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Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold

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journal contribution
posted on 24.05.2012, 00:00 by Haibin Zhou, Jianfang Chen, Jennifer L. Meagher, Chao-Yie Yang, Angelo Aguilar, Liu Liu, Longchuan Bai, Xin Cong, Qian Cai, Xueliang Fang, Jeanne A. Stuckey, Shaomeng Wang
Employing a structure-based strategy, we have designed a new class of potent small-molecule inhibitors of the anti-apoptotic proteins Bcl-2 and Bcl-xL. An initial lead compound with a new scaffold was designed based upon the crystal structure of Bcl-xL and U.S. Food and Drug Administration (FDA) approved drugs and was found to have an affinity of 100 μM for both Bcl-2 and Bcl-xL. Linking this weak lead to another weak-affinity fragment derived from Abbott’s ABT-737 led to an improvement of the binding affinity by a factor of >10 000. Further optimization ultimately yielded compounds with subnanomolar binding affinities for both Bcl-2 and Bcl-xL and potent cellular activity. The best compound (21) binds to Bcl-xL and Bcl-2 with Ki < 1 nM, inhibits cell growth in the H146 and H1417 small-cell lung cancer cell lines with IC50 values of 60–90 nM, and induces robust cell death in the H146 cancer cell line at 30–100 nM.