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Lee JH, Kim SG, Jang KM, Shin K, Jin H, Kim DW, Jeong BC, Lee SH. Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases. J Enzyme Inhib Med Chem 2024; 39:2318830. [PMID: 38488135 PMCID: PMC10946278 DOI: 10.1080/14756366.2024.2318830] [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: 12/30/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang-Gyu Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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Luo H, Yang Z, Lei T, Li C, Zhou Z, Wang M, Zhu D, Li P, Cheng A. RATA: A novel class A carbapenemase with broad geographic distribution and potential for global spread. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172873. [PMID: 38692330 DOI: 10.1016/j.scitotenv.2024.172873] [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: 12/28/2023] [Revised: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Carbapenem resistance's global proliferation poses a significant public health challenge. The primary resistance mechanism is carbapenemase production. In this study, we discovered a novel carbapenemase, RATA, located on the chromosome of Riemerella anatipestifer isolates. This enzyme shares ≤52 % amino acid sequence identity with other known β-lactamases. Antimicrobial susceptibility tests and kinetic assays demonstrated that RATA could hydrolyze not only penicillins and extended-spectrum cephalosporins but also monobactams, cephamycins, and carbapenems. Furthermore, its activity was readily inhibited by β-lactamase inhibitors. Bioinformatic analysis revealed 46 blaRATA-like genes encoding 27 variants in the NCBI database, involving 21 different species, including pathogens, host-associated bacteria, and environmental isolates. Notably, blaRATA-positive strains were globally distributed and primarily collected from marine environments. Concurrently, taxonomic analysis and GC content analysis indicated that blaRATA orthologue genes were predominantly located on the chromosomes of Flavobacteriaceae and shared a similar GC content as Flavobacteriaceae. Although no explicit mobile genetic elements were identified by genetic environment analysis, blaRATA-2 possessed the ability of horizontal transfer in R. anatipestifer via natural transformation. This work's data suggest that RATA is a new chromosome-encoded class A carbapenemase, and Flavobacteriaceae from marine environments could be the primary reservoir of the blaRATA gene.
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Affiliation(s)
- Hongyan Luo
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Ting Lei
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Caixia Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Zuoyong Zhou
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Pei Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China; National Center of Technology Innovation for Pigs, Rongchang, Chongqing, China.
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
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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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Javid A, Ahmed M. A computational odyssey: uncovering classical β-lactamase inhibitors in dry fruits. J Biomol Struct Dyn 2024; 42:4578-4604. [PMID: 37288775 DOI: 10.1080/07391102.2023.2220817] [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: 01/29/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
In the antibacterial arsenal, β-lactams have held a prominent position, but increasing resistance due to unauthorized use and genetic factors requires new strategies. Combining β-lactamase inhibitors with broad-spectrum β-lactams proves effective in combating this resistance. ESBL producers demand new inhibitors, leading to the exploration of plant-derived secondary metabolites for potent β-lactam antibiotics or alternative inhibitors. Using virtual screening, molecular docking, ADMET analysis, and molecular dynamic simulation, this study actively analyzed the inhibitory activity of figs, cashews, walnuts, and peanuts against SHV-1, NDM-1, KPC-2, and OXA-48 β-lactamases. Using AutoDock Vina, the docking affinities of various compounds for target enzymes were initially screened, revealing 12 bioactive compounds with higher affinities for the target enzymes compared to Avibactam and Tazobactam. Top-scoring metabolites, including Oleanolic acid, Protocatechuic acid, and Tannin, were subjected to MD simulation studies to further analyze the stability of the docked complexes using WebGro. The simulation coordinates, in terms of RMSD, RMSF, SASA, Rg, and hydrogen bonds formed, showed that these phytocompounds are stable enough to retain in the active sites at various orientations. The PCA and FEL analysis also showed the stability of the dynamic motion of Cα residues of phytochemical-bound enzymes. The pharmacokinetic analysis of the top phytochemicals was performed to analyze their bioavailability and toxicity. This study provides new insights into the therapeutic potential of phytochemicals of selected dry fruits and contributes to future experimental studies to identify βL inhibitors from plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amina Javid
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Mehboob Ahmed
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
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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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de Souza J, Vieira AZ, Dos Santos HG, Faoro H. Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group. BMC Genomics 2024; 25:508. [PMID: 38778284 PMCID: PMC11112869 DOI: 10.1186/s12864-024-10410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
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Affiliation(s)
- Joyce de Souza
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | - Alexandre Zanatta Vieira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | | | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil.
- Department of Microbiology, Infectious Disease and Immunology, CHU de Quebec Research Center, University Laval, Quebec, QC, G1V 0A6, Canada.
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Zakhour J, El Ayoubi LW, Kanj SS. Metallo-beta-lactamases: mechanisms, treatment challenges, and future prospects. Expert Rev Anti Infect Ther 2024; 22:189-201. [PMID: 38275276 DOI: 10.1080/14787210.2024.2311213] [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: 09/30/2023] [Accepted: 01/24/2024] [Indexed: 01/27/2024]
Abstract
INTRODUCTION Metallo-beta-lactamases (MBLs) are responsible for resistance to almost all beta-lactam antibiotics. Found predominantly in Gram-negative bacteria, they severely limit treatment options. Understanding the epidemiology, risk factors, treatment, and prevention of infections caused by MBL-producing organisms is essential to reduce their burden. AREAS COVERED The origins and structure of MBLs are discussed. We describe the mechanisms of action that differentiate MBLs from other beta-lactamases. We discuss the global epidemiology of MBL-producing organisms and their impact on patients' outcomes. By exposing the mechanisms of transmission of MBLs among bacterial populations, we emphasize the importance of infection prevention and control. EXPERT OPINION MBLs are spreading globally and challenging the majority of available antibacterial agents. Genotypic tests play an important role in the identification of MBL production. Phenotypic tests are less specific but may be used in low-resource settings, where MBLs are more predominant. Infection prevention and control are critical to reduce the spread of organisms producing MBL in healthcare systems. New combinations such as avibactam-aztreonam and new agents such as cefiderocol have shown promising results for the treatment of infections caused by MBL-producing organisms. New antibiotic and non-antibiotic agents are being developed and may improve the management of infections caused by MBL-producing organisms.
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Affiliation(s)
- Johnny Zakhour
- Internal Medicine Department, Henry Ford Hospital, Detroit, MI, USA
| | - L'Emir Wassim El Ayoubi
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Souha S Kanj
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Oliver A, Rojo-Molinero E, Arca-Suarez J, Beşli Y, Bogaerts P, Cantón R, Cimen C, Croughs PD, Denis O, Giske CG, Graells T, Daniel Huang TD, Iorga BI, Karatuna O, Kocsis B, Kronenberg A, López-Causapé C, Malhotra-Kumar S, Martínez LM, Mazzariol A, Meyer S, Naas T, Notermans DW, Oteo-Iglesias J, Pedersen T, Pirš M, Poeta P, Poirel L, Pournaras S, Sundsfjord A, Szabó D, Tambić-Andrašević A, Vatcheva-Dobrevska R, Vitkauskienė A, Jeannot K. Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group. Clin Microbiol Infect 2024; 30:469-480. [PMID: 38160753 DOI: 10.1016/j.cmi.2023.12.026] [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: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
SCOPE Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum β-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved β-lactams and β-lactam/β-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles. METHODS To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members. QUESTIONS ADDRESSED IN THE POSITION PAPER To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on β-lactams, (b) the susceptibility profiles associated with the most relevant β-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms. IMPLICATION The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.
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Affiliation(s)
- Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Estrella Rojo-Molinero
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Arca-Suarez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Yeşim Beşli
- Department of Medical Microbiology, Amerikan Hastanesi, Istanbul, Turkey
| | - Pierre Bogaerts
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Rafael Cantón
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany; Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter D Croughs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Olivier Denis
- Department of Microbiology, CHU Namur Site-Godinne, Université Catholique de Louvain, Yvoir, Belgium; Ecole de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Tíscar Graells
- Department of Neurobiology, Care Sciences and Society (NVS), Division of Family Medicine and Primary Care, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Te-Din Daniel Huang
- National Center for Antimicrobial Resistance in Gram, CHU UCL Namur, Yvoir, Belgium
| | - Bogdan I Iorga
- CNRS, Institut de Chimie des Substances Naturelles, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Béla Kocsis
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Andreas Kronenberg
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Luis Martínez Martínez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Annarita Mazzariol
- Microbiology and Virology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Sylvain Meyer
- INSERM UMR 1092 and Université of Limoges, Limoges, France
| | - Thierry Naas
- Laboratoire Associé du Centre National de Référence de la Résistance aux Antibiotiques: Entérobactéries Résistantes aux Carbapénèmes, Le Kremlin-Bicêtre, France; Équipe INSERM ReSIST, Faculté de Médecine, Université Paris-Saclay, Paris, France
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Mateja Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Patricia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Portugal; Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; University of Trás-os-Montes and Alto Douro, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Vila Real, Portugal
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland; University of Fribourg, Swiss National Reference Center for Emerging Antibiotic Resistance, Fribourg, Switzerland
| | - Spyros Pournaras
- Laboratory of Clinical Microbiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dora Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary; Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Arjana Tambić-Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Zagreb, Croatia; School of Dental Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Astra Vitkauskienė
- Department of Laboratory Medicine, Faculty of Medicine, Medical Academy, Lithuanian University of Health Science, Kaunas, Lithuania
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France; Laboratoire associé du Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France; Chrono-environnement UMR 6249, CNRS, Université Franche-Comté, Besançon, France
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9
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Papale F, Not F, Bapteste É, Haraoui LP. The evosystem: A centerpiece for evolutionary studies. Bioessays 2024; 46:e2300169. [PMID: 38344836 DOI: 10.1002/bies.202300169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 02/25/2024]
Abstract
In this paper, we redefine the target of evolutionary explanations by proposing the "evosystem" as an alternative to populations, lineages and species. Evosystems account for changes in the distribution of heritable variation within individual Darwinian populations (evolution by natural selection, drift, or constructive neutral evolution), but also for changes in the networks of interactions within or between Darwinian populations and changes in the abiotic environment (whether these changes are caused by the organic entities or not). The evosystem can thereby become a centerpiece for a redefined evolutionary science, that is, evolutionary studies, that apprehends through a single framework the variety of evolutionary processes that lie at various scales. To illustrate the importance of this broadened perspective on evolution, we use a case of antimicrobial resistance evolution: the spread of the blaNDM gene family and the related resistance to carbapenem antibiotics observed globally, and show how evolutionary studies can contribute to answering contemporary socially relevant challenges.
