Zinc-dependent histone deacetylases (HDACs) play a critical role       in transcriptional       repression and gene silencing, and are among the most attractive targets for the development of new         therapeutics         against cancer and various other diseases. By employing Born-Oppenheimer ab       initial QM/MM molecular dynamics with umbrella sampling, we have       determined       free energy profiles of several important zinc binding groups       (ZBGs) in their       binding to different HDACs. Our work aims to facilitate the design       of new HDAC       inhibitors, and provide reference results for the zinc-protein       force field       development.

Ranking of zinc binders for histone deacetylases with ab initio       QM/MM molecular dynamics simulations and umbrella sampling

243rd National Meeting (2012)

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