Design, synthesis, and computational studies of inhibitors of Bcl-X-L
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- Design, synthesis, and computational studies of inhibitors of Bcl-X-L
- Park, Cheol-Min; Oie, Tetsuro; Petros, Andrew M.; Zhang, Haichao; Nimmer, Paul M.; Henry, Rodger F.; Elmore, Steven W.
- Binding affinity; Global energy; Inhibition constant; Protein inhibitors; Steric interactions
- Issue Date
- AMER CHEMICAL SOC
- JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, v.128, no.50, pp.16206 - 16212
- One of the primary objectives in the design of protein inhibitors is to shape the three-dimensional structures of small molecules to be complementary to the binding site of a target protein. In the course of our efforts to discover potent inhibitors of Bcl-2 family proteins, we found a unique folded conformation adopted by tethered aromatic groups in the ligand that significantly enhanced binding affinity to Bcl-X L. This finding led us to design compounds that were biased by nonbonding interactions present in a urea tether to adopt this bioactive, folded motif. To characterize the key interactions that induce the desired conformational bias, a series of substituted N,N-diarylureas were prepared and analyzed using X-ray crystallography and quantum mechanical calculations. Stabilizing π-stacking interactions and destabilizing steric interactions were predicted to work in concert in two of the substitution patterns to promote the bioactive conformation as a global energy minimum and result in a high target binding affinity. Conversely, intramolecular hydrogen bonding present in the third substitution motif promotes a less active, extended conformer as the energetically favored geometry. These findings were corroborated when the inhibition constant of binding to BcL-X L was determined for fully elaborated analogues bearing these structural motifs. Finally, we obtained the NMR solution structure of the disubstituted N,N-diarylurea bound to Bcl-X L demonstrating the folded conformation of the urea motif engaged in extensive π-interactions with the protein.
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