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Shungube M, Hlophe AK, Girdhari L, Sabe VT, Peters BB, Reddy N, Omolabi KF, Chetty L, Arumugam T, Chuturgoon A, Kruger HG, Arvidsson PI, Qin HL, Naicker T, Govender T. Synthesis and biological evaluation of novel β-lactam-metallo β-lactamase inhibitors. RSC Adv 2023; 13:18991-19001. [PMID: 37362332 PMCID: PMC10285615 DOI: 10.1039/d3ra02490c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
β-lactamases are enzymes that deactivate β-lactam antibiotics through a hydrolysis mechanism. There are two known types of β-lactamases: serine β-lactamases (SBLs) and metallo β-lactamases (MBLs). The two existing strategies to overcome β-lactamase-mediated resistance are (a) to develop novel β-lactam antibiotics that are not susceptible to hydrolysis by these enzymes; or (b) to develop β-lactamase inhibitors that deactivate the enzyme and thereby restore the efficacy of the co-administered antibiotics. Many commercially available SBL inhibitors are used in combination therapy with antibiotics to treat antimicrobial resistant infections; however, there are only a handful of MBL inhibitors undergoing clinical trials. In this study, we present 11 novel potential MBL inhibitors (via multi-step chemical synthesis), that have shown to completely restore the efficacy of meropenem (≤2 mg L-1) against New Delhi metallo-β-lactamase (NDM) producing Klebsiella pneumoniae in vitro. These compounds contain a cyclic amino acid zinc chelator conjugated to various commercially available β-lactam antibiotic scaffolds with the aim to improve the overall drug transport, lipophilicity, and pharmacokinetic/pharmacodynamic properties as compared to the chelator alone. Biological evaluation of compounds 24b and 24c has further highlighted the downstream application of these MBLs, since they are non-toxic at the selected doses. Time-kill assays indicate that compounds 24b and 24c exhibit sterilizing activity towards NDM producing Klebsiella pneumoniae in vitro using minimal concentrations of meropenem. Furthermore, 24b and 24c proved to be promising inhibitors of VIM-2 (Ki = 0.85 and 1.87, respectively). This study has revealed a novel series of β-lactam MBLIs that are potent, efficacious, and safe leads with the potential to develop into therapeutic MBLIs.
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Affiliation(s)
- Mbongeni Shungube
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Ayanda K Hlophe
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Letisha Girdhari
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Victor T Sabe
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Byron B Peters
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Nakita Reddy
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Kehinde F Omolabi
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Lloyd Chetty
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal Durban South Africa
| | - Anil Chuturgoon
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal Durban South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Per I Arvidsson
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
- Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm Sweden
| | - Hua-Li Qin
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology 205 Luoshi Road Wuhan 430070 P. R. China
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Thavendran Govender
- Department of Chemistry, University of Zululand Private Bag X1001 KwaDlangezwa 3886 South Africa
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Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1. J Inorg Biochem 2020; 210:111123. [PMID: 32622213 DOI: 10.1016/j.jinorgbio.2020.111123] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
To probe the mechanism of inhibition of several previously-published metallo-β-lactamase (MBL) inhibitors for the clinically-important MBL Verona integron-encoded metallo-β-lactamase 2 (VIM-2), equilibrium dialyses with metal analyses, native state electrospray ionization mass spectrometry (ESI-MS), and UV-Vis spectrophotometry were utilized. The mechanisms of inhibition were analyzed for ethylenediaminetetraacetic acid (EDTA); dipicolinic acid (DPA) and DPA analogs 6-(1H-tetrazol-5-yl)picolinic acid (1T5PA) and 4-(3-aminophenyl)pyridine-2,6-dicarboxylic acid (3AP-DPA); thiol-containing compounds, 2,3-dimercaprol, thiorphan, captopril, and tiopronin; and 5-(pyridine-3-sulfonamido)-1,3-thiazole-4-carboxylic acid (ANT-431). UV-Vis spectroscopy and native-state ESI-MS results showed the formation of ternary complexes between VIM-2 and 1T5PA, ANT-431, thiorphan, captopril, and tiopronin, while a metal stripping mechanism was shown with VIM-2 and EDTA and DPA. The same approaches were used to show the formation of a ternary complex between New Delhi Metallo-β-lactamase (NDM-1) and ANT-431. The studies presented herein show that most of the inhibitors utilize a similar mechanism of inhibition as previously reported for NDM-1. These studies also demonstrate that native mass spectrometry can be used to probe the mechanism of inhibition at lower enzyme/inhibitor concentrations than has previously been achieved.
