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Al-Madboly LA, El-Salam MAA, Bastos JK, Aboukhatwa S, El-Morsi RM. Characterization of GQA as a novel β-lactamase inhibitor of CTX-M-15 and KPC-2 enzymes. Microb Cell Fact 2024; 23:221. [PMID: 39118086 PMCID: PMC11308155 DOI: 10.1186/s12934-024-02421-1] [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: 03/06/2024] [Accepted: 05/11/2024] [Indexed: 08/10/2024] Open
Abstract
β-lactam resistance is a significant global public health issue. Outbreaks of bacteria resistant to extended-spectrum β-lactams and carbapenems are serious health concerns that not only complicate medical care but also impact patient outcomes. The primary objective of this work was to express and purify two soluble recombinant representative serine β‑lactamases using Escherichia coli strain as an expression host and pET101/D as a cloning vector. Furthermore, a second objective was to evaluate the potential, innovative, and safe use of galloylquinic acid (GQA) from Copaifera lucens as a potential β-lactamase inhibitor.In the present study, blaCTX-M-15 and blaKPC-2 represented genes encoding for serine β-lactamases that were cloned from parent isolates of E. coli and K. pneumoniae, respectively, and expression as well as purification were performed. Moreover, susceptibility results demonstrated that recombinant cells became resistant to all test carbapenems (MICs; 64-128 µg/mL) and cephalosporins (MICs; 128-512 µg/mL). The MICs of the tested β-lactam antibiotics were determined in combination with 4 µg/mL of GQA, clavulanic acid, or tazobactam against E. coli strains expressing CTX-M-15 or KPC-2-β-lactamases. Interestingly, the combination with GQA resulted in an important reduction in the MIC values by 64-512-fold to the susceptible range with comparable results for other reference inhibitors. Additionally, the half-maximal inhibitory concentration of GQA was determined using nitrocefin as a β-lactamase substrate. Data showed that the test agent was similar to tazobactam as an efficient inhibitors of the test enzymes, recording smaller IC50 values (CTX-M-15; 17.51 for tazobactam, 28.16 µg/mL for GQA however, KPC-2; 20.91 for tazobactam, 24.76 µg/mL for GQA) compared to clavulanic acid. Our work introduces GQA as a novel non-β-lactam inhibitor, which interacts with the crucial residues involved in β-lactam recognition and hydrolysis by non-covalent interactions, complementing the enzyme's active site. GQA markedly enhanced the potency of β-lactams against carbapenemase and extended-spectrum β-lactamase-producing strains, reducing the MICs of β-lactams to the susceptible range. The β-lactamase inhibitory activity of GQA makes it a promising lead molecule for the development of more potent β-lactamase inhibitors.
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Affiliation(s)
- Lamiaa A Al-Madboly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Tanta University, Tanta, Egypt.
| | - Mohamed A Abd El-Salam
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, 11152, Egypt.
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, D02 VN51, Ireland.
