The Open Form Inducer Approach for Structure-Based Drug Design

PLoS One. 2016 Nov 28;11(11):e0167078. doi: 10.1371/journal.pone.0167078. eCollection 2016.

Abstract

Many open form (OF) structures of drug targets were obtained a posteriori by analysis of co-crystals with inhibitors. Therefore, obtaining the OF structure of a drug target a priori will accelerate development of potent inhibitors. In addition to its small active site, Trypanosoma cruzi dihydroorotate dehydrogenase (TcDHODH) is fully functional in its monomeric form, making drug design approaches targeting the active site and protein-protein interactions unrealistic. Therefore, a novel a priori approach was developed to determination the TcDHODH active site in OF. This approach consists of generating an "OF inducer" (predicted in silico) to bind the target and cause steric repulsion with flexible regions proximal to the active site that force it open. We provide the first proof-of-concept of this approach by predicting and crystallizing TcDHODH in complex with an OF inducer, thereby obtaining the OF a priori with its subsequent use in designing potent and selective inhibitors. Fourteen co-crystal structures of TcDHODH with the designed inhibitors are presented herein. This approach has potential to encourage drug design against diseases where the molecular targets are such difficult proteins possessing small AS volume. This approach can be extended to study open/close conformation of proteins in general, the identification of allosteric pockets and inhibitors for other drug targets where conventional drug design approaches are not applicable, as well as the effective exploitation of the increasing number of protein structures deposited in Protein Data Bank.

MeSH terms

  • Catalytic Domain
  • Computer Simulation
  • Dihydroorotate Dehydrogenase
  • Drug Design*
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / metabolism*
  • Models, Molecular
  • Oxidoreductases Acting on CH-CH Group Donors / chemistry*
  • Oxidoreductases Acting on CH-CH Group Donors / metabolism*
  • Protein Conformation
  • Trypanocidal Agents / chemistry
  • Trypanocidal Agents / metabolism*
  • Trypanosoma cruzi / drug effects
  • Trypanosoma cruzi / enzymology*

Substances

  • Dihydroorotate Dehydrogenase
  • Enzyme Inhibitors
  • Trypanocidal Agents
  • Oxidoreductases Acting on CH-CH Group Donors

Grants and funding

This work was supported in part by Creative Scientific Research Grant 18GS0314 (to K.K.), Grant-in-aid for Scientific Research 18073004 and 26253025 (to K.K.), 26870119 and 16K19114 (to D.K.I.) from the Japanese Society for the Promotion of Science, and Targeted Proteins Research Program (to K.K. and Sh.H.) from the Japanese Ministry of Education, Science, Culture, Sports and Technology (MEXT). The authors also acknowledge the support from Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry (to K.K. and Sh.H.) and JST/ JICA, SATREPS (Science and Technology Research Partnership for Sustainable Development) 10000284 (to K.K.) and 1400738 (to D.K.I.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.