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author:

Zhu, K. (Zhu, K..) [1] | Lu, J. (Lu, J..) [2] | Liang, Z. (Liang, Z..) [3] | Kong, X. (Kong, X..) [4] | Ye, F. (Ye, F..) [5] | Jin, L. (Jin, L..) [6] | Geng, H. (Geng, H..) [7] | Chen, Y. (Chen, Y..) [8] | Zheng, M. (Zheng, M..) [9] | Jiang, H. (Jiang, H..) [10] | Li, J.-Q. (Li, J.-Q..) [11] | Luo, C. (Luo, C..) [12]

Indexed by:

Scopus

Abstract:

New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies. © 2013 Springer Science+Business Media Dordrecht.

Keyword:

β-Lactam antibiotics; Catalytic mechanism; MD; NDM-1; QM/MM

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

Reprint 's Address:

  • [Chen, Y.]Department of Chemistry, Fuzhou University, Fujian 350108, China

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Source :

Journal of Computer-Aided Molecular Design

ISSN: 0920-654X

Year: 2013

Issue: 3

Volume: 27

Page: 247-256

2 . 7 8 2

JCR@2013

3 . 0 0 0

JCR@2023

JCR Journal Grade:1

CAS Journal Grade:2

Cited Count:

WoS CC Cited Count: 0

SCOPUS Cited Count: 36

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 4

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