Structural and functional insight of New Delhi Metallo β-lactamase-1 variants

Future Medicinal Chemistry

Volumn 10, Issue 2, 2018, Pages 221-229

  Khan, Sidra ^a   Ali, Abid ^a   Khan, Asad U ^a  

^a ALIGARH MUSLIM UNIVERSITY   (India)

Author keywords

antibiotics; hydrolysis; loops; mechanism; mutations; NDM 1; New Delhi Metallo lactamase 1; resistance; variants; lactam

Indexed keywords

BETA LACTAM ANTIBIOTIC; METALLO BETA LACTAMASE; NEW DELHI METALLO BETA LACTAMASE 1; UNCLASSIFIED DRUG; BETA LACTAMASE; BETA-LACTAMASE NDM-1;

ALPHA HELIX; AMINO ACID SUBSTITUTION; BETA SHEET; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STRUCTURE; GENE MUTATION; GENE SEQUENCE; GENETIC VARIATION; HYDROLYSIS; HYDROPHOBICITY; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FAMILY; REVIEW; CHEMISTRY; GENETICS; HUMAN; METABOLISM; PROTEIN CONFORMATION;

BETA-LACTAMASES; HUMANS; PROTEIN CONFORMATION;

EID: 85040177896     PISSN: 17568919     EISSN: 17568927     Source Type: Journal    
DOI: 10.4155/fmc-2017-0143     Document Type: Review

References (53)

