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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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Kang SJ, Kim DH, Lee BJ. Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance. Biophys Chem 2024; 309:107228. [PMID: 38552402 DOI: 10.1016/j.bpc.2024.107228] [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: 12/29/2023] [Revised: 03/18/2024] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.
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Affiliation(s)
- Su-Jin Kang
- College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Mastermeditech Ltd., Seoul 07793, Republic of Korea.
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Rout AK, Gautam S, Kumar Mishra V, Bopardikar M, Dehury B, Singh H. NMR insights into β-Lactamase activity of UVI31+ Protein from Chlamydomonas reinhardtii. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 362:107689. [PMID: 38677224 DOI: 10.1016/j.jmr.2024.107689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
β-Lactamases (EC 3.5.2.6) confer resistance against β-lactam group-containing antibiotics in bacteria and higher eukaryotes, including humans. Pathogenic bacterial resistance against β-lactam antibiotics is a primary concern for potential therapeutic developments and drug targets. Here, we report putative β-lactamase activity, sulbactam binding (a β-lactam analogue) in the low μM affinity range, and site-specific interaction studies of a 14 kDa UV- and dark-inducible protein (abbreviated as UVI31+, a BolA homologue) from Chlamydomonas reinhartii. Intriguingly, the solution NMR structure of UVI31 + bears no resemblance to other known β-lactamases; however, the sulbactam binding is found at two sites rich in positively charged residues, mainly at the L2 loop regions and the N-terminus. Using NMR spectroscopy, ITC and MD simulations, we map the ligand binding sites in UVI31 + providing atomic-level insights into its β-lactamase activity. Current study is the first report on β-lactamase activity of UVI31+, a BolA analogue, from C. reinhartii. Furthermore, our mutation studies reveal that the active site serine-55 is crucial for β-lactamase activity.
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Affiliation(s)
- Ashok K Rout
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; Institute of Chemistry and Metabolomics, University of Luebeck, 23562 Luebeck, Germany
| | - Saurabh Gautam
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Mandar Bopardikar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, 760010 Odisha, India
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, 760010 Odisha, India.
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Dos Santos S, Moussounda M, Togola M, Avoune Nguema E, Matteya C, Bignoumba M, Onanga R, Lekana-Douki JB, François P, van der Mee-Marquet N. Carbapenem-producing Enterobacteriaceae in mothers and newborns in southeast Gabon, 2022. Front Cell Infect Microbiol 2024; 14:1341161. [PMID: 38390622 PMCID: PMC10881798 DOI: 10.3389/fcimb.2024.1341161] [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: 11/20/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) pose a significant threat, leading to severe morbidity and mortality among newborns. Methods This study, conducted at Franceville hospital's maternity and neonatology wards from February 22nd to June 20th, 2022, investigated the prevalence of CPE in 197 parturients and 203 newborns. Rectal swabs were taken from parturients before delivery and from newborns 30 minutes after birth. Blood culture samples were collected if signs of infection were observed in newborns during a 28-day follow-up. A total of 152 environmental samples were obtained, comprising 18 from sinks, 14 from incubators, 27 from cradles, 39 from maternal beds, 14 from tables and desks, four from the two baby scales and 36 from bedside furniture. Results None of the 203 newborns were found to be CPE carriers 30 minutes after delivery. CPE carriage was found in 4.6% of mothers. When comparing colonized and uncolonized parturients, well-established risk factors for CPE carriage, such as recent hospitalization and antibiotic therapy, were more frequently observed among CPE carriers (33.3 vs 10.6% for hospitalization in the past 15 days; 55.5 vs 30.3% for hospitalization during pregnancy, and 55.5 vs 35.1% for antibiotic therapy during pregnancy). Notably, the prevalence of treatment with amoxicillin and clavulanic acid was 44.4% in CPE carriers compared to 17.0% in non-carriers. The incidence density of CPE-associated bloodstream infection was 0.49 per 100 newborns, accounting for a fatal case of CPE-associated bacteremia identified in one of the 203 newborns. Seven environmental samples returned positive for CPE (5 sinks and two pieces of furniture). Whole genome sequencing, performed on the 25 CPE isolates, revealed isolates carrying blaNDM-7 (n=10), blaNDM-5 (n=3), blaOXA181 (n=10), blaOXA48 (n=2) or blaOXA244 (n=1), along with genetic traits associated with the ability to cause severe and difficult-to-treat infections in newborns. Core genome comparison revealed nine CPE belonging to three international high-risk clones: E. coli ST410 (four mothers and a sink), two E. coli ST167 (a mother and a piece of furniture), and K. pneumoniae ST307 (a sink and a piece of furniture), with highly similar genetic backgrounds shared by maternal and environmental isolates, suggesting maternal contamination originating from the environment. Discussion Our study reveals key findings may guide the implementation of infection control measures to prevent nosocomial infections in newborns: the prevalence of CPE carriage in one out of 20 parturients, an infection occurring in one out of 400 newborns, substantial contamination of the care environment, clinical and environmental CPE isolates possessing genetic traits associated with the ability to cause severe and challenging infections, and clonal relationships between clinical and environmental isolates suggesting CPE spread within the wards, likely contributing to the acquisition and colonization of CPE by parturients during pregnancy.
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Affiliation(s)
- Sandra Dos Santos
- Centre d’appui pour la prévention des infections associées aux soins en région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, Tours, France
| | - Mesmin Moussounda
- Laboratoire d'Analyses médicales, Hôpital d'Instruction des Armées Omar Bongo Ondimba, Libreville, Gabon
- Equipe « bactéries et risque materno-fœtal », Unité Mixte de Recherche (UMR) 1282, Infectiologie et Santé Publique INRAE, Tours, France
| | - Moussa Togola
- Maternité, Centre Hospitalier Régional Amissa Bongo, Franceville, Gabon
| | - Evelyne Avoune Nguema
- Service de Néonatalogie, Centre Hospitalier Régional Amissa Bongo, Franceville, Gabon
| | - Christiane Matteya
- Service de Néonatalogie, Centre Hospitalier Régional Amissa Bongo, Franceville, Gabon
| | - Michelle Bignoumba
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Richard Onanga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Patrice François
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires et faculté de Médecine de Genève, Geneva, Switzerland
| | - Nathalie van der Mee-Marquet
- Centre d’appui pour la prévention des infections associées aux soins en région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, Tours, France
- Equipe « bactéries et risque materno-fœtal », Unité Mixte de Recherche (UMR) 1282, Infectiologie et Santé Publique INRAE, Tours, France
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Azman AA, Leow ATC, Noor NDM, Noor SAM, Latip W, Ali MSM. Worldwide trend discovery of structural and functional relationship of metallo-β-lactamase for structure-based drug design: A bibliometric evaluation and patent analysis. Int J Biol Macromol 2024; 256:128230. [PMID: 38013072 DOI: 10.1016/j.ijbiomac.2023.128230] [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: 05/25/2023] [Revised: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Metallo-β-lactamase (MBL) is an enzyme produced by clinically important bacteria that can inactivate many commonly used antibiotics, making them a significant concern in treating bacterial infections and the risk of having high antibiotic resistance issues among the community. This review presents a bibliometric and patent analysis of MBL worldwide research trend based on the Scopus and World Intellectual Property Organization databases in 2013-2022. Based on the keywords related to MBL in the article title, abstract, and keywords, 592 research articles were retrieved for further analysis using various tools such as Microsoft Excel to determine the frequency analysis, VOSviewer for bibliometric networks visualization, and Harzing's Publish or Perish for citation metrics analysis. Standard bibliometric parameters were analysed to evaluate the field's research trend, such as the growth of publications, topographical distribution, top subject area, most relevant journal, top cited documents, most relevant authors, and keyword trend analysis. Within 10 years, MBL discovery has shown a steady and continuous growth of interest among the community of researchers. United States of America, China, and the United Kingdom are the top 3 countries contribute high productivity to the field. The patent analysis also shows several impactful filed patents, indicating the significance of development research on the structural and functional relationship of MBL for an effective structure-based drug design (SBDD). Developing new MBL inhibitors using SBDD could help address the research gap and provide new successful therapeutic options for treating MBL-producing bacterial infections.
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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
| | - 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
| | - 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
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, 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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Bibi Z, Asghar I, Ashraf NM, Zeb I, Rashid U, Hamid A, Ali MK, Hatamleh AA, Al-Dosary MA, Ahmad R, Ali M. Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1). Pharmaceuticals (Basel) 2023; 16:1404. [PMID: 37895875 PMCID: PMC10610165 DOI: 10.3390/ph16101404] [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: 08/09/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.
