P02-07

Development of RIKEN Natural Products Depository Database

Xingmei OUYANG *¹, Hiroyuki HIRANO¹, Hiroyuki OSADA^{1, 2}

¹RIKEN Center for Sustainable Resource Science, RIKEN
²Institute of Microbial Chemistry
( * E-mail: xingmei.ouyang@riken.jp )

The RIKEN Natural Products Depository (NPDepo) is a public depository of chemical compounds. Currently, the NPDepo contains 66,313 pure compounds, about one-third of which are natural products and their derivatives. It has provided a chemical library at the requests of domestic and international researchers. The chemical library is an indispensable resource for exploring useful bio-active compounds.
To promote effective utilization of the NPDepo compounds, an effective structure database system must be constructed for this library. However, natural products remain difficult to encode by conventionally used molecular fingerprinting methods because of their complex and diverse structures. The database system for such a diverse range of compounds, including natural compounds, was insufficient to perform similar structure searches and clustering. We have studied the characteristics and steric features of complex fused ring systems of natural compounds and designed the NPDepo Informatics System (NIS) with 16 fragment types as parameters, focusing on evaluation and application. We compared the similarity search results of our system with results from the previously used fingerprinting methods available in RDKit (MACCS key, Morgan, RDKit, Topological Torsions, AtomPairs).
The results of our developed system show that it is a fast and effective tool for searching for structural analogues of hit compounds in biological evaluations and for clustering natural compounds in complex fused ring systems in the NPDepo library into general fused ring system structure groups.