Fragment-Based Drug Discovery: Difference between revisions

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Compounds 1 & 2 exhibited very poor binding affinity for Bcl-xl. The optimization of these two compounds resulted in <scene name='Sandbox_reserved_394/Compound_2/1'>Compound 3</scene>. In order to improve the binding affinity, the carboxylic acid of compound 1 was substituted with an acyl sulfonamide to capitalize on the hydrophilic interaction with the protein. This <scene name='Sandbox_reserved_394/Compound_2/3'>acylsulfonamide portion forms a hydrogen bond with Gly 142</scene> thereby increasing the affinity for Bcl-xl. The substitution of the sulfonamide actually allows the acidic proton to get closer to Gly 142 than it could in the carboxylic acid, which is why it is able to bind stronger to the amino acid.
Compounds 1 & 2 exhibited very poor binding affinity for Bcl-xl. The optimization of these two compounds resulted in <scene name='Sandbox_reserved_394/Compound_2/1'>Compound 3</scene>. In order to improve the binding affinity, the carboxylic acid of compound 1 was substituted with an acyl sulfonamide to capitalize on the hydrophilic interaction with the protein. This <scene name='Sandbox_reserved_394/Compound_2/3'>acylsulfonamide portion forms a hydrogen bond with Gly 142</scene> thereby increasing the affinity for Bcl-xl. The substitution of the sulfonamide actually allows the acidic proton to get closer to Gly 142 than it could in the carboxylic acid, which is why it is able to bind stronger to the amino acid.


Compound 2 was important in identifying the hydrophobicity of binding site 2 but was substituted with a <scene name='Sandbox_reserved_394/Nitro_thio_phenyl_sub/1'>3-nitro-4-(2-phenylthioethyl)aminophenyl group</scene>. This substitution more efficiently binds to site 2 through <scene name='Sandbox_reserved_394/Pi_stacking/3'>pi-pi interactions with Phe 101 and Tyr 199</scene>. This idea of using a known ligand to develop another ligand, and eventually drugs, is known as ligand-based drug design.
Compound 2 was important in identifying the hydrophobicity of binding site 2 but affinity was increased by substituting a <scene name='Sandbox_reserved_394/Nitro_thio_phenyl_sub/1'>3-nitro-4-(2-phenylthioethyl)aminophenyl group</scene>. This substitution more efficiently binds to site 2 through <scene name='Sandbox_reserved_394/Pi_stacking/3'>pi-pi interactions with Phe 101 and Tyr 199</scene>. This idea of using a known ligand to develop another ligand, and eventually drugs, is known as ligand-based drug design.


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One challenge in drug delivery is bioavailability. The bioavailibility may be decreased due to non-specific protein binding. Therefore, compound 3 required further optimization because the binding affinity for Bcl-xl is greatly reduced 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 3 by eliminating key binding groups of the compound to HSA without affecting Bcl-xl affinity.
One challenge in drug delivery is bioavailability. The bioavailibility may be decreased due to non-specific protein binding. Therefore, compound 3 required further optimization because Bcl-xl affinity is greatly reduced 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 3 by eliminating key binding groups of the compound to HSA without affecting Bcl-xl affinity.


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