| | - Jairo K Bastos
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, SP, 14040-903, Brazil
| | - Shaimaa Aboukhatwa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Rasha M El-Morsi
- Department of Microbiology and Immunology, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, 11152, Egypt
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Farhat N, Ali A, Waheed M, Gupta D, Khan AU. Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study. J Biomol Struct Dyn 2022:1-11. [PMID: 35848348 DOI: 10.1080/07391102.2022.2099977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The β-lactam antibiotics are the most effective medicines for treating bacterial infections. Resistance to them, particularly through the production of β-lactamases, which can hydrolyse all kinds of β-lactams, poses a threat to their continued use. The synthesised flavone and coumarin based isoxazole derivatives have the potential to be used as broad-spectrum inhibitors of the mechanistically different serine-(SBL) and metallo-β-lactamases (MBL). The synthesised compounds were discovered as potent β-lactamase inhibitors using molecular docking and in silico pharmacokinetic analysis. We studied the binding of chemically synthesised inhibitors to clinically significant β-lactamases of class A, B, and C using biophysical and biochemical approaches, and computational analyses. These molecules follow Lipinski's rule of five and have acceptable solubility, permeability, and oral bioavailability. These molecules were found to be non-toxic and non-carcinogenic. MIC results suggest that these molecules restore the antibiotic efficacy against class A, B, and C β-lactamases. Kinetics data showed that these molecules reduce the catalytic efficiency of clinically relevant class A, B, and C β-lactamases. Fluorescence study showed significant interaction between these flavone-/coumarin-based isoxazole derivatives and class A/B/ C β-lactamases. This study showed promising effect of these new generation compounds as broad spectrum β-lactamase inhibitors of both SBLs and MBLs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Abid Ali
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Mohd Waheed
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttrakhand, India
| | - Divya Gupta
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Monogue ML, Heil EL, Aitken SL, Pogue JM. The role of tazobactam-based combinations for the management of infections due to extended-spectrum β-lactamase-producing Enterobacterales: Insights from the Society of Infectious Diseases Pharmacists. Pharmacotherapy 2021; 41:864-880. [PMID: 34689349 DOI: 10.1002/phar.2623] [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: 07/12/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 11/07/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a global threat to public health due to their antimicrobial resistance profile and, consequently, their limited available treatment options. Tazobactam is a sulfone β-lactamase inhibitor with in vitro inhibitory activity against common ESBLs in Enterobacterales, including CTX-M. However, the role of tazobactam-based combinations in treating infections caused by ESBL-producing Enterobacterales remains unclear. In the United States, two tazobactam-based combinations are available, piperacillin-tazobactam and ceftolozane-tazobactam. We evaluated and compared the roles of tazobactam-based combinations against ESBL-producing organisms with emphasis on pharmacokinetic/pharmacodynamic exposures in relation to MIC distributions and established breakpoints, clinical outcomes data specific to infection site, and considerations for downstream effects with these agents regarding antimicrobial resistance development. While limited data with ceftolozane-tazobactam are encouraging for its potential role in infections due to ESBL-producing Enterobacterales, further evidence is needed to determine its place in therapy. Conversely, currently available microbiologic, pharmacokinetic, pharmacodynamic, and clinical data do not suggest a role for piperacillin-tazobactam, and we caution clinicians against its usage for these infections.
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Affiliation(s)
- Marguerite L Monogue
- Department of Pharmacy, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Emily L Heil
- Department of Pharmacy Services, University of Maryland Medical Center, Baltimore, Maryland, USA
- Department of Pharmacy Practice and Science, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Samuel L Aitken
- Department of Pharmacy, Michigan Medicine, Ann Arbor, Michigan, USA
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
| | - Jason M Pogue
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
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Lee H, Kim JL, Jung DH, Seo Y, Kim M, Yong D, Lee K, Chong Y. Evaluation of Disk carbapenemase test using improved disks for rapid detection and differentiation of clinical isolates of carbapenemase-producing Enterobacterales. J Infect Chemother 2021; 27:1205-1211. [PMID: 33888420 DOI: 10.1016/j.jiac.2021.03.020] [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: 12/22/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/01/2022]
Abstract
OBJECTIVES Rapid detection of carbapenemase-producing Enterobacterales (CPE) is important to control spread of the resistance. We previously reported that imipenem disks prepared from injectable imipenem-cilastatin could rapidly detect KPC- and NDM-type carbapenemases. In the present study, we evaluated performance of disks of IPM and combined disks of imipenem-tazobactam and imipenem-EDTA, which were prepared from powders of imipenem and inhibitors. METHODS Isolates of Enterobacterales were recovered from specimens of patients at a tertiary care hospital in Korea during January 2017 and March 2018. Routine CPE detection was performed by the CPE surveillance personnel whereas evaluation of the Disk carbapenemase test (DCT) was performed by the other personnel without knowing the results of surveillance. The DCT was carried out by pressing disks on to colonies and rehydrating in Petri plates and observing color change. RESULTS The DCT differentiated 688 of 694 (sensitivity 99.1%) carbapenemase-producing isolates in 2.5-20 min: 630 with KPC, 51 with NDM, three with IMP, one with VIM, two with KPC and IMP, and one with NDM and OXA-181. The DCT failed to detect six OXA- 48-like enzyme-producing isolates, but the modified method using 96-well flat-bottom microplates with mineral oil cover detected all 29 OXA-48-like enzyme-producing isolates in 20-120 min. The DCT was negative for all 440 ertapenem-nonsusceptible, carbapenemase gene-negative isolates (specificity 100%). CONCLUSION The procedure of DCT is simple and can differentiate isolates of Enterobacterales with KPC-, NDM-, IMP- and VIM-type carbapenemases rapidly, and the modified DCT can detect isolates with OXA-48-like enzymes rapidly.
