Designing a new Diels-Alderase: a combinatorial, semirational approach including dynamic optimization

J Chem Inf Model. 2011 Aug 22;51(8):1906-17. doi: 10.1021/ci200177d. Epub 2011 Aug 3.

Abstract

A computationally inexpensive design strategy involving 'semirational' screening for enzymatic catalysis is presented. The protocol is based on well-established computational methods and represents a holistic approach to the catalytic process. The model reaction studied here is the Diels-Alder, for which a successful computational design has recently been published (Siegel, J. B. et al. Science 2010, 329, 309-313). While it is a leap forward in the field of computational design, the focus on designing only a small fraction of the active site gives little control over dynamics. Our approach explicitly incorporates mutagenesis and the analysis of binding events and transition states, and a promising enzyme-substrate candidate is generated with relatively little effort. We estimate catalytic rate accelerations of up to 10⁵.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Biocatalysis
  • Catalytic Domain
  • Chemistry, Pharmaceutical / methods*
  • Combinatorial Chemistry Techniques
  • Computer Simulation
  • Data Mining
  • Databases, Protein
  • Drug Design
  • Drug Discovery / methods*
  • Humans
  • Kinetics
  • Ligands
  • Models, Molecular
  • Mutagenesis
  • Pharmaceutical Preparations / analysis*
  • Pharmaceutical Preparations / chemistry
  • Protein Binding
  • Proteins / analysis*
  • Proteins / chemistry
  • Proteins / metabolism
  • Small Molecule Libraries
  • Substrate Specificity
  • Thermodynamics

Substances

  • Ligands
  • Pharmaceutical Preparations
  • Proteins
  • Small Molecule Libraries