangita Dixit
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to Be University), Kalinga Nagar, Ghatikia, Bhubaneswar, 751029 Odisha India
| | - Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to Be University), Kalinga Nagar, Ghatikia, Bhubaneswar, 751029 Odisha India
| | - Enketeswara Subudhi
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to Be University), Kalinga Nagar, Ghatikia, Bhubaneswar, 751029 Odisha India
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9
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A modified bonded model approach for molecular dynamics simulations of New Delhi Metallo-β-lactamase. J Mol Graph Model 2023; 121:108431. [PMID: 36827734 DOI: 10.1016/j.jmgm.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Modelling metalloproteins using the classical force fields is challenging. Several methods have been devised to model metalloproteins in force fields. Of these methods, the bonded model, combined with Restrained Electrostatic Potential (RESP) charge fitting, proved its superiority. The latter method was facilitated by the development of the python-based Metal Centre Parameter Builder (MCPB.py) AmberTool. However, the standard bonded model method offered by the MCPB.py tool may not be appropriate for validating and refining the binding modes predicted by docking when crystal structures are lacking. That is because the representation of coordination interactions between any bound ligand and metal ions by covalent bonds can hinder the flexibility of the ligand. Therefore, a new modification to the standard bonded model approach is proposed here. Molecular dynamics (MD) simulations based on the new modified bonded model (MBM) approach avoid the bias caused by coordination bonds and, unlike hybrid QM/MM MD, allow for sufficient sampling of the binding mode given the currently available computational power. The MBM MD approach reproduced the studied crystal structure conformations of New Delhi Metallo-β-lactamase 1 (NDM-1). Furthermore, the MBM approach described the binding interactions of intact β-lactams with NDM-1 reasonably, and predicted a non-productive binding mode for the poor NDM-1 substrate aztreonam whilst predicting productive binding modes for known good substrates. This study presents a useful MD method for metallo-β-lactamases and provides better understanding of β-lactam substrates recognition by NDM-1. The proposed MBM approach might also be useful in the investigation of other metal-containing protein targets.
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A Cephalosporin-Tripodalamine Conjugate Inhibits Metallo-β-Lactamase with High Efficacy and Low Toxicity. Antimicrob Agents Chemother 2022; 66:e0035222. [PMID: 36094199 PMCID: PMC9578398 DOI: 10.1128/aac.00352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wide spread of metallo-β-lactamase (MBL)-expressing bacteria has greatly threatened human health, and there is an urgent need for inhibitors against MBLs. Herein, we present a cephalosporin-tripodalamine conjugate (DPASC) as a potent MBL inhibitor with a block-release design. The cephalosporin tag blocks the ligand binding site to reduce toxicity and is cleaved by MBLs to release active ligands to inhibit MBLs in situ. The screening of MBL-expressing pathogenic strains with 16 μg/mL DPASC showed a decrease of the minimum inhibitory concentration of meropenem (MEM) by 16 to 512-fold, and its toxicity was minimal to human HepG2 cells, with an IC50 exceeding 512 μg/mL. An in vivo infection model with Galleria mellonella larvae showed an increased 3-day survival rate of 87% with the coadministration of DPASC and MEM, compared to 50% with MEM alone and no toxicity at a dose of 256 mg/kg of DPASC. Our findings with DPASC demonstrate that it is an effective MBL inhibitor and that the block-release strategy could be useful for the development of new MBL inhibitors.
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Fung YH, Kong WP, Leung ASL, Du R, So PK, Wong WL, Leung YC, Chen YW, Wong KY. NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140833. [PMID: 35944887 DOI: 10.1016/j.bbapap.2022.140833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Bacteria expressing NDM-1 have been labeled as superbugs because it confers upon them resistance to a broad range of β-lactam antibiotics. The enzyme has a di‑zinc active centre, with the Zn2 site extensively studied. The roles of active-site Zn1 ligand residues are, however, still not fully understood. We carried out structure-function studies using the mutants, H116A, H116N, and H116Q. Zinc content analysis showed that Zn1 binding was weakened by 40 to 60% in the H116 mutants. The enzymatic-activity studies showed that the lower hydrolysis rates were mainly caused by their weaker substrate binding. The catalytic efficiency (kcat/Km) of the mutants followed the order: WT > > H116Q (decreased by 4-20 fold) > H116A (decreased by 20-700 fold) ≥ H116N (decreased by 6-800 fold). The maximum effect was observed on H116N against penicillin G, whereas ampicillin was not hydrolyzed at all. The fold-increase of Km values, which informs the weakening of substrate binding, were: H116A by 5-45 fold; H116N by 6-100 fold; H116Q by 2-10 fold. Molecular dynamics simulations suggested that the Zn1 site mutations affected the positions of Zn2 and the bridging hydroxide, by 0.8 to 1.2 Å, with the largest changes of ~1.5 Å observed on Zn2 ligand C221. A native hydrogen bond between H118 and D236 was disrupted in the H116N and H116Q mutants, which led to increased flexibility of loop 10. Consequently, residue N233 was no longer maintained at an optimal position for substrate binding. H116 connected loop 7 across Zn1 to loop 10, thereby contributed to the overall integrity. This work revealed that the H116-Zn1 interaction plays a critical role in defining the substrate-binding site. From these results, it can be inferred that inhibition strategies targeting the zinc ions may be a new direction for drug development.
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Affiliation(s)
- Yik-Hong Fung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wai-Po Kong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Alan Siu Lun Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Ruolan Du
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pu-Kin So
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wing-Leung Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Wai Chen
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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Evaluation of Tebipenem Hydrolysis by β-Lactamases Prevalent in Complicated Urinary Tract Infections. Antimicrob Agents Chemother 2022; 66:e0239621. [PMID: 35491852 DOI: 10.1128/aac.02396-21] [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: 01/07/2023] Open
Abstract
Tebipenem pivoxil is the first orally available carbapenem antibiotic and has been approved in Japan for treating ear, nose, and throat and respiratory infections in pediatric patients. Its active moiety, tebipenem, has shown potent antimicrobial activity in vitro against clinical isolates of Enterobacterales species from patients with urinary tract infections (UTIs), including those producing extended-spectrum β-lactamases (ESBLs) and/or AmpC β-lactamase. In the present study, tebipenem was tested for stability to hydrolysis by a set of clinically relevant β-lactamases, including TEM-1, AmpC, CTX-M, OXA-48, KPC, and NDM-1 enzymes. In addition, hydrolysis rates of other carbapenems, including imipenem, meropenem, and ertapenem, were determined for comparison. It was found that, similar to other carbapenems, tebipenem was resistant to hydrolysis by TEM-1, CTX-M, and AmpC β-lactamases but was susceptible to hydrolysis by KPC, OXA-48, and NDM-1 enzymes with catalytic efficiency values (kcat/Km) ranging from 0.1 to 2 × 106 M-1s-1. This supports the reported results of antimicrobial activity of tebipenem against ESBL- and AmpC-producing but not carbapenemase-producing Enterobacterales isolates. Considering that CTX-M and AmpC β-lactamases represent the primary determinants of multidrug-resistant complicated UTIs (cUTIs), the stability of tebipenem to hydrolysis by these enzymes supports the utility of its prodrug tebipenem, tebipenem pivoxil hydrobromide (TBP-PI-HBr), as an oral therapy for adult cUTIs.
