Abstract
Microbial pathogens including Enterobacteriaceae family members bear different antibiotic resistance genes comprising Extended-Spectrum-ß-Lactamases (ESBLs) and Metallo-ß-Lactamases (MBLs) on their chromosomes and mobile genetic elements such as plasmids and transposons. Because of the clinical concern regarding MBLs in global public healthcare system, this review focuses on different characteristics of MBLs. For preparing this review article, different databases, websites and search engines such as MEDLINE, SCOPUS, SCIENCEDIRECT and GOOGLE SCHOLAR were searched via MeSH keywords of Enterobacteriaceae, Escherichia coli, Klebsiella pneumoniae, MBL and Bioinformatics. Different types of papers comprising review articles and original articles which were published between the years of 1980 and 2020 were searched, studied and selected by the authors. The results show that, the importance of the spread of MBLs among microbial pathogens may lead to progressive studies for definite treatment. The use of computational biology and chemistry and bioinformatics has had effective consequences on recognition and identification of different properties of MBLs. The application of bioinformatic software tools and databases gives us a great promise regarding production of effective inhibitors against MBLs to have a definite treatment.
Similar content being viewed by others
References
Walsh C, Wencewicz T (2016) Antibiotics: challenges, mechanisms, opportunities. American Society for Microbiology (ASM), Washington
Lee W, McDonough MA, Kotra LP, Li Z-H, Silvaggi NR, Takeda Y et al (2001) A 1.2-Å snapshot of the final step of bacterial cell wall biosynthesis. Proc Natl Acad Sci. 98(4):1427–1431
Palzkill T (2013) Metallo-β-lactamase structure and function. Ann N Y Acad Sci 1277(1):91–104
Palacios AR, Mojica MF, Giannini E, Taracila MA, Bethel CR, Alzari PM et al (2019) The reaction mechanism of metallo-β-lactamases is tuned by the conformation of an active-site mobile loop. Antimicrob Agents Chemother 63(1):e01754–18
Fisher JF, Meroueh SO, Mobashery S (2005) Bacterial resistance to β-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 105(2):395–424
Mojica FM, Bonomo AR, Fast W (2016) B1-metallo-β-lactamases: where do we stand? Curr Drug Targets. 17(9):1029–1050
Issakhanian L, Behzadi P (2019) Antimicrobial agents and urinary tract infections. Curr Pharm Des 25(12):1409–1423
Öztürk H, Ozkirimli E, Özgür A (2015) Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models. PLoS ONE 10(2):e0117874
Wong D, van Duin D (2017) Novel beta-lactamase inhibitors: unlocking their potential in therapy. Drugs. 77(6):615–628
Naas T, Oueslati S, Bonnin RA, Dabos ML, Zavala A, Dortet L et al (2017) Beta-lactamase database (BLDB)–structure and function. J Enzyme Inhib Med Chem 32(1):917–919
Bonomo RA (2017) β-Lactamases: a focus on current challenges. Cold Spring Harbor Perspect Med. 7(1):a025239
Gupta V (2007) An update on newer beta-lactamases. Indian J Med Res 126(5):417
Hozzari A, Behzadi P, Khiabani PK, Sholeh M, Sabokroo N (2020) Clinical cases, drug resistance, and virulence genes profiling in uropathogenic Escherichia coli. J Appl Genet. https://doi.org/10.1007/s13353-020-00542-y
Crowder MW, Spencer J, Vila AJ (2006) Metallo-β-lactamases: novel weaponry for antibiotic resistance in bacteria. Acc Chem Res 39(10):721–728
Bebrone C (2007) Metallo-β-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Biochem Pharmacol 74(12):1686–1701
Ju LC, Cheng Z, Fast W, Bonomo RA, Crowder MW (2018) The continuing challenge of metallo-β-lactamase inhibition: mechanism matters. Trends Pharm Sci. 39(7):635–647
Meini M-R, Llarrull LI, Vila AJ (2015) Overcoming differences: the catalytic mechanism of metallo-β-lactamases. FEBS Lett 589(22):3419–3432