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Affiliation(s)
- Zainab Bibi
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Irfa Asghar
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Iftikhar Zeb
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Umer Rashid
- Department of Chemistry, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan;
| | - Arslan Hamid
- LIMES Institute, University of Bonn, D-53113 Bonn, Germany;
| | - Maria Kanwal Ali
- Institute of Nuclear Medicine, Oncology and Radiotherapy (INOR), Abbottabad 22060, Pakistan;
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Munirah Abdullah Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Raza Ahmad
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Muhammad Ali
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
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Au SX, Mohd Padzil A, Muhd Noor ND, Matsumura H, Raja Abdul Rahman RNZ, Normi YM. Probing the substrate binding modes and catalytic mechanisms of BLEG-1, a promiscuous B3 metallo-β-lactamase with glyoxalase II properties. PLoS One 2023; 18:e0291012. [PMID: 37672512 PMCID: PMC10482274 DOI: 10.1371/journal.pone.0291012] [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: 04/04/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open
Abstract
BLEG-1 from Bacillus lehensis G1 is an evolutionary divergent B3 metallo-β-lactamase (MBL) that exhibited both β-lactamase and glyoxalase II (GLXII) activities. Sequence, phylogeny, biochemical and structural relatedness of BLEG-1 to B3 MBL and GLXII suggested BLEG-1 might be an intermediate in the evolutionary path of B3 MBL from GLXII. The unique active site cavity of BLEG-1 that recognizes both β-lactam antibiotics and S-D-lactoylglutathione (SLG) had been postulated as the key factor for its dual activity. In this study, dynamic ensembles of BLEG-1 and its substrate complexes divulged conformational plasticity and binding modes of structurally distinct substrates to the enzyme, providing better insights into its structure-to-function relationship and enzymatic promiscuity. Our results highlight the flexible nature of the active site pocket of BLEG-1, which is governed by concerted loop motions involving loop7+α3+loop8 and loop12 around the catalytic core, thereby moulding the binding pocket and facilitate interactions of BLEG-1 with both ampicillin and SLG. The distribution of (i) predominantly hydrophobic amino acids in the N-terminal domain, and (ii) flexible amino acids with polar and/or charged side chains in both N- and C-termini provide additional advantages to BLEG-1 in confining the aromatic group of ampicillin, and polar groups of SLG, respectively. The importance of these residues for substrates binding was further confirmed by the reduction in MBL and GLXII activities upon alanine substitutions of Ile-10, Phe-57, Arg-94, Leu-95, and Arg-159. Based on molecular dynamics simulation, mutational, and biochemical data presented herein, the catalytic mechanisms of BLEG-1 toward the hydrolysis of β-lactams and SLG were proposed.
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Affiliation(s)
- Shaw Xian Au
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azyyati Mohd Padzil
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University, Noji-Higashi, Kusatsu, Japan
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Rosales-Hurtado M, Sannio F, Lari L, Verdirosa F, Feller G, Carretero E, Vo-Hoang Y, Licznar-Fajardo P, Docquier JD, Gavara L. Zidovudine-β-Lactam Pronucleoside Strategy for Selective Delivery into Gram-Negative Bacteria Triggered by β-Lactamases. ACS Infect Dis 2023; 9:1546-1557. [PMID: 37439673 DOI: 10.1021/acsinfecdis.3c00110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Addressing antibacterial resistance is a major concern of the modern world. The development of new approaches to meet this deadly threat is a critical priority. In this article, we investigate a new approach to negate bacterial resistance: exploit the β-lactam bond cleavage by β-lactamases to selectively trigger antibacterial prodrugs into the bacterial periplasm. Indeed, multidrug-resistant Gram-negative pathogens commonly produce several β-lactamases that are able to inactivate β-lactam antibiotics, our most reliable and widely used therapeutic option. The chemical structure of these prodrugs is based on a monobactam promoiety, covalently attached to the active antibacterial substance, zidovudine (AZT). We describe the synthesis of 10 prodrug analogues (5a-h) in four to nine steps and their biological activity. Selective enzymatic activation by a panel of β-lactamases is demonstrated, and subsequent structure-activity relationships are discussed. The best compounds are further evaluated for their activity on both laboratory strains and clinical isolates, preliminary stability, and toxicity.
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Affiliation(s)
- Miyanou Rosales-Hurtado
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, 34293 Montpellier, France
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Lindita Lari
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, 34293 Montpellier, France
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
| | - Georges Feller
- Laboratoire de Biochimie, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | - Elodie Carretero
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, 34293 Montpellier, France
| | - Yen Vo-Hoang
- HSM, Univ Montpellier, CNRS, IRD, CHU Montpellier, 34090 Montpellier, France
| | | | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, I-53100 Siena, Italy
- Laboratoire de Bactériologie Moléculaire, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, 34293 Montpellier, France
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9
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Maatouk M, Merhej V, Pontarotti P, Ibrahim A, Rolain JM, Bittar F. Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality. Microorganisms 2023; 11:1933. [PMID: 37630493 PMCID: PMC10459063 DOI: 10.3390/microorganisms11081933] [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: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
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Affiliation(s)
- Mohamad Maatouk
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Vicky Merhej
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Pierre Pontarotti
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Ahmad Ibrahim
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
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10
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Yang Y, Yan YH, Schofield CJ, McNally A, Zong Z, Li GB. Metallo-β-lactamase-mediated antimicrobial resistance and progress in inhibitor discovery. Trends Microbiol 2023; 31:735-748. [PMID: 36858862 DOI: 10.1016/j.tim.2023.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Resistance to β-lactam antibiotics is rapidly growing, substantially due to the spread of serine-β-lactamases (SBLs) and metallo-β-lactamases (MBLs), which efficiently catalyse β-lactam hydrolysis. Combinations of a β-lactam antibiotic with an SBL inhibitor have been clinically successful; however, no MBL inhibitors have been developed for clinical use. MBLs are a worrying resistance vector because they catalyse hydrolysis of all β-lactam antibiotic classes, except the monobactams, and they are being disseminated across many bacterial species worldwide. Here we review the classification, structures, substrate profiles, and inhibition mechanisms of MBLs, highlighting current clinical problems due to MBL-mediated resistance and progress in understanding and combating MBL-mediated resistance.
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Affiliation(s)
- Yongqiang Yang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, China.
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11
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Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
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12
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Krco S, Davis SJ, Joshi P, Wilson LA, Monteiro Pedroso M, Douw A, Schofield CJ, Hugenholtz P, Schenk G, Morris MT. Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup-emerging targets to combat antibiotic resistance. Front Chem 2023; 11:1196073. [PMID: 37408556 PMCID: PMC10318434 DOI: 10.3389/fchem.2023.1196073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical samples. B3-type MBLs display greater diversity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.
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Affiliation(s)
- Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Samuel J. Davis
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Pallav Joshi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Liam A. Wilson
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew Douw
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Marc T. Morris
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
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13
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Ashraf MV, Pant S, Khan MAH, Shah AA, Siddiqui S, Jeridi M, Alhamdi HWS, Ahmad S. Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:881. [PMID: 37375828 DOI: 10.3390/ph16060881] [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: 04/14/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.
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Affiliation(s)
- Mohammad Vikas Ashraf
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Shreekar Pant
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - M A Hannan Khan
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Ali Asghar Shah
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Mouna Jeridi
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Shoeb Ahmad
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
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14
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Huang W, Hu S, Zhu Y, Liu S, Zhou X, Fang Y, Lu Y, Wang R. Metagenomic surveillance and comparative genomic analysis of Chlamydia psittaci in patients with pneumonia. Front Microbiol 2023; 14:1157888. [PMID: 37323913 PMCID: PMC10265514 DOI: 10.3389/fmicb.2023.1157888] [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: 02/03/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023] Open
Abstract
Chlamydia psittaci, a strictly intracellular bacterium, is an underestimated etiologic agent leading to infections in a broad range of animals and mild illness or pneumonia in humans. In this study, the metagenomes of bronchoalveolar lavage fluids from the patients with pneumonia were sequenced and highly abundant C. psittaci was found. The target-enriched metagenomic reads were recruited to reconstruct draft genomes with more than 99% completeness. Two C. psittaci strains from novel sequence types were detected and these were closely related to the animal-borne isolates derived from the lineages of ST43 and ST28, indicating the zoonotic transmissions of C. psittaci would benefit its prevalence worldwide. Comparative genomic analysis combined with public isolate genomes revealed that the pan-genome of C. psittaci possessed a more stable gene repertoire than those of other extracellular bacteria, with ~90% of the genes per genome being conserved core genes. Furthermore, the evidence for significantly positive selection was identified in 20 virulence-associated gene products, particularly bacterial membrane-embedded proteins and type three secretion machines, which may play important roles in the pathogen-host interactions. This survey uncovered novel strains of C. psittaci causing pneumonia and the evolutionary analysis characterized prominent gene candidates involved in bacterial adaptation to immune pressures. The metagenomic approach is of significance to the surveillance of difficult-to-culture intracellular pathogens and the research into molecular epidemiology and evolutionary biology of C. psittaci.
