Inhibitor Discovery of Full-Length New Delhi Metallo-β-Lactamase-1 (NDM-1)

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Shen, Bingzheng ^a,b,e   Yu, Yan ^c   Chen, Hui ^b   Cao, Xin ^d   Lao, Xingzhen ^b   Fang, Yongliang ^a,b   Shi, Yun ^b   Chen, Jiao ^b   Zheng, Heng ^a,b  

^a INSTITUTE OF SOIL SCIENCE   (China)

^b CHINA PHARMACEUTICAL UNIVERSITY   (China)

^c HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^d SHANGHAI INSTITUTE OF ORGANIC CHEMISTRY   (China)

^e RENMIN HOSPITAL OF WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

2 [2,5 BIS[(1H TETRAZOL 5 YL)METHYL]THIOPHEN 3 YL]MALONIC ACID; 3 (BENZYLOXY)THIOPHENE 2,5 DICARBOXYLIC ACID DIMETHYL ESTER; 3,4 BIS(BENZYLOXY)THIOPHENE 2,5 DICARBOXYLIC ACID DIMETHYL ESTER; 3,4 BIS[(1H TETRAZOL 5 YL)METHOXY]THIOPHENE 2,5 DICARBOXYLIC ACID DIMETHYL ESTER; AMPICILLIN; AZTREONAM; BETA LACTAM ANTIBIOTIC; CARBOXYLIC ACID DERIVATIVE; CEFPIRAMIDE; CEFTAZIDIME; CEFTIZOXIME; CEFUROXIME; ENZYME INHIBITOR; HISTIDINE; IMIPENEM; MEROPENEM; METALLO BETA LACTAMASE; NEW DELHI METALLO BETA LACTAMASE 1; PENICILLIN G; SULFUR; THENOIC ACID DERIVATIVE; UNCLASSIFIED DRUG; ZINC ION;

ANTIBACTERIAL ACTIVITY; ARTICLE; CATALYSIS; DRUG ANTAGONISM; ENZYME INHIBITION; ENZYME KINETICS; HYDROGEN BOND; HYDROLYSIS; MOLECULAR DOCKING; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTUM MECHANICS; STATIC ELECTRICITY; STEADY STATE;

ANTI-BACTERIAL AGENTS; AZTREONAM; BACTERIAL PROTEINS; BETA-LACTAM RESISTANCE; BETA-LACTAMASES; BETA-LACTAMS; DRUG SYNERGISM; ENZYME INHIBITORS; ESCHERICHIA COLI; HYDROLYSIS; KINETICS; MOLECULAR DOCKING SIMULATION; RECOMBINANT FUSION PROTEINS; THIENAMYCINS;

EID: 84877663087     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062955     Document Type: Article

References (35)

