Chemaxon x Discngine webinar on Efficient biomolecular structural data handling and analysis

1. Biomolecule
structural data
management

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

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

4. 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

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

6. 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

7. 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

8. 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

9. 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?

10. 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.

11. 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

12. 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.

13. 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

14. Thank you
Mark Somogyi
msomogyi@chemaxon.com