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Affiliation(s)
- Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jung Lim Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Da Hee Jung
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Younghee Seo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea; Seoul Clinical Laboratories Academy, Yongin, 16954, South Korea.
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea
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Zhao B, Zhang X, Yu T, Liu Y, Zhang X, Yao Y, Feng X, Liu H, Yu D, Ma L, Qin S. Discovery of thiosemicarbazone derivatives as effective New Delhi metallo- β-lactamase-1 (NDM-1) inhibitors against NDM-1 producing clinical isolates. Acta Pharm Sin B 2021; 11:203-221. [PMID: 33532189 PMCID: PMC7838035 DOI: 10.1016/j.apsb.2020.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/02/2020] [Accepted: 06/28/2020] [Indexed: 12/23/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is capable of hydrolyzing nearly all β-lactam antibiotics, posing an emerging threat to public health. There are currently less effective treatment options for treating NDM-1 positive “superbug”, and no promising NDM-1 inhibitors were used in clinical practice. In this study, structure–activity relationship based on thiosemicarbazone derivatives was systematically characterized and their potential activities combined with meropenem (MEM) were evaluated. Compounds 19bg and 19bh exhibited excellent activity against 10 NDM-positive isolate clinical isolates in reversing MEM resistance. Further studies demonstrated compounds 19bg and 19bh were uncompetitive NDM-1 inhibitors with Ki = 0.63 and 0.44 μmol/L, respectively. Molecular docking speculated that compounds 19bg and 19bh were most likely to bind in the allosteric pocket which would affect the catalytic effect of NDM-1 on the substrate meropenem. Toxicity evaluation experiment showed that no hemolysis activities even at concentrations of 1000 mg/mL against red blood cells. In vivo experimental results showed combination of MEM and compound 19bh was markedly effective in treating infections caused by NDM-1 positive strain and prolonging the survival time of sepsis mice. Our finding showed that compound 19bh might be a promising lead in developing new inhibitor to treat NDM-1 producing superbug.
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Key Words
- (Boc)2O, di-tert-butyl decarbonate
- 3-AP, 3-aminopyridine carboxaldehyde thiosemicarbazone
- AcOH, acetic acid
- Antibiotic resistance
- Boc, tert-butoxycarbonyl
- CLSI, Clinical and Laboratory Standards Institute
- DMAP, 4-dimethylaminopyridine
- DpC, di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone
- E. coli, Escherichia coli
- EDTA, ethylene diamine tetraacetic acid
- ESI, electrospray ionization
- HR-MS, high-resolution mass spectra
- IC50, half-maximal inhibitory concentrations
- Inhibitor
- K. pneumoniae, Klebsiella pneumoniae
- LQTS, long QT syndrome
- MBLs, metallo-β-lactamases class B
- MEM, meropenem
- MHA, Mueller-Hinton Agar
- MHB, Mueller-Hinton Broth
- MIC, minimum inhibitory concentration
- NDM-1, New Delhi metallo-β-lactamase-1
- New Delhi metallo-β-lactamase-1
- PBS, phosphate-buffered saline
- PK, pharmacokinetic
- RBCs, red blood cells
- SAR, structure–activity relationship
- THF, tetrahydrofuran
- TLC, thin layer chromatography
- TMS, tetramethylsilane
- Thiosemicarbazone derivatives
- UPLC, ultra-performance liquid chromatography
- conc. HCl, concentrated hydrochloric acid
- r.t., room temperature
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Inhibition Activity of Avibactam against Nocardia farcinica β-Lactamase FAR IFM10152. Antimicrob Agents Chemother 2020; 64:AAC.01551-19. [PMID: 31712200 DOI: 10.1128/aac.01551-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/04/2019] [Indexed: 11/20/2022] Open
Abstract
Nocardia farcinica, one of the most frequent pathogenic species responsible for nocardiosis, is characterized by frequent brain involvement and resistance to β-lactams mediated by a class A β-lactamase. Kinetic parameters for hydrolysis of various β-lactams by FARIFM10152 from strain IFM 10152 were determined by spectrophotometry revealing a high catalytic activity (k cat/Km ) for amoxicillin, aztreonam, and nitrocefin. For cephems, k cat/Km was lower but remained greater than 104 M-1 s-1 A low catalytic activity was observed for meropenem, imipenem, and ceftazidime hydrolysis. FARIFM10152 inhibition by avibactam and clavulanate was compared using nitrocefin as a reporter substrate. FARIFM10152 was efficaciously inhibited by avibactam with a carbamoylation rate constant (k 2/Ki ) of (1.7 ± 0.3) × 104 M-1 s-1 The 50% effective concentrations (EC50s) of avibactam