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13
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Alfei S, Schito AM. β-Lactam Antibiotics and β-Lactamase Enzymes Inhibitors, Part 2: Our Limited Resources. Pharmaceuticals (Basel) 2022; 15:ph15040476. [PMID: 35455473 PMCID: PMC9031764 DOI: 10.3390/ph15040476] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
β-lactam antibiotics (BLAs) are crucial molecules among antibacterial drugs, but the increasing emergence of resistance to them, developed by bacteria producing β-lactamase enzymes (BLEs), is becoming one of the major warnings to the global public health. Since only a small number of novel antibiotics are in development, a current clinical approach to limit this phenomenon consists of administering proper combinations of β-lactam antibiotics (BLAs) and β-lactamase inhibitors (BLEsIs). Unfortunately, while few clinically approved BLEsIs are capable of inhibiting most class-A and -C serine β-lactamases (SBLEs) and some carbapenemases of class D, they are unable to inhibit most part of the carbapenem hydrolyzing enzymes of class D and the worrying metallo-β-lactamases (MBLEs) of class B. Particularly, MBLEs are a set of enzymes that catalyzes the hydrolysis of a broad range of BLAs by a zinc-mediated mechanism, and currently no clinically available molecule capable of inhibiting MBLEs exists. Additionally, new types of alarming “superbugs”, were found to produce the New Delhi metallo-β-lactamases (NDMs) encoded by increasing variants of a plasmid-mediated gene capable of rapidly spreading among bacteria of the same species and even among different species. Particularly, NDM-1 possesses a flexible hydrolysis mechanism that inactivates all BLAs, except for aztreonam. The present review provides first an overview of existing BLAs and the most clinically relevant BLEs detected so far. Then, the BLEsIs and their most common associations with BLAs already clinically applied and those still in development are reviewed.
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Affiliation(s)
- Silvana Alfei
- Department of Pharmacy (DIFAR), University of Genoa, Viale Cembrano, 4, 16148 Genoa, Italy
- Correspondence: ; Tel.: +39-010-355-2296
| | - Anna Maria Schito
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, 16132 Genoa, Italy;
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14
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Thomas PW, Cho EJ, Bethel CR, Smisek T, Ahn YC, Schroeder JM, Thomas CA, Dalby KN, Beckham JT, Crowder MW, Bonomo RA, Fast W. Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM). ACS Infect Dis 2022; 8:811-824. [PMID: 35353502 DOI: 10.1021/acsinfecdis.1c00577] [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: 12/20/2022]
Abstract
To identify novel inhibitors of the carbapenemase New Delhi metallo-β-lactamase (NDM) as possible therapeutic compounds, we conducted a high-throughput screen of a 43,358-compound library. One of these compounds, a 2-quinazolinone linked through a diacylhydrazine to a phenyl ring (QDP-1) (IC50 = 7.9 ± 0.5 μM), was characterized as a slow-binding reversible inhibitor (Kiapp = 4 ± 2 μM) with a noncompetitive mode of inhibition in which substrate and inhibitor enhance each other's binding affinity. These studies, along with differential scanning fluorimetry, zinc quantitation, and selectivity studies, support an allosteric mechanism of inhibition. Cotreatment with QDP-1 effectively lowers minimum inhibitory concentrations of carbapenems for a panel of resistant Escherichia coli and Klebsiella pneumoniae clinical isolates expressing NDM-1 but not for those expressing only serine carbapenemases. QDP-1 represents a novel allosteric approach for NDM drug development for potential use alone or with other NDM inhibitors to counter carbapenem resistance in enterobacterales.
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Affiliation(s)
- Pei W. Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Thomas Smisek
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - John M. Schroeder
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Josh T. Beckham
- Texas Institute for Discovery Education in Science, University of Texas, Austin, Texas 78712, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- LaMontagne Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
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15
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Recommendations to Synthetize Old and New β-Lactamases Inhibitors: A Review to Encourage Further Production. Pharmaceuticals (Basel) 2022; 15:ph15030384. [PMID: 35337181 PMCID: PMC8954882 DOI: 10.3390/ph15030384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 01/06/2023] Open
Abstract
The increasing emergence of bacteria producing β-lactamases enzymes (BLEs), able to inactivate the available β-lactam antibiotics (BLAs), causing the hydrolytic opening of their β-lactam ring, is one of the global major warnings. According to Ambler classification, BLEs are grouped in serine-BLEs (SBLEs) of class A, C, and D, and metal-BLEs (MBLEs) of class B. A current strategy to restore no longer functioning BLAs consists of associating them to β-lactamase enzymes inhibitors (BLEsIs), which, interacting with BLEs, prevent them hydrolyzing to the associated antibiotic. Worryingly, the inhibitors that are clinically approved are very few and inhibit only most of class A and C SBLEs, leaving several class D and all MBLEs of class B untouched. Numerous non-clinically approved new molecules are in development, which have shown broad and ultra-broad spectrum of action, some of them also being active on the New Delhi metal-β-lactamase-1 (NDM-1), which can hydrolyze all available BLAs except for aztreonam. To not duplicate the existing review concerning this topic, we have herein examined BLEsIs by a chemistry approach. To this end, we have reviewed both the long-established synthesis adopted to prepare the old BLEsIs, those proposed to achieve the BLEsIs that are newly approved, and those recently reported to prepare the most relevant molecules yet in development, which have shown high potency, providing for each synthesis the related reaction scheme.
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16
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Twidale RM, Hinchliffe P, Spencer J, Mulholland AJ. Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-β-Lactamase in the Imine Form. J Chem Inf Model 2021; 61:5988-5999. [PMID: 34637298 DOI: 10.1021/acs.jcim.1c00663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Widespread bacterial resistance to carbapenem antibiotics is an increasing global health concern. Resistance has emerged due to carbapenem-hydrolyzing enzymes, including metallo-β-lactamases (MβLs), but despite their prevalence and clinical importance, MβL mechanisms are still not fully understood. Carbapenem hydrolysis by MβLs can yield alternative product tautomers with the potential to access different binding modes. Here, we show that a combined approach employing crystallography and quantum mechanics/molecular mechanics (QM/MM) simulations allow tautomer assignment in MβL:hydrolyzed antibiotic complexes. Molecular simulations also examine (meta)stable species of alternative protonation and tautomeric states, providing mechanistic insights into β-lactam hydrolysis. We report the crystal structure of the hydrolyzed carbapenem ertapenem bound to the L1 MβL from Stenotrophomonas maltophilia and model alternative tautomeric and protonation states of both hydrolyzed ertapenem and faropenem (a related penem antibiotic), which display different binding modes with L1. We show how the structures of both complexed β-lactams are best described as the (2S)-imine tautomer with the carboxylate formed after β-lactam ring cleavage deprotonated. Simulations show that enamine tautomer complexes are significantly less stable (e.g., showing partial loss of interactions with the L1 binuclear zinc center) and not consistent with experimental data. Strong interactions of Tyr32 and one zinc ion (Zn1) with ertapenem prevent a C6 group rotation, explaining the different binding modes of the two β-lactams. Our findings establish the relative stability of different hydrolyzed (carba)penem forms in the L1 active site and identify interactions important to stable complex formation, information that should assist inhibitor design for this important antibiotic resistance determinant.
