Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation

Abstract

The 3-amino-2-methylpyridine derivative 1 was identified as ligand of the BAZ2B bromodomain by automatic docking of nearly 500 compounds, selected on the basis of previous fragment hits. Hit expansion by two in silico approaches, pharmacophore search followed by docking, and substructure search resulted in five additional ligands. The predicted binding mode of the six 3-amino-2-methylpyridine derivatives was validated by protein crystallography. A small displacement of residues 1894-1899 of the ZA loop is observed for two of the six ligands. In all structures, the pyridine head is involved in a water-mediated hydrogen bond with the side chain of the conserved Tyr1901 while the 3-amino linker acts as hydrogen bond donor for the backbone carbonyl of Pro1888. Heterogeneous orientations are observed for the tail groups (i.e., the 3-amino substituents). The sulfonyl group in the tail of compounds 1 and 2 is involved in a hydrogen bond with the backbone amide of Asn1894.

Structural Analysis of Small‐Molecule Binding to the BAZ2A and BAZ2B Bromodomains

“…We present eight new structures of the BAZ2A bromodomain in complex with small molecules that originate from the expansion of fragment hits identified by docking. Whereas the BAZ2A/B ligands 6 – 8 were reported previously, compounds 1 – 5 are disclosed here for the first time. They are derivatives of the N ‐methyl‐2‐pyridone‐5‐carboxamide head group (i.e., fragment 1 of Ref.…”

“…The 1‐methylpyridinones 1 – 5 were prioritized following in silico screening and competition binding assays, starting from a parent fragment identified in a previous screening campaign . The 3‐amino‐2‐methylpyridine derivatives 6 – 7 and the acetylindole compound 8 had been identified previously as BAZ2B ligands and they represent interesting molecules for further optimization of their potency and selectivity . We first present the results of a substructure search (fragment 1 from Ref.…”

“…[d] Reported in Ref. , determined by Alphascreen. [e] Residual binding at 0.05 m m measured by AlphaScreen in Ref.…”

“…Compounds 6 and 7 show similar binding modes in the two bromodomains (Figure a). Despite containing a stereogenic center, a single enantiomer is present or at least largely predominant in the X‐ray structures in complex with BAZ2B . The lower resolution of the BAZ2A crystallographic structures makes questionable whether a similar specificity is possible also for this bromodomain, in which the smaller gatekeeper residue might result in a less stringent enantiomeric selectivity, a possibility worth further investigation.…”

“…[9] The3 -amino-2-methylpyridine derivatives 6-7 and the acetylindole compound 8 had been identified previously as BAZ2B ligandsa nd they represent interesting molecules for further optimization of their potency and selectivity. [10,11] We first present the resultso fasubstructure search (fragment 1 from Ref. [9]) followedb yacomparison of the binding sites of BAZ2A andB AZ2B, and then we analyze the differences in binding modes and interaction motifs.…”