Oelschlaeger P, Mayo SL (2005) Hydroxyl groups in the ββ sandwich of metallo-β-lactamases favor enzyme activity: a computational protein design study. J Mol Biol 350(3):395–401
Bradford PA (2001) Extended-spectrum β-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev 14(4):933–951
Behzadi P (2018) Introductory chapter: an overview on urinary tract infections, pathogens, and risk factors. Microbiology of urinary tract infections. Microbial agents and predisposing factorsMicrobial agents and predisposing factors. IntechOpen, London
Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–433
Drawz SM, Bonomo RA (2010) Three decades of β-lactamase inhibitors. Clin Microbiol Rev 23(1):160–201
Jacoby GA (2009) AmpC β-lactamases. Clin Microbiol Rev 22(1):161–182
Bush K, Jacoby GA, Medeiros AA (1995) A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 39(6):1211
Ambler RP (1980) The structure of β-lactamases. Phil Trans R Soc Lond B. 289(1036):321–331
Bush K, Jacoby GA (2010) Updated functional classification of β-lactamases. Antimicrob Agents Chemother 54(3):969–976
Ghafourian S, Sadeghifard N, Soheili S, Sekawi Z (2014) Extended spectrum beta-lactamases: definition, classification and epidemiology. Curr Issues Mol Biol. 17(1):11–22
Bush K, Bradford PA (2019) Interplay between β-lactamases and new β-lactamase inhibitors. Nat Rev Microbiol 17(5):295
Silveira MC, da Silva AR, da Mota FF, Catanho M, Jardim R, Guimarães RAC et al (2018) Systematic identification and classification of β-lactamases based on sequence similarity criteria: β-lactamase annotation. Evol Bioinform. 14:1176934318797351
Behzadi P, Ranjbar R (2019) DNA microarray technology and bioinformatic web services. Acta microbiol immunol hung 66(1):19–30
Ranjbar R, Behzadi P, Najafi A, Roudi R (2017) DNA microarray for rapid detection and identification of food and water borne Bacteria: from dry to wet lab. Open Microbiol J. 11:330
Queenan AM, Bush K (2007) Carbapenemases: the versatile β-lactamases. Clin Microbiol Rev 20(3):440–458
Wang J-F, Chou K-C (2013) Metallo-β-lactamases: structural features, antibiotic recognition, inhibition, and inhibitor design. Curr Top Med Chem 13(10):1242–1253
Bush K (2013) The ABCD’s of β-lactamase nomenclature. J Infect Chemother. 19(4):549–559
Oelschlaeger P, Schmid RD, Pleiss J (2003) Modeling domino effects in enzymes: molecular basis of the substrate specificity of the bacterial metallo-β-lactamases IMP-1 and IMP-6. Biochemistry 42(30):8945–8956
Aravind L (1999) An evolutionary classification of the metallo-ß-lactamase fold proteins. Silico Biol. 1(2):69–91
Carfi A, Pares S, Duee E, Galleni M, Duez C, Frère J-M et al (1995) The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. EMBO J. 14(20):4914–4921
Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlić A, Rose PW (2018) NGL viewer: web-based molecular graphics for large complexes. Bioinformatics 34(21):3755–3758
Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VH, Takebayashi Y et al (2019) β-lactamases and β-lactamase inhibitors in the 21st Century. J Mol Biol. 431:3472–3500
Herzberg O, Fitzgerald PM. Metallo β‐Lactamases. Encyclopedia of Inorganic and Bioinorganic Chemistry. 2011
Somboro AM, Sekyere JO, Amoako DG, Essack SY, Bester LA (2018) Diversity and proliferation of metallo-β-lactamases: a clarion call for clinically effective metallo-β-lactamase inhibitors. Appl Environ Microbiol 84(18):e00698–18
Hawk MJ, Breece RM, Hajdin CE, Bender KM, Hu Z, Costello AL et al (2009) Differential binding of Co (II) and Zn (II) to metallo-β-lactamase Bla2 from Bacillus anthracis. J Am Chem Soc 131(30):10753–10762