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Affiliation(s)
- François Papale
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- Faculty of Philosophy, Université Laval, Quebec, Canada
| | - Fabrice Not
- CNRS, Adaptation and Diversity in Marine Environment laboratory (AD2M-UMR7144), Sorbonne University, Roscoff, France
| | - Éric Bapteste
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Louis-Patrick Haraoui
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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10
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Ben Abderrazek R, Hamdi E, Piccirilli A, Dhaouadi S, Muyldermans S, Perilli M, Bouhaouala-Zahar B. Camel-Derived Nanobodies as Potent Inhibitors of New Delhi Metallo-β-Lactamase-1 Enzyme. Molecules 2024; 29:1431. [PMID: 38611711 PMCID: PMC11013165 DOI: 10.3390/molecules29071431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/14/2024] Open
Abstract
The injudicious usage of antibiotics during infections caused by Gram-negative bacteria leads to the emergence of β-lactamases. Among them, the NDM-1 enzyme poses a serious threat to human health. Developing new antibiotics or inhibiting β-lactamases might become essential to reduce and prevent bacterial infections. Nanobodies (Nbs), the smallest antigen-binding single-domain fragments derived from Camelidae heavy-chain-only antibodies, targeting enzymes, are innovative alternatives to develop effective inhibitors. The biopanning of an immune VHH library after phage display has helped to retrieve recombinant antibody fragments with high inhibitory activity against recombinant-NDM-1 enzyme. Nb02NDM-1, Nb12NDM-1, and Nb17NDM-1 behaved as uncompetitive inhibitors against NDM-1 with Ki values in the nM range. Remarkably, IC50 values of 25.0 nM and 8.5 nM were noted for Nb02NDM-1 and Nb17NDM-1, respectively. The promising inhibition of NDM-1 by Nbs highlights their potential application in combating particular Gram-negative infections.
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Affiliation(s)
- Rahma Ben Abderrazek
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
| | - Emna Hamdi
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Alessandra Piccirilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Sayda Dhaouadi
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleenlaan, 9, 1050 Brussels, Belgium;
| | - Mariagrazia Perilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Veteoio Coppito, 67100 L’Aquila, Italy; (A.P.); (M.P.)
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Biomolécules Venins et Applications Théranostiques, Institut Pasteur Tunis, 13 Place Pasteur, Tunisie Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia; (E.H.); (S.D.); (B.B.-Z.)
- Faculté de Médecine de Tunis, Université Tunis El Manar, B.P N 93, Tunis 1068, Tunisia
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11
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Dong S, Zhao Z, Tang H, Li G, Pan J, Gu X, Jiang J, Xiao L, Scapin G, Hunter DN, Yang D, Huang Y, Bennett F, Yang SW, Mandal M, Tang H, Su J, Tudge C, deJesus RK, Ding FX, Lombardo M, Hicks JD, Fischmann T, Mirza A, Dayananth P, Painter RE, Villafania A, Garlisi CG, Zhang R, Mayhood TW, Si Q, Li N, Amin RP, Bhatt B, Chen F, Regan CP, Regan H, Lin X, Wu J, Leithead A, Pollack SR, Scott JD, Nargund RP, Therien AG, Black T, Young K, Pasternak A. Structure Guided Discovery of Novel Pan Metallo-β-Lactamase Inhibitors with Improved Gram-Negative Bacterial Cell Penetration. J Med Chem 2024; 67:3400-3418. [PMID: 38387069 DOI: 10.1021/acs.jmedchem.3c01614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The use of β-lactam (BL) and β-lactamase inhibitor combination to overcome BL antibiotic resistance has been validated through clinically approved drug products. However, unmet medical needs still exist for the treatment of infections caused by Gram-negative (GN) bacteria expressing metallo-β-lactamases. Previously, we reported our effort to discover pan inhibitors of three main families in this class: IMP, VIM, and NDM. Herein, we describe our work to improve the GN coverage spectrum in combination with imipenem and relebactam. This was achieved through structure- and property-based optimization to tackle the GN cell penetration and efflux challenges. A significant discovery was made that inhibition of both VIM alleles, VIM-1 and VIM-2, is essential for broad GN coverage, especially against VIM-producing P. aeruginosa. In addition, pharmacokinetics and nonclinical safety profiles were investigated for select compounds. Key findings from this drug discovery campaign laid the foundation for further lead optimization toward identification of preclinical candidates.
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Affiliation(s)
- Shuzhi Dong
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhiqiang Zhao
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haiqun Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Guoqing Li
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jianping Pan
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xin Gu
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jinlong Jiang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Li Xiao
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Giovanna Scapin
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David N Hunter
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dexi Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuhua Huang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Frank Bennett
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shu-Wei Yang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mihirbaran Mandal
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Haifeng Tang
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Su
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Clare Tudge
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Fa-Xiang Ding
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew Lombardo
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jacqueline D Hicks
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Asra Mirza
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Priya Dayananth
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Ronald E Painter
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Artjohn Villafania
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Charles G Garlisi
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rumin Zhang
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Qian Si
- Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nianyu Li
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rupesh P Amin
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Bhavana Bhatt
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Feifei Chen
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Christopher P Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Hillary Regan
- Nonclinical Drug Safety, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Xinjie Lin
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jin Wu
- Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew Leithead
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Scott R Pollack
- Discovery Process Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jack D Scott
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ravi P Nargund
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Alex G Therien
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02139, United States
| | - Todd Black
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Katherine Young
- Antibacterial/Antifungal, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Alexander Pasternak
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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12
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Villamil V, Rossi MA, Mojica MF, Hinchliffe P, Martínez V, Castillo V, Saiz C, Banchio C, Macías MA, Spencer J, Bonomo RA, Vila A, Moreno DM, Mahler G. Rational Design of Benzobisheterocycle Metallo-β-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes. J Med Chem 2024; 67:3795-3812. [PMID: 38373290 DOI: 10.1021/acs.jmedchem.3c02209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Antimicrobial resistance is a global public health threat. Metallo-β-lactamases (MBLs) inactivate β-lactam antibiotics, including carbapenems, are disseminating among Gram-negative bacteria, and lack clinically useful inhibitors. The evolving bisthiazolidine (BTZ) scaffold inhibits all three MBL subclasses (B1-B3). We report design, synthesis, and evaluation of BTZ analogues. Structure-activity relationships identified the BTZ thiol as essential, while carboxylate is replaceable, with its removal enhancing potency by facilitating hydrophobic interactions within the MBL active site. While the introduction of a flexible aromatic ring is neutral or detrimental for inhibition, a rigid (fused) ring generated nM benzobisheterocycle (BBH) inhibitors that potentiated carbapenems against MBL-producing strains. Crystallography of BBH:MBL complexes identified hydrophobic interactions as the basis of potency toward B1 MBLs. These data underscore BTZs as versatile, potent broad-spectrum MBL inhibitors (with activity extending to enzymes refractory to other inhibitors) and provide a rational approach to further improve the tricyclic BBH scaffold.