1. Feng H, Ding J, Zhu D et al. Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins. J. Am. Chem. Soc. 136(42), 14694-14697 (2014).
2. Toleman MA, Bennett PM, Walsh TR. Common regions e.g. orf513 and antibiotic resistance: IS91-like elements evolving complex class 1 integrons. J. Antimicrob. Chemother. 58(1), 1-6 (2006).
3. Saini A, Bansa R. Insights on the structural characteristics of NDM-1: The journey so far. Adv. Biol. Chem. 2, 323-334 (2012).
4. Wilke MS, Lovering AL, Strynadka NC.-lactam antibiotic resistance: A current structural perspective. Curr. Opin. Microbiol. 8(5), 525-533 (2005).
5. Chiou J, Leung TY, Chen S. Molecular mechanisms of substrate recognition and specificity of New Delhi metallo-lactamase. Antimicrob. Agents Chemother. 58(9), 5372-5378 (2014).
6. Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A. NDM-1, the ultimate promiscuous enzyme: Substrate recognition and catalytic mechanism. FASEB J. 27(5), 1917-1927 (2013).
7. Hammoudi D, Moubareck CA, Sarkis DK. How to detect carbapenemase producers A literature review of phenotypic and molecular methods. J. Microbiol. Methods 107, 106-118 (2014).
8. Queenan AM, Bush K. Carbapenemases: The versatile-lactamases. Clin. Microbiol. Rev. 20(3), 440-458 (2007).
9. Yang H, Aitha M, Hetrick AM, Richmond TK, Tierney DL, Crowder MW. Mechanistic and spectroscopic studies of metallo-lactamase NDM-1. Biochemistry 51(18), 3839-3847 (2012).
10. Kim Y, Tesar C, Mire J et al. Structure of apo-A nd monometalated forms of NDM-1-a highly potent carbapenem-hydrolyzing metallo-lactamase. PLoS ONE 6, e24621 (2011).
11. Poirel L, Pitout JD, Nordmann P. Carbapenemases: Molecular diversity and clinical consequences. Future Microbiol. 2(5), 501-512 (2007).
12. Yong D, Toleman MA, Giske CG et al. Characterization of a new metallo-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 (2009).
13. Galleni M, Lamotte-Brasseur J, Rossolini GM, Spencer J, Dideberg O, Frère JM. A standard numbering scheme for the Class A-lactamases. Biochem. J. 276, 269-270 (1991).
14. Bush K, Jacoby GA, Medeiros AA. A functional classification scheme for-lactamases and its correlation with molecular structure. Antimicrob. Agents Chemother. 39(6), 1211-1233 (1995).
15. Kumarasamy KK, Toleman MA, Walsh TR et al. 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 (2010).
16. Bonnin RA, Poirel L, Carattoli A, Nordmann P. Characterization of an IncFII plasmid encoding NDM-1 from Escherichia coli ST131. PloS ONE 7, e34 752 (2012).
17. Lahey clinic. ß-lactamase classification and amino acid sequences for TEM, SHV and OXA extended-spectrum and inhibitor resistant enzymes. www.lahey.org/studies/
18. Kaase M, Nordmann P, Wichelhaus TA, Gatermann SG, Bonnin RA, Poirel L. NDM-2 carbapenemase in Acinetobacter baumannii from Egypt. J. Antimicrob. Chemother. 66(6), 1260-1262 (2011).
19. Tada T, Miyoshi-Akiyama T, Shimada K, Kirikae T. Biochemical analysis of metallo-lactamase NDM-3 from a multidrug-resistant Escherichia coli strain isolated in Japan. Antimicrob. Agents Chemother. 58(6), 3538-3540 (2014).
20. Nordmann P, Boulanger AE, Poirel L. NDM-4 metallo-lactamase with increased carbapenemase activity from Escherichia coli. Antimicrob. Agents Chemother. 56(4), 2184-2186 (2012).
21. Hornsey M, Phee L, Wareham DW. A novel variant, NDM-5, of the New Delhi metallo-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrob. Agents Chemother. 55(12), 5952-5954 (2011).
22. Williamson DA, Sidjabat HE, Freeman JT et al. Identification and molecular characterisation of New Delhi metallo-lactamase-1 (NDM-1)-A nd NDM-6-producing Enterobacteriaceae from New Zealand hospitals. Int. J. Antimicrob. Agents 39(6), 529-533 (2012).
23. Göttig S, Hamprecht AG, Christ S, Kempf VA, Wichelhaus TA. Detection of NDM-7 in Germany, a new variant of the New Delhi metallo-lactamase with increased carbapenemase activity. J. Antimicrob. Chemother. 68(8), 1737-1740 (2013).
24. Tada T, Miyoshi-Akiyama T, Dahal RK et al. NDM-8 metallo-lactamase in a multidrug-resistant Escherichia coli strain isolated in Nepal. Antimicrob. Agents Chemother. 57(5), 2394-2396 (2013).
25. Wang X, Li H, Zhao C et al. Novel NDM-9 metallo-lactamase identified from a ST107 Klebsiella pneumoniae strain isolated in China. Int. J. Antimicrob. Agents 44(1), 90-101 (2014).
26. Khajuria A, Praharaj AK, Kumar M, Grover N. Presence of a novel variant NDM-10, of the New Delhi metallo-beta-lactamase in a Klebsiella pneumoniae isolate. Indian J. Med. Microbiol. 34(1), 121-123 (2016).
27. Khan AU, Ali A, Srivastava G, Sharma A. Potential inhibitors designed against NDM-1 type metallo-lactamases: An attempt to enhance efficacies of antibiotics against multidrug-resistant bacteria. Sci. Rep. 7(1), 9207 (2017).
