Transcript po1_Chemaxons chemo-informatics toolkit integration into the

Chemaxon's chemo-informatics toolkit integration into the
Affectis Data Management System
Nkemdilim Uwaje and Markus
1
Panhuysen
– Affectis Pharmaceuticals * Kraepelinstr. 2 * 80804 Munich / Germany -
Abstract
Data Management System Architecture
We developed a Java-/PSQL based data management
solution for our R&D. Sources of our data are as
diverse as immunohistochemistry and in situ
hybridization experiments, in vitro screening and
EC50/ IC50 curves (plate reader), in vivo experiments,
and last but not least small molecule structures and
whole compound libraries.
Here, we present the architecture of our growing data
management system and delineate the integration of
JChemBase and the Marvin API.
Molecular
Pharmacology
Behavioral
Pharmacology
open field
MHB
forced swim
darklightbox
RNAi
screening data
validation data
EC50 / IC50
specificity
toxicity
GUI client
GUI client
PostgreSQL Database Server
compound structures & fingerprints * compound properties *
pharmacological annotations *
assay / experimental metadata
SSL connectivity
GUI client
Compound Database
JChemBase
Expression
Profiling
Compounds
IHC
ISH
Microarray
RT-PCR / Q-PCR
libraries
hit-to-lead
agonists
antagonists
properties
GUI client
Thick Clients
Java+Jchem Applets
Compounds are introduced into the database via
JChemBase either by importing or drawing.
Additional data can also be entered (physical
properties, R&S, pharmacological action, batch
data…). Screening results and other experimental data
are stored in a searchable, sortable meta-data style.
Graphic files and images are annotated with contentrelated searchable data.
Aim of the data management software is to integrate data from our different
R&D groups, provide comprehensive access to the accumulating data, allow
rapid analysis of structure activity relationships from the point of view of
different assays and offer a customizable report functionality. The compound
management aspect of our database was implemented using Chemaxon's
JChemBase tools. The JChemBase developers API functionalities were integrated
for the handling and presentation of chemical structures as well as for
compound-related calculations.
Automated Data Integration
- Example: IC50 Data generated with Flex-Station II -
SAR Tools
FlexStation
Experiment
SAR / Compound
Export functionality
raw data
GUI client
Parser
Module
temporary storage of raw
data in database
Compare 3D structure of
two or more molecules
Data Analysis
Sort search results
according to activity
About Us
Affectis Pharmaceuticals AG (located in Munich /
Germany) is a young biopharmaceutical company
dedicated to development of innovative drugs for the
treatment of psychiatric disorders. Our expertise runs
from target identification, in vitro / in vivo target
validation and behavioral pharmacology to assay
development, compound screening and lead
optimization. Our main programs are in preclinical
development or clinical phase II, respectively.
Additionally,
we
perform
service
research
collaborations with big pharma (Mitsubishi Pharma,
Organon).
Database
registration of
meta data
Future Directions
The presented database serves as a starting point for further developments. We
are currently working on the improvement of the report generation capabilities,
and of the overall-performance of the software. In the future, data from external
databases will be integrated / linked (PubChem etc.). Searches will not be
restricted to our own compound database but optionally include public database
searches. The user management will be optimized in a way that users with
specific functions will have specific perspectives and defined rights to
read/edit/create data points within the database. We plan to implement a “3DSAR-Viewer” which will be used to simultaneously visualize the structure
activity relationship for a large set of compounds.
1
contact for correspondence: [email protected]