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Affiliation(s)
- Weifeng Huang
- Department of Intensive Care Medicine, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuqin Hu
- Department of Critical Care Medicine, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Yongzhe Zhu
- Department of Microbiology, Navy Medical University, Shanghai, China
| | - Shijia Liu
- Department of Pulmonary Disease, PLA 905 Hospital, Shanghai, China
| | - Xingya Zhou
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
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15
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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [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] [Indexed: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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16
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Ren H, Lu Z, Sun R, Wang X, Zhong J, Su T, He Q, Liao X, Liu Y, Lian X, Sun J. Functional metagenomics reveals wildlife as natural reservoirs of novel β-lactamases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161505. [PMID: 36626997 DOI: 10.1016/j.scitotenv.2023.161505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
The antibiotic resistances in bacteria are believed to rapidly evolve over time in the anthropogenic environments which enriched with selection pressures. However, the knowledge regarding the development of antibiotic resistance in wildlife and their habitats is scarce. It is, therefore, of great interest and significance to unveil the yet-unknown antibiotic resistances in wildlife in accordance with One Health concept. To this end, we analyzed the samples taken from wildlife and surrounding environments using a functional metagenomics approach. By functional screening in combination with Illumina sequencing, a total of 32 candidate genes which encoding putative novel β-lactamase were identified. These putative β-lactamase were taxonomically assigned into bacteria of 23 genera from 7 phyla, where Proteobacteria, Actinobacteria and Firmicutes were dominant. The following functional assessment demonstrated that 4 novel β-lactamases, namely blaSSA, blaSSB1, blaSSB2 and blaSSD, were functionally active to confer the phenotypical resistance to bacteria by increasing MICs up to 128-fold. Further analysis indicated that the novel β-lactamases identified in the current study were able to hydrolyze a broad spectrum of β-lactams including cephalosporins, and they were genetically unique comparing with known β-lactamases. The plausible transmission of some novel β-lactamase genes was supported by our results as the same gene was detected in different samples from different sites. This study shed the light on the active role of wildlife and associated environments as natural reservoirs of novel β-lactamases, implying that the antibiotic resistances might evolve in absence of selection pressure and threaten public health once spread into clinically important pathogens.
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Affiliation(s)
- Hao Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Zhaoxiang Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ruanyang Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Xiran Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jiahao Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Su
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Qian He
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yahong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xinlei Lian
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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17
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Cheng K, Wu Q, Yao C, Chai Z, Jiang L, Liu M, Li C. Distinct Inhibition Modes of New Delhi Metallo-β-lactamase-1 Revealed by NMR Spectroscopy. JACS AU 2023; 3:849-859. [PMID: 37006760 PMCID: PMC10052233 DOI: 10.1021/jacsau.2c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
The wide spread of antibiotic-resistant "superbugs" containing New Delhi metallo-β-lactamase-1 (NDM-1) has become a threat to human health. However, clinically valid antibiotics to treat the superbugs' infection are not available now. Quick, simple, and reliable methods to assess the ligand-binding mode are key to developing and improving inhibitors against NDM-1. Herein, we report a straightforward NMR method to distinguish the NDM-1 ligand-binding mode using distinct NMR spectroscopy patterns of apo- and di-Zn-NDM-1 titrations with various inhibitors. Elucidating the inhibition mechanism will aid the development of efficient inhibitors for NDM-1.
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Affiliation(s)
- Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qiong Wu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chendie Yao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaofei Chai
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ling Jiang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
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18
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The activity and mechanism of vidofludimus as a potent enzyme inhibitor against NDM-1-positive E. coli. Eur J Med Chem 2023; 250:115225. [PMID: 36870273 DOI: 10.1016/j.ejmech.2023.115225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the most important and prevalent enzyme among all metallo-β-lactamases. NDM-1 can hydrolyze almost all-available β-lactam antibiotics including carbapenems, resulting in multidrug resistance, which poses an increasing clinical threat. However, there is no NDM-1 inhibitor approved for clinical treatment. Therefore, identifying a novel and potential enzyme inhibitor against NDM-1-mediated infections is an urgent need. In this study, vidofludimus was identified as a potential NDM-1 inhibitor by structure-based virtual screening and an enzyme activity inhibition assay. Vidofludimus significantly inhibited NDM-1 hydrolysis activity with a significant dose-dependent effect. When the vidofludimus concentration was 10 μg/ml, the inhibition rate and 50% inhibitory concentration were 93.3% and 13.8 ± 0.5 μM, respectively. In vitro, vidofludimus effectively restored the antibacterial activity of meropenem against NDM-1-positive Escherichia coli (E. coli), and the minimum inhibitory concentration of meropenem was decreased from 64 μg/ml to 4 μg/ml, a 16-fold reduction. The combination of vidofludimus and meropenem showed a significant synergistic effect with a fractional inhibitory concentration index of 0.125 and almost all the NDM-1-positive E. coli were killed within 12 h. Furthermore, the synergistic therapeutic effect of vidofludimus and meropenem in vivo was evaluated in mice infected with NDM-1 positive E. coli. Compared with the control treatment, vidofludimus combined with meropenem significantly improved the survival rate of mice infected with NDM-1-positive E. coli (P < 0.05), decreased the white blood cell count, the bacterial burden and inflammatory response induced by NDM-1-positive E. coli (P < 0.05), and alleviated histopathological damage in infected mice. It was demonstrated by molecular dynamic simulation, site-directed mutagenesis and biomolecular interaction that vidofludimus could interact directly with the key amino acids (Met67, His120, His122 and His250) and Zn2+ in the active site of NDM-1, thereby competitively inhibiting the hydrolysis activity of NDM-1 on meropenem. In summary, vidofludimus holds promise as anNDM-1 inhibitor, and the combination of vidofludimus and meropenem has potential as a therapeutic strategy for NDM-1-mediated infections.
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19
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Hinchliffe P, Calvopiña K, Rabe P, Mojica M, Schofield C, Dmitrienko G, Bonomo R, Vila A, Spencer J. Interactions of hydrolyzed β-lactams with the L1 metallo-β-lactamase: Crystallography supports stereoselective binding of cephem/carbapenem products. J Biol Chem 2023; 299:104606. [PMID: 36924941 PMCID: PMC10148155 DOI: 10.1016/j.jbc.2023.104606] [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: 10/05/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/15/2023] Open
Abstract
L1 is a dizinc subclass B3 metallo-β-lactamase (MBL) that hydrolyzes most β-lactam antibiotics and is a key resistance determinant in the Gram-negative pathogen Stenotrophomonas maltophilia, an important cause of nosocomial infections in immunocompromised patients. L1 is not usefully inhibited by MBL inhibitors in clinical trials, underlying the need for further studies on L1 structure and mechanism. We describe kinetic studies and crystal structures of L1 in complex with hydrolyzed β-lactams from the penam (mecillinam), cephem (cefoxitin/cefmetazole) and carbapenem (tebipenem, doripenem and panipenem) classes. Despite differences in their structures, all the β-lactam-derived products hydrogen bond to Tyr33, Ser221 and Ser225 and are stabilized by interactions with a conserved hydrophobic pocket. The carbapenem products were modelled as Δ1-imines, with (2S)-stereochemistry. Their binding mode is determined by the presence of a 1β-methyl substituent: the Zn-bridging hydroxide either interacts with the C-6 hydroxyethyl group (1β-hydrogen-containing carbapenems), or is displaced by the C-6 carboxylate (1β-methyl-containing carbapenems). Unexpectedly, the mecillinam product is a rearranged N-formyl amide rather than penicilloic acid, with the N-formyl oxygen interacting with the Zn-bridging hydroxide. NMR studies imply mecillinam rearrangement can occur non-enzymatically in solution. Cephem-derived imine products are bound with (3R)-stereochemistry and retain their 3' leaving groups, likely representing stable endpoints, rather than intermediates, in MBL-catalyzed hydrolysis. Our structures show preferential complex formation by carbapenem- and cephem-derived species protonated on the equivalent (β) faces, and so identify interactions that stabilize diverse hydrolyzed antibiotics. These results may be exploited in developing antibiotics, and β-lactamase inhibitors, that form long-lasting complexes with dizinc MBLs.