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Affiliation(s)
- Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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17
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Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Int J Mol Sci 2021; 23:ijms23010197. [PMID: 35008622 PMCID: PMC8745225 DOI: 10.3390/ijms23010197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Multidrug bacterial resistance endangers clinically effective antimicrobial therapy and continues to cause major public health problems, which have been upgraded to unprecedented levels in recent years, worldwide. β-Lactam antibiotics have become an important weapon to fight against pathogen infections due to their broad spectrum. Unfortunately, the emergence of antibiotic resistance genes (ARGs) has severely astricted the application of β-lactam antibiotics. Of these, New Delhi metallo-β-lactamase-1 (NDM-1) represents the most disturbing development due to its substrate promiscuity, the appearance of variants, and transferability. Given the clinical correlation of β-lactam antibiotics and NDM-1-mediated resistance, the discovery, and development of combination drugs, including NDM-1 inhibitors, for NDM-1 bacterial infections, seems particularly attractive and urgent. This review summarizes the research related to the development and optimization of effective NDM-1 inhibitors. The detailed generalization of crystal structure, enzyme activity center and catalytic mechanism, variants and global distribution, mechanism of action of existing inhibitors, and the development of scaffolds provides a reference for finding potential clinically effective NDM-1 inhibitors against drug-resistant bacteria.
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18
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A Novel Cooperative Metallo-β-Lactamase Fold Metallohydrolase from Pathogen Vibrio vulnificus Exhibits β-Lactam Antibiotic-Degrading Activities. Antimicrob Agents Chemother 2021; 65:e0032621. [PMID: 34228542 DOI: 10.1128/aac.00326-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus is a pathogen that accounts for one of the highest mortality rates and is responsible for most reported seafood-related illnesses and deaths worldwide. Owing to the threats of pathogens with β-lactamase activity, it is important to identify and characterize β-lactamases with clinical significance. In this study, the protein sequence of the metallo-β-lactamase (MBL) fold metallohydrolase from V. vulnificus (designated Vmh) was analyzed, and its oligomeric state, β-lactamase activity, and metal binding ability were determined. BLASTp analysis indicated that the V. vulnificus Vmh protein showed no significant sequence identity with any experimentally identified Ambler class B MBLs or enzymes containing the MBL protein fold; it was also predicted to have a signal peptide of 19 amino acids at its N terminus and an MBL protein fold from amino acid residues 23 to 216. Recombinant V. vulnificus Vmh protein was overexpressed and purified. Analytical ultracentrifugation and electrospray ionization-mass spectrometry (MS) data demonstrated its monomeric state in an aqueous solution. Recombinant V. vulnificus Vmh protein showed broad degrading activities against β-lactam antibiotics, such as penicillins, cephalosporins, and imipenems, with kcat/Km values ranging from 6.23 × 102 to 1.02 × 104 M-1 s-1. The kinetic reactions of this enzyme exhibited sigmoidal behavior, suggesting the possibility of cooperativity. Zinc ions were required for the enzyme activity, which was abolished by adding the metal chelator EDTA. Inductively coupled plasma-MS indicated that this enzyme might bind two zinc ions per molecule as a cofactor.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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20
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Wang T, Xu K, Zhao L, Tong R, Xiong L, Shi J. Recent research and development of NDM-1 inhibitors. Eur J Med Chem 2021; 223:113667. [PMID: 34225181 DOI: 10.1016/j.ejmech.2021.113667] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Bacteria carrying New Delhi metallo-β-lactamase-1 (New Delhi metallo-β-lactamase, NDM-1) resistance gene is a new type of "superbug", which can hydrolyze almost all β-lactam antibiotics, rapidly spread among the same species and even spread among different species. NDM-1 belongs to the class B1 broad-spectrum enzyme of β-lactamase. The two positively charged zinc ions in the active center have electrostatic interaction with the hydroxyl ions in them to seize the hydrogen atom near the water molecule to form a bridging ring water molecule, which strengthens its nucleophilicity and attacks the carbonyl group on the lactam ring; thus, catalyzing the hydrolysis of β-lactam antibiotics. Since NDM-1 has an open active site and unique electrostatic structure, it essentially provides a wider range of substrate specificity. Due to its flexible hydrolysis mechanism and more and more variants also aggravate the threat of drug-resistant bacteria infection, there is still no effective inhibitor in clinic, which is a serious threat to human health and public health safety. The electron-rich substituents of NDM-1 inhibitors coordinate with two positively charged zinc ions in the active center of the enzyme through ion-dipole interaction to produce NDM-1 inhibitory activity. In this review, the research progress of NDM-1 enzyme and its inhibitors in the past 5 years was reviewed. The crystal structure, active center structure, surrounding important amino acid residues, newly discovered inhibitors and their action mechanism are classified and summarized in detail, which can be used as a reference for the development of effective drugs against drug-resistant bacteria targeting NDM-1.
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Affiliation(s)
- Ting Wang
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Kaiju Xu
- Department of Infectious Diseases, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, China
| | - Liyun Zhao
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Rongsheng Tong
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Liang Xiong
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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21
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Zhang H, Yang K, Cheng Z, Thomas C, Steinbrunner A, Pryor C, Vulcan M, Kemp C, Orea D, Paththamperuma C, Chen AY, Cohen SM, Page RC, Tierney DL, Crowder MW. Spectroscopic and biochemical characterization of metallo-β-lactamase IMP-1 with dicarboxylic, sulfonyl, and thiol inhibitors. Bioorg Med Chem 2021; 40:116183. [PMID: 33965839 PMCID: PMC8170513 DOI: 10.1016/j.bmc.2021.116183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 02/02/2023]
Abstract
In an effort to probe the biophysical mechanisms of inhibition for ten previously-reported inhibitors of metallo-β-lactamases (MBL) with MBL IMP-1, equilibrium dialysis, metal analyses coupled with atomic absorption spectroscopy (AAS), native state mass spectrometry (native MS), and ultraviolet-visible spectrophotometry (UV-VIS) were used. 6-(1H-tetrazol-5-yl) picolinic acid (1T5PA), ANT431, D/l-captopril, thiorphan, and tiopronin were shown to form IMP-1/Zn(II)/inhibitor ternary complexes, while dipicolinic acid (DPA) and 4-(3-aminophenyl)pyridine-2,6-dicarboxylic acid (3AP-DPA) stripped some metal from the active site of IMP but also formed ternary complexes. DPA and 3AP-DPA stripped less metal from IMP-1 than from VIM-2 but stripped more metal from IMP-1 than from NDM-1. In contrast to a previous report, pterostilbene does not appear to bind to IMP-1 under our conditions. These results, along with previous studies, demonstrate similar mechanisms of inhibition toward different MBLs for different MBL inhibitors.