and clavulanate were 0.060 ± 0.007 μM and 0.28 ± 0.06 μM, respectively. Amoxicillin, cefotaxime, imipenem, and meropenem MICs were measured for ten clinical strains in the presence of avibactam and clavulanate. At 4 μg/ml, avibactam and clavulanate restored amoxicillin susceptibility in all but one of the tested strains but had no effect on the MICs of cefotaxime, imipenem, and meropenem. At 0.4 μg/ml, amoxicillin susceptibility (MIC ≤ 8 μg/ml) was restored for 9 out of 10 strains by avibactam but only for 4 out of 10 strains by clavulanate. Together, these results indicate that avibactam was at least as potent as clavulanate, suggesting that the amoxicillin-avibactam combination could be considered as an option for the rescue treatment of N. farcinica infections if clavulanate cannot be used.
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Chandar B, Bhattacharya D. Role of Natural Product in Modulation of Drug Transporters and New Delhi Metallo-β Lactamases. Curr Top Med Chem 2019; 19:874-885. [PMID: 30987566 DOI: 10.2174/1871529x19666190415110724] [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: 02/17/2019] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 11/22/2022]
Abstract
A rapid growth in drug resistance has brought options for treating antimicrobial resistance to a halt. Bacteria have evolved to accumulate a multitude of genes that encode resistance for a single drug within a single cell. Alternations of drug transporters are one of the causes for the development of resistance in drug interactions. Conversely, the production of enzymes also inactivates most antibiotics. The discovery of newer classes of antibiotics and drugs from natural products is urgently needed. Alternative medicines play an integral role in countries across the globe but many require validation for treatment strategies. It is essential to explore this chemical diversity in order to find novel drugs with specific activities which can be used as alternative drug targets. This review describes the interaction of drugs with resistant pathogens with a special focus on natural product-derived efflux pump and carbapenemase inhibitors.
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Affiliation(s)
- Brinda Chandar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States
| | - Debdutta Bhattacharya
- ICMRRegional Medical Research Centre (Dept. of Health Research, Govt. of India), Chandrasekharpur, Bhubaneswar, India
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8
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Linciano P, Cendron L, Gianquinto E, Spyrakis F, Tondi D. Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design. ACS Infect Dis 2019; 5:9-34. [PMID: 30421910 DOI: 10.1021/acsinfecdis.8b00247] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The worldwide emergence of New Delhi metallo-β-lactamase-1 (NDM-1) as a carbapenemase able to hydrolyze nearly all available β-lactam antibiotics has characterized the past decade, endangering efficacious antibacterial treatments. No inhibitors for NDM-1 are available in therapy, nor are promising compounds in the pipeline for future NDM-1 inhibitors. We report the studies dedicated to the design and development of effective NDM-1 inhibitors. The discussion for each agent moves from the employed design strategy to the ability of the identified inhibitor to synergize β-lactam antibiotics. A structural analysis of NDM-1 mechanism of action based on selected X-ray complexes is also reported: the intrinsic flexibility of the binding site and the comparison between penicillin/cephalosporin and carbapenem mechanisms of hydrolysis are evaluated. Despite the valuable progress in terms of structural and mechanistic information, the design of a potent NDM-1 inhibitor to be introduced in therapy remains challenging. Certainly, only the deep knowledge of NDM-1 architecture and of the variable mechanism of action that NDM-1 employs against different classes of substrates could orient a successful drug discovery campaign.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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9
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Ali A, Kumar R, Iquebal MA, Jaiswal S, Kumar D, Khan AU. The role of conserved residues in the catalytic activity of NDM-1: an approach involving site directed mutagenesis and molecular dynamics. Phys Chem Chem Phys 2019; 21:17821-17835. [DOI: 10.1039/c9cp02734c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug degraded by enzyme and hence not targeted on to the cell leading to cell survival. After mutation leading to conformational changes and loss of function hence drug was not degraded and remained available for the target to lyse the cell.