Galleni M, Lamotte-Brasseur J, Rossolini GM, Spencer J, Dideberg O, Frère J-M (2001) Standard numbering scheme for class B β-lactamases. Antimicrob Agents Chemother 45(3):660–663
Walsh TR, Toleman MA, Poirel L, Nordmann P (2005) Metallo-β-lactamases: the quiet before the storm? Clin Microbiol Rev 18(2):306–325
Carruthers TJ, Carr PD, Loh CT, Jackson CJ, Otting G (2014) Iron (III) located in the dinuclear metallo-β-lactamase IMP-1 by pseudocontact shifts. Angew Chem Int Ed 53(51):14269–14272
Mammeri H, Bellais S, Nordmann P (2002) Chromosome-encoded β-lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odoratimimus (formerly Flavobacterium odoratum), new members of the lineage of molecular subclass B1 metalloenzymes. Antimicrob Agents Chemother 46(11):3561–3567
Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K et al (2009) Characterization of a new metallo-β-lactamase gene, blaNDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 53(12):5046–5054
Wu W, Feng Y, Tang G, Qiao F, McNally A, Zong Z (2019) NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin Microbiol Rev. https://doi.org/10.1128/CMR.00115-18
Orellano EG, Girardini JE, Cricco JA, Ceccarelli EA, Vila AJ (1998) Spectroscopic characterization of a binuclear metal site in Bacillus cereus β-lactamase II. Biochemistry 37(28):10173–10180
Concha NO, Rasmussen BA, Bush K, Herzberg O (1996) Crystal structure of the wide-spectrum binuclear zinc β-lactamase from Bacteroides fragilis. Structure. 4(7):823–836
Carfi A, Paul-Soto R, Martin L, Petillot Y, Frère J-M, Dideberg O (1997) Purification, crystallization and preliminary X-ray analysis of Bacteroides fragilis Zn2 + β-lactamase. Acta Crystallogr D Biol Crystallogr 53(4):485–487
Yang H, Aitha M, Hetrick AM, Richmond TK, Tierney DL, Crowder MW (2012) Mechanistic and spectroscopic studies of metallo-β-lactamase NDM-1. Biochemistry 51(18):3839–3847
Lisa M-N, Palacios AR, Aitha M, González MM, Moreno DM, Crowder MW et al (2017) A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases. Nat Commun. 8(1):538
Wachino J. Crystal structure of IMP-1 metallo-beta-lactamase in a complex with MCR. To be published
Garau G, García-Sáez I, Bebrone C, Anne C, Mercuri P, Galleni M et al (2004) Update of the standard numbering scheme for class B β-lactamases. Antimicrob Agents Chemother 48(7):2347–2349
Thomas CA, Cheng Z, Yang K, Hellwarth E, Yurkiewicz CJ, Baxter FM et al (2020) Probing the mechanisms of inhibition for various inhibitors of metallo-β-lactamases VIM-2 and NDM-1. J Inorganic Biochem. https://doi.org/10.1016/j.jinorgbio.2020.111123
Campos-Bermudez VA, González JM, Tierney DL, Vila AJ (2010) Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily. J Biol Inorg Chem 15(8):1209–1218
Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJ, Chothia C et al (2007) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36(suppl_1):D419–D425
Chandonia J-M, Fox NK, Brenner SE (2018) SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database. Nucleic Acids Res 47(D1):D475–D481
Gomes CM, Frazão C, Xavier AV, Legall J, Teixeira M (2002) Functional control of the binuclear metal site in the metallo-β-lactamase-like fold by subtle amino acid replacements. Protein Sci 11(3):707–712
Khan NH, Bui AA, Xiao Y, Sutton RB, Shaw RW, Wylie BJ et al (2019) A DNA aptamer reveals an allosteric site for inhibition in metallo-β-lactamases. PLoS ONE 14(4):e0214440
Furuyama T, Nonomura H, Ishii Y, Hanson ND, Shimizu-Ibuka A (2016) Structural and mutagenic analysis of metallo-β-lactamase IMP-18. Antimicrob Agents Chemother 60(9):5521–5526
Moali C, Anne C, Lamotte-Brasseur J, Groslambert S, Devreese B, Van Beeumen J et al (2003) Analysis of the importance of the metallo-β-lactamase active site loop in substrate binding and catalysis. Chem Biol 10(4):319–329
