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Transcript Drug_desig_vs6

Drug Design for high school students, high school teachers
and the public at large
Blatter Marie-Claude1,5, Daina Antoine2,3, Baillie Gerritsen Vivienne1, Marek Diana4,5, Palagi Patricia M.5,
Xenarios Ioannis1,3,4,6, Schwede Torsten7,8, Michielin Olivier2,3, Zoete Vincent2,3
1 Swiss-Prot
group, Geneva, 2 Molecular Modeling group, Lausanne, 3University of Lausanne,
4 Vital-IT
Structural Biology group, Basel, 8University of Basel,
all SIB
group, Lausanne, 5 Training and Outreach group, 6University of Geneva,
Swiss Institute of Bioinformatics, Switzerland
Our aim is to introduce, in an engaging and challenging way, concepts such as 3D structure, protein function,
diseases and the role played by bioinformatics in drug discovery and development.
Our workshop involves…
1. a short film produced by Studio KO graphic
designers, which introduces the key notions for drug
design (protein target, disease, ligand, docking,…)
2. the ‘manual docking’ of 3D-printed small molecules into a
3D printed COX2
protein with 6 of its
known ligands (nonsteroidal antiinflammatory drugs)
3D-printed structure representing the target protein on a one-to-one
scale, and ‘manual docking’ with a camera system (leap motion)
3. tools embedded into a user friendly freely accessible
web interface: www.atelier-drug-design.ch
participants can design new ‘virtual’ molecules, visualize their binding
mode and estimate their affinity for the target protein, which they can
then compare with existing drugs
draw a new
molecule in 2D
(Marvin JS,
ChemAxon, Ltd.)
a molecular docking
simulation (AutoDock Vina)
predicts the binding mode
and compares moleculeprotein affinity with existing
drugs (score)
iterative approach
4. direct links to expert tools for predicting possible targets
(SwissTargetPrediction) as well as important properties of the molecule in
order to evaluate its potential of becoming a drug (SwissADME)
5. pen and pencil activities to understand how a computer encodes
chemical structures (fingerprints) and how similarities between
molecules are calculated.
The workshops give a simple yet realistic picture of how bioinformatics is used to design
drug candidates. Hands-on sessions are for cancer (target BRAF and IDO1) and pain (target
COX) treatments. Over 200 people attended our pilot workshops. Many of them, even with a very
limited knowledge of chemistry, were inspired by the challenge to sketch a molecule whose
properties – compared to well-known drugs - they could perhaps improve, in competition
with other participants. According to a first evaluation (n=35), the participants (over 16 years) really
appreciate using bona fide bioinformatics tools. Those interested in science for their future
studies also appreciated discovering a new professional field. The workshops are currently
given by 2 public labs: ‘Chimiscope’ in Geneva and ‘l’Éprouvette’ in Lausanne. There will soon be
an English and German version of the workshops, which will broaden the area to the whole of
Switzerland as well as abroad. Interested? Please, contact us!
Funded by the FNS (Agora) and the Swiss Federal Government through
the State Secretariat for Education, Research and Innovation (SERI)
See also:
[email protected]