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Affiliation(s)
- Huan Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Caitlyn Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Abbie Steinbrunner
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Cecily Pryor
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Maya Vulcan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Claire Kemp
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Diego Orea
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | - Allie Y Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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22
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Mehta R, Rivera DD, Reilley DJ, Tan D, Thomas PW, Hinojosa A, Stewart AC, Cheng Z, Thomas CA, Crowder MW, Alexandrova AN, Fast W, Que EL. Visualizing the Dynamic Metalation State of New Delhi Metallo-β-lactamase-1 in Bacteria Using a Reversible Fluorescent Probe. J Am Chem Soc 2021; 143:8314-8323. [PMID: 34038127 DOI: 10.1021/jacs.1c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) grants resistance to a broad spectrum of β-lactam antibiotics, including last-resort carbapenems, and is emerging as a global antibiotic resistance threat. Limited zinc availability adversely impacts the ability of NDM-1 to provide resistance, but a number of clinical variants have emerged that are more resistant to zinc scarcity (e.g., NDM-15). To provide a novel tool to better study metal ion sequestration in host-pathogen interactions, we describe the development of a fluorescent probe that reports on the dynamic metalation state of NDM within Escherichia coli. The thiol-containing probe selectively coordinates the dizinc metal cluster of NDM and results in a 17-fold increase in fluorescence intensity. Reversible binding enables competition and time-dependent studies that reveal fluorescence changes used to detect enzyme localization, substrate and inhibitor engagement, and changes to metalation state through the imaging of live E. coli using confocal microscopy. NDM-1 is shown to be susceptible to demetalation by intracellular and extracellular metal chelators in a live-cell model of zinc dyshomeostasis, whereas the NDM-15 metalation state is shown to be more resistant to zinc flux. The development of this reversible turn-on fluorescent probe for the metalation state of NDM provides a new tool for monitoring the impact of metal ion sequestration by host defense mechanisms and for detecting inhibitor-target engagement during the development of therapeutics to counter this resistance determinant.
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Affiliation(s)
- Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Dann D Rivera
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - David J Reilley
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Emily L Que
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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23
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Dong X, Xue P, Ma X, Bai Y, Shi P, Bian L. Recognition and binding of FEZ-1 from Legionella with penicillin V and cefoxitin by fluorescence spectra in combination with molecular dynamics simulation. Enzyme Microb Technol 2021; 149:109819. [PMID: 34311875 DOI: 10.1016/j.enzmictec.2021.109819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 04/15/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
The recognition and interaction of FEZ-1 from Legionella (FEZ-1) with penicillin V(PV) and cefoxitin(CFX) were investigated using fluorescence spectra in combination with molecular dynamics simulation (MD). The results revealed that the CFX bind with FEZ-1 in stronger interaction and induced larger conformational change than PV, despite all being forced by the electrostatic interaction and along with the changing in an environment of amino acid residues as well as the polypeptide skeleton inside the FEZ-1. Moreover, only the loop1, loop2, and N-terminal were observed locating near the binding pocket of FEZ-1, consisting of a flexible "gate-like" zone with better adaptability that controlled the entrance of antibiotic into the pocket by allowing the newly introduced antibiotic to match the pocket better through the conformational changes of these three substructures in the binding procedure. The current study may provide some valuable information on the antibiotic hydrolytic process by metallo-beta-lactamase and thus the references for the development of new antibiotics for super bacteria.
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Affiliation(s)
- Xiaoting Dong
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Pengli Xue
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xian Ma
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Yifan Bai
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Penghui Shi
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an, 710069, China.
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24
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Docking and antibacterial activity of novel nontoxic 5-arylidenepyrimidine-triones as inhibitors of NDM-1 and MetAP-1. Future Med Chem 2021; 13:1041-1055. [PMID: 33913733 DOI: 10.4155/fmc-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Antibiotic resistance, which occurs through the action of metallo-β-lactamases (NDM-1), is a serious problem in the treatment of infectious diseases. Therefore, the discovery of new NDM-1 inhibitors and promising antibacterial agents as inhibitors of alternative targets (MetAP-1) is important. Method & results: In this study, a virtual library of 5-arylidene barbituric acids was created and molecular docking was performed for identification of novel possible inhibitors of NDM-1 and MetAP-1. Antibacterial activity (agar well-diffusion assay) and cytotoxicity (alamarBlue assay) of perspective compounds were evaluated. Pharmacokinetic profiles and molecular properties were predicted. Conclusion: We have identified possible novel inhibitors of NDM-1 and MetAP-1 with bacteriostatic activity, most of which are not cytotoxic and have potential excellent drug-likeness properties.
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25
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Carbapenem Use Is Driving the Evolution of Imipenemase 1 Variants. Antimicrob Agents Chemother 2021; 65:AAC.01714-20. [PMID: 33468463 DOI: 10.1128/aac.01714-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are a growing clinical threat because they inactivate nearly all β-lactam-containing antibiotics, and there are no clinically available inhibitors. A significant number of variants have already emerged for each MBL subfamily. To understand the evolution of imipenemase (IMP) genes (bla IMP) and their clinical impact, 20 clinically derived IMP-1 like variants were obtained using site-directed mutagenesis and expressed in a uniform genetic background in Escherichia coli strain DH10B. Strains of IMP-1-like variants harboring S262G or V67F substitutions exhibited increased resistance toward carbapenems and decreased resistance toward ampicillin. Strains expressing IMP-78 (S262G/V67F) exhibited the largest changes in MIC values compared to IMP-1. In order to understand the molecular mechanisms of increased resistance, biochemical, biophysical, and molecular modeling studies were conducted to compare IMP-1, IMP-6 (S262G), IMP-10 (V67F), and IMP-78 (S262G/V67F). Finally, unlike most New Delhi metallo-β-lactamase (NDM) and Verona integron-encoded metallo-β-lactamase (VIM) variants, the IMP-1-like variants do not confer any additional survival advantage if zinc availability is limited. Therefore, the evolution of MBL subfamilies (i.e., IMP-6, -10, and -78) appears to be driven by different selective pressures.
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26
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Jin WB, Xu C, Qi XL, Zeng P, Gao W, Lai KH, Chiou J, Chan EWC, Leung YC, Chan TH, Wong KY, Chen S, Chan KF. Synthesis of 1,3,4-trisubstituted pyrrolidines as meropenem adjuvants targeting New Delhi metallo-β-lactamase. NEW J CHEM 2021. [DOI: 10.1039/d0nj06090a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A promising NDM-1 inhibitor was discovered by the construction of pyrrolidine library via boric acid-catalyzed 1,3-dipolar cycloaddition and cell-based screens.
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27
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Bassetti M, Di Pilato V, Giani T, Vena A, Rossolini GM, Marchese A, Giacobbe DR. Treatment of severe infections due to metallo-β-lactamases-producing Gram-negative bacteria. Future Microbiol 2020; 15:1489-1505. [PMID: 33140656 DOI: 10.2217/fmb-2020-0210] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the last decades, there was an important paucity of agents for adequately treating infections due to metallo-β-lactamases-producing Gram-negative bacteria (MBL-GNB). Cefiderocol, a novel siderophore cephalosporin showing in vitro activity against MBL-GNB, has been recently marketed, and a combination of aztreonam and ceftazidime/avibactam has shown a possible favorable effect on survival of patients with severe MBL-GNB infections in observational studies. Other agents showing in vitro activity against MBL-GNB are currently in clinical development (e.g., cefepime/taniborbactam, LYS228, cefepime/zidebactam) that could be an important addition to our future armamentarium for severe MBL-GNB infections. Nonetheless, we should not discontinue our efforts to optimize the use of non-β-lactams agents, since they could remain an essential last-resort or alternative option in selected cases.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences & Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Tommaso Giani
- Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
- Microbiology & Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Antonio Vena
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
| | - Gian Maria Rossolini
- Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
- Microbiology & Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Anna Marchese
- Department of Surgical Sciences & Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- Microbiology Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
| | - Daniele R Giacobbe
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
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28
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Chen C, Yang K. Ruthenium complexes as prospective inhibitors of metallo-β-lactamases to reverse carbapenem resistance. Dalton Trans 2020; 49:14099-14105. [PMID: 32996954 DOI: 10.1039/d0dt02430a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The widespread prevalence of metallo-β-lactamase (MβL)-mediated pathogens has seriously caused a loss of efficacy of carbapenem antibacterials, the last resort for the treatment of severe infectious diseases. The development of effective MβL inhibitors is an ideal alternative to restore the efficacy of carbapenems. Here we report that Ru complexes can irreversibly inhibit clinically relevant B1 subclass MβLs (NDM-1, IMP-1 and VIM-2) and potentiate meropenem efficacy against MβL-expressing bacteria in vitro and in a mice infection model. The Cys208 residue at the Zn(ii)-binding site and Met67 residue at the β-hairpin loop of an enzyme active pocket are critical for Ru complexes to inhibit NDM-1, which was verified by enzyme kinetics, thermodynamics, NDM-1-C208A mutation and MALDI-TOF-MS analysis. This study will undoubtedly aid efforts to develop metal-based MβL inhibitors in combination with carbapenems to deal with the clinical crisis of carbapenem-resistant E. coli harboring MβLs.