King DT, Worrall LJ, Gruninger R, Strynadka NC (2012) New Delhi metallo-β-lactamase: structural insights into β-lactam recognition and inhibition. J Am Chem Soc 134(28):11362–11365
Zhang H, Hao Q (2011) Crystal structure of NDM-1 reveals a common β-lactam hydrolysis mechanism. FASEB J 25(8):2574–2582
Kupper MB, Herzog K, Bennink S, Schlömer P, Bogaerts P, Glupczynski Y et al (2015) The three-dimensional structure of VIM-31–a metallo-β-lactamase from Enterobacter cloacae in its native and oxidized form. FEBS J. 282(12):2352–2360
Green VL, Verma A, Owens RJ, Phillips SE, Carr SB (2011) Structure of New Delhi metallo-β-lactamase 1 (NDM-1). Acta Crystallogr Sect F Struct Biol Cryst Commun 67(10):1160–1164
Guo Y, Wang J, Niu G, Shui W, Sun Y, Zhou H et al (2011) A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Protein Cell. 2(5):384–394
King D, Strynadka N (2011) Crystal structure of New Delhi metallo-β-lactamase reveals molecular basis for antibiotic resistance. Protein Sci 20(9):1484–1491
Yamaguchi Y, Matsueda S, Matsunaga K, Takashio N, Toma-Fukai S, Yamagata Y et al (2015) Crystal structure of IMP-2 metallo-β-lactamase from Acinetobacter spp. Biol Pharm Bull. 38(1):96–101
Wu S, Xu D, Guo H (2010) QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme—intermediate complex represents a minor pathway. J Am Chem Soc 132(51):17986–17988
Bebrone C, Delbrück H, Kupper MB, Schlömer P, Willmann C, Frère J-M et al (2009) The structure of the dizinc subclass B2 metallo-β-lactamase CphA reveals that the second inhibitory zinc ion binds in the histidine site. Antimicrob Agents Chemother 53(10):4464–4471
Simona F, Magistrato A, Dal Peraro M, Cavalli A, Vila AJ, Carloni P (2009) Common mechanistic features among metallo-β-lactamases A COMPUTATIONAL STUDY OF AEROMONAS HYDROPHILA CphA ENZYME. J Biol Chem 284(41):28164–28171
Wang Z, Fast W, Benkovic SJ (1999) On the mechanism of the metallo-β-lactamase from Bacteroides fragilis. Biochemistry 38(31):10013–10023
Park H, Brothers EN, Merz KM (2005) Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-β-lactamase CcrA from Bacteroides fragilis. J Am Chem Soc 127(12):4232–4241
Makena A, Brem J, Pfeffer I, Geffen RE, Wilkins SE, Tarhonskaya H et al (2014) Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability. J Antimicrob Chemother 70(2):463–469
Iyobe S, Kusadokoro H, Ozaki J, Matsumura N, Minami S, Haruta S et al (2000) Amino acid substitutions in a variant of IMP-1 metallo-β-lactamase. Antimicrob Agents Chemother 44(8):2023–2027
Behzadi P, Issakhanian L (2019) Introductory chapter: gene regulation, an RNA network-dependent architecture. Gene regulation. IntechOpen, London
Daiyasu H, Osaka K, Ishino Y, Toh H (2001) Expansion of the zinc metallo-hydrolase family of the β-lactamase fold. FEBS Lett 503(1):1–6
Toney J (2003) Metallo-beta-lactamase inhibitors: could they give old antibacterials new life? Curr Opin Investig Drugs (London England:2000). 4(2):115
Stewart AC, Bethel CR, VanPelt J, Bergstrom A, Cheng Z, Miller CG et al (2017) Clinical variants of New Delhi metallo-β-lactamase are evolving to overcome zinc scarcity. ACS infectious diseases. 3(12):927–940
Bahr G, Vitor-Horen L, Bethel CR, Bonomo RA, González LJ, Vila AJ (2018) Clinical evolution of New Delhi metallo-β-lactamase (NDM) optimizes resistance under Zn (II) deprivation. Antimicrob Agents Chemother 62(1):e01849–17
Pitout J (2012) Extraintestinal pathogenic Escherichia coli: a combination of virulence with antibiotic resistance. Front Microbiol. 3:9
Kumarasamy KK, Toleman MA, Walsh TR, Bagaria J, Butt F, Balakrishnan R et al (2010) Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis 10(9):597–602