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Affiliation(s)
- Valentina Villamil
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay
| | - Maria-Agustina Rossi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Maria F Mojica
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 44106 Cleveland, Ohio, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), 44106 Cleveland, Ohio, United States
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, U.K
| | - Verónica Martínez
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay
| | - Valerie Castillo
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay
| | - Cecilia Saiz
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay
| | - Claudia Banchio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - Mario A Macías
- Crystallography and Chemistry of Materials, CrisQuimMat, Department of Chemistry, Universidad de los Andes, 111711 Bogotá, Colombia
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, U.K
| | - Robert A Bonomo
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 44106 Cleveland, Ohio, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), 44106 Cleveland, Ohio, United States
- Departments of Medicine, Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 44106 Cleveland, Ohio, United States
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 44106 Cleveland, Ohio, United States
- Clinical Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 44106 Cleveland, Ohio, United States
| | - Alejandro Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), 44106 Cleveland, Ohio, United States
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - Diego M Moreno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
- Instituto de Química Rosario (IQUIR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Graciela Mahler
- Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay
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13
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Wang Y, Sapula SA, Whittall JJ, Blaikie JM, Lomovskaya O, Venter H. Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics. Commun Biol 2024; 7:282. [PMID: 38454015 PMCID: PMC10920655 DOI: 10.1038/s42003-024-05940-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
The increasing rate of carbapenem-resistant bacteria within healthcare environments is an issue of great concern that needs urgent attention. This resistance is driven by metallo-β-lactamases (MBLs), which can catalyse the hydrolysis of almost all clinically available β-lactams and are resistant to all the clinically utilized β-lactamase inhibitors. In this study, an uncharacterized MBL is identified in a multidrug resistant isolate of the opportunistic pathogen, Chryseobacterium indologenes. Sequence analysis predicts this MBL (CIM-1) to be a lipoprotein with an atypical lipobox. Characterization of CIM-1 reveals it to be a high-affinity carbapenemase with a broad spectrum of activity that includes all cephalosporins and carbapenems. Results also shown that CIM-1 is potentially a membrane-associated MBL with an uncharacterized lipobox. Using prediction tools, we also identify more potentially lipidated MBLs with non-canonical lipoboxes highlighting the necessity of further investigation of lipidated MBLs.
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Affiliation(s)
- Yu Wang
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- School of Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Sylvia A Sapula
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Jonathan J Whittall
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Jack M Blaikie
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | | | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia.
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14
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Araten AH, Brooks RS, Choi SDW, Esguerra LL, Savchyn D, Wu EJ, Leon G, Sniezek KJ, Brynildsen MP. Cephalosporin resistance, tolerance, and approaches to improve their activities. J Antibiot (Tokyo) 2024; 77:135-146. [PMID: 38114565 DOI: 10.1038/s41429-023-00687-y] [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: 07/11/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023]
Abstract
Cephalosporins comprise a β-lactam antibiotic class whose first members were discovered in 1945 from the fungus Cephalosporium acremonium. Their clinical use for Gram-negative bacterial infections is widespread due to their ability to traverse outer membranes through porins to gain access to the periplasm and disrupt peptidoglycan synthesis. More recent members of the cephalosporin class are administered as last resort treatments for complicated urinary tract infections, MRSA, and other multi-drug resistant pathogens, such as Neisseria gonorrhoeae. Unfortunately, there has been a global increase in cephalosporin-resistant strains, heteroresistance to this drug class has been a topic of increasing concern, and tolerance and persistence are recognized as potential causes of cephalosporin treatment failure. In this review, we summarize the cephalosporin antibiotic class from discovery to their mechanisms of action, and discuss the causes of cephalosporin treatment failure, which include resistance, tolerance, and phenomena when those qualities are exhibited by only small subpopulations of bacterial cultures (heteroresistance and persistence). Further, we discuss how recent efforts with cephalosporin conjugates and combination treatments aim to reinvigorate this antibiotic class.
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Affiliation(s)
- Alison H Araten
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel S Brooks
- Department of English, Princeton University, Princeton, NJ, USA
| | - Sarah D W Choi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laura L Esguerra
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Diana Savchyn
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Emily J Wu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Katherine J Sniezek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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15
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Elena A, Cejas D, Gutkind G, Radice M. Genomic characterization of bla VIM-11-harbouring plasmids recovered from Pseudomonas aeruginosa. J Glob Antimicrob Resist 2024; 36:190-192. [PMID: 38154753 DOI: 10.1016/j.jgar.2023.12.014] [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: 08/25/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023] Open
Abstract
OBJECTIVES To the best of our knowledge, no genomic descriptions of blaVIM-11-harbouring plasmids are available in literature so far. The aim of this study was to describe the genomic features of three blaVIM-11-harbouring plasmids recovered from Pseudomonas aeruginosa isolated in Argentina in different periods. METHODS blaVIM-11-harbouring plasmids from three clinical P. aeruginosa isolates were transferred by transformation into P. aeruginosa PAO-1. Then, genomic DNA of these transformants was extracted and sequenced using NovaSeq 6000 System-Illumina. De novo assemblies were generated using Unicycler program and reads were mapped against a reference genome of P. aeruginosa PAO-1. Plasmids sequences were predicted identifying the reads that did not map the reference sequence of PAO-1. These reads were recovered and assembled de novo. In silico predictions were carried out using bioinformatics tools. RESULTS One Plasmid (pP6VIM-11) was distributed in 2 contigs, a second plasmid (pPOta2VIM-11) was found in a single contig, and the last one (pP936401VIM-11) was fragmented into 4 contigs. pP6VIM-11 and pPOta2VIM-11 belonged to the IncP-1β group, displaying 64% of coverage and 83.9% of identity among them. pP936401VIM-1 plasmid corresponded to the IncN group. The bioinformatic analysis revealed that blaVIM-11 was located in a class 1 integron, flanked by insertion sequences, exhibiting potential for its dissemination. However, none of the plasmids were conjugative. CONCLUSION This study corresponded to the first description and deposit of blaVIM-11-harbouring plasmids in P. aeruginosa, which expands the limited knowledge about their molecular epidemiology.
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Affiliation(s)
- Alan Elena
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina; Institute of Hydrobiology, Technische Universität Dresden, Germany
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcela Radice
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina
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16
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Ding L, Yang Z, Sun B. Understanding blaNDM-1 gene regulation in CRKP infections: toward novel antimicrobial strategies for hospital-acquired pneumonia. Mol Med 2024; 30:29. [PMID: 38395744 PMCID: PMC10893750 DOI: 10.1186/s10020-024-00794-y] [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: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The escalating challenge of Carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospital-acquired pneumonia (HAP) is closely linked to the blaNDM-1 gene. This study explores the regulatory mechanisms of blaNDM-1 expression and aims to enhance antibacterial tactics to counteract the spread and infection of resistant bacteria. METHODS KP and CRKP strains were isolated from HAP patients' blood samples. Transcriptomic sequencing (RNA-seq) identified significant upregulation of blaNDM-1 gene expression in CRKP strains. Bioinformatics analysis revealed blaNDM-1 gene involvement in beta-lactam resistance pathways. CRISPR-Cas9 was used to delete the blaNDM-1 gene, restoring sensitivity. In vitro and in vivo experiments demonstrated enhanced efficacy with Imipenem and Thanatin or Subatan combination therapy. RESULTS KP and CRKP strains were isolated with significant upregulation of blaNDM-1 in CRKP strains identified by RNA-seq. The Beta-lactam resistance pathway was implicated in bioinformatics analysis. Knockout of blaNDM-1 reinstated sensitivity in CRKP strains. Further, co-treatment with Imipenem, Thanatin, or Subactam markedly improved antimicrobial effectiveness. CONCLUSION Silencing blaNDM-1 in CRKP strains from HAP patients weakens their Carbapenem resistance and optimizes antibacterial strategies. These results provide new theoretical insights and practical methods for treating resistant bacterial infections.
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Affiliation(s)
- Liang Ding
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Zheng Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Baier Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China.
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17
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Kondratieva A, Palica K, Frøhlich C, Hovd RR, Leiros HKS, Erdelyi M, Bayer A. Fluorinated captopril analogues inhibit metallo-β-lactamases and facilitate structure determination of NDM-1 binding pose. Eur J Med Chem 2024; 266:116140. [PMID: 38242072 DOI: 10.1016/j.ejmech.2024.116140] [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: 10/26/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
Bacterial resistance to the majority of clinically used β-lactam antibiotics is a global health threat and, consequently, the driving force for the development of metallo-β-lactamase (MBL) inhibitors. The rapid evolution of new MBLs calls for new strategies and tools for inhibitor development. In this study, we designed and developed a series of trifluoromethylated captopril analogues as probes for structural studies of enzyme-inhibitor binding. The new compounds showed activity comparable to the non-fluorinated inhibitors against the New Delhi Metallo-β-lactamase-1 (NDM-1). The most active compound, a derivative of D-captopril, exhibited an IC50 value of 0.3 μM. Several compounds demonstrated synergistic effects, restoring the effect of meropenem and reducing the minimum inhibitory concentration (MIC) values in NDM-1 (up to 64-fold), VIM-2 (up to 8-fold) and IMP-26 (up to 8-fold) harbouring Escherichia coli. NMR spectroscopy and molecular docking of one representative inhibitor determined the binding pose in NDM-1, demonstrating that fluorinated analogues of inhibitors are a valuable tool for structural studies of MBL-inhibitor complexes.
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Affiliation(s)
- Alexandra Kondratieva
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Katarzyna Palica
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University, 752 37, Uppsala, Sweden
| | - Christopher Frøhlich
- Department of Pharmacy, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Mate Erdelyi
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University, 752 37, Uppsala, Sweden
| | - Annette Bayer
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway.
