Ongoing projects

Computational and systems approaches to early stage drug discovery

Computational methods can potentially improve target identification and validation at the earliest possible stage of drug development by providing a better understanding of the biology of the target network. Such a knowledge should also lead to new therapeutic strategies based on molecular mechanisms.

Identification and validation of novel drug targets

What is target prioritization and why?

We have developed TargetMine, an integrated data warehouse for assisting early stage drug discovery. (See the previous NEDO-funded project page.)

Here are specific applications, in which we hypothesized novel host factors to be involved in the pathogen life cycle and validated it experimentally:

◾HCV pathogenesis (yeast two-hybrid assays): Tripathi et al. 2010.
◾HCV pathogenesis (proteomic data): Tripathi et al. 2012.
◾Lung tumorigenesis (gene expression): Ihara et al. 2012.
◾HCV pathogenesis (yeast two-hybrid assays and literature): Tripathi et al. 2013.

More details can be found here.

What is target validation?

New therapeutic strategies based on molecular mechanisms

We are developing a range of computational biology techniques, utilizing information about protein sequence, structure and interaction

Prediction of protein-protein interactions with an application to breast cancer therapies
Enzyme structures and functions

Biomarker discovery

We are developing databases for biomarker discovery and toxicity prediction.

An Integrated Platform for Toxicogenomics Data Analysis
The Adjuvant Database Project

Other projects

Large-scale data integration (in collaboration with the NBDC)
Development of an international pharmaceutical innovation value chain for in silico drug discovery
Development of a novel method for modelling dynamic structures of membrane proteins
High throughput algorithms for predicting specificity in regulatory interactions