Title: Dr. Zhiwei Cao
1Computational Platform for Mechanistic Study of
Chinese Herb
- Dr. Zhiwei Cao
- College of life science and biotechnology,
- Tongji University
- Shanghai Center for Bioinformation Technology
2Overview
- Introduction of Mechanistic Study of Chinese Herb
- Computational Platform Resources and
Technologies - Case Study
- Ongoing and future development
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41. Introduction Mechanism of Herbs Multiple
Ingredients, Multiple Targets, Network
Pharmacology Therapeutics 2000, 86191-198
5Questions about Herb Mechanism
- What ingredients are active compounds?
- What are their potential targets?
- What are their targeted pathways?
- How can we analyze the network?
- ..
62. Platform Resources and Technologies
- 1. China patent filed
- Identification of main active ingredients of
herbs based on database technology (SCBIT) - 2. US patent obtained
- INVDOCK to identify potential drug targets (BIDD)
- 3. Software license obtained
- Human intergrated PPI database (SCBIT)
- 4. China patent filed
- Computational platform and methodologies to
support herbal mechanistic study (SCBIT)
72.1 Herbal Ingredient and Content database(HICD)
- Above 30 related journals
- gt3200 literatures being curated
- Herbs from 39 countries
- gt15,000 ingredient with Content information
- Including all potential factors affecting
ingredient content - Collecting time, site
- herbal part
- Processing methods
- Method to measure the content
- Therapeutic effects
- Diseases
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92.2. Computational Method to Identify Potential
Targets (INVDOCK)
- US patent authorized 6,519,611 B1
(Feb.11.2003 ) - German Merck testing in 2006
- Getting improved both in BIDD and SCBIT
- Getting Co-developed with Bridgeway
high-computing company ( www.bridgeway.com.cn) in
Oct, 2007
102.3 Target network construction based on (ISHIP)
- Experimental and predicted PPI gt 610,000 pairs
- gt 29,000 with experimental evidence
- Covering whole human genome, with confidence
scoring system - Linking to genetic disease database (OMIM)
- Software licensed 2006SR05464?
111.3 Integrated Source of Human interacting
proteins(ISHIP)
12Supporting various queries
- ????????
- Protein accession
- Gene symbol
- GeneID
- IPI accession
- Keyword
- BLAST
Gene symbol search
132.4 Network analysis System biology
14Network Decomposition Technology
Complex networks theory for analyzing metabolic
networks Chinese Science Bulletin 2006 vol. 51
No. 13, 1529-1537
15E.Coli????12??????GSC??????.???????????????????
Zhao J, , Cao ZW, Li YX. Hierarchical
modularity of nested bow-ties in metabolic
networks. BMC Bioinformatics. 2006 Aug 187386.
16E.Coli?????12?????????.??????????????,????????
17Identifying topological modules and their
functions
Modular co-evolution of metabolic networks. BMC
Bioinformatics 2007,8311.
183. Case study ganoderic acid D
- Main ingredient of tri-terpenoids in Ganoderma
lucidum (??). - Inhibit hela cell proliferation? apoptosis
- Target 2-DE 21 proteins
- Question whats the target pathway?
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20Minimization 21 proteins (steiner)
Proteomic characterization of the cytotoxic
mechanism of ganoderic acid D and computer
automated estimation of the possible drug-target
network Molecular Cell Proteomics 2007.12.31
214. Future development
- Improvement of target-searching technology (
with BIDD, NUS) - Clustering and similarity search of active
ingredients (with BIDD and Tongji) - Herbal toxicity study ( with Shanghai TCM
university) - Formula validation. ( with .? )
22Collaborative Opportunities
- Experts on Chinese Herb
- Experts on computational chemistry and physics
- Experts on biologists
23Acknowledgements
- Funding from Shanghai Commission of Science and
Technology - 863 funding from China Ministry of Science and
Technology
- Prof. Chen yuzong BIDD group, NUS
- Prof. Li Yixue, SCBIT
- Shanghai TCM Modernizations Center
Whether from the East or the West, we share the
same goal of improving human health.
24If there is any technology that could lead to a
breakthrough in traditional Chinese medicine, it
will be systems biology, NATUREVol 44812
July 2007