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18
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Le Terrier C, Viguier C, Nordmann P, Vila AJ, Poirel L. Relative inhibitory activities of the broad-spectrum β-lactamase inhibitor taniborbactam against metallo-β-lactamases. Antimicrob Agents Chemother 2024; 68:e0099123. [PMID: 38047644 PMCID: PMC10848752 DOI: 10.1128/aac.00991-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/07/2023] [Indexed: 12/05/2023] Open
Abstract
Taniborbactam (TAN) is a novel broad-spectrum β-lactamase inhibitor with significant activity against subclass B1 metallo-β-lactamases (MBLs). Here, we showed that TAN exhibited an overall excellent activity against B1 MBLs including most NDM- and VIM-like as well as SPM-1, GIM-1, and DIM-1 enzymes, but not against SIM-1. Noteworthy, VIM-1-like enzymes (particularly VIM-83) were less inhibited by TAN than VIM-2-like. Like NDM-9, NDM-30 (also differing from NDM-1 by a single amino acid substitution) was resistant to TAN.
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Affiliation(s)
- Christophe Le Terrier
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Division of Intensive Care Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Clément Viguier
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Infectious Disease Department, University Hospital of Toulouse, Toulouse, France
| | - Patrice Nordmann
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Alejandro J. Vila
- 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
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Laurent Poirel
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
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19
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Ono D, Mojica MF, Bethel CR, Ishii Y, Drusin SI, Moreno DM, Vila AJ, Bonomo RA. Structural role of K224 in taniborbactam inhibition of NDM-1. Antimicrob Agents Chemother 2024; 68:e0133223. [PMID: 38174924 PMCID: PMC10848753 DOI: 10.1128/aac.01332-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Taniborbactam (TAN; VNRX-5133) is a novel bicyclic boronic acid β-lactamase inhibitor (BLI) being developed in combination with cefepime (FEP). TAN inhibits both serine and some metallo-β-lactamases. Previously, the substitution R228L in VIM-24 was shown to increase activity against oxyimino-cephalosporins like FEP and ceftazidime (CAZ). We hypothesized that substitutions at K224, the homologous position in NDM-1, could impact FEP/TAN resistance. To evaluate this, a library of codon-optimized NDM K224X clones for minimum inhibitory concentration (MIC) measurements was constructed; steady-state kinetics and molecular docking simulations were next performed. Surprisingly, our investigation revealed that the addition of TAN restored FEP susceptibility only for NDM-1, as the MICs for the other 19 K224X variants remained comparable to those of FEP alone. Moreover, compared to NDM-1, all K224X variants displayed significantly lower MICs for imipenem, tebipenem, and cefiderocol (32-, 133-, and 33-fold lower, respectively). In contrast, susceptibility to CAZ was mostly unaffected. Kinetic assays with the K224I variant, the only variant with hydrolytic activity to FEP comparable to NDM-1, confirmed that the inhibitory capacity of TAN was modestly compromised (IC50 0.01 µM vs 0.14 µM for NDM-1). Lastly, structural modeling and docking simulations of TAN in NDM-1 and in the K224I variant revealed that the hydrogen bond between TAN's carboxylate with K224 is essential for the productive binding of TAN to the NDM-1 active site. In addition to the report of NDM-9 (E149K) as FEP/TAN resistant, this study demonstrates the fundamental role of single amino acid substitutions in the inhibition of NDM-1 by TAN.
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Affiliation(s)
- Daisuke Ono
- Department of Medicine, Division of Infectious Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Maria F. Mojica
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Salvador I. Drusin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Química Rosario (IQUIR), CONICET, Rosario, Argentina
| | - Diego M. Moreno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Química Rosario (IQUIR), CONICET, Rosario, Argentina
| | - Alejandro J. Vila
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Robert A. Bonomo
- Department of Medicine, Division of Infectious Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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20
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Tamma PD, Munita JM. The metallo-β-lactamases strike back: emergence of taniborbactam escape variants. Antimicrob Agents Chemother 2024; 68:e0151023. [PMID: 38174925 PMCID: PMC10848767 DOI: 10.1128/aac.01510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Metallo-β-lactamases (MBLs) have evolved relatively rapidly to become an international public health threat. There are no clinically available β-lactamase inhibitors with activity against MBLs. This may change with the introduction of cefepime-taniborbactam. Herein, we review three manuscripts (S. I. Drusin, C. Le Terrier, L. Poirel, R. A. Bonomo, et al., Antimicrob Agents Chemother 68:e01168-23, 2024, https://doi.org/10.1128/aac.01168-23; C. Le Terrier, C. Viguier, P. Nordmann, A. J. Vila, and L. Poirel, Antimicrob Agents Chemother 68:e00991-23, 2024, https://doi.org/10.1128/aac.00991-23; D. Ono, M. F. Mojica, C. R. Bethel, Y. Ishii, et al., Antimicrob Agents Chemother 68:e01332-23, 2024, https://doi.org/10.1128/aac.01332-23) in which investigators describe elegant experiments to explore MBL/taniborbactam interactions and modifications to MBLs, in response, to reduce the affinity of taniborbactam. Challenges with MBL inhibition will not disappear; rather, they will evolve commensurate with advancements in medicinal chemistry.
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Affiliation(s)
- Pranita D. Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jose M. Munita
- Genomics and Resistant Microbes Group, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
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21
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Drusin SI, Le Terrier C, Poirel L, Bonomo RA, Vila AJ, Moreno DM. Structural basis of metallo-β-lactamase resistance to taniborbactam. Antimicrob Agents Chemother 2024; 68:e0116823. [PMID: 38063400 PMCID: PMC10848773 DOI: 10.1128/aac.01168-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024] Open
Abstract
The design of inhibitors against metallo-β-lactamases (MBLs), the largest family of carbapenemases, has been a strategic goal in designing novel antimicrobial therapies. In this regard, the development of bicyclic boronates, such as taniborbactam (TAN) and xeruborbactam, is a major achievement that may help in overcoming the threat of MBL-producing and carbapenem-resistant Gram-negative pathogens. Of concern, a recent report has shown that New Delhi MBL-9 (NDM-9) escapes the inhibitory action of TAN by a single amino acid substitution with respect to New Delhi MBL-1 (NDM-1), the most widely disseminated MBL. Here, we report a docking and computational analysis that identifies that "escape variants" against TAN can arise by disruption of the electrostatic interaction of negative charges in the active site loops of MBLs with the N-(2-aminoethyl)cyclohexylamine side chain of TAN. These changes result in non-productive binding modes of TAN that preclude reaction with the MBLs, a phenomenon that is not restricted to NDM-9. This analysis demonstrates that single amino acid substitutions in non-essential residues in MBL loops can unexpectedly elicit resistance to TAN.
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Affiliation(s)
- Salvador I. Drusin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Christophe Le Terrier
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Division of Intensive care unit, University hospitals of Geneva, Geneva, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Robert A. Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J. Vila
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- CONICET, Universidad Nacional de Rosario, Instituto de Biología Molecular y Celular de Rosario (IBR), Rosario, Argentina
| | - Diego M. Moreno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- CONICET, Universidad Nacional de Rosario, Instituto de Química Rosario (IQUIR), Rosario, Argentina
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22
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Zheng Z, Cheng Q, Ye L, Xu Y, Chen S. Characterization of VIM-71, a novel VIM-type metallo-β-lactamase variant encoded by an integrative and conjugative element recovered from a Vibrio alginolyticus strain in China. Microbiol Res 2024; 278:127532. [PMID: 37879253 DOI: 10.1016/j.micres.2023.127532] [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] [Received: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
A novel VIM-type metallo-β-lactamase variant, VIM-71, which is encoded by a multidrug-resistant Vibrio alginolyticus strain recovered from a shrimp sample in China, was identified. Compared to VIM-1, VIM-71 differs in 22 amino acid positions based on the primary protein sequence and confers a similar resistance profile to penicillins, but the level of resistance to carbapenems encoded by this enzyme was lower than that of VIM-1. The blaVIM-71 gene was found located in an integrative and conjugative element of the SXT/R391 family in the chromosome. These findings implied that genetic elements that encode clinically important carbapenemases continue to evolve in Vibrio spp.
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Affiliation(s)
- Zhiwei Zheng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China; State Key Lab for Chemical Biology and Drug Discovery, and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Qipeng Cheng
- College of Life Sciences, Anhui Normal University, Wuhu, PR China; State Key Lab for Chemical Biology and Drug Discovery, and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Lianwei Ye
- State Key Lab for Chemical Biology and Drug Discovery, and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Yating Xu
- State Key Lab for Chemical Biology and Drug Discovery, and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China; State Key Lab for Chemical Biology and Drug Discovery, and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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23
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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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24
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Feuillard J, Couston J, Benito Y, Hodille E, Dumitrescu O, Blaise M. Biochemical and structural characterization of a class A β-lactamase from Nocardia cyriacigeorgica. Acta Crystallogr F Struct Biol Commun 2024; 80:13-21. [PMID: 38168018 PMCID: PMC10833343 DOI: 10.1107/s2053230x23010671] [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: 10/02/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Nocardia are Gram-positive bacteria from the Actinobacteria phylum. Some Nocardia species can infect humans and are usually considered to be opportunist pathogens, as they often infect immunocompromised patients. Although their clinical incidence is low, many Nocardia species are now considered to be emerging pathogens. Primary sites of infection by Nocardia are the skin or the lungs, but dissemination to other body parts is very frequent. These disseminated infections are very difficult to treat and thus are tackled with multiple classes of antibiotics, in addition to the traditional treatment targeting the folate pathway. β-Lactams are often included in the regimen, but many Nocardia species present moderate or strong resistance to some members of this drug class. Genomic, microbiological and biochemical studies have reported the presence of class A β-lactamases (ABLs) in a handful of Nocardia species, but no structural investigation of Nocardia β-lactamases has yet been performed. In this study, the expression, purification and preliminary biochemical characterization of an ABL from an N. cyriacigeorgica (NCY-1) clinical strain are reported. The crystallization and the very high resolution crystal structure of NCY-1 are also described. The sequence and structural analysis of the protein demonstrate that NCY-1 belongs to the class A1 β-lactamases and show its very high conservation with ABLs from other human-pathogenic Nocardia. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future drug development to specifically target Nocardia spp. β-lactamases.
