Fragment-Based Drug Discovery
From Proteopedia
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Three ligands with moderate affinity for Bcl-xl were analyzed using SAR by NMR in order to develop ABT-737. The structural components that allow the ligands to bind to the protein were then linked together to form ABT-737 - the final compound with high-affinity for Bcl-xl. | Three ligands with moderate affinity for Bcl-xl were analyzed using SAR by NMR in order to develop ABT-737. The structural components that allow the ligands to bind to the protein were then linked together to form ABT-737 - the final compound with high-affinity for Bcl-xl. | ||
| - | <scene name='Sandbox_reserved_394/Compound_1/2'>Compound 1</scene> is 4'-fluoro-biphenyl-4-carboxylic acid. SAR by NMR was used to identify the interactions that this compound forms with Bcl-xl. The fluorobiphenyl system is hydrophobic and its interactions form a <scene name='Sandbox_reserved_394/Compound_1/4'>"hydrophobic pocket"</scene> around the fluorobiphenyl system. The <scene name='Sandbox_reserved_394/Compound_1/5'>carboxyilic acid portion binds near Gly 142</scene> of Bcl-xl. The carboxylic acid is later substituted with an acyl sulfonamide (shown in compounds 2 & 3) which provides increased affinity. | + | <scene name='Sandbox_reserved_394/Compound_1/2'>Compound 1</scene> is a 4'-fluoro-biphenyl-4-carboxylic acid. SAR by NMR was used to identify the interactions that this compound forms with Bcl-xl. The fluorobiphenyl system is hydrophobic and its interactions form a <scene name='Sandbox_reserved_394/Compound_1/4'>"hydrophobic pocket"</scene> around the fluorobiphenyl system. The <scene name='Sandbox_reserved_394/Compound_1/5'>carboxyilic acid portion binds near Gly 142</scene> of Bcl-xl. The carboxylic acid is later substituted with an acyl sulfonamide (shown in compounds 2 & 3) which provides increased affinity. |
<scene name='Sandbox_reserved_394/Compound_2/1'>Compound 2</scene> binds with high affinity to Bcl-xl. However, this affinity was decreased in the presence of human serum albumin (HSA). In order to decrease HSA affinity, and therefore increase Bcl-xl affinity, SAR by NMR was used to modify compound 1 by eliminating key binding groups of compound 1 without affecting Bcl-xl affinity. | <scene name='Sandbox_reserved_394/Compound_2/1'>Compound 2</scene> binds with high affinity to Bcl-xl. However, this affinity was decreased in the presence of human serum albumin (HSA). In order to decrease HSA affinity, and therefore increase Bcl-xl affinity, SAR by NMR was used to modify compound 1 by eliminating key binding groups of compound 1 without affecting Bcl-xl affinity. | ||
Revision as of 19:21, 29 October 2012
Drug Design: SAR by NMR
Traditionally, new drugs are developed by either making small changes to existing drugs or by individually testing thousands of compounds. Both of these methods require many hours of laborious chemical synthesis. However, new techniques that capitalize on the advances of modern technology are being applied in the drug industry to develop new drugs which decrease the cost and time required to discover and develop new drugs. Nuclear magnetic resonance (NMR) and x-ray crystallography can be used to analyze compounds in order to create three-dimensional images for detailed, visual analysis of those compounds. Applying these 3-D structures to the drug design process involves using either structure-based drug design (SBDD) or ligand-based drug design (LBDD).
| Structure-Based Drug Design |
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| Structure-based drug design is utilized when the 3-D structure of a protein, or other drug target, is used to predict drug candidates. A visual representation of the structure allows developers to pinpoint binding sites and more effectively design a drug that will have high affinity for the target. |
| Ligand-Based Drug Design |
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| "Ligand-based drug design (LBDD) techniques are applied when the structure of the receptor is unknown but when a series of compounds or ligands have been identified that show the biological activity of the interest."[1] In other words, once it is known how a ligand binds to a protein or any other molecule, new ligands, and eventually drugs, can be designed to bind in a similar manner and get the desired effect. It involves modifying a known ligand to develop another ligand with a higher binding affinity for the target. |
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References
- ↑ Pandit D. LIGAND-BASED DRUG DESIGN: I. CONFORMATIONAL STUDIES OF GBR 12909 ANALOGS AS COCAINE ANTAGONISTS; II. 3D-QSAR STUDIES OF SALVINORIN A ANALOGS AS εΑΡΡΑ OPIOID AGONISTS. http://archives.njit.edu/vol01/etd/2000s/2007/njit-etd2007-051/njit-etd2007-051.pdf
- ↑ Shuker S. B., Hajduk P. J., Meadows R. P., Fesik S. W. Discovering High-Affinity Ligands for Proteins: SAR by NMR. Science; Nov 29, 1996; 274, 5292; ProQuest Central pg. 1531.
- ↑ Oltersdorf T., Elmore S. W., Shoemaker A. R. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Vol 435|2 June 2005|doi:10.1038/nature03579
