Disco Docking - Computational Drug Design

Example of computational drug design: virtual screening, followed by lead optimization with Glide.

Modeling Software:
Schrodinger Suite 2009 and PyMOL
(www.schrodinger.com)

Target:
Thrombin (PDB: 1mue)

Ligands Series:
1. Burgey 2003 - Bioorg Med Chem Lett - Pharmacokinetic optimization of 3-amino-6-chloropyrazinone acetamide thrombin inhibitors. implementation of P3 pyridine N-Oxides to deliver an orally bioavailable series containing P1 N-Benzylamides
2. Young 2004 - J Med Chem - Discovery and Evaluation of Potent P1 Aryl Heterocycle-Based Thrombin Inhibitors

Note: for the true experimental dG divide values by 1.76 kcal/mol.

- Noeris Salam

Category:

Science & Technology

Tags:

• computational drug design
• computer aided drug design
• molecular modeling
• docking
• virtual screening
• schrodinger
• maestro
• pymol
• structure based drug design
• thrombin
• computational chemistry
• rational drug design
• noeris salam
• noeris

[msilberg]

That song is sweet! What is it?

[CompChemist]

@msilberg. The song is "Sinnerman (Felix Da Housecat's Heavenly House Mix), Verve remixed. The original is Nina Simone- Sinnerman (The Thomas Crown Affair)"

[Yeclanoide]

is the protein flexible? which scoring function?

[CompChemist]

@Yeclanoide. The protein is rigid. We used the Glide SP scoring function.

[romfeastore]

can it work based on pdb models??

[CompChemist]

@romfeastore. Yes, both Maestro and PyMOL can work with PDB (.pdb) models.

[mtgau]

Genius!