Structure–activity relationships of bipyridine inotropic cardiac agents

Structural analysis of human dihydrofolate reductase as a binary complex with the potent and selective inhibitor 2,4-diamino-6-{2′-O-(3-carboxypropyl)oxydibenz[b,f]-azepin-5-yl}methylpteridine reveals an unusual binding mode

“…These data revealed that the carboxylate side chain of PT684 occupies two alternate positions, neither of which interacts with the conserved Arg70 in the active-site pocket, which in turn hydrogen bonds to water. These observations are in contrast to those reported for the ternary complex of mouse DHFR (mDHFR) with NADPH [Cody et al (2008), Acta Cryst. D64, 977-984], in which the 3-carboxypropyl side chain of PT684 was hydrolyzed to its hydroxyl derivative, PT684a.…”

“…The side chain of Gln35 does make intermolecular contact with the carboxylate side chain of PT684. Additionally, only one conformer is observed for the side chains of Phe31 and Gln35 in the hDHFR binary complex, unlike the two conformers that are observed for these residues in the mDHFR-PT684a ternary complex (Cody et al, 2008). In this structure, the side chain of Gln35 is pointing away from the active site and does not make contact with Arg70 as observed for one of the conformers in the mDHFR complex (Fig.…”

“…Initial interpretation of the difference electron-density map suggested that the inhibitor was hydrolyzed to PT684a ( Fig. 2a) as observed in the structure of the ternary complex of mDHFR with NADPH and PT684a (Cody et al, 2008). However, further analysis revealed that the carboxylate side chain was present and refinement of the side chain at full occupancy showed that the thermal parameters for the carboxypropyl group were twice those of the rest of the molecule (35-45 Å 2 versus 15-20 Å 2 ).…”

“…The crystal structure of PT684 in complex with hDHFR was obtained in order to understand these structure-activity correlations. These data are compared with previously reported structural data of PT684a in complex with mDHFR (Cody et al, 2008) and the parent compound PT653 ( Fig. 1; Cody et al, 2002).…”

“…Structural studies of the mouse DHFR (mDHFR) complex with PT684 and NADPH could not validate the computational binding data for PT684 as this inhibitor had hydrolyzed to the hydroxyl analogue PT648a (Fig. 1) under the crystallization conditions used (15 mM Tris pH 8.3, 75 mM sodium cacodylate, PEG 4000; Cody et al, 2008). The crystal structure of PT684 in complex with hDHFR was obtained in order to understand these structure-activity correlations.…”