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Affiliation(s)
| | - Julie Couston
- IRIM, Montpellier University, CNRS, Montpellier, France
| | - Yvonne Benito
- Institut des Agents Infectieux, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Centre de Biologie Nord, Lyon, France
| | - Elisabeth Hodille
- Institut des Agents Infectieux, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Centre de Biologie Nord, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Lyon 1, Lyon, France
| | - Oana Dumitrescu
- Institut des Agents Infectieux, Hospices Civils de Lyon, Hôpital de la Croix-Rousse, Centre de Biologie Nord, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Université Lyon 1, Lyon, France
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25
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Li J, Ma D, Huang Q, Du Y, He Q, Ji H, Ma W, Zhao J. Cu 2+ coordination-induced in situ photo-to-heat on catalytic sites to hydrolyze β-lactam antibiotics pollutants in waters. Proc Natl Acad Sci U S A 2023; 120:e2302761120. [PMID: 38109527 PMCID: PMC10756305 DOI: 10.1073/pnas.2302761120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/26/2023] [Indexed: 12/20/2023] Open
Abstract
For degradation of β-lactam antibiotics pollution in waters, the strained β-lactam ring is the most toxic and resistant moiety to biodegrade and redox-chemically treat among their functional groups. Hydrolytically opening β-lactam ring with Lewis acid catalysts has long been recognized as a shortcut, but at room temperature, such hydrolysis is too slow to be deployed. Here, we found when Cu2+ was immobilized on imine-linked COF (covalent organic framework) (Cu2+/Py-Bpy-COF, Cu2+ load is 1.43 wt%), as-prepared composite can utilize the light irradiation (wavelength range simulated sunlight) to in situ heat anchored Cu2+ Lewis acid sites through an excellent photothermal conversion to open the β-lactam ring followed by a desired full-decarboxylation of hydrolysates. Under 1 W/cm2 simulated sunlight, Cu2+/Py-Bpy-COF powders placed in a microfiltration membrane rapidly cause a temperature rising even to ~211.7 °C in 1 min. It can effectively hydrolyze common β-lactam antibiotics in waters and even antibiotics concentration is as high as 1 mM and it takes less than 10 min. Such photo-heating hydrolysis rate is ~24 times as high as under dark and ~2 times as high as Cu2+ homogenous catalysis. Our strategy significantly decreases the interference from generally coexisting common organics in waters and potential toxicity concerns of residual carboxyl groups in hydrolysates and opens up an accessible way for the settlement of β-lactam antibiotics pollutants by the only energy source available, the sunlight.
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Affiliation(s)
- Jiazhen Li
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Dongge Ma
- Department of Chemistry, College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing100048, People’s Republic of China
| | - Qiang Huang
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Yangyang Du
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Qin He
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Hongwei Ji
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Wanhong Ma
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Jincai Zhao
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing100190, People’s Republic of China
- Beijing National Laboratory for Molecular Sciences, Beijing100190, People’s Republic of China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
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Oelschlaeger P, Kaadan H, Dhungana R. Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues. Antibiotics (Basel) 2023; 12:1746. [PMID: 38136780 PMCID: PMC10740994 DOI: 10.3390/antibiotics12121746] [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: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Heba Kaadan
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Rinku Dhungana
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts & Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Voráčová M, Zore M, Yli-Kauhaluoma J, Kiuru P. Harvesting phosphorus-containing moieties for their antibacterial effects. Bioorg Med Chem 2023; 96:117512. [PMID: 37939493 DOI: 10.1016/j.bmc.2023.117512] [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: 09/12/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Clinically manifested resistance of bacteria to antibiotics has emerged as a global threat to society and there is an urgent need for the development of novel classes of antibacterial agents. Recently, the use of phosphorus in antibacterial agents has been explored in quite an unprecedent manner. In this comprehensive review, we summarize the use of phosphorus-containing moieties (phosphonates, phosphonamidates, phosphonopeptides, phosphates, phosphoramidates, phosphinates, phosphine oxides, and phosphoniums) in compounds with antibacterial effect, including their use as β-lactamase inhibitors and antibacterial disinfectants. We show that phosphorus-containing moieties can serve as novel pharmacophores, bioisosteres, and prodrugs to modify pharmacodynamic and pharmacokinetic properties. We further discuss the mechanisms of action, biological activities, clinical use and highlight possible future prospects.
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Affiliation(s)
- Manuela Voráčová
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Matej Zore
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Paula Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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28
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Bersani M, Failla M, Vascon F, Gianquinto E, Bertarini L, Baroni M, Cruciani G, Verdirosa F, Sannio F, Docquier JD, Cendron L, Spyrakis F, Lazzarato L, Tondi D. Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-β-Lactamases and Synergistic Activity on Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1682. [PMID: 38139809 PMCID: PMC10747250 DOI: 10.3390/ph16121682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.
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Affiliation(s)
- Matteo Bersani
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Mariacristina Failla
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Filippo Vascon
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Laura Bertarini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, UK;
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università Degli Studi di Perugia, Via Elce di Sotto, 06132 Perugia, Italy;
| | - Federica Verdirosa
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Filomena Sannio
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
- Laboratoire de Bactériologie Moléculaire, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
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Nafaee ZH, Egyed V, Jancsó A, Tóth A, Gerami AM, Dang TT, Heiniger‐Schell J, Hemmingsen L, Hunyadi‐Gulyás É, Peintler G, Gyurcsik B. Revisiting the hydrolysis of ampicillin catalyzed by Temoneira-1 β-lactamase, and the effect of Ni(II), Cd(II) and Hg(II). Protein Sci 2023; 32:e4809. [PMID: 37853808 PMCID: PMC10661098 DOI: 10.1002/pro.4809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/18/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
β-Lactamases grant resistance to bacteria against β-lactam antibiotics. The active center of TEM-1 β-lactamase accommodates a Ser-Xaa-Xaa-Lys motif. TEM-1 β-lactamase is not a metalloenzyme but it possesses several putative metal ion binding sites. The sites composed of His residue pairs chelate borderline transition metal ions such as Ni(II). In addition, there are many sulfur-containing donor groups that can coordinate soft metal ions such as Hg(II). Cd(II) may bind to both types of the above listed donor groups. No significant change was observed in the circular dichroism spectra of TEM-1 β-lactamase on increasing the metal ion content of the samples, with the exception of Hg(II) inducing a small change in the secondary structure of the protein. A weak nonspecific binding of Hg(II) was proven by mass spectrometry and 119m Hg perturbed angular correlation spectroscopy. The hydrolytic process of ampicillin catalyzed by TEM-1 β-lactamase was described by the kinetic analysis of the set of full catalytic progress curves, where the slow, yet observable conversion of the primary reaction product into a second one, identified as ampilloic acid by mass spectrometry, needed also to be considered in the applied model. Ni(II) and Cd(II) slightly promoted the catalytic activity of the enzyme while Hg(II) exerted a noticeable inhibitory effect. Hg(II) and Ni(II), applied at 10 μM concentration, inhibited the growth of E. coli BL21(DE3) in M9 minimal medium in the absence of ampicillin, but addition of the antibiotic could neutralize this toxic effect by complexing the metal ions.