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Affiliation(s)
- Katrin Ackermann
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
| | - Bela E. Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
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Ackermann K, Pliotas C, Valera S, Naismith JH, Bode BE. Sparse Labeling PELDOR Spectroscopy on Multimeric Mechanosensitive Membrane Channels. Biophys J 2017; 113:1968-1978. [PMID: 29117521 PMCID: PMC5685675 DOI: 10.1016/j.bpj.2017.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/17/2022] Open
Abstract
Pulse electron paramagnetic resonance (EPR) is being applied to ever more complex biological systems comprising multiple subunits. Membrane channel proteins are of great interest as pulse EPR reports on functionally significant but distinct conformational states in a native environment without the need for crystallization. Pulse EPR, in the form of pulsed electron-electron double resonance (PELDOR), using site-directed spin labeling, is most commonly employed to accurately determine distances (in the nanometer range) between different regions of the structure. However, PELDOR data analysis is more challenging in systems containing more than two spins (e.g., homomultimers) due to distorting multispin effects. Without suppression of these effects, much of the information contained in PELDOR data cannot be reliably retrieved. Thus, it is of utmost importance for future PELDOR applications in structural biology to develop suitable approaches that can overcome the multispin problem. Here, two different approaches for suppressing multispin effects in PELDOR, sparse labeling of the protein (reducing the labeling efficiency f) and reducing the excitation probability of spins (λ), are compared on two distinct bacterial mechanosensitive channels. For both the pentameric channel of large conductance (MscL) and the heptameric channel of small conductance (MscS) of Escherichia coli, mutants containing a spin label in the cytosolic or the transmembrane region were tested. Data demonstrate that distance distributions can be significantly improved with either approach compared to the standard PELDOR measurement, and confirm that λ < 1/(n−1) is needed to sufficiently suppress multispin effects (with n being the number of spins in the system). A clear advantage of the sparse labeling approach is demonstrated for the cytosolic mutants due to a significantly smaller loss in sensitivity. For the transmembrane mutants, this advantage is less pronounced but still useful for MscS, but performance is inferior for MscL possibly due to structural perturbations by the bulkier diamagnetic spin label analog.
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Affiliation(s)
- Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - James H Naismith
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom.
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Aitha M, Moller AJ, Sahu ID, Horitani M, Tierney DL, Crowder MW. Investigating the position of the hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis and inhibitor binding. J Inorg Biochem 2016; 156:35-9. [PMID: 26717260 PMCID: PMC4843777 DOI: 10.1016/j.jinorgbio.2015.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 12/29/2022]
Abstract
In an effort to examine the relative position of a hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis, rapid freeze quench double electron electron resonance (RFQ-DEER) spectroscopy was used. A doubly-labeled mutant of NDM-1, which had one spin label on the invariant loop at position 69 and another label at position 235, was prepared and characterized. The reaction of the doubly spin labeled mutant with chromacef was freeze quenched at 500μs and 10ms. DEER results showed that the average distance between labels decreased by 4Å in the 500μs quenched sample and by 2Å in the 10ms quenched sample, as compared to the distance in the unreacted enzyme, although the peaks corresponding to distance distributions were very broad. DEER spectra with the doubly spin labeled enzyme with two inhibitors showed that the distance between the loop residue at position 69 and the spin label at position 235 does not change upon inhibitor binding. This study suggests that the hairpin loop in NDM-1 moves over the metal ion during the catalysis and then moves back to its original position after hydrolysis, which is consistent with a previous hypothesis based on NMR solution studies on a related metallo-β-lactamase. This study also demonstrates that this loop motion occurs in the millisecond time domain.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Abraham J Moller
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, OH 45056, USA.
