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Chemaxon's chemo-informatics toolkit integration into the Affectis Data Management System
Database
Automated Data Integration- Example: IC50 Data generated with Flex-Station II -
Data Analysis
GUI client
FlexStation Experiment
raw data
Nkemdilim Uwaje and Markus Panhuysen1
– Affectis Pharmaceuticals * Kraepelinstr. 2 * 80804 Munich / Germany -
JChemBase
Compounds
librarieshit-to-leadagonists
antagonistsproperties
PostgreSQL Database Servercompound structures & fingerprints * compound properties *
pharmacological annotations * assay / experimental metadata
BehavioralPharmacology
open fieldMHB
forced swimdarklightbox
RNAi
Molecular Pharmacology
screening datavalidation dataEC50 / IC50 specificity
toxicity
ExpressionProfiling
IHCISH
MicroarrayRT-PCR / Q-PCR
GUI client
GUI client
GUI client
GUI client
Data Management System Architecture
SSL connectivity
Thick ClientsJava+Jchem Applets
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.
1 contact for correspondence: [email protected]
SAR Tools
Sort search results according to activity
Compare 3D structure oftwo or more molecules
Compound Database
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 content-related searchable data.
registration of meta data
temporary storage of raw data in database
ParserModule
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.
Abstract
Future DirectionsAbout UsAffectis 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).
SAR / Compound Export functionality
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 “3D-SAR-Viewer” which will be used to simultaneously visualize the structure activity relationship for a large set of compounds.