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Affiliation(s)
- Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Karina Calvopiña
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - MariaF Mojica
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; CWRU-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - ChristopherJ Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - GaryI Dmitrienko
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada; School of Pharmacy, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - RobertA Bonomo
- CWRU-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Departments of Medicine, Biochemistry, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH
| | - AlejandroJ Vila
- CWRU-Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA; Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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20
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Castronovo S, Helmholz L, Wolff D, Poulsen JS, Nielsen JL, Ternes TA, Schmidt TC, Wick A. Protein fractionation and shotgun proteomics analysis of enriched bacterial cultures shed new light on the enzymatically catalyzed degradation of acesulfame. WATER RESEARCH 2023; 230:119535. [PMID: 36610183 DOI: 10.1016/j.watres.2022.119535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/08/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
The removal of organic micropollutants in municipal wastewater treatment is an extensively studied field of research, but the underlying enzymatic processes have only been elucidated to a small extent so far. In order to shed more light on the enzymatic degradation of the artificial sweetener acesulfame (ACE) in this context, we enriched two bacterial taxa which were not yet described to be involved in the degradation of ACE, an unknown Chelatococcus species and Ensifer adhaerens, by incubating activated sludge in chemically defined media containing ACE as sole carbon source. Cell-free lysates were extracted, spiked with ACE and analyzed via target LC-MS/MS, demonstrating for the first time enzymatically catalyzed ACE degradation outside of living cells. Fractionation of the lysate via two-dimensional fast protein liquid chromatography (FPLC) succeeded in a partial separation of the enzymes catalyzing the initial transformation reaction of ACE from those catalyzing the further transformation pathway. Thereby, an accumulation of the intermediate transformation product acetoacetamide-n-sulfonic acid (ANSA) in the ACE-degrading fractions was achieved, providing first quantitative evidence that the cleavage of the sulfuric ester moiety of ACE is the initial transformation step. The metaproteome of the enrichments was analyzed in the FPLC fractions and in the unfractionated lysate, using shotgun proteomics via UHPLC-HRMS/MS and label-free quantification. The comparison of protein abundances in the FPLC fractions to the corresponding ACE degradation rates revealed a metallo-β-lactamase fold metallo-hydrolase as most probable candidate for the enzyme catalyzing the initial transformation from ACE to ANSA. This enzyme was by far the most abundant of all detected proteins and amounted to a relative protein abundance of 91% in the most active fraction after the second fractionation step. Moreover, the analysis of the unfractionated lysate resulted in a list of further proteins possibly involved in the transformation of ACE, most striking a highly abundant amidase likely catalyzing the further transformation of ANSA, and an ABC transporter substrate-binding protein that may be involved in the uptake of ACE into the cell.
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Affiliation(s)
- Sandro Castronovo
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Lissa Helmholz
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - David Wolff
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Thomas A Ternes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Arne Wick
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
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21
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Kong WP, Chen YW, Wong KY. The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions. J Struct Biol 2022; 214:107922. [PMID: 36375744 DOI: 10.1016/j.jsb.2022.107922] [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: 08/16/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
New Delhi metallo-β-lactamase 1 (NDM-1) is an important causative factor of antimicrobial resistance due to its efficient hydrolysis of a broad range of β-lactam compounds. The two zinc ions at the active site play essential roles in the NDM-1 catalytic activities. In a previous work, H116, one of the three ligands at the Zn1 site, was mutated in order to investigate the nature of zinc ion chelation. We report here the crystal structure of the NDM-1 H116Q mutant, that was designed to convert a B1 di-zinc enzyme into a B3 type, which either still binds two zinc ions or binds only one at the Zn2 site. The effect of mutation on the overall structure is minimal. Unexpectedly, no zinc ion was observed in the crystal structure. The Zn2-site ligating residue C221 forms a covalent bond with the nearby K121, a residue important in maintaining the active-site structure. The largest conformational changes were found at main-chain and side-chain atoms at residues 232-236 (loop 10), the proper configuration of which is known to be essential for substrate binding. The catalytic-site mutation caused little local changes, yet the effects were amplified and propagated to the substrate binding residues. There were big changes in the ψ angles of residues G232 and L234, which resulted in the side chain of N233 being displaced away from the substrate-binding site. In summary, we failed in turning a B1 enzyme into a B3 enzyme, yet we produced a zinc-less NDM-1 with residual activities.
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Affiliation(s)
- Wai-Po Kong
- 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
- 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
- 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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22
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Wilamowski M, Sherrell DA, Kim Y, Lavens A, Henning RW, Lazarski K, Shigemoto A, Endres M, Maltseva N, Babnigg G, Burdette SC, Srajer V, Joachimiak A. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase. Nat Commun 2022; 13:7379. [PMID: 36450742 PMCID: PMC9712583 DOI: 10.1038/s41467-022-35029-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia. Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.
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Affiliation(s)
- M Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology of Jagiellonian University, 30387, Krakow, Poland
| | - D A Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Y Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Lavens
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - R W Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - K Lazarski
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - A Shigemoto
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - M Endres
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - N Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - G Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - S C Burdette
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - V Srajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, 60637, USA
| | - A Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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23
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Dong R, Yang H, Ai C, Duan G, Wang J, Guo F. DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction. J Chem Inf Model 2022; 62:5830-5840. [PMID: 36245217 DOI: 10.1021/acs.jcim.2c01008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogens producing β-lactamase pose a great challenge to antibiotic-resistant infection treatment; thus, it is urgent to discover novel β-lactamase inhibitors for drug development. Conventional high-throughput screening is very costly, and structure-based virtual screening is limited with mechanisms. In this study, we construct a novel multichannel deep neural network (DeepBLI) for β-lactamase inhibitor screening, pretrained with a label reversal KIBA data set and fine-tuned on β-lactamase-inhibitor pairs from BindingDB. First, the pairs of encoders (Conv and Att) fuse the information spatially and sequentially for both enzymes and inhibitors. Then, a co-attention module creates the connection between the inhibitor and enzyme embeddings. Finally, multichannel outputs fuse with an element-wise product and then are fed into 3-layer fully connected networks to predict interactions. Comparing the state-of-the-art methods, DeepBLI yields an AUROC of 0.9240 and an AUPRC of 0.9715, which indicates that it can identify new β-lactamase-inhibitor interactions. To demonstrate its prediction ability, an application of DeepBLI is described to screen potential inhibitor compounds for metallo-β-lactamase AIM-1 and repurpose rottlerin for four classes of β-lactamase targets, showing the possibility of being a broad-spectrum inhibitor. DeepBLI provides an effective way for antibacterial drug development, contributing to antibiotic-resistant therapeutics.
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Affiliation(s)
- Ruihan Dong
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Hongpeng Yang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina29208, United States
| | - Chengwei Ai
- College of Intelligence and Computing, Tianjin University, Tianjin300350, China
| | - Guihua Duan
- School of Computer Science and Engineering, Central South University, Changsha410083, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha410083, China
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha410083, China
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24
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Fang L, Liu Z, Lu Z, Huang R, Xiang R. Identification and characterization of a novel metallo β-lactamase, SZM-1, in Shenzhen Bay, South China. Front Microbiol 2022; 13:996834. [PMID: 36225370 PMCID: PMC9549060 DOI: 10.3389/fmicb.2022.996834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Metallo β-Lactamases (MBLs) degrade most clinical β-lactam antibiotics, especially Carbapenem, posing a huge threat to global health. Studies on environmental MBLs are important for risk assessment of the MBLs transmission among connected habitats, and between environment and human. Here, we described a novel metallo β-Lactamases, named SZM-1 (Shenzhen metallo-β-lactamase), from an Arenimonas metagenome-assembled genome recovered from the river sediment in the Shenzhen Bay area, south China. Phylogenetic analysis, primary sequence comparison, structural modeling suggested that the SZM-1 belongs to B1 MBL family, likely harboring a typical di-zinc catalytic center. Furthermore, the gene encoding the MBLs was cloned into Escherichia coli TOP10 for Carba NP test and antimicrobial susceptibility test. The results indicated that the SZM-1 had carbapenemase activity, and conferred the carrier to increased resistance toward carbapenems. Taken together, our results raise alarms about the emergence and spread of the SZM-1, and suggest further surveillance, especially in hospital settings and clinical isolates, to determine whether blaSZM–1 is a mobilizable antibiotic resistance.
