The FMP has developed a database of commercially available compounds which is used to design our in-house HTS collection and is additionally applied to create focused libraries. But the dramatically increase of unique compounds of one order of magnitude from less than 10 to around 30 to 40 million compounds currently and approximately hundred million compounds in the next years requires a reorganization and redevelopment of our storage and searching strategy. To manage such a massive amount of data we developed a Registration Database for registration and normalisation of vendor catalogues. This database contains the highly redundant data of the vendor catalogues and is converted in a second step into the non-redundant Unique Structure Database which represents a data warehouse combining vendor data, structural descriptors and in-house classification tools including our earlier developed ADMET- and reactivity filters as well as our in-house fragment-based fingerprints used for library design tasks. The management of both database systems is part of a new developed Java application, which handles the user management for the data upload in the Registration Database and the conversion into the Unique Structure Database. Further a first version of a Web service is in preparation. This service allows the scientist not only to search for compounds and fragments in the Unique Structure Database but also to combine such a search with the FMP tools to classify compounds for their usability in biological assays.

1. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
BERND RUPP
Chemical Information systems:
From compound collections to rationally
designed HTS library

2. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
The Library Design Team
Head: Ronald Kühne
Module Cheminformatic/Drug Design
M. Lisurek
 Design and enhancement of
Screening- Libraries
 Maintenance of Vendor-Data
- Library Design:
 Design of focussed Libraries
 Design of Virtual Screens
 Design of Docking Studies
 Development of Homology Models
- Modelling:
 Pharmacophore Models
 QSAR
Module Database Design and IT
M. Pawletta, R. AL-Yamori and B. Rupp
- Database design:
 Development and Maintenance of relational
Database of Screening results
 Development of commercial available
compound library
- Software development
- Hardware Management
 Tools for Processing Structural Data

3. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Screening Libraries @ FMP
[CBB 6: - 1.280 Cpds, LOPAC-library of
pharmacologically active annotated Cpds]
2005 CBB 1: - 16.544 Cpds from ChemDiv
2006/07 CBB 4: - 4.224 Cpds, ArtChem-library
CBB 3: - 4.576 Cpds, fragment library
2008/09 CBB 2: - 3.520 Cpds from Enamine, IBS,
ChemDiv, KeyOrganics, Maybridge
2011 CBB X: - 1.765 Cpds from IBS
2012 CBB Y: - 2.600 Cpds from Enamine
and UORSY
[CBB 5: - 1.780 Cpds synthesized by academic
groups, collected by E. Specker]
∑ ~35.000 Cpds
€ 130.000
€ ~10.000
€ ~30.000
€ ~80.000
€ ~45.000
€ ~45.000
€ 20.000
∑ € ~360.000

4. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Database of Available Chemical Substances (DACS)
Usage:
- Experimental:
design of HTS, Ligation,
Building Block und focused
Libraries
- Theoretical:
Virtual Screening, Docking
Testing new Methods
Advantages:
- Effective Data Control
- Individual Tagging and Search
functionality

5. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
DACS 2005
~20 vendors
~ 2 million Cpds

6. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Upload History
147 311
12 489 623
13 996 350
4 350 900
42 659 022
0
5 000 000
10 000 000
15 000 000
20 000 000
25 000 000
30 000 000
35 000 000
40 000 000
45 000 000
2006 2007 2008 2009 2010 2011 2012 2013
Import Year
Records
Structures

7. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Data Processing Routine
SD-File
SDB
UDB
FMP-Data
Management
Tool
SD-File
Webinterface
Searchtools
Vendor collections
SD-File registration
Unique Structure

8. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
SD File collection 2012
Vendor collection_count file_count mol_count Vendor collection_count file_count mol_count
enamine 38 89 21.238.992,00 labotest 4 5 122.867,00
ukrorgsynthesis 16 54 14.918.628,00 sigma_aldrich 3 4 118.392,00
chemdiv 50 134 6.826.433,00 apollo_scientific 6 16 111.361,00
aurora 9 31 5.494.875,00 zylexa 5 6 107.425,00
vitas_m_lab 7 41 4.255.322,00 matrix_scientific 1 2 91.556,00
otava 32 47 4.099.533,00 analyticon 5 15 84.037,00
chembridge 20 41 4.038.934,00 nano_syn 2 9 65.327,00
life_chemicals 76 95 2.875.379,00 toslab 9 15 47.944,00
Ibs 4 24 1.908.031,00 arkad 1 1 31.102,00
amri 9 18 1.258.137,00 fluorochem 1 1 29.304,00
asinex 14 20 1.253.381,00 emc 1 1 28.932,00
specs 16 19 1.140.632,00 asis_chem 19 19 24.485,00
princeton_bio 12 15 949.659,00 peakdale 2 2 15.462,00
timtec 11 21 535.435,00 spectrum_info 1 1 8.678,00
pharmeks 2 5 524.224,00 evoblocks 1 1 8.367,00
aronis 3 12 278.177,00 acb_blocks 3 3 6.561,00
chemical_block 2 6 258.925,00 microsource 7 7 5.120,00
nch_laboratories 3 3 230.831,00 sequoia 1 1 2.323,00
ko_bionet 25 57 192.096,00 selleckchem 7 7 1.828,00
arvi 2 58 180.728,00 combi_blocks 1 1 1.747,00
maybridge 13 15 171.881,00 menai_organics_limited 1 3 652,00
synthon_labs 3 3 129.544,00 Total: 43 448 928 73.673.247,00

9. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
DACS 2012
1
10
100
1 000
10 000
100 000
1 000 000
10 000 000
100 000 000
Records
Structures
Unique Structures

10. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
SDB-Routine
SD-File
SDB
UDB
FMP-Data
Management
Tool
SD-File
SDB
Webinterface
Searchtools

11. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
SD-File Registration
- Determination of key data (Orderno., saltdata, vendor,
file, catalog, import_date, user...)
- Testing of correct Syntax for Structure and Property
block
- Upload into SD-File registration Database
- Upload verification

12. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Catalog (SD-File) Registration

13. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Import Application Form

14. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Import controlling

15. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Import controlling

16. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
ER-Model of the SD-File Registration
ER-model := Entity relationship model

17. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
UDB Routine
SD-File
SDB
UDB
FMP-Data
Management
Tool
SDB
UDB
Webinterface
Searchtools

18. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Unique structure database
- Standardization of chemical Structures
- Normalization of the Data (removal of
redundancy)
- Storage in a Data Warehouse system

19. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
ER-Model of the UDB

20. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Summary
SDF-Registration 2007-2011: 99.2GB
SDF-Registration 2012 : 116.7GB
UDB 2012 : 142.9GB
Molecule Records: 73.64 Mill
Structure Records: 37.89 Mill
Property Records: 65.72 Mill
SaltData Records: 2386
Smallfragment Records: 4838
Lost-molecule Records: 6360
Duplicate Records: 2070
Empty Records: 3582
Error Records: 708
Java 7 (jdk 1.7.10)
Chemaxon 5.12
MySQL 5.5.
12 Missing files (42179 Records):
error in count line of SD-File:
Is fixed with jchem later than 5.12.3
3 2 0 0 0 0 0 0 0
3 2 0 0 0 0 0 0 0 0999 V2000
Wrong count line:
correct count line:

21. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Outlook
 Web interface and start of the Webserver
 Implementation of FMP Reactivity
and Tox. Tag
 Implementation of FMP Solubility
Prediction and other in-house models
 Development of a GUI for UDB Routine
 Connection to other Public recourses like
PubChem and ChEMBL
 Development of virtual Screening and
Docking interfaces
 Update and Bug fix for SDF-Registration
and UDB-Routine
Further Targets:
Coming Soon:

22. LEIBNIZ-INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE
Acknowledgment
Drug Design / Molecular Modeling
• Ronald Kühne, Dr.
• Daniela Müller, Dr.
• Kirill Piotukh, Dr.
• Martyna Pawletta , master student
• Raed Al-Yamori, tech. Informatics
• Robert Opitz, Dr. student
• Matthias Barone, Dr. student
• Matthias Müller, Dr. student
• Michael Lisurek, Dr.
• Frank Eisenmenger, Dr.
Screnning Unit/ Compound
Managment
• Jens-Peter von Kries, Dr.
• Martin Neuenschwander, Dr.
• Edgar Specker, Dr.
Former member:
• Jörg Wichard, Dr. (Bayer AG)
• Lara Kuhnke , master student
Funding:
• Helmholtz Drug Research
initiative; Ronald Frank, Dr.
Partner:
• Prof. Gerhard Wolber (FU Berlin)
• Chemaxon