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Affiliation(s)
- Zeyad H. Nafaee
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
- College of PharmacyUniversity of BabylonBabelIraq
| | - Viktória Egyed
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Attila Jancsó
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Annamária Tóth
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Adeleh Mokhles Gerami
- School of Particles and AcceleratorsInstitute for Research in Fundamental Sciences (IPM)TehranIran
- European Organization for Nuclear Research (CERN)GenevaSwitzerland
| | - Thanh Thien Dang
- Institute for Materials Science and Center for Nanointegration Duisburg‐Essen (CENIDE)University of Duisburg‐EssenEssenGermany
| | - Juliana Heiniger‐Schell
- European Organization for Nuclear Research (CERN)GenevaSwitzerland
- Institute for Materials Science and Center for Nanointegration Duisburg‐Essen (CENIDE)University of Duisburg‐EssenEssenGermany
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenCopenhagenDenmark
| | - Éva Hunyadi‐Gulyás
- Laboratory of Proteomics Research, Biological Research CentreHungarian Research Network (HUN‐REN)SzegedHungary
| | - Gábor Peintler
- Department of Physical Chemistry and Material SciencesUniversity of SzegedSzegedHungary
| | - Béla Gyurcsik
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
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Chen C, Li J, Dan H, He J, Wang D, Oelschlaeger P, Wang N, Zhang Y, Pei Y, Yang KW. A self-reported inhibitor of metallo-carbapenemases for reversing carbapenem resistance. Int J Biol Macromol 2023; 252:126441. [PMID: 37607651 DOI: 10.1016/j.ijbiomac.2023.126441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/08/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
Metallo-carbapenemases-mediated carbapenem-resistant Enterobacterales (CREs) has been acknowledged as "urgent threat" by the World Health Organization. The discovery of new strategies that block metallo-carbapenemases activity to reverse carbapenem resistance is an urgent need. In this study, a coumarin copper complex containing a PEG linker and glucose ligand, GluC-Cu, was used to reverse carbapenem resistance. Interestingly, it could effectively inhibit metallo-carbapenemases (NDM-1, IMP-1 and ImiS) with an IC50 value in the range of 0.23-1.21 μM, and simultaneously release the green fluorescence signal (GluC), therefore exhibiting self-reported inhibition performance. The inhibition mechanism of oxidizing Zn(II) thiolate site of NDM-1 from Cu2+ to Cu+ was verified by fluorescence assay, HR-MS, and XPS. Moreover, GluC-Cu in combination with meropenem showed excellent synergistic antibacterial effect to effectively combat E. coli expressing metallo-carbapenemases in vitro and in a mice infection model. This bifunctional metallo-carbapenemases inhibitor provides a novel chemical tool to overcome carbapenem resistance.
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Affiliation(s)
- Cheng Chen
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, PR China; Key laboratory synthetic and Natural Functional Molecular Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jiahui Li
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, PR China
| | - Heng Dan
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, PR China
| | - Jingyi He
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, PR China
| | - Dongmei Wang
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, PR China.
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, 91766, CA, United States
| | - Nana Wang
- Shaanxi Key Laboratory of Economic Plant Resources Development and Utilization, College of Forestry, Northwest A&F University, Yangling 712100, PR China
| | | | - Yuxin Pei
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, PR China.
| | - Ke-Wu Yang
- Key laboratory synthetic and Natural Functional Molecular Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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31
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Thomas CA, Cheng Z, Bethel CR, Hujer AM, Sturgill AM, Onuoha K, Page RC, Bonomo RA, Crowder MW. The directed evolution of NDM-1. Antimicrob Agents Chemother 2023; 67:e0071423. [PMID: 37874296 PMCID: PMC10649027 DOI: 10.1128/aac.00714-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/10/2023] [Indexed: 10/25/2023] Open
Abstract
β-Lactam antibiotics are among the most frequently prescribed therapeutic agents. A common mechanism of resistance toward β-lactam antibiotics is the production of β-lactamases. These enzymes are capable of hydrolyzing the β-lactam bond, rendering the drug inactive. Among the four described classes, the metallo- β-lactamases (MBLs, class B) employ one or two zinc ions in the active site for catalysis. One of the three most clinically relevant MBLs is New Delhi Metallo- β-Lactamase (NDM-1). The current study sought to investigate the in vitro protein evolution of NDM-1 β-lactamase using error-prone polymerase chain reaction. Evaluation revealed that variants were not found to confer higher levels of resistance toward meropenem based on amino acid substitutions. Thus, we postulate that increases in transcription or changes in zinc transport may be clinically more relevant to meropenem resistance than amino acid substitutions.
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Affiliation(s)
- Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aidan M. Sturgill
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Kelechi Onuoha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Clinician Scientist Investigator, Ohio, Cleveland, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes. Sci Rep 2023; 13:19207. [PMID: 37932283 PMCID: PMC10628120 DOI: 10.1038/s41598-023-44172-w] [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: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Benin BM, Hillyer T, Crugnale AS, Fulk A, Thomas CA, Crowder MW, Smith MA, Shin WS. Taxifolin as a Metallo-β-Lactamase Inhibitor in Combination with Augmentin against Verona Imipenemase 2 Expressing Pseudomonas aeruginosa. Microorganisms 2023; 11:2653. [PMID: 38004664 PMCID: PMC10673258 DOI: 10.3390/microorganisms11112653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Among the various mechanisms that bacteria use to develop antibiotic resistance, the multiple expression of β-lactamases is particularly problematic, threatening public health and increasing patient mortality rates. Even if a combination therapy-in which a β-lactamase inhibitor is administered together with a β-lactam antibiotic-has proven effective against serine-β-lactamases, there are no currently approved metallo-β-lactamase inhibitors. Herein, we demonstrate that quercetin and its analogs are promising starting points for the further development of safe and effective metallo-β-lactamase inhibitors. Through a combined computational and in vitro approach, taxifolin was found to inhibit VIM-2 expressing P. aeruginosa cell proliferation at <4 μg/mL as part of a triple combination with amoxicillin and clavulanate. Furthermore, we tested this combination in mice with abrasive skin infections. Together, these results demonstrate that flavonol compounds, such as taxifolin, may be developed into effective metallo-β-lactamase inhibitors.
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Affiliation(s)
- Bogdan M. Benin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
| | - Trae Hillyer
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
| | - Aylin S. Crugnale
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
| | - Andrew Fulk
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; (C.A.T.); (M.W.C.)
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; (C.A.T.); (M.W.C.)
| | - Matthew A. Smith
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
- Akron Children’s Hospital, Rebecca D. Considine Research Institute, Akron, OH 44302, USA
| | - Woo Shik Shin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (B.M.B.); (T.H.); (A.F.); (M.A.S.)
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Dong X, Liu W, Dong Y, Wang K, Li K, Bian L. Metallo-β-lactamase SMB-1 evolves into a more efficient hydrolase under the selective pressure of meropenem. J Inorg Biochem 2023; 247:112323. [PMID: 37478781 DOI: 10.1016/j.jinorgbio.2023.112323] [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: 04/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Metallo-β-lactamases (MβLs) are the primary mechanism of resistance to carbapenem antibiotics. To elucidate how MβLs have evolved with the introduction and use of antibiotics, the mutation and evolution of SMB-1 from Serratia marcescens were investigated in microbial evolution plates containing discontinuous meropenem (MEM) concentration gradients. The results revealed 2-point mutations, A242G and S257R; 1 double-site mutation, C240G/E258G; and 3 frameshift mutations, M5, M12, and M13, which are all missense mutations situated at the C-terminus. Compared with that of the wild-type (WT), the minimum inhibitory concentrations (MICs) of MEM for A242G, C240G/E258G, M5, M12, and M13 increased at least 120-fold, and that of S257R increased 8-fold. The catalytic efficiency kcat/Km increased by 365% and 647%, respectively. Concerning the structural changes, the structure at the active site changed from an ordered structure to an unordered conformation. Simultaneously, the flexibility of loop 1 was enhanced. These changes increased the volume of the active site cavity; thus, this was more conducive to exposing the Zn2+ site, facilitating substrate binding and conversion to products. In A242G, structural changes in Gly-242 can be transmitted to the active region via a network of interactions between the side chains of Gly-242 and the amino acid side chains near the active pocket. Together, these results pointed to the process of persistent drug tolerance and resistance, the SMB-1 enzyme evolved into a more exquisite structure with increased flexibility and stability, and stronger hydrolysis activity via genetic mutations and structural changes.
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Affiliation(s)
- Xiaoting Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Wenli Liu
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Yuxuan Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kun Wang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kewei Li
- 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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Dos Santos PAS, Silva MJA, Gouveia MIM, Lima LNGC, Quaresma AJPG, De Lima PDL, Brasiliense DM, Lima KVB, Rodrigues YC. The Prevalence of Metallo-Beta-Lactamese-(MβL)-Producing Pseudomonas aeruginosa Isolates in Brazil: A Systematic Review and Meta-Analysis. Microorganisms 2023; 11:2366. [PMID: 37764210 PMCID: PMC10534863 DOI: 10.3390/microorganisms11092366] [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: 07/26/2023] [Revised: 08/12/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The purpose of the current study is to describe the prevalence of Pseudomonas aeruginosa (PA)-producing MβL among Brazilian isolates and the frequency of blaSPM-1 in MβL-PA-producing isolates. From January 2009 to August 2023, we carried out an investigation on this subject in the internet databases SciELO, PubMed, Science Direct, and LILACS. A total of 20 papers that met the eligibility requirements were chosen by comprehensive meta-analysis software v2.2 for data retrieval and analysis by one meta-analysis using a fixed-effects model for the two investigations. The prevalence of MβL-producing P. aeruginosa was 35.8% or 0.358 (95% CI = 0.324-0.393). The studies' differences were significantly different from one another (x2 = 243.15; p < 0.001; I2 = 92.18%), so they were divided into subgroups based on Brazilian regions. There was indication of asymmetry in the meta-analyses' publishing bias funnel plot; so, a meta-regression was conducted by the study's publication year. According to the findings of Begg's test, no discernible publishing bias was found. blaSPM-1 prevalence was estimated at 66.9% or 0.669 in MβL-PA isolates (95% CI = 0.593-0.738). The analysis of this one showed an average heterogeneity (x2 = 90.93; p < 0.001; I2 = 80.20%). According to the results of Begg's test and a funnel plot, no discernible publishing bias was found. The research showed that MβL-P. aeruginosa and SPM-1 isolates were relatively common among individuals in Brazil. P. aeruginosa and other opportunistic bacteria are spreading quickly and causing severe infections, so efforts are needed to pinpoint risk factors, reservoirs, transmission pathways, and the origin of infection.