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Affiliation(s)
- Lingxu Fang
- Department of Stomatology, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Rongzhong Huang
- Precision Medicine Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Rongzhong Huang,
| | - Rong Xiang
- Precision Medicine Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Rong Xiang,
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25
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Kulyar MFEA, Chen X, Bhutta ZA, Boruah P, Shabbir S, Akhtar M, Aqib AI, Ashar A, Li K. Editorial: Antimicrobials alternatives for the prevention and treatment of veterinary infectious diseases. Front Vet Sci 2022; 9:1025150. [PMID: 36157178 PMCID: PMC9501705 DOI: 10.3389/fvets.2022.1025150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Muhammad Fakhar-e-Alam Kulyar
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiushuang Chen
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, South Korea
| | - Prerona Boruah
- DY Patil, Deemed to be University, Navi Mumbai, Maharastra, India
| | - Samina Shabbir
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Muhammad Akhtar
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
- Amjad Islam Aqib
| | - Ambreen Ashar
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
- Ambreen Ashar
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Li
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26
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Kaderabkova N, Bharathwaj M, Furniss RCD, Gonzalez D, Palmer T, Mavridou DAI. The biogenesis of β-lactamase enzymes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35943884 DOI: 10.1099/mic.0.001217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of penicillin by Alexander Fleming marked a new era for modern medicine, allowing not only the treatment of infectious diseases, but also the safe performance of life-saving interventions, like surgery and chemotherapy. Unfortunately, resistance against penicillin, as well as more complex β-lactam antibiotics, has rapidly emerged since the introduction of these drugs in the clinic, and is largely driven by a single type of extra-cytoplasmic proteins, hydrolytic enzymes called β-lactamases. While the structures, biochemistry and epidemiology of these resistance determinants have been extensively characterized, their biogenesis, a complex process including multiple steps and involving several fundamental biochemical pathways, is rarely discussed. In this review, we provide a comprehensive overview of the journey of β-lactamases, from the moment they exit the ribosomal channel until they reach their final cellular destination as folded and active enzymes.
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Affiliation(s)
- Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Manasa Bharathwaj
- Centre to Impact AMR, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - R Christopher D Furniss
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Diego Gonzalez
- Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Tracy Palmer
- Microbes in Health and Disease, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.,John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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27
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Aromatic Schiff bases confer inhibitory efficacy against New Delhi metallo-β-lactamase-1 (NDM-1). Bioorg Chem 2022; 126:105910. [PMID: 35653899 DOI: 10.1016/j.bioorg.2022.105910] [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] [Received: 01/14/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022]
Abstract
The irregular use of antibiotics has created a natural selection pressure for bacteria to adapt resistance. Bacterial resistance caused by metallo-β-lactamases (MβLs) has been the most prevalent in terms of posing a threat to human health. The New Delhi metallo-β-lactamase-1 (NDM-1) has been shown to be capable of hydrolyzing almost all β-lactams. In this work, eight aromatic Schiff bases 1-8 were prepared and identified by enzyme kinetic assays to be the potent inhibitors of NDM-1 (except 4). These molecules exhibited a more than 95 % inhibition, and an IC50 value in the range of 0.13-19 μM on the target enzyme, and 3 was found to be the most effective inhibitor (IC50 = 130 nM). Analysis of structure-activity relationship revealed that the o-hydroxy phenyl improved the inhibitory activity of Schiff bases on NDM-1. The inhibition mode assays including isothermal titration calorimetry (ITC) disclosed that both compounds 3 and 5 exhibited a reversibly mixed inhibition on NDM-1, with a Ki value of 1.9 and 10.8 μM, respectively. Antibacterial activity tests indicated that a dose of 64 μg·mL-1 Schiff bases resulted in 2-128-fold reduction in MICs of cefazolin on E. coli producing NDM-1 (except 4). Cytotoxicity assays showed that both Schiff bases 3 and 5 have low cytotoxicity on the mouse fibroblast (L929) cells at a concentration of up to 400 μM. Docking studies suggested that the hydroxyl group interacts with Gln123 and Glu152 of NDM-1, and the amino groups interact with the backbone amide groups of Glu152 and Asp223. This study provided a novel scaffold for the development of NDM-1 inhibitors.
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28
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Antibiotic Use in Livestock and Residues in Food-A Public Health Threat: A Review. Foods 2022; 11:foods11101430. [PMID: 35627000 PMCID: PMC9142037 DOI: 10.3390/foods11101430] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 01/05/2023] Open
Abstract
The usage of antibiotics has been, and remains, a topic of utmost importance; on the one hand, for animal breeders, and on the other hand, for food safety. Although many countries have established strict rules for using antibiotics in animal husbandry for the food industry, their misuse and irregularities in compliance with withdrawal periods are still identified. In addition to animal-origin foods that may cause antibiotic residue problems, more and more non-animal-origin foods with this type of non-compliance are identified. In this context, we aim to summarize the available information regarding the presence of antibiotic residues in food products, obtained in various parts of the world, as well as the impact of consumption of food with antibiotic residues on consumer health. We also aim to present the methods of analysis that are currently used to determine antibiotic residues in food, as well as methods that are characterized by the speed of obtaining results or by the possibility of identifying very small amounts of residues.
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29
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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30
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Heo Y, Park SB, Jeon YE, Yun JH, Jeong BG, Cha SS, Lee W. Structural and functional identification of the uncharacterized metallo-β-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination. Acta Crystallogr D Struct Biol 2022; 78:532-541. [DOI: 10.1107/s2059798322002108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
Metallo-β-lactamase (MBL) superfamily proteins have a common αβ/βα sandwich fold and perform a variety of functions through metal-mediated catalysis. However, because of the enormous scale of this superfamily, only a small percentage of the proteins belonging to the superfamily have been annotated structurally or functionally to date. Therefore, much remains unknown about the MBL superfamily proteins. Here, TW9814, a hypothetical MBL superfamily protein, was structurally and functionally investigated. Guided by the crystal structure of dimeric TW9814, it was demonstrated that TW9814 functions as a phosphodiesterase (PDE) in the presence of divalent metal ions such as manganese(II) or nickel(II). A docking model between TW9814 and the substrate bis(p-nitrophenyl)phosphate (bpNPP) showed the importance of the dimerization of TW9814 for its bpNPP-hydrolyzing activity and for the interaction between the enzyme and the substrate. TW9814 showed outstanding catalytic efficiency (k
cat/K
m) under alkaline conditions compared with other PDEs. The activity of TW9814 appears to be regulated through a disulfide bond, which is a feature that is not present in other MBL superfamily members. This study provides a platform for the functional characterization of other hypothetical proteins of the MBL or other superfamilies.
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31
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Song L, Xue X, Wang S, Li J, Jin K, Xia Y. MaAts, an Alkylsulfatase, Contributes to Fungal Tolerances against UV-B Irradiation and Heat-Shock in Metarhizium acridum. J Fungi (Basel) 2022; 8:jof8030270. [PMID: 35330272 PMCID: PMC8951457 DOI: 10.3390/jof8030270] [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: 02/11/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Sulfatases are commonly divided into three classes: type I, type II, and type III sulfatases. The type III sulfatase, alkylsulfatase, could hydrolyze the primary alkyl sulfates, such as sodium dodecyl sulfate (SDS) and sodium octyl sulfate. Thus, it has the potential application of SDS biodegradation. However, the roles of alkylsulfatase in biological control fungus remain unclear. In this study, an alkylsulfatase gene MaAts was identified from Metarhizium acridum. The deletion strain (ΔMaAts) and the complemented strain (CP) were constructed to reveal their functions in M. acridum. The activity of alkylsulfatase in ΔMaAts was dramatically reduced compared to the wild-type (WT) strain. The loss of MaAts delayed conidial germination, conidiation, and significantly declined the fungal tolerances to UV-B irradiation and heat-shock, while the fungal conidial yield and virulence were unaffected in M. acridum. The transcription levels of stress resistance-related genes were significantly changed after MaAts inactivation. Furthermore, digital gene expression profiling showed that 512 differential expression genes (DEGs), including 177 up-regulated genes and 335 down-regulated genes in ΔMaAts, were identified. Of these DEGs, some genes were involved in melanin synthesis, cell wall integrity, and tolerances to various stresses. These results indicate that MaAts and the DEGs involved in fungal stress tolerances may be candidate genes to be adopted to improve the stress tolerances of mycopesticides.