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Affiliation(s)
- Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China.
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29
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Mehaffey MR, Ahn YC, Rivera DD, Thomas PW, Cheng Z, Crowder MW, Pratt RF, Fast W, Brodbelt JS. Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry. Chem Sci 2020; 11:8999-9010. [PMID: 34123154 PMCID: PMC8163344 DOI: 10.1039/d0sc02503h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We use mass spectrometry (MS), under denaturing and non-denaturing solution conditions, along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation. Mapping changes in the abundances and distributions of fragment ions enables sensitive detection of structural alterations throughout the protein. Binding of three covalent inhibitors was characterized: a pentafluorphenyl ester, an O-aryloxycarbonyl hydroxamate, and ebselen. The first two inhibitors modify Lys211 and maintain dizinc binding, although the pentafluorophenyl ester is not selective (Lys214 and Lys216 are also modified). Ebselen reacts with the sole Cys (Cys208) and ejects Zn2 from the active site. For each inhibitor, native UVPD-MS enabled simultaneous detection of the closing of a substrate-binding beta-hairpin loop, identification of covalently-modified residue(s), reporting of the metalation state of the enzyme, and in the case of ebselen, observation of the induction of partial disorder in the C-terminus of the protein. Owing to the ability of native UVPD-MS to track structural changes and metalation state with high sensitivity, we further used this method to evaluate the impact of mutations found in NDM clinical variants. Changes introduced by NDM-4 (M154L) and NDM-6 (A233V) are revealed to propagate through separate networks of interactions to direct zinc ligands, and the combination of these two mutations in NDM-15 (M154L, A233V) results in additive as well as additional structural changes. Insight from UVPD-MS helps to elucidate how distant mutations impact zinc affinity in the evolution of this antibiotic resistance determinant. UVPD-MS is a powerful tool capable of simultaneous reporting of ligand binding, conformational changes and metalation state of NDM, revealing structural aspects of ligand recognition and clinical variants that have proven difficult to probe. We use mass spectrometry (MS) along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation.![]()
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Dann D Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Pei W Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University Middletown CT 06459 USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
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30
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Thomas CS, Braun DR, Olmos JL, Rajski SR, Phillips GN, Andes D, Bugni TS. Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo -Lactamase-1. Mar Drugs 2020; 18:md18060295. [PMID: 32498259 PMCID: PMC7374359 DOI: 10.3390/md18060295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae continue to threaten human health worldwide with few effective treatment options. New Delhi metallo-β-lactamase (NDM) enzymes are a contributing element that drive resistance to many β-lactam- and carbapenem-based antimicrobials. Many NDM inhibitors are known, yet none are clinically viable. In this study, we present and characterize a new class of NDM-1 inhibitors based on a pyridine-2,6-dithiocarboxylic acid metal complex scaffold. These complexes display varied and unique activity profiles against NDM-1 in kinetic assays and serve to increase the effectiveness of meropenem, an established antibacterial, in assays using clinical Enterobacteriaceae isolates.
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Affiliation(s)
- Chris S. Thomas
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, WI 53705, USA; (C.S.T.); (D.R.B.); (S.R.R.)
| | - Doug R. Braun
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, WI 53705, USA; (C.S.T.); (D.R.B.); (S.R.R.)
| | - Jose Luis Olmos
- Department of Biosciences, Rice University, Houston, TX 77005, USA; (J.L.O.J.); (G.N.P.J.)
| | - Scott R. Rajski
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, WI 53705, USA; (C.S.T.); (D.R.B.); (S.R.R.)
| | - George N. Phillips
- Department of Biosciences, Rice University, Houston, TX 77005, USA; (J.L.O.J.); (G.N.P.J.)
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - David Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA;
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin–Madison, Madison, WI 53705, USA; (C.S.T.); (D.R.B.); (S.R.R.)
- Correspondence: ; Tel.: +1-608-263-2519
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31
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Wang X, Yang Y, Gao Y, Niu X. Discovery of the Novel Inhibitor Against New Delhi Metallo-β-Lactamase Based on Virtual Screening and Molecular Modelling. Int J Mol Sci 2020; 21:ijms21103567. [PMID: 32443639 PMCID: PMC7279046 DOI: 10.3390/ijms21103567] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
New Delhi metallo-β-lactamase (NDM-1), one of the metallo-β-lactamases (MBLs), leads to antibiotic resistance in clinical treatments due to the strong ability of hydrolysis to almost all kinds of β-lactam antibiotics. Therefore, there is the urgent need for the research and development of the novel drug-resistant inhibitors targeting NDM-1. In this study, ZINC05683641 was screened as potential NDM-1 inhibitor by virtual screening and the inhibitor mechanism of this compound was explored based on molecular dynamics simulation. The nitrocefin assay showed that the IC50 value of ZINC05683641 was 13.59 ± 0.52 μM, indicating that the hydrolytic activity of NDM-1 can be obviously suppressed by ZINC05683641. Further, the binding mode of ZINC05683641 with NDM-1 was obtained by molecular modeling, binding free energy calculation, mutagenesis assays and fluorescence-quenching assays. As results, ILE-35, MET-67, VAL-73, TRP-93, CYS-208, ASN-220 and HIS-250 played the key roles in the binding of NDM-1 with ZINC05683641. Interestingly, these key residues were exactly located in the catalytic activity region of NDM-1, implying that the inhibitor mechanism of ZINC05683641 against NDM-1 was the competitive inhibition. These findings will provide an available approach to research and develop new drug against NDM-1 and treatment for bacterial resistance.
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32
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Rivière G, Oueslati S, Gayral M, Créchet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors. ACS OMEGA 2020; 5:10466-10480. [PMID: 32426604 PMCID: PMC7226869 DOI: 10.1021/acsomega.0c00590] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 05/22/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix α2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.