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Affiliation(s)
- Pabllo Antonny Silva Dos Santos
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Marcos Jessé Abrahão Silva
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Maria Isabel Montoril Gouveia
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Luana Nepomuceno Gondim Costa Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Ana Judith Pires Garcia Quaresma
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
| | - Patrícia Danielle Lima De Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
| | - Danielle Murici Brasiliense
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Karla Valéria Batista Lima
- Program in Parasitic Biology in the Amazon Region (PPGBPA), State University of Pará (UEPA), Belém 66087-662, PA, Brazil; (P.A.S.D.S.); (L.N.G.C.L.); (P.D.L.D.L.); (D.M.B.); (K.V.B.L.)
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
| | - Yan Corrêa Rodrigues
- Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil; (M.I.M.G.); (A.J.P.G.Q.)
- Program in Epidemiology and Health Surveillance (PPGEVS), Evandro Chagas Institute (IEC), Ministry of Health, Ananindeua 67030-000, PA, Brazil
- Department of Natural Science, State University of Pará (DCNA/UEPA), Belém 66050-540, PA, Brazil
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Escamilla P, Bartella L, Sanz-Navarro S, Percoco RM, Di Donna L, Prejanò M, Marino T, Ferrando-Soria J, Armentano D, Leyva-Pérez A, Pardo E. Degradation of Penicillinic Antibiotics and β-Lactamase Enzymatic Catalysis in a Biomimetic Zn-Based Metal-Organic Framework. Chemistry 2023; 29:e202301325. [PMID: 37279057 DOI: 10.1002/chem.202301325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/07/2023]
Abstract
β-Lactam antibiotics are one of the most commonly prescribed drugs to treat bacterial infections. However, their use has been somehow limited given the emergence of bacteria with resistance mechanisms, such as β-lactamases, which inactivate them by degrading their four-membered β-lactam rings. So, a total knowledge of the mechanisms governing the catalytic activity of β-lactamases is required. Here, we report a novel Zn-based metal-organic framework (MOF, 1), possessing functional channels capable to accommodate and interact with antibiotics, which catalyze the selective hydrolysis of the penicillinic antibiotics amoxicillin and ceftriaxone. In particular, MOF 1 degrades, very efficiently, the four-membered β-lactam ring of amoxicillin, acting as a β-lactamase mimic, and expands the very limited number of MOFs capable to mimic catalytic enzymatic processes. Combined single-crystal X-ray diffraction (SCXRD) studies and density functional (DFT) calculations offer unique snapshots on the host-guest interactions established between amoxicillin and the functional channels of 1. This allows to propose a degradation mechanism based on the activation of a water molecule, promoted by a Zn-bridging hydroxyl group, concertedly to the nucleophilic attack to the carbonyl moiety and the cleaving of C-N bond of the lactam ring.
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Affiliation(s)
- Paula Escamilla
- Instituto de Ciencia Molecular (ICMOL), Universitat deValència Paterna, 46980, València, Spain
| | - Lucia Bartella
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
- QUASIORA Laboratory, AGRINFRA Research Net, Università della Calabria, 87036, Rende, Cosenza, Italy
| | - Sergio Sanz-Navarro
- Instituto de Tecnología Química, Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), 46022, Valencia, Spain
| | - Rita Maria Percoco
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
| | - Leonardo Di Donna
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
- QUASIORA Laboratory, AGRINFRA Research Net, Università della Calabria, 87036, Rende, Cosenza, Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
| | - Jesús Ferrando-Soria
- Instituto de Ciencia Molecular (ICMOL), Universitat deValència Paterna, 46980, València, Spain
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87030, Rende, Cosenza, Italy
| | - Antonio Leyva-Pérez
- Instituto de Tecnología Química, Universidad Politècnica de València-Consejo Superior de Investigaciones Científicas (UPV-CSIC), 46022, Valencia, Spain
| | - Emilio Pardo
- Instituto de Ciencia Molecular (ICMOL), Universitat deValència Paterna, 46980, València, Spain
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37
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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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38
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González LJ, Bahr G, González MM, Bonomo RA, Vila AJ. In-cell kinetic stability is an essential trait in metallo-β-lactamase evolution. Nat Chem Biol 2023; 19:1116-1126. [PMID: 37188957 DOI: 10.1038/s41589-023-01319-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
Protein stability is an essential property for biological function. In contrast to the vast knowledge on protein stability in vitro, little is known about the factors governing in-cell stability. Here we show that the metallo-β-lactamase (MBL) New Delhi MBL-1 (NDM-1) is a kinetically unstable protein on metal restriction that has evolved by acquiring different biochemical traits that optimize its in-cell stability. The nonmetalated (apo) NDM-1 is degraded by the periplasmic protease Prc that recognizes its partially unstructured C-terminal domain. Zn(II) binding renders the protein refractory to degradation by quenching the flexibility of this region. Membrane anchoring makes apo-NDM-1 less accessible to Prc and protects it from DegP, a cellular protease degrading misfolded, nonmetalated NDM-1 precursors. NDM variants accumulate substitutions at the C terminus that quench its flexibility, enhancing their kinetic stability and bypassing proteolysis. These observations link MBL-mediated resistance with the essential periplasmic metabolism, highlighting the importance of the cellular protein homeostasis.
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Affiliation(s)
- Lisandro J González
- 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
| | - Guillermo Bahr
- 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
| | - Mariano M González
- 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
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alejandro J Vila
- 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.
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.
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Kurz JL, Pedroso MM, Richard E, McGeary RP, Schenk G. Inhibitors for metallo-β-lactamases from the B1 and B3 subgroups provide an avenue to combat a major mechanism of antibiotic resistance. Bioorg Med Chem Lett 2023; 92:129387. [PMID: 37369333 DOI: 10.1016/j.bmcl.2023.129387] [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: 04/17/2023] [Revised: 06/12/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023]
Abstract
Metallo-β-lactamases (MBLs) are a group of Zn(II)-dependent enzymes that pose a major threat to global health. They are linked to an increasing number of multi-drug resistant bacterial pathogens, but no clinically useful inhibitor is yet available. Since β-lactam antibiotics, which are inactivated by MBLs, constitute ∼65% of all antibiotics used to treat infections, the search for clinically relevant MBL inhibitors is urgent. Here, derivatives of a 2-amino-1-benzyl-4,5-diphenyl-1H-pyrrole-3-carbonitrile (1a) were synthesised and their inhibitory effects assessed against prominent representatives of the MBL family. Several compounds are potent inhibitors of each MBL tested, making them promising candidates for the development of broad-spectrum drug leads. In particular, compound 5f is highly potent across the MBL family, with Ki values in the low µM range. Furthermore, this compound also appears to display synergy in combination with antibiotics such as penicillin G, cefuroxime or meropenem. This molecule thus represents a promising starting point to develop new drugs to inhibit a major mechanism of antibiotic resistance.
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Affiliation(s)
- Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emmanuelle Richard
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.
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40
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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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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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Papastergiou T, Azé J, Bringay S, Louet M, Poncelet P, Rosales-Hurtado M, Vo-Hoang Y, Licznar-Fajardo P, Docquier JD, Gavara L. Discovering NDM-1 inhibitors using molecular substructure embeddings representations. J Integr Bioinform 2023; 0:jib-2022-0050. [PMID: 37498676 PMCID: PMC10389050 DOI: 10.1515/jib-2022-0050] [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: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/29/2023] Open
Abstract
NDM-1 (New-Delhi-Metallo-β-lactamase-1) is an enzyme developed by bacteria that is implicated in bacteria resistance to almost all known antibiotics. In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison to the classical Machine Learning paradigm. Moreover, we investigate different compact molecular representations, based on atomic or bi-atomic substructures. Finally, we scanned the Drugbank for strongly active compounds and we present the top-15 ranked compounds.
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Affiliation(s)
- Thomas Papastergiou
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | - Jérôme Azé
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
| | - Sandra Bringay
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
- AMIS, Paul Valery University, 34199 Montpellier, France
| | - Maxime Louet
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | - Pascal Poncelet
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
| | | | - Yen Vo-Hoang
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | | | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, I-53100 Siena, Italy
| | - Laurent Gavara
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
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Arbour CA, Fay EM, McGouran JF, Imperiali B. Deploying solid-phase synthesis to access thymine-containing nucleoside analogs that inhibit DNA repair nuclease SNM1A. Org Biomol Chem 2023; 21:5873-5879. [PMID: 37417819 PMCID: PMC10529636 DOI: 10.1039/d3ob00836c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Nucleoside analogs show useful bioactive properties. A versatile solid-phase synthesis that readily enables the diversification of thymine-containing nucleoside analogs is presented. The utility of the approach is demonstrated with the preparation of a library of compounds for analysis with SNM1A, a DNA damage repair enzyme that contributes to cytotoxicity. This exploration provided the most promising nucleoside-derived inhibitor of SNM1A to date with an IC50 of 12.3 μM.
