Structure-Based Discovery of Highly Selective Phosphodiesterase-9A Inhibitors and Implications for Inhibitor Design

Abstract

A new series of phosphodiesterase-9 (PDE9) inhibitors that contain a scaffold of 6-amino-pyrazolopyrimidinone have been discovered by a combination of structure-based design and computational docking. This procedure significantly saved load of chemical synthesis and is an effective method for the discovery of inhibitors. The best compound 28 has an IC50 of 21 nM and 3.3 µM respectively for PDE9 and PDE5, and about three orders of magnitude of selectivity against other PDE families. The crystal structure of the PDE9 catalytic domain in complex with 28 has been determined and shows a hydrogen bond between 28 and Tyr424. This hydrogen bond may account for the 860-fold selectivity of 28 against PDE1B, in comparison with about 30-fold selectivity of BAY73-6691. Thus, our studies suggest that Tyr424, a unique residue of PDE8 and PDE9, is a potential target for improvement of selectivity of PDE9 inhibitors.

Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor

“…However, in terms of bioavailability and in vivo stability, C33 shows significant improvement over 3r. The oral administration of racemic C33 yielded a C max value of 373 ng/ml and bioavailability of 56.5% (Table 4), in comparison with C max values of 16 and 217 ng/ml and bioavailability of 1.3% and 9.8% for 28s (Meng et al, 2012) and 3r (Shao et al, 2014), respectively. The blood concentration of C33 in the oral administration mode was 113 ng/ml after 6 hours, which is about 19-fold higher than the IC 50 value of 6 ng/ml, indicating practical usability and the potential for C33 as a drug lead.…”

“…The early studies on the crystal structures of PDE9 in the complex with BAY73-6691 (Wang et al, 2010) and 28s (Meng et al, 2012) showed a small pocket neighboring the inhibitor binding site. This study revealed that the chlorophenyl tail of inhibitor (S)-C33 interacts with the small subpocket that is composed of a portion of helices H14 and H15 and the M-loop, which we thus tentatively named the M-pocket (Fig.…”

“…The default values were used for the rest of the docking parameters. The PDE9A inhibitor 28s (Meng et al, 2012) was used as a reference for the docking test. The reliability of the docking results is also confirmed by a comparison between the docking poses and the crystal structure of PDE9-(S)-C33 (Supplemental Fig.…”

“…In this paper, we report a novel category of PDE9 inhibitors that have been discovered by using the rational structure-based design and docking on the basis of our early analogs of 28s and 3r (Meng et al, 2012;Shao et al, 2014). The crystal structures of PDE9 in the complex with the best compound, (S)-6-((1-(4-chlorophenyl)ethyl)amino)-1-cyclopentyl-1,5,6,7-tetrahydro-4H-pyrazolo [3,4-day]pyrimidin-4-one [(S)-C33], and a systematic comparison among PDE9 structures in the RCSB Protein Data Bank (www.rcsb.org/pdb) revealed subtle but significant conformation differences between two M-loops in the PDE9 dimers.…”

The Use of PDE10A and PDE9 Inhibitors for Treating Schizophrenia

“…Several X-ray crystal structures of inhibitors bound to the catalytic domain of PDE9A have been published, providing insight into substrate and inhibitor binding modes and isozyme selectivity profiles [163][164][165][166][167][168]. A mechanism for cGMP hydrolysis was proposed based on PDE9A X-ray crystal structures obtained by a freeze trapping technique [163].…”