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author:

Zhu, K. (Zhu, K..) [1] | Lu, J. (Lu, J..) [2] | Ye, F. (Ye, F..) [3] | Jin, L. (Jin, L..) [4] | Kong, X. (Kong, X..) [5] | Liang, Z. (Liang, Z..) [6] | Chen, Y. (Chen, Y..) [7] | Yu, K. (Yu, K..) [8] | Jiang, H. (Jiang, H..) [9] | Li, J.-Q. (Li, J.-Q..) [10] | Luo, C. (Luo, C..) [11]

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Scopus

Abstract:

New Delhi metallo-β-lactmase-1 (NDM-1) is an enzyme that confers antibiotic resistance to bacteria and is thus a serious threat to human health. Almost all clinically available β-lactam antibiotics can be hydrolyzed by NDM-1. To determine the mechanism behind the wide substrate diversity and strong catalytic ability of NDM-1, we explored the molecular interactions between NDM-1 and different β-lactam antibiotics using computational methods. Molecular dynamics simulations and binding free energy calculations were performed on enzyme-substrate (ES) complex models of NDM-1-Meropenem, NDM-1-Nitrocefin, and NDM-1-Ampicillin constructed by molecular docking. Our computational results suggest that mutant residues Ile35 and Lys216, and active site loop L1 residues 65-73 in NDM-1 play crucial roles in substrate recognition and binding. The results of our study provide new insights into the mechanism behind the enhanced substrate binding and wider substrate spectrum of NDM-1 compared with its homologous enzymes CcrA and IMP-1. These insights may be useful in the discovery and design of specific and potent inhibitors against NDM-1. © 2013 Elsevier Inc.

Keyword:

Metallo-β-lactamase; Molecular dynamics simulations; Molecular mechanics/Poisson-Boltzmann surface area; New Delhi metallo-β-lactmase-1

Community:

  • [ 1 ] [Zhu, K.]Department of Chemistry, Fuzhou University, Fujian 350108, China
  • [ 2 ] [Zhu, K.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 3 ] [Lu, J.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 4 ] [Ye, F.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 5 ] [Jin, L.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 6 ] [Kong, X.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 7 ] [Liang, Z.]Center for Systems Biology, Soochow University, Jiangsu 215006, China
  • [ 8 ] [Chen, Y.]Department of Chemistry, Fuzhou University, Fujian 350108, China
  • [ 9 ] [Yu, K.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 10 ] [Jiang, H.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 11 ] [Li, J.-Q.]Department of Chemistry, Fuzhou University, Fujian 350108, China
  • [ 12 ] [Luo, C.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
  • [ 13 ] [Luo, C.]Center for Systems Biology, Soochow University, Jiangsu 215006, China

Reprint 's Address:

  • [Chen, Y.]State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China

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Source :

Biochemical and Biophysical Research Communications

ISSN: 0006-291X

Year: 2013

Issue: 1

Volume: 431

Page: 2-7

2 . 2 8 1

JCR@2013

2 . 5 0 0

JCR@2023

JCR Journal Grade:3

CAS Journal Grade:3

Cited Count:

WoS CC Cited Count: 0

SCOPUS Cited Count: 11

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 0

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