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Affiliation(s)
- Gwladys Rivière
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Saoussen Oueslati
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Maud Gayral
- Institut
de Chimie Moléculaire et des Matériaux d’Orsay
(ICMMO), CNRS, Université Paris Sud, Université Paris-Saclay, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | | | - Naïma Nhiri
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Eric Jacquet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Jean-Christophe Cintrat
- Service
de Chimie Bio-organique et Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif/Yvette, France
| | - François Giraud
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Ewen Lescop
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Stéphanie Pethe
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Bogdan I. Iorga
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361
“Structure, Dynamic, Function and Expression of Broad Spectrum
β-Lactamases”, Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- . Phone:(33)145212019 or (33)145213030. Fax: (33)145216340
| | - Eric Guittet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Nelly Morellet
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université
Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- . Phone:(33)169823762. Fax: (33)169823784
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33
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Jackson AC, Zaengle-Barone JM, Puccio EA, Franz KJ. A Cephalosporin Prochelator Inhibits New Delhi Metallo-β-lactamase 1 without Removing Zinc. ACS Infect Dis 2020; 6:1264-1272. [PMID: 32298084 DOI: 10.1021/acsinfecdis.0c00083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antibacterial drug resistance is a rapidly growing clinical threat, partially due to expression of β-lactamase enzymes, which confer resistance to bacteria by hydrolyzing and inactivating β-lactam antibiotics. The increasing prevalence of metallo-β-lactamases poses a unique challenge, as currently available β-lactamase inhibitors target the active site of serine β-lactamases but are ineffective against the zinc-containing active sites of metallo-β-lactamases. There is an urgent need for metallo-β-lactamase inhibitors and antibiotics that circumvent resistance mediated by metallo-β-lactamases in order to extend the utility of existing β-lactam antibiotics for treating infection. Here we investigated the antibacterial chelator-releasing prodrug PcephPT (2-((((6R,7R)-2-carboxy-8-oxo-7-(2-phenylacetamido)-5-thia-1-azabicyclo[4.2.0]oct-2-en-3-yl)methyl)thio) pyridine 1-oxide) as an inhibitor of New Delhi metallo-β-lactamase 1 (NDM-1). PcephPT is an experimental compound that we have previously shown inhibits growth of β-lactamase-expressing E. coli using a mechanism that is dependent on both copper availability and β-lactamase expression. Here, we found that PcephPT, in addition to being a copper-dependent antibacterial compound, inhibits hydrolysis activity of purified NDM-1with an IC50 of 7.6 μM without removing zinc from the active site and restores activity of the carbapenem antibiotic meropenem against NDM-1-producing E. coli. This work demonstrates that targeting a metal-binding pharmacophore to β-lactamase-producing bacteria is a promising strategy for inhibition of both bacterial growth and metallo-β-lactamases.
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Affiliation(s)
- Abigail C. Jackson
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | | | - Elena A. Puccio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Katherine J. Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
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34
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Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M. Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates. Int J Biol Macromol 2020; 158:104-115. [PMID: 32353499 DOI: 10.1016/j.ijbiomac.2020.04.219] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Two accessory loop regions that are present in numerous variants of New Delhi metallo-β-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Ω loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Ω loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Ω loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Ω loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the β-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins.
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Affiliation(s)
- Joanna E Raczynska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Imiolczyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marlena Komorowska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Justyna Czyrko-Horczak
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland
| | - Krzysztof Brzezinski
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland.
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
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35
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Zalucki YM, Jen FEC, Pegg CL, Nouwens AS, Schulz BL, Jennings MP. Evolution for improved secretion and fitness may be the selective pressures leading to the emergence of two NDM alleles. Biochem Biophys Res Commun 2020; 524:555-560. [DOI: 10.1016/j.bbrc.2020.01.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/24/2020] [Indexed: 01/07/2023]
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36
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Suppression of β-Lactam Resistance by Aspergillomarasmine A Is Influenced by both the Metallo-β-Lactamase Target and the Antibiotic Partner. Antimicrob Agents Chemother 2020; 64:AAC.01386-19. [PMID: 31932375 DOI: 10.1128/aac.01386-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
The rise of Gram-negative pathogens expressing metallo-β-lactamases (MBLs) is a growing concern, threatening the efficacy of β-lactam antibiotics, in particular, the carbapenems. There are no inhibitors of MBLs in current clinical use. Aspergillomarasmine A (AMA) is an MBL inhibitor isolated from Aspergillus versicolor with the ability to rescue meropenem activity in MBL-producing bacteria both in vitro and in vivo Here, we systematically explored the pairing of AMA with six β-lactam antibiotic partners against 19 MBLs from three subclasses (B1, B2, and B3). Cell-based assays performed with Escherichia coli and Klebsiella pneumoniae showed that bacteria producing NDM-1 and VIM-2 of subclass B1 were the most susceptible to AMA inhibition, whereas bacteria producing CphA2 and AIM-1 of subclasses B2 and B3, respectively, were the least sensitive. Intracellular antibiotic accumulation assays and in vitro enzyme assays demonstrated that the efficacy of AMA/β-lactam combinations did not correlate with outer membrane permeability or drug efflux. We determined that the optimal β-lactam partners for AMA are the carbapenem antibiotics and that the efficacy of AMA is linked to the Zn2+ affinity of specific MBLs.
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37
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Mu X, Xu D. QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism. J Mol Model 2020; 26:71. [PMID: 32146530 DOI: 10.1007/s00894-020-4330-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/23/2020] [Indexed: 11/25/2022]
Abstract
Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of Oδ2-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
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Affiliation(s)
- Xia Mu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China. .,Research Center for Material Genome Engineering, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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38
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Gao H, Ge Y, Jiang MH, Chen C, Sun LY, Li JQ, Yang KW. Real-time monitoring and inhibition of the activity of carbapenemase in live bacterial cells: application to screening of β-lactamase inhibitors. NEW J CHEM 2020. [DOI: 10.1039/d0nj03475d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance mediated by β-lactamases including metallo-β-lactamases (MβLs) has become an emerging threat.