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Aitha M, Al-Adbul-Wahid S, Tierney DL, Crowder MW. Probing substrate binding to the metal binding sites in metallo-β-lactamase L1 during catalysis. MEDCHEMCOMM 2016; 7:194-201. [PMID: 27087914 DOI: 10.1039/c5md00358j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions in metallo-β-lactamases (MBLs) play a major role in catalysis. In this study we investigated the role of the metal ions in the Zn1 and Zn2 sites of MBL L1 during catalysis. A ZnCo (with Zn(II) in the invariant Zn1 site and Co(II) in the Zn2 site) analog of MBL L1 was prepared by using a biological incorporation method. Extended X-ray Absorption Fine Structure (EXAFS) spectroscopic studies were used to confirm that the ZnCo analog was prepared. To study the roles of the Zn(II) and Co(II) ions during catalysis, rapid freeze quench (RFQ)-EXAFS studies were used to probe the reaction of the ZnCo-L1 analog with chromacef when quenched at 10 ms, 50 ms, and 100 ms. The L1-product complex was also analyzed with EXAFS spectroscopy. The data show that the Zn-Co distance is 3.49 Å in the resting enzyme and that this distance increases by 0.3 Å in the sample that was quenched at 10 ms. The average Zn-Co distance decreases at the other time points until reaching a distance of 3.58 Å in the L1-product complex. The data also show that a Co-S interaction is present in the 100 ms quenched sample and in the L1-product complex, which suggests that there is a significant rearrangement of product in the active site.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Sameer Al-Adbul-Wahid
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
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Meini MR, Llarrull LI, Vila AJ. Overcoming differences: The catalytic mechanism of metallo-β-lactamases. FEBS Lett 2015; 589:3419-32. [PMID: 26297824 DOI: 10.1016/j.febslet.2015.08.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/27/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
Metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. The worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. Inhibitor design has been mostly impeded by the structural diversity of these enzymes. Here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyzed at the light of structural and mutagenesis investigations. We propose that these enzymes present a modular structure in their active sites that can be dissected into two halves: one providing the attacking nucleophile, and the second one stabilizing a negatively charged reaction intermediate. These are common mechanistic elements in all metallo-β-lactamases. Nucleophile activation does not necessarily requires a Zn(II) ion, but a Zn(II) center is essential for stabilization of the anionic intermediate. Design of a common inhibitor could be therefore approached based in these convergent mechanistic features despite the structural differences.
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Affiliation(s)
- María-Rocío Meini
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina
| | - Leticia I Llarrull
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina; Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 2000 Rosario, Argentina.
| | - Alejandro J Vila
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina; Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 2000 Rosario, Argentina.
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Aitha M, Moritz L, Sahu ID, Sanyurah O, Roche Z, McCarrick R, Lorigan GA, Bennett B, Crowder MW. Conformational dynamics of metallo-β-lactamase CcrA during catalysis investigated by using DEER spectroscopy. J Biol Inorg Chem 2015; 20:585-94. [PMID: 25827593 PMCID: PMC4733638 DOI: 10.1007/s00775-015-1244-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Previous crystallographic and mutagenesis studies have implicated the role of a position-conserved hairpin loop in the metallo-β-lactamases in substrate binding and catalysis. In an effort to probe the motion of that loop during catalysis, rapid-freeze-quench double electron-electron resonance (RFQ-DEER) spectroscopy was used to interrogate metallo-β-lactamase CcrA, which had a spin label at position 49 on the loop and spin labels (at positions 82, 126, or 233) 20-35 Å away from residue 49, during catalysis. At 10 ms after mixing, the DEER spectra show distance increases of 7, 10, and 13 Å between the spin label at position 49 and the spin labels at positions 82, 126, and 233, respectively. In contrast to previous hypotheses, these data suggest that the loop moves nearly 10 Å away from the metal center during catalysis and that the loop does not clamp down on the substrate during catalysis. This study demonstrates that loop motion during catalysis can be interrogated on the millisecond time scale.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Lindsay Moritz
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Omar Sanyurah
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Zahilyn Roche
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Robert McCarrick
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Brian Bennett
- Physics Department, Marquette University, 540 N. 15th Street, Milwaukee, Wisconsin 53233, USA, and Department of Biophysics, Medical College of Wisconsin, 8701 W. Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
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