Derivatives of 3‑Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation
datasetposted on 12.10.2016, 00:00 by Jean-Rémy Marchand, Graziano Lolli, Amedeo Caflisch
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.
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silico approachesside chainligandSilico DiscoveryTyr 1901ZA loop500 compoundsCrystallo Validationsulfonyl grouptail groupsfragment hitsbackbone amidebinding mode-2-methylpyridine derivatives3-protein crystallographybackbone carbonyllinker actshydrogen bond donorcompounds 1Pro 1888. Heterogeneous orientationssubstructure searchpyridine headpharmacophore searchwater-mediated hydrogen bonddockingBAZ 2B bromodomainBAZ 2B Bromodomain Ligandshydrogen bond