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Affiliation(s)
- Lei Song
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Xiaoning Xue
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Shuqin Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Juan Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
| | - Kai Jin
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
- Correspondence: (K.J.); (Y.X.); Tel.: +86-23-65120990 (Y.X.)
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing 401331, China; (L.S.); (X.X.); (S.W.); (J.L.)
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing 401331, China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing 401331, China
- Correspondence: (K.J.); (Y.X.); Tel.: +86-23-65120990 (Y.X.)
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32
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Extraintestinal Pathogenic Escherichia coli: Beta-Lactam Antibiotic and Heavy Metal Resistance. Antibiotics (Basel) 2022; 11:antibiotics11030328. [PMID: 35326791 PMCID: PMC8944441 DOI: 10.3390/antibiotics11030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Multiple-antibiotic-resistant (MAR) extra-intestinal pathogenic Escherichia coli (ExPEC) represents one of the most frequent causes of human nosocomial and community-acquired infections, whose eradication is of major concern for clinicians. ExPECs may inhabit indefinitely as commensal the gut of humans and other animals; from the intestine, they may move to colonize other tissues, where they are responsible for a number of diseases, including recurrent and uncomplicated UTIs, sepsis and neonatal meningitis. In the pre-antibiotic era, heavy metals were largely used as chemotherapeutics and/or as antimicrobials in human and animal healthcare. As with antibiotics, the global incidence of heavy metal tolerance in commensal, as well as in ExPEC, has increased following the ban in several countries of antibiotics as promoters of animal growth. Furthermore, it is believed that extensive bacterial exposure to heavy metals present in soil and water might have favored the increase in heavy-metal-tolerant microorganisms. The isolation of ExPEC strains with combined resistance to both antibiotics and heavy metals has become quite common and, remarkably, it has been recently shown that heavy metal resistance genes may co-select antibiotic-resistance genes. Despite their clinical relevance, the mechanisms underlining the development and spread of heavy metal tolerance have not been fully elucidated. The aim of this review is to present data regarding the development and spread of resistance to first-line antibiotics, such as beta-lactams, as well as tolerance to heavy metals in ExPEC strains.
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33
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Kaya C, Konstantinović J, Kany AM, Andreas A, Kramer JS, Brunst S, Weizel L, Rotter MJ, Frank D, Yahiaoui S, Müller R, Hartmann RW, Haupenthal J, Proschak E, Wichelhaus TA, Hirsch AKH. N-Aryl Mercaptopropionamides as Broad-Spectrum Inhibitors of Metallo-β-Lactamases. J Med Chem 2022; 65:3913-3922. [PMID: 35188771 DOI: 10.1021/acs.jmedchem.1c01755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Drug-resistant pathogens pose a global challenge to public health as they cause diseases that are extremely difficult to cure. Metallo-β-lactamases (MBLs) are a diverse set of zinc-containing enzymes that catalyze the hydrolysis of β-lactam drugs, including carbapenems, which are considered as the last resort to fight severe infections. To restore the activity of current β-lactam antibiotics and to offer an orthogonal strategy to the discovery of new antibiotics, we have identified a series of polar N-aryl mercaptopropionamide derivatives as potent inhibitors of several class B1 MBLs. We have identified a hit structure with high selectivity restoring the effect of imipenem and reducing minimum inhibitory concentration (MIC) values up to 256-fold in resistant isolates from Escherichia coli. Furthermore, the combination of imipenem with our inhibitor showed in vivo efficacy in a Galleria mellonella model, increasing the survival rate of infected larvae by up to 31%.
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Affiliation(s)
- Cansu Kaya
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jelena Konstantinović
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Anastasia Andreas
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Marco J Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | - Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
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34
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Duan M, Bai J, Yang J, Qiao P, Bian L. Molecular recognition and binding of CcrA from Bacteroides fragilis with cefotaxime and ceftazidime by fluorescence spectra and molecular docking. J Biol Inorg Chem 2022; 27:283-295. [PMID: 35190875 DOI: 10.1007/s00775-022-01927-6] [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: 07/20/2021] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
Abstract
In search of new super-bacterial inhibitor agents, the recognition and binding mechanism of the B1 subclass MβL CcrA from Bacteroides fragilis with cefotaxime (CTX) and ceftazidime (CAZ) were studied using spectroscopy analysis and molecular docking. The results showed that the fluorescence quenching of CcrA induced by CTX and CAZ were all due to the complex formation, which belonged to static quenching and was forced by hydrogen bonds and Van der Waals forces, despite the greater binding ability of CTX with CcrA than CAZ. Upon recognizing CTX or CAZ, the CcrA opened its binding pocket by the microenvironmental and conformational of three loops changing to promote an induced-fit of the freshly introduced antibiotics. In addition, the whole antibiotic molecule ultimately entered the active pocket of CcrA with its original carbonate replaced by the carboxyl oxygen of the hexatomic ring adjacent to the β-lactam ring in CTX or CAZ, forming a new tetrahedral coordination structure at the Zn2 site. Moreover, the difference in steric hindrance and electrostatic effects of the side chain affected the binding ability of the two antibiotics to the CcrA. This work showed the refined procedures of the antibiotics binding to CcrA and might provide useful information hint for the new strategy of developing the novel and innovative super-bacterial antibiotics.
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Affiliation(s)
- Meijiao Duan
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jiakun Bai
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jian Yang
- College of Life Science, Northwest University, Xi'an, 710069, China
| | - Pan Qiao
- 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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35
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Abstract
The widely distributed, essential redox factor pyrroloquinoline quinone (PQQ, methoxatin) (1) was discovered in the mid-1960s. The breadth and depth of its biological effects are steadily being revealed, and understanding its biosynthesis at the genomic level is a continuing process. In this review, aspects of the chemistry, biology, biosynthesis, and commercial production of 1 at the gene level, and some applications, are presented from discovery through to mid-2021.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, Illinois 60202, United States.,Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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36
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Grigorenko VG, Khrenova MG, Andreeva IP, Rubtsova MY, Lev AI, Novikova TS, Detusheva EV, Fursova NK, Dyatlov IA, Egorov AM. Drug Repurposing of the Unithiol: Inhibition of Metallo-β-Lactamases for the Treatment of Carbapenem-Resistant Gram-Negative Bacterial Infections. Int J Mol Sci 2022; 23:ijms23031834. [PMID: 35163756 PMCID: PMC8837113 DOI: 10.3390/ijms23031834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 02/05/2023] Open
Abstract
The increasing antibiotic resistance is a clinical problem worldwide. Numerous Gram-negative bacteria have already become resistant to the most widely used class of antibacterial drugs, β-lactams. One of the main mechanisms is inactivation of β-lactam antibiotics by bacterial β-lactamases. Appearance and spread of these enzymes represent a continuous challenge for the clinical treatment of infections and for the design of new antibiotics and inhibitors. Drug repurposing is a prospective approach for finding new targets for drugs already approved for use. We describe here the inhibitory potency of known detoxifying antidote 2,3-dimercaptopropane-1-sulfonate (unithiol) against metallo-β-lactamases. Unithiol acts as a competitive inhibitor of meropenem hydrolysis by recombinant metallo-β-lactamase NDM-1 with the KI of 16.7 µM. It is an order of magnitude lower than the KI for l-captopril, the inhibitor of angiotensin-converting enzyme approved as a drug for the treatment of hypertension. Phenotypic methods demonstrate that the unithiol inhibits natural metallo-β-lactamases NDM-1 and VIM-2 produced by carbapenem-resistant K. pneumoniae and P. aeruginosa bacterial strains. The 3D full atom structures of unithiol complexes with NDM-1 and VIM-2 are obtained using QM/MM modeling. The thiol group is located between zinc cations of the active site occupying the same place as the catalytic hydroxide anion in the enzyme–substrate complex. The sulfate group forms both a coordination bond with a zinc cation and hydrogen bonds with the positively charged residue, lysine or arginine, responsible for proper orientation of antibiotics upon binding to the active site prior to hydrolysis. Thus, we demonstrate both experimentally and theoretically that the unithiol is a prospective competitive inhibitor of metallo-β-lactamases and it can be utilized in complex therapy together with the known β-lactam antibiotics.
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Affiliation(s)
- Vitaly G. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
- Correspondence: (V.G.G.); (M.G.K.)