Edelstein MV, Skleenova EN, Shevchenko OV, D’souza JW, Tapalski DV, Azizov IS et al (2013) Spread of extensively resistant VIM-2-positive ST235 Pseudomonas aeruginosa in Belarus, Kazakhstan, and Russia: a longitudinal epidemiological and clinical study. Lancet Infect Dis. 13(10):867–876
Everett M, Sprynski N, Coelho A, Castandet J, Bayet M, Bougnon J et al (2018) Discovery of a novel metallo-β-lactamase inhibitor that potentiates meropenem activity against carbapenem-resistant Enterobacteriaceae. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.00074-18
Emeraud C, Escaut L, Boucly A, Fortineau N, Bonnin RA, Naas T et al (2019) Aztreonam plus clavulanate, tazobactam, or avibactam for treatment of infections caused by metallo-β-lactamase-producing gram-negative bacteria. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.00010-19
Chauzy A, Torres SGB, Buyck J, de Jonge B, Adier C, Marchand S et al (2019) Semimechanistic pharmacodynamic modeling of aztreonam-avibactam combination to understand its antimicrobial activity against multidrug-resistant gram-negative bacteria. CPT Pharmacometrics Syst Pharmacol. 8(11):815–824
Abboud MI, Damblon C, Brem J, Smargiasso N, Mercuri P, Gilbert B et al (2016) Interaction of avibactam with class B metallo-β-lactamases. Antimicrob Agents Chemother 60(10):5655–5662
Somboro AM, Amoako DG, Sekyere JO, Kumalo HM, Khan R, Bester LA et al (2019) 1, 4, 7-triazacyclononane restores the activity of β-lactam antibiotics against metallo-β-lactamase-producing Enterobacteriaceae: exploration of potential metallo-β-lactamase inhibitors. Appl Environ Microbiol. https://doi.org/10.1128/AEM.02077-18
Barnes MD, Kumar V, Bethel CR, Moussa SH, O’Donnell J, Rutter JD et al (2019) Targeting multidrug-resistant Acinetobacter spp: sulbactam and the diazabicyclooctenone β-lactamase inhibitor ETX2514 as a novel therapeutic agent. MBio. https://doi.org/10.1128/mBio.00159-19
Tehrani KH, Martin NI (2018) β-lactam/β-lactamase inhibitor combinations: an update. MedChemComm. 9(9):1439–1456
Revers L, Furczon E (2010) An introduction to biologics and biosimilars. Part II: subsequent entry biologics: biosame or biodifferent? Can Pharmacists J/Revue des Pharmaciens du Canada. 143(4):184–191
Klingler F-M, Wichelhaus TA, Frank D, Cuesta-Bernal J, El-Delik J, Müller HF et al (2015) Approved drugs containing thiols as inhibitors of metallo-β-lactamases: strategy to combat multidrug-resistant bacteria. J Med Chem 58(8):3626–3630
Büttner D, Kramer JS, Klingler F-M, Wittmann SK, Hartmann MR, Kurz CG et al (2017) Challenges in the development of a thiol-based broad-spectrum inhibitor for metallo-β-lactamases. ACS infectious diseases. 4(3):360–372
Park B, Naisbitt D, Gordon S, Kitteringham N, Pirmohamed M (2001) Metabolic activation in drug allergies. Toxicology 158(1–2):11–23
Bergstrom A, Katko A, Adkins Z, Hill J, Cheng Z, Burnett M et al (2017) Probing the interaction of aspergillomarasmine A with metallo-β-lactamases NDM-1, VIM-2, and IMP-7. ACS Infect Dis. 4(2):135–145
Funding
No funding.
Author information
Authors and Affiliations
Contributions
PB, HAGP, TMK and LI had the idea for the article, PB, HAGP, TMK and LI performed the literature search, PB, HAGP and TMK performed data analysis, PB, HAGP, TMK and LI drafted the manuscript, and PB critically revised the work.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Ethical approval
Not required.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Behzadi, P., García-Perdomo, H.A., Karpiński, T.M. et al. Metallo-ß-lactamases: a review. Mol Biol Rep 47, 6281–6294 (2020). https://doi.org/10.1007/s11033-020-05651-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-020-05651-9