Compound property enhancement by virtual compound synthesis

J Bioinform Comput Biol. 2018 Jun;16(3):1840016. doi: 10.1142/S0219720018400164.


During drug discovery, drug candidates are narrowed down over several steps to develop pharmaceutical products. The theoretical chemical space in such steps is estimated to be [Formula: see text]. To cover that space, extensive virtual compound libraries have been developed; however, the compilation of extensive libraries comes at large computational cost. Thus, to reduce the computational cost, researchers have constructed custom-made virtual compound libraries that focus on target diseases. In this study, we develop a system that generates virtual compound libraries from input compounds. When a user inputs a compound, the system recursively applies virtual synthetic reaction rules to the compound to improve its properties. The synthetic pathway can also be traced by the user because the reaction rules in this system are based on real organic synthesis reactions. This system has useful functions for effective drug design, such as structural preservation, allowing the substructures necessary for potency to be maintained. In this paper, to confirm the effect of directional reaction sets, we applied the reaction sets to 100 compounds. Moreover, to confirm that the system can reproduce real synthetic pathways, the synthetic pathways of Ibuprofen and Ofloxacin were explored by inputting isobutyl benzene and 7,8-difluoro-2,3-dihydro-3-methyl-4H-benzoxazine. This application is available at the following URL: .

Keywords: Computational chemistry; drug design; virtual compound library; web system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Inflammatory Agents, Non-Steroidal / chemistry
  • Computational Biology / methods*
  • Ibuprofen / chemistry
  • Libraries, Digital*
  • Ofloxacin / chemistry
  • Pharmaceutical Preparations / chemistry*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*


  • Anti-Inflammatory Agents, Non-Steroidal
  • Pharmaceutical Preparations
  • Small Molecule Libraries
  • Ofloxacin
  • Ibuprofen