About DB

About PPI Library

This database contains over 15,000 compounds expected to PPI inhibitions. These library compounds were selected from a virtual compound library (K-Library developed by the Kishida Chemical Co. Ltd., ~8M compounds). We conducted docking calculation against the virtual library on PDB structures of known PPI targets. Then, we selected and synthesized about 100 compounds from each target. Furthermore, our PPI library also includes novel scaffolds and non-flat 3D shapes (sphere-like structures). Thus, our PPI library is useful for small and medium-sized drug discovery.

About Database

This database has been developed by Keio University and PeptiDream Inc. During this development, NIBIOHN supports and advises this project. This work was supported by AMED (Japan Agency for Medical Research and Development) grant.


  1. Ikeda K, Maezawa Y, Yonezawa T, Shimizu Y, Tashiro T, Kanai S, Sugaya N, Masuda Y, Inoue N, Niimi T, Masuya K, Mizuguchi K, Furuya T, Osawa M. DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions. Front Chem. 2023;10:1090643.
  2. Shimizu Y, Yonezawa T, Sakamoto J, Furuya T, Osawa M, Ikeda K. Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein-protein interaction-oriented library and machine learning. Sci Rep. 2021 ;11(1):7420.
  3. Shimizu Y, Yonezawa T, Bao Y, Sakamoto J, Yokogawa M, Furuya T, Osawa M, Ikeda K. Applying deep learning to iterative screening of medium-sized molecules for protein-protein interaction-targeted drug discovery. Chem Commun (Camb). 2023 May 30;59(44):6722-6725. doi: 10.1039/d3cc01283b. PMID: 37191131.