Reshaping acetylated peptide selectivity between human BET Brd2 bromodomains BD-I and BD-II in glioblastoma by rationally grafting secondary anchor residues

Selective inhibition of BET Brd2 BD-I and BD-II bromodomains is expected to elicit subtle pharmacological difference in anti-glioblastoma therapy. Here, structural basis and energetic property underlying the selective interaction of acetylated peptide ligands with Brd2 BD-I and BD-II were investigated in detail using molecular simulation and computational analysis. It is revealed that the acetyl-lysine is, as expected, a primary anchor residue that confers affinity and stability to bromodomain-peptide binding, while few secondary anchor residues flanking the acetyl-lysine determine specificity and selectivity of peptide interaction with different bromodomains. We also demonstrated that peptide selectivity can be totally reversed by only grafting the secondary anchor residues from one to another. As an instance, fluorescence-based assays showed that the Stat3-derived acetylated peptide Stat3_K87 possesses a high affinity to BD-II (KdBD-II = 9.7 μM) and a strong selectivity for BD-II over BD-I (S = 0.21-fold). Grafting the three secondary anchor residues Lys8, Gly11 and Gly13 of a BD-I-over-BD-II selective H4 N-terminal peptide to the corresponding residue positions of Stat3_K87, which results in a grafted counterpart Stat3(KGG)_K87, can completely change the peptide selectivity from the BD-II-over-BD-I (S = 0.21-fold) of Stat3_K87 to the BD-I-over-BD-II (S = 2.5-fold) of Stat3(KGG)_K87.