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Affiliation(s)
- Christine A Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ellen M Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland
| | - Joanna F McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St., Dublin 2, Ireland
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Venkatesan M, Fruci M, Verellen LA, Skarina T, Mesa N, Flick R, Pham C, Mahadevan R, Stogios PJ, Savchenko A. Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat Commun 2023; 14:4031. [PMID: 37419898 PMCID: PMC10328974 DOI: 10.1038/s41467-023-39778-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
The sulfonamides (sulfas) are the oldest class of antibacterial drugs and inhibit the bacterial dihydropteroate synthase (DHPS, encoded by folP), through chemical mimicry of its co-substrate p-aminobenzoic acid (pABA). Resistance to sulfa drugs is mediated either by mutations in folP or acquisition of sul genes, which code for sulfa-insensitive, divergent DHPS enzymes. While the molecular basis of resistance through folP mutations is well understood, the mechanisms mediating sul-based resistance have not been investigated in detail. Here, we determine crystal structures of the most common Sul enzyme types (Sul1, Sul2 and Sul3) in multiple ligand-bound states, revealing a substantial reorganization of their pABA-interaction region relative to the corresponding region of DHPS. We use biochemical and biophysical assays, mutational analysis, and in trans complementation of E. coli ΔfolP to show that a Phe-Gly sequence enables the Sul enzymes to discriminate against sulfas while retaining pABA binding and is necessary for broad resistance to sulfonamides. Experimental evolution of E. coli results in a strain harboring a sulfa-resistant DHPS variant that carries a Phe-Gly insertion in its active site, recapitulating this molecular mechanism. We also show that Sul enzymes possess increased active site conformational dynamics relative to DHPS, which could contribute to substrate discrimination. Our results reveal the molecular foundation for Sul-mediated drug resistance and facilitate the potential development of new sulfas less prone to resistance.
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3E2, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station. RESEARCH SQUARE 2023:rs.3.rs-3126314. [PMID: 37461605 PMCID: PMC10350232 DOI: 10.21203/rs.3.rs-3126314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS). Results The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Conclusions Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D. Rekha
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Fay EM, Newton A, Berney M, El‐Sagheer AH, Brown T, McGouran JF. Two-Step Validation Approach for Tools To Study the DNA Repair Enzyme SNM1A. Chembiochem 2023; 24:e202200756. [PMID: 36917742 PMCID: PMC10962688 DOI: 10.1002/cbic.202200756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023]
Abstract
We report a two-step validation approach to evaluate the suitability of metal-binding groups for targeting DNA damage-repair metalloenzymes using model enzyme SNM1A. A fragment-based screening approach was first used to identify metal-binding fragments suitable for targeting the enzyme. Effective fragments were then incorporated into oligonucleotides using the copper-catalysed azide-alkyne cycloaddition reaction. These modified oligonucleotides were recognised by SNM1A at >1000-fold lower concentrations than their fragment counterparts. The exonuclease SNM1A is a key enzyme involved in the repair of interstrand crosslinks, a highly cytotoxic form of DNA damage. However, SNM1A and other enzymes of this class are poorly understood, as there is a lack of tools available to facilitate their study. Our novel approach of incorporating functional fragments into oligonucleotides is broadly applicable to generating modified oligonucleotide structures with high affinity for DNA damage-repair enzymes.
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Affiliation(s)
- Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Ailish Newton
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Mark Berney
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Tom Brown
- Department of ChemistryUniversity of OxfordMansfield RoadOX1 3TAOxfordUK
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences InstituteTrinity College DublinThe University of DublinDublin 2D02 R590Ireland
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47
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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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Shungube M, Hlophe AK, Girdhari L, Sabe VT, Peters BB, Reddy N, Omolabi KF, Chetty L, Arumugam T, Chuturgoon A, Kruger HG, Arvidsson PI, Qin HL, Naicker T, Govender T. Synthesis and biological evaluation of novel β-lactam-metallo β-lactamase inhibitors. RSC Adv 2023; 13:18991-19001. [PMID: 37362332 PMCID: PMC10285615 DOI: 10.1039/d3ra02490c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
β-lactamases are enzymes that deactivate β-lactam antibiotics through a hydrolysis mechanism. There are two known types of β-lactamases: serine β-lactamases (SBLs) and metallo β-lactamases (MBLs). The two existing strategies to overcome β-lactamase-mediated resistance are (a) to develop novel β-lactam antibiotics that are not susceptible to hydrolysis by these enzymes; or (b) to develop β-lactamase inhibitors that deactivate the enzyme and thereby restore the efficacy of the co-administered antibiotics. Many commercially available SBL inhibitors are used in combination therapy with antibiotics to treat antimicrobial resistant infections; however, there are only a handful of MBL inhibitors undergoing clinical trials. In this study, we present 11 novel potential MBL inhibitors (via multi-step chemical synthesis), that have shown to completely restore the efficacy of meropenem (≤2 mg L-1) against New Delhi metallo-β-lactamase (NDM) producing Klebsiella pneumoniae in vitro. These compounds contain a cyclic amino acid zinc chelator conjugated to various commercially available β-lactam antibiotic scaffolds with the aim to improve the overall drug transport, lipophilicity, and pharmacokinetic/pharmacodynamic properties as compared to the chelator alone. Biological evaluation of compounds 24b and 24c has further highlighted the downstream application of these MBLs, since they are non-toxic at the selected doses. Time-kill assays indicate that compounds 24b and 24c exhibit sterilizing activity towards NDM producing Klebsiella pneumoniae in vitro using minimal concentrations of meropenem. Furthermore, 24b and 24c proved to be promising inhibitors of VIM-2 (Ki = 0.85 and 1.87, respectively). This study has revealed a novel series of β-lactam MBLIs that are potent, efficacious, and safe leads with the potential to develop into therapeutic MBLIs.
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Affiliation(s)
- Mbongeni Shungube
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Ayanda K Hlophe
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Letisha Girdhari
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Victor T Sabe
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Byron B Peters
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Nakita Reddy
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Kehinde F Omolabi
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Lloyd Chetty
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal Durban South Africa
| | - Anil Chuturgoon
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal Durban South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Per I Arvidsson
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
- Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm Sweden
| | - Hua-Li Qin
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology 205 Luoshi Road Wuhan 430070 P. R. China
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu Natal Durban 4001 South Africa +27 312601845
| | - Thavendran Govender
- Department of Chemistry, University of Zululand Private Bag X1001 KwaDlangezwa 3886 South Africa
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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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Maia JCDS, Silva GADA, Cunha LSDB, Gouveia GV, Góes-Neto A, Brenig B, Araújo FA, Aburjaile F, Ramos RTJ, Soares SC, Azevedo VADC, Costa MMD, Gouveia JJDS. Genomic Characterization of Aeromonas veronii Provides Insights into Taxonomic Assignment and Reveals Widespread Virulence and Resistance Genes throughout the World. Antibiotics (Basel) 2023; 12:1039. [PMID: 37370358 DOI: 10.3390/antibiotics12061039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Aeromonas veronii is a Gram-negative bacterial species that causes disease in fish and is nowadays increasingly recurrent in enteric infections of humans. This study was performed to characterize newly sequenced isolates by comparing them with complete genomes deposited at the NCBI (National Center for Biotechnology Information). Nine isolates from fish, environments, and humans from the São Francisco Valley (Petrolina, Pernambuco, Brazil) were sequenced and compared with complete genomes available in public databases to gain insight into taxonomic assignment and to better understand virulence and resistance profiles of this species within the One Health context. One local genome and four NCBI genomes were misidentified as A. veronii. A total of 239 virulence genes were identified in the local genomes, with most encoding adhesion, motility, and secretion systems. In total, 60 genes involved with resistance to 22 classes of antibiotics were identified in the genomes, including mcr-7 and cphA. The results suggest that the use of methods such as ANI is essential to avoid misclassification of the genomes. The virulence content of A. veronii from local isolates is similar to those complete genomes deposited at the NCBI. Genes encoding colistin resistance are widespread in the species, requiring greater attention for surveillance systems.
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Affiliation(s)
- José Cleves da Silva Maia
- Graduate Program in Animal Science, Agricultural Sciences Campus, Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
| | - Gabriel Amorim de Albuquerque Silva
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
| | - Letícia Stheffany de Barros Cunha
- Graduate Program in Animal Science, Agricultural Sciences Campus, Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
| | - Gisele Veneroni Gouveia
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
| | - Aristóteles Góes-Neto
- Laboratory of Molecular Computational Biology of Fungi (LBMCF), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Niedersachsen, Germany
| | - Fabrício Almeida Araújo
- Biological Engineering Laboratory, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-110, Pará, Brazil
| | - Flávia Aburjaile
- Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Rommel Thiago Jucá Ramos
- Biological Engineering Laboratory, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-110, Pará, Brazil
| | - Siomar Castro Soares
- Department of Microbiology, Immunology, and Parasitology, Federal University of Triângulo Mineiro, Uberaba 38025-180, Minas Gerais, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Mateus Matiuzzi da Costa
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
| | - João José de Simoni Gouveia
- Center for Open Access Genomic Analysis (CALAnGO), Federal University of Vale of São Francisco (Univasf), Petrolina 56304-917, Pernambuco, Brazil
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