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: (V.G.G.); (M.G.K.)
| | - Irina P. Andreeva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
| | - Maya Yu. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
| | - Anastasia I. Lev
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Tatiana S. Novikova
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Elena V. Detusheva
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Nadezhda K. Fursova
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Ivan A. Dyatlov
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Russia; (A.I.L.); (T.S.N.); (E.V.D.); (N.K.F.); (I.A.D.)
| | - Alexey M. Egorov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.P.A.); (M.Y.R.); (A.M.E.)
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37
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López C, Delmonti J, Bonomo RA, Vila AJ. Deciphering the evolution of metallo-β-lactamases: a journey from the test tube to the bacterial periplasm. J Biol Chem 2022; 298:101665. [PMID: 35120928 DOI: 10.1016/j.jbc.2022.101665] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the evolution of metallo-β-lactamases (MBLs) is fundamental to deciphering the mechanistic basis of resistance to carbapenems in pathogenic and opportunistic bacteria. Presently, these MBL producing pathogens are linked to high rates of morbidity and mortality worldwide. However, the study of the biochemical and biophysical features of MBLs in vitro provides an incomplete picture of their evolutionary potential, since this limited and artificial environment disregards the physiological context where evolution and selection take place. Herein, we describe recent efforts aimed to address the evolutionary traits acquired by different clinical variants of MBLs in conditions mimicking their native environment (the bacterial periplasm) and considering whether they are soluble or membrane-bound proteins. This includes addressing the metal content of MBLs within the cell under zinc starvation conditions, and the context provided by different bacterial hosts that result in particular resistance phenotypes. Our analysis highlights recent progress bridging the gap between in vitro and in-cell studies.
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Affiliation(s)
- Carolina López
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Juliana Delmonti
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA; Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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38
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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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Medina FE, Jaña GA. QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fabiola E. Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
- Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, 4051381 Concepción, Chile
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
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Qin Y, Duan X, Peng Y, Rui Y. Rapid detection of a novel B1-β-lactamase gene, blaAFM-1 using a loop-mediated isothermal amplification (LAMP) assay. Ann Clin Microbiol Antimicrob 2021; 20:80. [PMID: 34876146 PMCID: PMC8650397 DOI: 10.1186/s12941-021-00486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022] Open
Abstract
Background BlaAFM-1 (GenBank Accession No. 143105.1) is a new B1 subclass metallo-β-lactamase gene discovered by our group, and isolated from an Alcaligenes faecalis plasmid that renders carbapenem antibiotics ineffective. In this study, we generated a fast and reliable assay for blaAFM-1 detection. Methods We designed optimum loop-mediated isothermal amplification (LAMP) primers and constructed a recombinant plasmid AFM-1 to specifically detect blaAFM-1. Optimal LAMP primers were used to assess sensitivity of the recombinant plasmid AFM-1 and blaAFM-1-supplemented samples (simulated sputum and simulated feces). Fifty two samples, without blaAFM-1, were used to assess LAMP real-time assay specificity; these samples were verified by conventional PCR and sequencing for the absence of blaAFM-1. Three hundred clinical Gram-negative carbapenem-resistant strains were tested by LAMP assay for strains carrying blaAFM-1, which were confirmed by conventional PCR and Sanger sequencing. We calculated the sensitivity and its 95% confidence interval (95% CI), specificity and its 95% CI, and predictive values of the LAMP assay and conventional PCR/sequencing by investigating positive and negative clinical strains. Results The lowest limit of detection for the recombinant plasmid AFM-1 and blaAFM-1-supplemented samples (in both simulated sputum and simulated feces) was 101 copies/reaction. All amplification curves of the 52 blaAFM-1-free bacteria strains were negative, suggesting the LAMP assay had excellent specificity for detecting blaAFM-1. Among the 300 clinical strains, eight were positive for blaAFM-1 using LAMP. These LAMP results were consistent with conventional PCR and Sanger sequencing data. As with conventional PCR/sequencing, the LAMP method exhibits 100% sensitivity (95% CI 59.8–100%) and 100% specificity (95% CI 98.4–100%) for blaAFM-1 detection. The LAMP assay is also time-efficient (1 h) for blaAFM-1 detection. Conclusions We established a new LAMP assay with high sensitivity and specificity to detect the novel B1-β-lactamase gene, blaAFM-1. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-021-00486-z.
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Affiliation(s)
- Yingcheng Qin
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaonv Duan
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yuan Peng
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Cafiero JH, Martini MC, Lozano MJ, Vacca C, Lagares A, Tomatis PE, Del Papa MF. BioF is a novel B2 metallo-β-lactamase from Pseudomonas sp. isolated from an on-farm biopurification system. Environ Microbiol 2021; 24:1247-1262. [PMID: 34725905 DOI: 10.1111/1462-2920.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022]
Abstract
Antimicrobial resistance represents a major global health concern and environmental bacteria are considered a source of resistance genes. Carbapenems are often used as the last antibiotic option to treat multidrug-resistant bacteria. Metallo-β-lactamases (MBLs) are able to render resistance to almost all β-lactam antibiotics, including carbapenems. Unfortunately, there are no inhibitors against MBLs for clinical use. Subclass B2 MBLs are the only enzymes working as strict carbapenemases, under-represented, encoded in chromosome genes and only functional as mono-zinc enzymes. Despite current efforts in MBLs inhibitor development, B2 carbapenemase activity is especially difficult to suppress, even in vitro. In this study we characterized BioF, a novel subclass B2 MBL identified in a new environmental Pseudomonas sp. strain isolated from an on-farm biopurification system (BPS). Although blaBioF is most likely a chromosomal gene, it is found in a genomic island and may represent a step previous to the horizontal transmission of B2 genes. The new B2 MBL is active as a mono-zinc enzyme and is a potent carbapenemase with incipient activity against some cephalosporins. BioF activity is not affected by excess zinc and is only inhibited at high metal chelator concentrations. The discovery and characterization of B2 MBL BioF as a potent carbapenemase in a BPS bacterial isolate emphasizes the importance of exploring antibiotic resistances existing in the environmental microbiota under the influence of human activities before they could emerge clinically.
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Affiliation(s)
- Juan Hilario Cafiero
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - María Carla Martini
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Mauricio Javier Lozano
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Carolina Vacca
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Antonio Lagares
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Pablo Emiliano Tomatis
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario, 2000, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - María Florencia Del Papa
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
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Yahiaoui S, Voos K, Haupenthal J, Wichelhaus TA, Frank D, Weizel L, Rotter M, Brunst S, Kramer JS, Proschak E, Ducho C, Hirsch AKH. N-Aryl mercaptoacetamides as potential multi-target inhibitors of metallo-β-lactamases (MBLs) and the virulence factor LasB from Pseudomonas aeruginosa. RSC Med Chem 2021; 12:1698-1708. [PMID: 34778771 PMCID: PMC8528214 DOI: 10.1039/d1md00187f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/23/2021] [Indexed: 12/18/2022] Open
Abstract
Increasing antimicrobial resistance is evolving to be one of the major threats to public health. To reduce the selection pressure and thus to avoid a fast development of resistance, novel approaches aim to target bacterial virulence instead of growth. Another strategy is to restore the activity of antibiotics already in clinical use. This can be achieved by the inhibition of resistance factors such as metallo-β-lactamases (MBLs). Since MBLs can cleave almost all β-lactam antibiotics, including the “last resort” carbapenems, their inhibition is of utmost importance. Here, we report on the synthesis and in vitro evaluation of N-aryl mercaptoacetamides as inhibitors of both clinically relevant MBLs and the virulence factor LasB from Pseudomonas aeruginosa. All tested N-aryl mercaptoacetamides showed low micromolar to submicromolar activities on the tested enzymes IMP-7, NDM-1 and VIM-1. The two most promising compounds were further examined in NDM-1 expressing Klebsiella pneumoniae isolates, where they restored the full activity of imipenem. Together with their LasB-inhibitory activity in the micromolar range, this class of compounds can now serve as a starting point for a multi-target inhibitor approach against both bacterial resistance and virulence, which is unprecedented in antibacterial drug discovery. Simultaneous inhibition of metallo-β-lactamases (MBLs) and virulence factors such as LasB from Pseudomonas aeruginosa offers a new approach to combat antibiotic-resistant pathogens.![]()
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Affiliation(s)
- Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt Paul-Ehrlich-Straße 40 60596 Frankfurt Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Marco Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8 1 66123 Saarbrücken Germany .,Department of Pharmacy, Saarland University Campus Building E8 1 66123 Saarbrücken Germany
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Melenotte C, Pontarotti P, Pinault L, Mège JL, Devaux C, Raoult D. Could β-Lactam Antibiotics Block Humoral Immunity? Front Immunol 2021; 12:680146. [PMID: 34603278 PMCID: PMC8480522 DOI: 10.3389/fimmu.2021.680146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
It has been reported that treatment with β-lactam antibiotics induces leukopenia and candidemia, worsens the clinical response to anticancer immunotherapy and decreases immune response to vaccination. β-lactamases can cleave β-lactam antibiotics by blocking their activity. Two distincts superfamilies of β-lactamases are described, the serine β-lactamases and the zinc ion dependent metallo-β-lactamases. In human, 18 metallo-β-lactamases encoding genes (hMBLs) have been identified. While the physiological role of most of them remains unknown, it is well established that the SNM1A, B and C proteins are involved in DNA repair. The SNM1C/Artemis protein is precisely associated in the V(D)J segments rearrangement, that leads to immunoglobulin (Ig) and T-cell receptor variable regions, which have a crucial role in the immune response. Thus in humans, SNM1C/Artemis mutation is associated with severe combined immunodeficiency characterized by hypogammaglobulinemia deficient cellular immunity and opportunistic infections. While catalytic site of hMBLs and especially that of the SNM1 family is highly conserved, in vitro studies showed that some β-lactam antibiotics, and precisely third generation of cephalosporin and ampicillin, inhibit the metallo-β-lactamase proteins SNM1A & B and the SNM1C/Artemis protein complex. By analogy, the question arises as to whether β-lactam antibiotics can block the SNM1C/Artemis protein in humans inducing transient immunodeficiency. We reviewed here the literature data supporting this hypothesis based on in silico, in vitro and in vivo evidences. Understanding the impact of β-lactam antibiotics on the immune cell will offer new therapeutic clues and new clinical approaches in oncology, immunology, and infectious diseases.