1. Ambler RP, (1980) The structure of beta-lactamases. Philos Trans R Soc Lond B Biol Sci 289: 321-31.
2. Galleni M, Lamotte-Brasseur J, Rossolini GM, Spencer J, Dideberg O, et al. (2001) Standard numbering scheme for class B β-lactamases. Antimicrob Agents Chemother 45: 660-663.
3. Garau G, García-Sáez I, Bebrone C, Anne C, Mercuri P, et al. (2004) Update of the standard numbering scheme for class B β-lactamases. Antimicrob Agents Chemother 48: 2347-2349.
4. Yong D, Toleman MA, Giske CG, Cho HS, Sundman 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: 5046-5054.
5. Rolain JM, Parola P, Cornaglia G, (2010) New Delhi metallo-β-lactamase (NDM-1): towards a new pandemia? Clin Microbiol Infect 16: 1699-1701.
6. Cornaglia G, Giamarellou H, Rossolini GM, (2011) Metallo-β-lactamases: a last frontier for β-lactams? Lancet Infect Dis 11: 381-393.
7. Williamson DA, Sidjabat HE, Freeman JT, Roberts SA, Silvey A, et al. (2012) Identification and molecular characterisation of New Delhi metallo-β-lactamase-1 (NDM-1)- and NDM-6-producing Enterobacteriaceae from New Zealand hospitals. Int J Antimicrob Agents 39: 529-533.
8. Jamal W, Rotimi VO, Albert MJ, Khodakhast F, Udo EE, et al. (2012) Emergence of nosocomial New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae in patients admitted to a tertiary care hospital in Kuwait. Int J Antimicrob Agents 39: 183-184.
9. Kumarasamy KK, Toleman MA, Walsh TR, Bagaria J, Butt F, 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: 597-602.
10. Moellering RC Jr, (2010) NDM-1-a cause for worldwide concern. N Engl J Med 363: 2377-2379.
11. Zhang H, Hao Q, (2011) Crystal structure of NDM-1 reveals a common β-lactam hydrolysis mechanism. FASEB J 25: 2574-2582.
12. Kim Y, Tesar C, Mire J, Jedrzejczak R, Binkowski A, et al. (2011) Structure of apo- and monometalated forms of NDM-1-a highly potent carbapenem-hydrolyzing metallo-β- lactamase. PLoS One 6: e24621.
13. Guo Y, Wang J, Niu G, Shui W, Sun Y, et al. (2011) A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Protein Cell 2: 384-394.
14. Poirel L, Lagrutta E, Taylor P, Pham J, Nordmann P, (2010) Emergence of metallo-β-lactamase NDM-1-producing multidrug-resistant Escherichia coli in Australia. Antimicrob Agents Chemother 54: 4914-4916.
15. Laraki N, Franceschini N, Rossolini GM, Santucci P, Meunier C, et al. (1999) Biochemical characterization of the Pseudomonas aeruginosa 101/1477 metallo-β-lactamase IMP-1 produced by Escherichia coli. Antimicrob Agents Chemother 43: 902-906.
16. Thomas PW, Zheng M, Wu S, Guo H, Liu D, et al. (2011) Characterization of purified New Delhi metallo-β-lactamase-1. Biochemistry 50: 10102-10113.
17. Shen B, Zheng H, Lao X, Zhou Y (2012) Preparation of five-membered heterocycle dicarbonyl derivatives as multidrug-resistant antibacterial agents. Faming Zhuanli Shenqing CN102304108A.
18. Wachino J, Yoshida H, Yamane K, Suzuki S, Matsui M, et al. (2011) SMB-1, a novel subclass B3 metallo-β-lactamase, associated with ISCR1 and a class 1 integron, from a carbapenem-resistant Serratia marcescens clinical isolate. Antimicrob Agents Chemother 55: 5143-5149.
19. Hao Q, Wang H, Wang J, Dou J, Zhang M, et al. (2013) Effective antimicrobial activity of Cbf-K16 and Cbf-A7A13 against NDM-1-carrying Escherichia coli by DNA binding after penetrating the cytoplasmic membrane in vitro. J Pept Sci 19: 173-180.
20. Clinical and Laboratory Standards Institute (2010) Performance standards for antimicrobial susceptibility testing; twentieth informational supplement. CLSI DocumentM100-S20.
21. Hammond GG, Huber JL, Greenlee ML, Laub JB, Young K, et al. (1999) Inhibition of IMP-1 metallo-β-lactamase and sensitization of IMP-1-producing bacteria by thioester derivatives. FEMS Microbiol Lett 459: 289-296.
22. Moloughney JG, D Thomas J, Toney JH, (2005) Novel IMP-1 metallo-β-lactamase inhibitors can reverse meropenem resistance in Escherichia coli expressing IMP-1. FEMS Microbiol Lett 243: 65-71.
23. Koska J, Spassov VZ, Maynard AJ, Yan L, Austin N, et al. (2008) Fully automated molecular mechanics based induced fit protein-ligand docking method. J Chem Inf Model 48: 1965-1973.
24. Discovery Studio Version 2.5 (2009) User Manual. San Diego, CA; Accelrys Inc.
25. Teague SJ, (2003) Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2: 527-541.
26. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: A program for macromolecular energy minimization and dynamics calculations. J Comp Chem 4: 187-217.
27. Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow C, et al. (2003) QUASI: a general purpose implementation of the QM/MM approach and its application to problems in catalysis. J Mol Struct (Theochem) 632: 1-28.
28. Hohenberg P, Kohn W, (1964) Inhomogeneous electron gas. Phys Rev B 136: 864-871.
29. Levy M, (1979) Universal variational functionals of electron densities, first-order density matrices, and natural spin-orbitals and solution of the v-representability problem. Proc Natl Acad Sci 76: 6062-6065.
30. Riley KE, Op't Holt BT, Merz Jr. KM, (2007) Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. J Chem Theory Comput 3: 407-433.
31. Becke AD, (1988) A multicenter numerical integration scheme for polyatomic molecules. J Phys Chem 88: 2547-2553.
32. Lee C, Yang W, Parr RG, (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37: 785-789.
33. Ververs TF, van Dijk A, Vinks SA, Blankestijn PJ, Savelkoul TJF, et al. (2000) Pharmacokinetics and dosing regimen of meropenem in critically ill patients receiving continuous venovenous hemofiltration. Crit Care Med 28: 3412-3416.
34. Menikarachchi LC, Gascón JA, (2010) QM/MM approaches in medicinal chemistry research. Curr Top Med Chem 10: 46-54.
35. Yang H, Aitha M, Hetrick AM, Richmond TK, Tierney DL, et al. (2012) Mechanistic and spectroscopic studies of metallo-β-lactamase NDM-1. Biochemistry 51: 3839-3847.