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Affiliation(s)
- Abid Ali
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
| | - Rakesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
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10
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Klein R, Linciano P, Celenza G, Bellio P, Papaioannou S, Blazquez J, Cendron L, Brenk R, Tondi D. In silico identification and experimental validation of hits active against KPC-2 β-lactamase. PLoS One 2018; 13:e0203241. [PMID: 30496182 PMCID: PMC6264499 DOI: 10.1371/journal.pone.0203241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/06/2018] [Indexed: 01/25/2023] Open
Abstract
Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, as putative hit candidates. We performed a structure-based in silico screening of commercially available compounds for non-β-lactam KPC-2 inhibitors. Thirty-two commercially available high-scoring, fragment-like hits were selected for in vitro validation and their activity and mechanism of action vs the target was experimentally evaluated using recombinant KPC-2. N-(3-(1H-tetrazol-5-yl)phenyl)-3-fluorobenzamide (11a), in light of its ligand efficiency (LE = 0.28 kcal/mol/non-hydrogen atom) and chemistry, was selected as hit to be directed to chemical optimization to improve potency vs the enzyme and explore structural requirement for inhibition in KPC-2 binding site. Further, the compounds were evaluated against clinical strains overexpressing KPC-2 and the most promising compound reduced the MIC of the β-lactam antibiotic meropenem by four-fold.
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Affiliation(s)
- Raphael Klein
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Pasquale Linciano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Giuseppe Celenza
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell’Aquila,L’Aquila, Italy
| | - Pierangelo Bellio
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell’Aquila,L’Aquila, Italy
| | - Sofia Papaioannou
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Jesus Blazquez
- Department of Microbial Biotechnology, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Campus de la Universidad Autonoma-Cantoblanco, Madrid, Spain
| | - Laura Cendron
- Dipartimento di Biologia, Università di Padova, Padova, Italy
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Bergen, Norway
- * E-mail: (DT); (RB)
| | - Donatella Tondi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
- * E-mail: (DT); (RB)
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11
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Saravanan M, Ramachandran B, Barabadi H. The prevalence and drug resistance pattern of extended spectrum β–lactamases (ESBLs) producing Enterobacteriaceae in Africa. Microb Pathog 2018; 114:180-192. [DOI: 10.1016/j.micpath.2017.11.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
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12
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Potential inhibitors designed against NDM-1 type metallo-β-lactamases: an attempt to enhance efficacies of antibiotics against multi-drug-resistant bacteria. Sci Rep 2017; 7:9207. [PMID: 28835636 PMCID: PMC5569068 DOI: 10.1038/s41598-017-09588-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/25/2017] [Indexed: 11/08/2022] Open
Abstract
NDM-1 and its variants are the most prevalent types of metallo-β-lactamases, hydrolyze almost all antibiotics of β-lactam group leading to multiple-drug resistance in bacteria. No inhibitor has yet been obtained for NDM-1 or other class of metallo-β-lactamases. Therefore, strategies to identify novel anti-β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we have reported the discovery of novel non-β-lactam inhibitors against NDM-1 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Five chemical compounds were finally purchased and evaluated experimentally for their efficacies to inhibit NDM-1 producing bacterial cells, in vitro. The dissociation constants (Kd), association constant (Ka), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets were determined using isothermal titration calorimetry (ITC). Molecular dynamic simulation carried out for 25 ns revealed that these complexes were stable throughout the simulation with relative RMSD in acceptable range. Moreover, Microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as lead molecules for future drug candidates.