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Affiliation(s)
- Cléa Melenotte
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Lucile Pinault
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Jean-Louis Mège
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
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Dor S, Prusky D, Afriat-Jurnou L. Bacterial Quorum-Quenching Lactonase Hydrolyzes Fungal Mycotoxin and Reduces Pathogenicity of Penicillium expansum-Suggesting a Mechanism of Bacterial Antagonism. J Fungi (Basel) 2021; 7:jof7100826. [PMID: 34682247 PMCID: PMC8537011 DOI: 10.3390/jof7100826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Penicillium expansum is a necrotrophic wound fungal pathogen that secrets virulence factors to kill host cells including cell wall degrading enzymes (CWDEs), proteases, and mycotoxins such as patulin. During the interaction between P. expansum and its fruit host, these virulence factors are strictly modulated by intrinsic regulators and extrinsic environmental factors. In recent years, there has been a rapid increase in research on the molecular mechanisms of pathogenicity in P. expansum; however, less is known regarding the bacteria–fungal communication in the fruit environment that may affect pathogenicity. Many bacterial species use quorum-sensing (QS), a population density-dependent regulatory mechanism, to modulate the secretion of quorum-sensing signaling molecules (QSMs) as a method to control pathogenicity. N-acyl homoserine lactones (AHLs) are Gram-negative QSMs. Therefore, QS is considered an antivirulence target, and enzymes degrading these QSMs, named quorum-quenching enzymes, have potential antimicrobial properties. Here, we demonstrate that a bacterial AHL lactonase can also efficiently degrade a fungal mycotoxin. The mycotoxin is a lactone, patulin secreted by fungi such as P. expansum. The bacterial lactonase hydrolyzed patulin at high catalytic efficiency, with a kcat value of 0.724 ± 0.077 s−1 and KM value of 116 ± 33.98 μM. The calculated specific activity (kcat/KM) showed a value of 6.21 × 103 s−1M−1. While the incubation of P. expansum spores with the purified lactonase did not inhibit spore germination, it inhibited colonization by the pathogen in apples. Furthermore, adding the purified enzyme to P. expansum culture before infecting apples resulted in reduced expression of genes involved in patulin biosynthesis and fungal cell wall biosynthesis. Some AHL-secreting bacteria also express AHL lactonase. Here, phylogenetic and structural analysis was used to identify putative lactonase in P. expansum. Furthermore, following recombinant expression and purification of the newly identified fungal enzyme, its activity with patulin was verified. These results indicate a possible role for patulin and lactonases in inter-kingdom communication between fungi and bacteria involved in fungal colonization and antagonism and suggest that QQ lactonases can be used as potential antifungal post-harvest treatment.
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Affiliation(s)
- Shlomit Dor
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Dov Prusky
- Department of Postharvest Science, Agricultural Research Organization, Rishon LeZion 7505101, Israel
- Correspondence: (D.P.); (L.A.-J.)
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence: (D.P.); (L.A.-J.)
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Dual Activity BLEG-1 from Bacillus lehensis G1 Revealed Structural Resemblance to B3 Metallo-β-Lactamase and Glyoxalase II: An Insight into Its Enzyme Promiscuity and Evolutionary Divergence. Int J Mol Sci 2021; 22:ijms22179377. [PMID: 34502284 PMCID: PMC8431146 DOI: 10.3390/ijms22179377] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 11/16/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are class B β-lactamases from the metallo-hydrolase-like MBL-fold superfamily which act on a broad range of β-lactam antibiotics. A previous study on BLEG-1 (formerly called Bleg1_2437), a hypothetical protein from Bacillus lehensis G1, revealed sequence similarity and activity to B3 subclass MBLs, despite its evolutionary divergence from these enzymes. Its relatedness to glyoxalase II (GLXII) raises the possibility of its enzymatic promiscuity and unique structural features compared to other MBLs and GLXIIs. This present study highlights that BLEG-1 possessed both MBL and GLXII activities with similar catalytic efficiencies. Its crystal structure revealed highly similar active site configuration to YcbL and GloB GLXIIs from Salmonella enterica, and L1 B3 MBL from Stenotrophomonas maltophilia. However, different from GLXIIs, BLEG-1 has an insertion of an active-site loop, forming a binding cavity similar to B3 MBL at the N-terminal region. We propose that BLEG-1 could possibly have evolved from GLXII and adopted MBL activity through this insertion.
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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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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Nagulapalli Venkata KC, Ellebrecht M, Tripathi SK. Efforts towards the inhibitor design for New Delhi metallo-beta-lactamase (NDM-1). Eur J Med Chem 2021; 225:113747. [PMID: 34391033 DOI: 10.1016/j.ejmech.2021.113747] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial stewardship is imperative when treating bacterial infections because the misuse and overuse of antibiotics have caused pathogens to develop life-threatening resistance mechanisms. The New Delhi metallo-beta-lactamase (NDM-1) is one of many enzymes that enable bacterial resistance. NDM-1 is a more recently discovered beta-lactamase with the ability to inactivate a wide range of beta-lactam antibiotics. Multiple NDM-1 inhibitors have been designed and tested; however, due to the complexity of the NDM-1 active site, there is currently no inhibitor on the market. Consequently, an infection caused by bacteria possessing the gene for the NDM-1 enzyme is a serious and potentially fatal complication. An abundance of research has been invested over the past decade in search of an NDM-1 inhibitor. This review aims to summarize various NDM-1 inhibitor designs that have been developed in recent years.
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Affiliation(s)
| | - Morgan Ellebrecht
- St. Louis College of Pharmacy, University of Health Sciences and Pharmacy, St. Louis, MO, 63110, USA
| | - Siddharth K Tripathi
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
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Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active Site Glutamic Acid. Antimicrob Agents Chemother 2021; 65:e0093621. [PMID: 34310207 DOI: 10.1128/aac.00936-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations were reported previously. Here, we describe the structure and kinetic properties of the first example (SIE-1) of a fourth variant containing the EHH/DHH active site motif (B3-E). SIE-1 was identified in the hexachlorocyclohexane-degrading bacterium Sphingobium indicum, and kinetic analyses demonstrate that although it is active against a wide range of antibiotics its efficiency is lower than that of other B3 MBLs, but with improved efficiency towards cephalosporins relative to other β-lactam substrates. The overall fold of SIE-1 is characteristic of the MBLs; the notable variation is observed in the Zn1 site due to the replacement of the canonical His116 by a glutamate. The unusual preference of SIE-1 for cephalosporins and its occurrence in a widespread environmental organism suggests scope for increased MBL-mediated β-lactam resistance. It is thus relevant to include SIE-1 into MBL inhibitor design studies to widen the therapeutic scope of much needed anti-resistance drugs.
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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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