Peptide-Based Drug Design

108 Westermann and Craik
5.5.2. Discovery of Small Molecule Ligands Inhibiting Protein–Peptide
Interactions Through SAR-by-NMR
The SAR-by-NMR (33) strategy has not yet been widely applied in screening
peptides despite that fact that numerous publications demonstrate the use of this
technique in the discovery of nonpeptide compounds as inhibitors of protein–
protein interactions. Petros et al. demonstrated the application of SAR-by-NMR
to discover small molecule inhibitors for interaction of the anti-apoptotic protein
Bcl-xL with a peptide derived from its endogenous binding partner Bad (52).
The fluorescein-labeled peptide NLWAAQRYGRELRRMSDKFVD showed a
dissociation constant (Kd) of 20 nM. SAR-by-NMR screening of a 10,000
compound library identified a fluorobiaryl acid compound. Using an excess
of this compound in the screening mixture, a second molecule was identified,
binding in a site in close vicinity to the first ligand. A linking strategy was
devised and a molecule featuring a biphenyl system linked to the biaryl acid via
a trans-olefin linker was developed, exhibiting an IC50 of 1.4 �M. Optimization
of the lead compound yielded a small molecule inhibitor of the protein–protein
interaction with an IC50 of 36 nM.
6. Conclusions
NMR has proven to be a versatile and robust method for the study of
biomolecular interactions involving peptides. The information gained from
NMR experiments ranges from the identification of binding partners to determination
of conformations in the bound state and characterization of the binding
interface between ligand and receptor. This information is extremely valuable
for the design of new drugs from bioactive peptides.
References
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challenging targets. Mini. Rev. Med. Chem. 6, 979–987.
2. Valente, A. P., Miyamoto, C. A. and Almeida, F. C. (2006) Implications of protein
conformational diversity for binding and development of new biological active
compounds. Curr. Med. Chem. 13, 3697–3703.
3. Craik, D. J. and Clark, R. J. (2005) Structure-based drug design and NMR-based
screening. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine
(Meyers R. A., ed.). 2nd ed. Wiley-VCH, Weinheim, pp. 517–605.
4. Fu, R. and Cross, T. A. (1999) Solid-state nuclear magnetic resonance investigation
of protein and polypeptide structure. Annu. Rev. Biophys. Biomol. Struct. 28,
235–268.
5. Guthrie, D. J. (1997) 1H nuclear magnetic resonance (NMR) in the elucidation of
peptide structure. Methods Mol. Biol. 73, 163–184.