Flux (1): a virtual synthesis scheme for fragment-based de novo design

J Chem Inf Model. 2006 Mar-Apr;46(2):699-707. doi: 10.1021/ci0503560.


It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builder reaxions) facilitated the generation of new molecules using a single known reference compound as a template. This molecule assembly method is applicable in the absence of receptor-structure information. In a case study, we used imantinib (Gleevec) and a Factor Xa inhibitor as the reference structures. The algorithm succeeded in redesigning the templates from scratch and suggested several alternative molecular structures. The resulting designed molecules were chemically reasonable and contained essential substructure motifs. A comparison of molecular descriptors suggests that holographic descriptors might be advantageous over binary fingerprints for ligand-based de novo design.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms*
  • Drug Design*
  • Factor Xa / genetics
  • Factor Xa Inhibitors
  • Ligands*
  • Molecular Structure
  • Mutation
  • Phosphotransferases / antagonists & inhibitors
  • Phosphotransferases / genetics
  • Software Validation*
  • Thrombin / chemistry


  • Factor Xa Inhibitors
  • Ligands
  • Phosphotransferases
  • Thrombin
  • Factor Xa