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Schillaci D, Spanò V, Parrino B, Carbone A, Montalbano A, Barraja P, Diana P, Cirrincione G, Cascioferro S. Pharmaceutical Approaches to Target Antibiotic Resistance Mechanisms. J Med Chem 2017; 60:8268-8297. [PMID: 28594170 DOI: 10.1021/acs.jmedchem.7b00215] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is urgent need for new therapeutic strategies to fight the global threat of antibiotic resistance. The focus of this Perspective is on chemical agents that target the most common mechanisms of antibiotic resistance such as enzymatic inactivation of antibiotics, changes in cell permeability, and induction/activation of efflux pumps. Here we assess the current landscape and challenges in the treatment of antibiotic resistance mechanisms at both bacterial cell and community levels. We also discuss the potential clinical application of chemical inhibitors of antibiotic resistance mechanisms as add-on treatments for serious drug-resistant infections. Enzymatic inhibitors, such as the derivatives of the β-lactamase inhibitor avibactam, are closer to the clinic than other molecules. For example, MK-7655, in combination with imipenem, is in clinical development for the treatment of infections caused by carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa, which are difficult to treat. In addition, other molecules targeting multidrug-resistance mechanisms, such as efflux pumps, are under development and hold promise for the treatment of multidrug resistant infections.
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Affiliation(s)
- Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Carbone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
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Proteomic analysis of a carbapenem-resistant Klebsiella pneumoniae strain in response to meropenem stress. J Glob Antimicrob Resist 2017; 8:172-178. [PMID: 28219823 DOI: 10.1016/j.jgar.2016.12.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES Antibiotic resistance has become a major problem in treating bacterial infections. The aim of this study was to elucidate the effects of meropenem on a blaKPC-2-harbouring multidrug-resistant clinical strain of Klebsiella pneumoniae through a proteomics approach in order to attain a deeper understanding of bacterial resistance strategies. METHODS Analysis was performed by two-dimensional gel electrophoresis of whole-cell extracts of bacteria exposed to a sublethal concentration of meropenem compared with the untreated control. Differentially expressed proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF). RESULTS Based on Quantity One® software and MALDI-TOF analysis, 16 overexpressed proteins were identified in meropenem-treated bacteria. These proteins were primarily enzymes involved in defence against oxidative stress as well as glycolytic enzymes. LysM domain/BON superfamily protein was found overexpressed by >12-fold. STRING-10 was used to determine protein-protein interaction among the overexpressed proteins and to predict their functional associations. This study demonstrated that treatment with meropenem resulted in upregulation of various proteins involved in defence and repair mechanisms along with enzymes of energy metabolism. CONCLUSIONS These overexpressed proteins may play an important role in bacterial resistance mechanisms against carbapenems, however their role in resistance needs to be further validated. High expression of lysine M domain/BON superfamily protein may indicate its possible involvement in modulating the bacterial response to antibiotic stress, but its actual role requires more investigation. These findings may also help in the development of newer therapeutic agents or diagnostic markers against carbapenem resistance.
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The analysis of the antibiotic resistome offers new opportunities for therapeutic intervention. Future Med Chem 2016; 8:1133-51. [DOI: 10.4155/fmc-2016-0027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most efforts in the development of antimicrobials have focused on the screening of lethal targets. Nevertheless, the constant expansion of antimicrobial resistance makes the antibiotic resistance determinants themselves suitable targets for finding inhibitors to be used in combination with antibiotics. Among them, inhibitors of antibiotic inactivating enzymes and of multidrug efflux pumps are suitable candidates for improving the efficacy of antibiotics. In addition, the application of systems biology tools is helping to understand the changes in bacterial physiology associated to the acquisition of resistance, including the increased susceptibility to other antibiotics displayed by some antibiotic-resistant mutants. This information is useful for implementing novel strategies based in metabolic interventions or combination of antibiotics for improving the efficacy of antibacterial therapy.
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