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Affiliation(s)
- Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Min-Hao Jiang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education
- Chemical Biology Innovation Laboratory
- College of Chemistry and Materials Science
- Northwest University
- Xi’an 710127
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39
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Kim Y, Maltseva N, Wilamowski M, Tesar C, Endres M, Joachimiak A. Structural and biochemical analysis of the metallo-β-lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di-metal scaffold for catalytic activity. Protein Sci 2019; 29:723-743. [PMID: 31846104 PMCID: PMC7020990 DOI: 10.1002/pro.3804] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023]
Abstract
Emergence of Enterobacteriaceae harboring metallo‐β‐lactamases (MBL) has raised global threats due to their broad antibiotic resistance profiles and the lack of effective inhibitors against them. We have been studied one of the emerging environmental MBL, the L1 from Stenotrophomonas maltophilia K279a. We determined several crystal structures of L1 complexes with three different classes of β‐lactam antibiotics (penicillin G, moxalactam, meropenem, and imipenem), with the inhibitor captopril and different metal ions (Zn+2, Cd+2, and Cu+2). All hydrolyzed antibiotics and the inhibitor were found binding to two Zn+2 ions mainly through the opened lactam ring and some hydrophobic interactions with the binding pocket atoms. Without a metal ion, the active site is very similarly maintained as that of the native form with two Zn+2 ions, however, the protein does not bind the substrate moxalactam. When two Zn+2 ions were replaced with other metal ions, the same di‐metal scaffold was maintained and the added moxalactam was found hydrolyzed in the active site. Differential scanning fluorimetry and isothermal titration calorimetry were used to study thermodynamic properties of L1 MBL compared with New Deli Metallo‐β‐lactamase‐1 (NDM‐1). Both enzymes are significantly stabilized by Zn+2 and other divalent metals but showed different dependency. These studies also suggest that moxalactam and its hydrolyzed form may bind and dissociate with different kinetic modes with or without Zn+2 for each of L1 and NDM‐1. Our analysis implicates metal ions, in forming a distinct di‐metal scaffold, which is central to the enzyme stability, promiscuous substrate binding and versatile catalytic activity. Statement The L1 metallo‐β‐lactamase from an environmental multidrug‐resistant opportunistic pathogen Stenotrophomonas maltophilia K279a has been studied by determining 3D structures of L1 enzyme in the complexes with several β‐lactam antibiotics and different divalent metals and characterizing its biochemical and ligand binding properties. We found that the two‐metal center in the active site is critical in the enzymatic process including antibiotics recognition and binding, which explains the enzyme's activity toward diverse antibiotic substrates. This study provides the critical information for understanding the ligand recognition and for advanced drug development.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Christine Tesar
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
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40
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Cheng Z, Shurina BA, Bethel CR, Thomas PW, Marshall SH, Thomas CA, Yang K, Kimble RL, Montgomery JS, Orischak MG, Miller CM, Tennenbaum JL, Nix JC, Tierney DL, Fast W, Bonomo RA, Page RC, Crowder MW. A Single Salt Bridge in VIM-20 Increases Protein Stability and Antibiotic Resistance under Low-Zinc Conditions. mBio 2019; 10:e02412-19. [PMID: 31744917 PMCID: PMC6867895 DOI: 10.1128/mbio.02412-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/04/2019] [Indexed: 12/31/2022] Open
Abstract
To understand the evolution of Verona integron-encoded metallo-β-lactamase (VIM) genes (blaVIM) and their clinical impact, microbiological, biochemical, and structural studies were conducted. Forty-five clinically derived VIM variants engineered in a uniform background and expressed in Escherichia coli afforded increased resistance toward all tested antibiotics; the variants belonging to the VIM-1-like and VIM-4-like families exhibited higher MICs toward five out of six antibiotics than did variants belonging to the widely distributed and clinically important VIM-2-like family. Generally, maximal MIC increases were observed when cephalothin and imipenem were tested. Additionally, MIC determinations under conditions with low zinc availability suggested that some VIM variants are also evolving to overcome zinc deprivation. The most profound increase in resistance was observed in VIM-2-like variants (e.g., VIM-20 H229R) at low zinc availability. Biochemical analyses reveal that VIM-2 and VIM-20 exhibited similar metal binding properties and steady-state kinetic parameters under the conditions tested. Crystal structures of VIM-20 in the reduced and oxidized forms at 1.25 Å and 1.37 Å resolution, respectively, show that Arg229 forms an additional salt bridge with Glu171. Differential scanning fluorimetry of purified proteins and immunoblots of periplasmic extracts revealed that this difference increases thermostability and resistance to proteolytic degradation when zinc availability is low. Therefore, zinc scarcity appears to be a selective pressure driving the evolution of multiple metallo-β-lactamase families, although compensating mutations use different mechanisms to enhance resistance.IMPORTANCE Antibiotic resistance is a growing clinical threat. One of the most serious areas of concern is the ability of some bacteria to degrade carbapenems, drugs that are often reserved as last-resort antibiotics. Resistance to carbapenems can be conferred by a large group of related enzymes called metallo-β-lactamases that rely on zinc ions for function and for overall stability. Here, we studied an extensive panel of 45 different metallo-β-lactamases from a subfamily called VIM to discover what changes are emerging as resistance evolves in clinical settings. Enhanced resistance to some antibiotics was observed. We also found that at least one VIM variant developed a new ability to remain more stable under conditions where zinc availability is limited, and we determined the origin of this stability in atomic detail. These results suggest that zinc scarcity helps drive the evolution of this resistance determinant.
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Affiliation(s)
- Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Ben A Shurina
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Christopher R Bethel
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Pei W Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center for Infectious Disease, University of Texas, Austin, Texas, USA
| | - Steven H Marshall
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert L Kimble
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | | | - Matthew G Orischak
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Callie M Miller
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Jordan L Tennenbaum
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Jay C Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center for Infectious Disease, University of Texas, Austin, Texas, USA
| | - Robert A Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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41
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González-Bello C, Rodríguez D, Pernas M, Rodríguez Á, Colchón E. β-Lactamase Inhibitors To Restore the Efficacy of Antibiotics against Superbugs. J Med Chem 2019; 63:1859-1881. [PMID: 31663735 DOI: 10.1021/acs.jmedchem.9b01279] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Infections caused by resistant bacteria are nowadays too common, and some pathogens have even become resistant to multiple types of antibiotics, in which case few or even no treatments are available. In recent years, the most successful strategy in anti-infective drug discovery for the treatment of such problematic infections is the combination therapy "antibiotic + inhibitor of resistance". These inhibitors allow the repurposing of antibiotics that have already proven to be safe and effective for clinical use. Three main types of compounds have been developed to block the principal bacterial resistance mechanisms: (i) β-lactamase inhibitors; (ii) outer membrane permeabilizers; (iii) efflux pump inhibitors. This Perspective is focused on β-lactamase inhibitors that disable the most prevalent cause of antibiotic resistance in Gram-negative bacteria, i.e., the deactivation of the most widely used antibiotics, β-lactams (penicillins, cephalosporines, carbapenems, and monobactams), by the production of β-lactamases. An overview of the most recently identified β-lactamase inhibitors and of combination therapy is provided. The article also covers the mechanism of action of the different types of β-lactamase enzymes as a basis for inhibitor design and target inactivation.
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Affiliation(s)
- 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
| | - Diana Rodríguez
- 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
| | - Marina Pernas
- 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
| | - Ángela Rodríguez
- 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
| | - Esther Colchón
- 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
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42
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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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43
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Chen AY, Thomas PW, Cheng Z, Xu NY, Tierney DL, Crowder MW, Fast W, Cohen SM. Investigation of Dipicolinic Acid Isosteres for the Inhibition of Metallo-β-Lactamases. ChemMedChem 2019; 14:1271-1282. [PMID: 31124602 DOI: 10.1002/cmdc.201900172] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/24/2019] [Indexed: 12/31/2022]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) poses an immediate threat to our most effective and widely prescribed drugs, the β-lactam-containing class of antibiotics. There are no clinically relevant inhibitors to combat NDM-1, despite significant efforts toward their development. Inhibitors that use a carboxylic acid motif for binding the ZnII ions in the active site of NDM-1 make up a large portion of the >500 inhibitors reported to date. New and structurally diverse scaffolds for inhibitor development are needed urgently. Herein we report the isosteric replacement of one carboxylate group of dipicolinic acid (DPA) to obtain DPA isosteres with good inhibitory activity against NDM-1 (and related metallo-β-lactamases, IMP-1 and VIM-2). It was determined that the choice of carboxylate isostere influences both the potency of NDM-1 inhibition and the mechanism of action. Additionally, we show that an isostere with a metal-stripping mechanism can be re-engineered into an inhibitor that favors ternary complex formation. This work provides a roadmap for future isosteric replacement of routinely used metal binding motifs (i.e., carboxylic acids) for the generation of new entities in NDM-1 inhibitor design and development.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas Austin, Austin, TX, 78712, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Nasa Y Xu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas Austin, Austin, TX, 78712, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas Austin, Austin, TX, 78712, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
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Kaushik A, Kaushik M, Lather V, Dua J. Recent Review on Subclass B1 Metallo-β-lactamases Inhibitors: Sword for Antimicrobial Resistance. Curr Drug Targets 2019; 20:756-762. [DOI: 10.2174/1389450120666181217101812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/03/2018] [Accepted: 12/11/2018] [Indexed: 01/17/2023]
Abstract
An emerging crisis of antibiotic resistance for microbial pathogens is alarming all the nations,
posing a global threat to human health. The production of the metallo-β-lactamase enzyme is the
most powerful strategy of bacteria to produce resistance. An efficient way to combat this global health
threat is the development of broad/non-specific type of metallo-β-lactamase inhibitors, which can inhibit
the different isoforms of the enzyme. Till date, there are no clinically active drugs against metallo-
β-lactamase. The lack of efficient drug molecules against MBLs carrying bacteria requires continuous
research efforts to overcome the problem of multidrug-resistance bacteria. The present review will
discuss the clinically potent molecules against different variants of B1 metallo-β-lactamase.
