Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Prediction of Relative Stability between TACE/Gelastatin and TACE/Gelastatin Hydroxamate

  • Nam, Ky-Youb (Research Institute Bioinformatics & Molecular Design (BMD), Yonsei Engineering Research Complex) ;
  • Han, Gyoon-Hee (Department of Biotechnology, Yonsei University) ;
  • Kim, Hwan-Mook (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • No, Kyoung-Tai (Department of Biotechnology, Yonsei University)
  • Received : 2010.04.12
  • Accepted : 2010.09.15
  • Published : 2010.11.20
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Abstract

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.

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