Fragment-Based Drug Discovery

Apoptosis by Inhibition of Bcl-2 Family ProteinsApoptosis by Inhibition of Bcl-2 Family Proteins

Apoptosis, or programmed cell death, is a natural mechanism in which a damaged cell dies in order to prevent further damage to the multicellular organism. The absence of apoptosis may occur in damaged cells and can lead to many types of cancers and other diseases. In certain types of cancers, a family of proteins, known as the Bcl-2 family, has been observed as being over-expressed compared to normal, healthy cells. There is also evidence to suggest that Bcl-2 over-expression may also contribute to chemo-resistance.

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Bcl-xl: a member of the Bcl-2 familyBcl-xl: a member of the Bcl-2 family

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is a member of the Bcl-2 family. The protein is comprised of seven , no beta sheets, and 221 amino acid residues.

Bcl-xl Inhibition with ABT-737Bcl-xl Inhibition with ABT-737

Inhibiting the over-expression of this protein has been shown to effectively induce tumor regression and increase chemo-sensitivity. This can be done with .

ABT-737 is not a naturally occurring compound but is a result of ligand-based design using SAR by NMR.

Ligand-Based DesignLigand-Based Design

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Once it is known how a ligand binds to a protein or any other molecule, new ligands can be designed to bind in a similar manner and get the desired effect. This process is known as ligand-based design. The use of this method has resulted in the discovery and production of many medicinal agents available for phramacologic therapy.

SAR by NMRSAR by NMR

One tool used in ligand-based design is structure-activity relationship (SAR) by nuclear magnetic resonance (NMR). This is a process "in which small organic molecules that bind to proximal subsites of a protein are identified, optimized, and linked together to produce high-affinity ligands." Using this tool allows drug developers to create new drugs with minimal chemical synthesis, which then decreases the cost and time required to discover and develop new drugs.

Discovering ABT-737 involved a process of analyzing a series of precursors to the final ligand. Several compounds were found to have affinity for Bcl-xl. Using SAR by NMR, each of these precursors were analyzed for functional groups that were critical for high affinity binding.

For example:

actually consists of two ligands: a and a . The fluorobiphenyl system is significant to the high affinity of ABT-737. It is involved in hydrophobic interactions with Bcl-xl forming a and is also contained in the two subsequent compounds. Notice the stability of the biphenyl system. Because of of the ortho-hydrogens, the two benzene rings adopt a of about 28.6° as opposed to an angle of 0° (or perfectly lined up).

and are very similar in structure and contribute many of the same groups needed for high affinity. Coumpound 1 is an acylsulfonamide-based ligand while compound 2 is a nitrobenzenesulfonamide-based ligand. Both of these compounds have the same core structure with the exception of the (shown with yellow halos) on the terminal benzene ring. These compounds also exhibit hydrophobic bonding with the fluorobiphenyl system but they also include a between an oxygen from the sulfoxone portion of the ligand to an "N-H" group of a glycine amino acid.

SAR by NMR is also useful for analyzing a drug target to obtain a better understanding of its function and activity as well as identifying similar targets. For example, Bcl-2 and Bcl-w are proteins that were discovered to have structures very closely related to Bcl-xl as well as similar roles as anti-apoptotic proteins.

ReferencesReferences

Justin Weekley 03:20, 16 October 2012 (IST)