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Affiliation(s)
| | | | - Viney Lather
- Amity institute of Pharmacy, Amity University, Noida, India
| | - J.S. Dua
- School of Pharmacy, MMU, Sadopur, Ambala, India
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Duan H, Liu X, Zhuo W, Meng J, Gu J, Sun X, Zuo K, Luo Q, Luo Y, Tang D, Shi H, Cao S, Hu J. 3D-QSAR and molecular recognition of Klebsiella pneumoniae NDM-1 inhibitors. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1579327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Huaichuan Duan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Xinyu Liu
- Laboratory of tumor targeted and immune therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, People’s Republic of China
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jian Meng
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, People’s Republic of China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Ke Zuo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Qing Luo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Yafei Luo
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, Chongqing, People’s Republic of China
| | - Dianyong Tang
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, Chongqing, People’s Republic of China
| | - Hubing Shi
- Laboratory of tumor targeted and immune therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, People’s Republic of China
| | - Shenghua Cao
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, People’s Republic of China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
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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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The Reaction Mechanism of Metallo-β-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop. Antimicrob Agents Chemother 2018; 63:AAC.01754-18. [PMID: 30348667 DOI: 10.1128/aac.01754-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022] Open
Abstract
Carbapenems are "last resort" β-lactam antibiotics used to treat serious and life-threatening health care-associated infections caused by multidrug-resistant Gram-negative bacteria. Unfortunately, the worldwide spread of genes coding for carbapenemases among these bacteria is threatening these life-saving drugs. Metallo-β-lactamases (MβLs) are the largest family of carbapenemases. These are Zn(II)-dependent hydrolases that are active against almost all β-lactam antibiotics. Their catalytic mechanism and the features driving substrate specificity have been matter of intense debate. The active sites of MβLs are flanked by two loops, one of which, loop L3, was shown to adopt different conformations upon substrate or inhibitor binding, and thus are expected to play a role in substrate recognition. However, the sequence heterogeneity observed in this loop in different MβLs has limited the generalizations about its role. Here, we report the engineering of different loops within the scaffold of the clinically relevant carbapenemase NDM-1. We found that the loop sequence dictates its conformation in the unbound form of the enzyme, eliciting different degrees of active-site exposure. However, these structural changes have a minor impact on the substrate profile. Instead, we report that the loop conformation determines the protonation rate of key reaction intermediates accumulated during the hydrolysis of different β-lactams in all MβLs. This study demonstrates the existence of a direct link between the conformation of this loop and the mechanistic features of the enzyme, bringing to light an unexplored function of active-site loops on MβLs.
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Shi M, Xu D, Zeng J. GPU Accelerated Quantum Virtual Screening: Application for the Natural Inhibitors of New Dehli Metalloprotein (NDM-1). Front Chem 2018; 6:564. [PMID: 30515379 PMCID: PMC6255897 DOI: 10.3389/fchem.2018.00564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/31/2018] [Indexed: 11/13/2022] Open
Abstract
Quantum mechanical approaches for the massive computation on large biological system such as virtual screening in drug design and development have presented a challenge to computational chemists for many years. In this study, we demonstrated that by taking advantage of rapid growth of GPU-based hardware and software (i.e., teraChem), it is feasible to perform virtual screening of a refined chemical library at quantum mechanical level in order to identify the lead compounds with improved accuracy, especially for the drug targets such as metalloproteins in which significant charge transfer and polarization occur amongst the metal ions and their coordinated amino acids. Our calculations predicted four nature compounds (i.e., Curcumin, Catechin, menthol, and Ferulic acid) as the suitable inhibitors for antibiotics resistance against New Delhi Metallo-β-lactamase-1 (NDM-1). Molecular orbitals (MOs) of the QM region of metal ions and their coordinated residues indicate that the bridged hydroxide ion delocalized the electron over the Zn-OH-Zn group at HOMO, different from MOs when the OH- is not presented in NDM-1. This indicates that the bridged hydroxide ion plays an important role in the design of antibiotics and other inhibitors targeting the metalloproteins.
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Affiliation(s)
- Mingsong Shi
- College of Chemistry, Sichuan University, Chengdu, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jun Zeng
- MedChemSoft Solutions, Wheelers Hill, VIC, Australia
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Differential active site requirements for NDM-1 β-lactamase hydrolysis of carbapenem versus penicillin and cephalosporin antibiotics. Nat Commun 2018; 9:4524. [PMID: 30375382 PMCID: PMC6207675 DOI: 10.1038/s41467-018-06839-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 09/24/2018] [Indexed: 01/26/2023] Open
Abstract
New Delhi metallo-β-lactamase-1 exhibits a broad substrate profile for hydrolysis of the penicillin, cephalosporin and 'last resort' carbapenems, and thus confers bacterial resistance to nearly all β-lactam antibiotics. Here we address whether the high catalytic efficiency for hydrolysis of these diverse substrates is reflected by similar sequence and structural requirements for catalysis, i.e., whether the same catalytic machinery is used to achieve hydrolysis of each class. Deep sequencing of randomized single codon mutation libraries that were selected for resistance to representative antibiotics reveal stringent sequence requirements for carbapenem versus penicillin or cephalosporin hydrolysis. Further, the residue positions required for hydrolysis of penicillins and cephalosporins are a subset of those required for carbapenem hydrolysis. Thus, while a common core of residues is used for catalysis of all substrates, carbapenem hydrolysis requires an additional set of residues to achieve catalytic efficiency comparable to that for penicillins and cephalosporins.
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50
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Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Antimicrob Agents Chemother 2018; 62:AAC.01579-18. [PMID: 30150473 DOI: 10.1128/aac.01579-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 01/05/2023] Open
Abstract
β-Lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-β-lactamases (MBLs) has become a global concern. New Delhi metallo-β-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all β-lactam antibiotics, has rapidly spread all over the world and poses serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs toward different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products and by using biochemical and biophysical studies, site-directed mutagenesis, and molecular dynamics computation. The structural studies reveal the consistency of the active-site conformations in NDM-1/product complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active-site fluctuation, with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active-site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism studies and inhibitor design.
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