In this joint event our experts are coming together to elaborate on the technical and scientific opportunities coming from this partnership. If you are working on the discovery of next generation drugs and using structure-based approach in your research, join us to learn how to leverage vast biomolecular structural data with innovative technologies.

2. Biomolecule structural
data management

3. Agenda
Introduction
Who are we?
Biotherapeutics
Opportunities, challenges
What is a biomolecule?
Overview
Features for handling complex
biomolecules

4. Chemaxon facts in a nutshell
Founded in 1998 (HQ in Budapest)
100% independent software & service provider
~250 employees worldwide
>30 software products

5. Identify &
validate
targets
Lead design
& discovery
Lead
optimization
Preclinical
candidate
selection
Clinical
Trials (I,
IIa/IIb, III)
Post-
approval
Phase
Chemaxon software supported workflows
Design Hub
Marvin
Phys-chem
calculators
JChem
Engines
Reactor
technology
Chemicalize
JChem for
Office
Registration Patent
drafting
Compliance
Checker
ChemCurator
Instant JChem
Where do we fit in a drug discovery workflow

6. Biotherapeutic fields
Synthetic peptides Therapeutic RNAs
Recombinant proteins Antibodies
Conjugates

7. Opportunities in biotherapeutics
Emerging trend in developing novel biotherapeutics
● “Drugging the undruggable”
● Improving biological/chemical stability, specificity and potency
● Improving biomolecule delivery
Specialized teams and organizations need to collaborate
● Chemistry and biology meet
● Outsourcing R&D activities

8. Data management challenges
Understanding biological and chemical structural context
● internal and external R&D departments
● manufacturers
Data silos
● Excel spreadsheets
Increasing complexity of biomolecules
● decreases the visual interpretation efficiency
● increases the time spent on designing structure

9. What is a biomolecule?
eBmt
MeV
MeL
MeL
dA
A
MeL
MeV
MeL
Abu
Sar
https://pubchem.ncbi.nlm.nih.gov/compound/Ciclosporin#section=3D-Status
Abu-Sar-MeL-MeV-MeL-A-dA-MeL-MeL-MeV-eBmt

10. https://www.researchgate.net/publication/51538736_Functionalized_polystyrene_supports_for_solid-phase_syn
thesis_of_glycyl-_alanyl-_and_isoleucyl-RNA_conjugates_as_hydrolysis-resistant_mimics_of_peptidyl-tRNAs
What is a biomolecule?

11. Biomolecule features overview
Model and register biological entities
Chemically modified entities
● peptides, oligonucleotides, conjugates etc.
Biological entities
● proteins, antibodies etc.
Biological tools and reagents
● plasmids, cell lines etc.

12. Biomolecule features overview
Standardize biomolecules
Standardize complex biomolecules
● with HELM (Hierarchical Editing Language for Macromolecules)
● set nomenclature and chemical definition of building blocks
Standardize chemical structures
● to achieve uniformity in your chemical representation
● modify chemistry and perform visual transformations

13. Biomolecule features overview
Visualize and design entities
Interpret complex structures
Scientists can easily read and share
biomolecule structure information
(peptides, oligonucleotides and
conjugates)
Design modifications
Introduce novel sequence and/or chemical
patterns.

14. Biomolecule features overview
Monomer library management
Capture atomic level of detail
The monomer library enables fast and
easy way for scientists to interpret and
construct atomic level representations
Customize monomers
Work with generic or novel chemistry

15. Thank you
Mark Somogyi
msomogyi@chemaxon.com

16. Challenges in
data handling
Biomolecular structures –
beyond the small molecule
paradigm
16
Peter Schmidtke, PhD

17. Discngine
17

18. Company
Paris
2004 ~58 employees >70 customers worldwide
More Information: www.discngine.com
SOFTWARE FOR LIFE SCIENCES RESEARCH

19. Our Focus
19
Data acquisition and
analysis – Sample
management
Cheminformatics &
Bioinformatics
Scientific Data
Science
New Molecule Discovery

20. Discngine
Strategic Partners
▪ ChemAxon
▪ Dassault Systèmes BIOVIA
▪ Oracle
▪ TIBCO & Perkin Elmer (Spotfire)
▪ KNIME
▪ LabVoice
▪ Nanome
▪ Schrödinger
Combine & integrate key research IT component to provide Scientific IT solutions

21. 3decision
SaaS platform for 3d Biomolecular Structures
21

22. Collaborative Platform for Structural Analytics and Knowledge Management
Knowledge
Base
Structural
Analytics
Toolkit
Web
Interface
What is 3decision®
?

23. Main purpose of 3decision
Foster and analyze structural knowledge
▪ Centralize all knowledge in one structured database
▪ Use collective intelligence & learn from the past
Enhance collaboration between interdisciplinary teams
▪ Allow scientist to work individually and share ideas within the team
Enable easy access to complex knowledge
▪ Provide visual analytics and predictive tools
▪ Streamline common analyses
▪ Integrate with molecular modeling tools / pipelines

24. 3decision®
Knowledge Base
STRUCTURES
o Docking results
o Homology models
o MD snapshots
public private in silico
SEQUENCES ASSOCIATED DATA

25. 3decision®
Knowledge Base
STRUCTURES SEQUENCES ASSOCIATED DATA
annotations
sequences

26. 3decision®
Knowledge Base
pockets ligand
interactions
electron
density maps
assay data project data
STRUCTURES SEQUENCES ASSOCIATED DATA

27. 27

28. Enhancing scope towards
biologics
Beyond the small molecule universe
28

29. On the menu this year
Full peptide support
▪ Integration in existing UI & API with minimal changes
Antibody registration
▪ Dedicated analyses workflows
▪ Dedicated UI
29

30. Peptide support
Chemaxon integrations
▪ Monomer registration & management
▪ Depiction
▪ Search
▪ Edition
Functionalities
▪ Registration & analysis same as for small molecules
▪ Edition & constrained docking
30

31. Antibody registration
Chemaxon integrations
▪ Sequence registration
▪ ADC’s POC
Functionalities
▪ Sequence Search
▪ Structure Search
▪ Proper entity handling
▪ Sequence Property Relationship
31

32. Integration
32

33. 3decision®
- Setup
User
3decision Web-UI 3decision
knowledge
database

34. Current integrations
34

35. Current Chemaxon integrations
Sketching
▪ MarvinJS new default sketcher
Search
▪ Choral novel molecular DB cartridge
JChem Webservices
▪ Standardization
▪ Atom/Molecular property calculation
▪ Depiction
▪ …
35

36. +33 1 80 48 66 70
contact@discngine.com
Discngine, 79 avenue Ledru-Rollin, 75012 Paris – France
www.discngine.com
Thanks!
More on 3decision.discngine.com
36