Exploring the Chemical Space of Known and Unknown Organic Small Molecules at www.gdb.unibe.ch

Authors

  • Jean-Louis Reymond Department of Chemistry and Biochemistry, NCCR TransCure and NCCR Chemical Biology, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland. jean-louis.reymond@ioc.unibe.ch
  • Lorenz C. Blum Department of Chemistry and Biochemistry, NCCR TransCure and NCCR Chemical Biology, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
  • Ruud van Deursen Biomolecular Screening Facility, NCCR Chemical Biology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

DOI:

https://doi.org/10.2533/chimia.2011.863

Keywords:

Cheminformatics, Computer-aided drug design, Chemical space, Databases, Virtual screening

Abstract

Organic small molecules are of particular interest for medicinal chemistry since they comprise many biologically active compounds which are potential drugs. To understand this vast chemical space, we are enumerating all possible organic molecules to create the chemical universe database GDB, which currently comprises 977 million molecules up to 13 atoms of C, N, O, Cl and S. Furthermore, we have established a simple classification method for organic molecules in form of the MQN (molecular quantum numbers) system, which is an equivalent of the periodic system of the elements. Despite its simplicity the 42 dimensional MQN system is surprisingly relevant with respect to bioactivity, as evidenced by the fact that groups of biosimilar compounds form close groups in MQN space. The MQN space of the known organic molecules in PubChem and of the unknown molecules in the Chemical Universe Database GDB-13 can be searched interactively using browser tools freely accessible at www.gdb.unibe.ch.

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Published

2011-11-23

Issue

Section

Scientific Articles

How to Cite

[1]
J.-L. Reymond, L. C. Blum, R. van Deursen, Chimia 2011, 65, 863, DOI: 10.2533/chimia.2011.863.