Drug Design

See also:

www.isb- sib.org

See also:

www.isb- sib.org

1.

^a

short film

produced by Studio KO graphic designers, which introduces the key notions for drug

design (protein target, disease, ligand, docking,…)

Contact

[email protected]

Drug Design for high school students, high school teachers and the public at large

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…

Blatter Marie-Claude^1,5, Daina Antoine^2,3, Baillie Gerritsen Vivienne¹, Marek Diana^4,5, Palagi Patricia M.⁵, Xenarios Ioannis^1,3,4,6, Schwede Torsten^7,8, Michielin Olivier^2,3, Zoete Vincent^2,3

1 Swiss-Prot group, Geneva, ² Molecular Modeling group, Lausanne, ³University of Lausanne, ⁴ Vital-IT group, Lausanne, ⁵ Training and Outreach group, ⁶University of Geneva,

7Computational Structural Biology group, Basel, ⁸University of Basel, ^all SIB Swiss Institute of Bioinformatics, Switzerland

Funded by the FNS (Agora) and the Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI)

2.

^the ‘manual docking’ of 3D-printed small molecules into a

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

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!

a molecular docking simulation (AutoDock Vina)

predicts the binding mode and compares molecule- protein affinity with existing

drugs (score)

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)

draw a new molecule in 2D

(Marvin JS, ChemAxon, Ltd.) 3D printed COX2

protein with 6 of its known ligands (non- steroidal anti-

inflammatory drugs)

iterative approach