28. Tada T, Shrestha B, Miyoshi-Akiyama T et al. NDM-12, a novel New Delhi metallo-lactamase variant from a carbapenem-resistant Escherichia coli clinical isolate in Nepal. Antimicrob. Agents Chemother. 58(10), 6302-6305 (2014).
29. Shrestha B, Tada T, Miyoshi-Akiyama T et al. Identification of a novel NDM variant, NDM-13, from a multidrug-resistant Escherichia coli clinical isolate in Nepal. Antimicrob. Agents Chemother. 59(9), 5847-5850 (2015).
30. Zou D, Huang Y, Zhao X et al. A novel New Delhi metallo-lactamase variant, NDM-14, isolated in a Chinese hospital possesses increased enzymatic activity against carbapenems. Antimicrob. Agents Chemother. 59(4), 2450-2453 (2015).
31. Liu Z, Wang Y, Walsh TR et al. Plasmid-mediated novel blaNDM-17 gene encoding a carbapenemase with enhanced activity in a ST48 Escherichia coli strain. Antimicrob. Agents Chemother. 61(5), pii:AAC.02233-16 (2017).
32. Brown MC, Verma D, Russell C, Jacobs DJ, Livesay DR. A case study comparing quantitative stability-flexibility relationships across five metallo-lactamases highlighting differences within NDM-1. Methods Mol. Biol. 1084, 227-238 (2014).
33. Khan AU, Nordmann P. NDM-1-producing Enterobacter cloacae and Klebsiella pneumoniae from diabetic foot ulcers in India. J. Med. Microbiol. 61(Pt 3), 454-456 (2012).
34. Zheng B, Tan S, Gao J et al. An unexpected similarity between antibiotic-resistant NDM-1 and-lactamase II from Erythrobacter litoralis. Protein Cell 2(3), 250-258 (2011).
35. Thomas PW, Zheng M, Wu S et al. Characterization of purified New Delhi metallo-lactamase-1. Biochemistry 50(46), 10102-10113 (2011)
36. Guo Y, Wang J, Niu Get al. A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Protein Cell 2(5), 384-394 (2011).
37. Bebrone C. Metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Biochem. Pharmacol. 74(12), 1686-1701 (2007).
38. Zhang H, Hao Q. Crystal structure of NDM-1 reveals a common-lactam hydrolysis mechanism. FASEB J. 25(8), 2574-2582 (2011)
39. King D, Strynadka N. Crystal structure of New Delhi metallo-lactamase reveals molecular basis for antibiotic resistance. Protein Sci. 20(9), 1484-1491 (2011).
40. Chen J, Chen H, Shi Y et al. Probing the effect of the nonactive-site mutation Y229W in New Delhi metallo-lactamase-1 by site-directed mutagenesis, kinetic studies and molecular dynamics simulations. PLoS ONE 8, e820-80 (2013).
41. Green VL, Verma A, Owens RJ, Phillips SE, Carr SB. Structure of New Delhi metallo-lactamase 1 (NDM-1). Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67(Pt 10), 1160-1164 (2011).
42. Toleman MA, Bennett PM, Walsh TR. ISCR elements: Novel gene-capturing systems of the 21st century Microbiol. Mol. Biol. Rev. 70(2), 296-316 (2006).
43. Concha NO, Rasmussen BA, Bush K, Herzberg O. Crystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis. Structure 4(7), 823-836 (1996).
44. King DT, Worrall LJ, Gruninger R, Strynadka NC. New Delhi metallo-lactamase: Structural insights into-lactam recognition and inhibition. J. Am. Chem. Soc. 134(28), 11362-11365 (2012).
45. Wang Z, Fast W, Valentine AM, Benkovic SJ. Metallo-beta-lactamase: Structure and mechanism. Curr. Opin. Chem. Biol. 3(5), 614-622 (1999).
46. Zhu K, Lu J, Ye F et al. Structure-based computational study of the hydrolysis of New Delhi metallo-lactmase-1. Biochem. Biophys. Res. Commun. 431(1), 2-7 (2013).
47. Chen J, Chen H, Zhu T, Zhou D. Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-lactamase: Experimental and computational study. Phys. Chem. Chem. Phys. 16(14), 6709-6716 (2014).
48. Kazmierczak KM, Rabine S, Hackel M et al. Multiyear, multinational survey of the incidence and global distribution of metallo-lactamase-producing enterobacteriaceae and Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 60(2), 1067-1078 (2015).
49. Makena A, Brem J, Pfeffer I et al. Biochemical characterization of New Delhi metallo-lactamase variants reveals differences in protein stability. J. Antimicrob. Chemother. 70(2), 463-469 (2015).
50. Kaase M, Nordmann P, Wichelhaus TA et al. NDM-2 carbapenemase in Acinetobacter baumanii from Egypt. J. Antimicrob. Chemother. 66(6), 1260-1262 (2011).
51. Khan AU, Rehman MT. Role of nonactive-site residue Trp-93 in the function and stability of New Delhi metallo-lactamase 1. Antimicrob. Agents Chemother. 60(1), 356-360 (2016).
52. Groundwater PW, Xu S, Lai F et al. New Delhi metallo-lactamase-1: Structure, inhibitors and detection of producers. Future Med. Chem. 8(9), 993-1012 (2016).
53. Khan AU, Maryam L, Zarrilli R. Structure, genetics and worldwide spread of New Delhi metallo-lactamase (NDM): A threat to public health. BMC Microbiol. 17(1), 101 (2017).