Application of Structure-Based Drug Design and Parallel Chemistry to Identify Selective, Brain Penetrant, In Vivo Active Phosphodiesterase 9A Inhibitors

Abstract

Phosphodiesterase 9A inhibitors have shown activity in preclinical models of cognition with potential application as novel therapies for treating Alzheimer's disease. Our clinical candidate, PF-04447943 (2), demonstrated acceptable CNS permeability in rats with modest asymmetry between central and peripheral compartments (free brain/free plasma = 0.32; CSF/free plasma = 0.19) yet had physicochemical properties outside the range associated with traditional CNS drugs. To address the potential risk of restricted CNS penetration with 2 in human clinical trials, we sought to identify a preclinical candidate with no asymmetry in rat brain penetration and that could advance into development. Merging the medicinal chemistry strategies of structure-based design with parallel chemistry, a novel series of PDE9A inhibitors was identified that showed improved selectivity over PDE1C. Optimization afforded preclinical candidate 19 that demonstrated free brain/free plasma ≥ 1 in rat and reduced microsomal clearance along with the ability to increase cyclic guanosine monophosphosphate levels in rat CSF.

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

“…The remaining PDE families are capable of degrading both substrates. PDE9 inhibitors have been studied for their potential applications to treat diabetes (Deninno et al, 2009;Shao et al, 2014) and central nervous system diseases such as Alzheimer's disease (Wunder et al, 2005;van der Staay et al, 2008;Verhoest et al, 2009Verhoest et al, , 2012Hutson et al, 2011;Vardigan et al, 2011;Claffey et al, 2012;Kleiman et al, 2012;Kroker et al, 2012Kroker et al, , 2014Liddie et al, 2012;Schwam et al, 2014;Singh and Patra, 2014;Heckman et al, 2015;Nagy et al, 2015).…”

The Use of PDE10A and PDE9 Inhibitors for Treating Schizophrenia

“…40) and 73 (PDB ID: 4G2L) bound to PDE9A reveal the expected binding modes [166,167], with the pyrazolopyrimidinone core sandwiched between the P clamp residues and forming two HBs with Gln-453. The N1 4-tetrahydropyran (4-THP) substituent interacts with residues in the M pocket and the C6 substituent accesses the Q 2 and S pockets with the pyrrolidine methyl and the pyrimidine, respectively.…”

“…Pfizer has published several papers describing the discovery of the PDE9A clinical candidate, PF-04447943, 70 (IC 50 ¼ 8.3 nM) [167], related PDE9A inhibitors, PF-04181366 71 (IC 50 ¼ 1.8 nM) [169] and PF-04449613 72 (IC 50 ¼ 14 nM) [166,200], and preclinical PDE9A candidate 73 (IC 50 ¼ 32.4 nM) [166] (Fig. 39).…”

“…Physiological effects were seen at~5x the PDE9A IC50. Compound 73 has a brain/ plasma ratio of 1.4 and free brain/free plasma and free CSF/free plasma ratios of 1.4, indicating no brain impairment [166]. It has an oral bioavailability of 63% in rat and 71% in dog and was predicted to be 80% bioavailable in human.…”

“…The basic nitrogen of the azetidines and pyrrolidines are oriented to interact with Tyr-424. An aryl substituent either directly attached or ether-linked to the azetidine or pyrrolidine is found in most of the exemplified compounds, which is oriented to interact with Phe-441 and/or Phe-456 to obtain selectivity over other PDEs, evident in the X-ray crystal structures of 73 and 83 (PDB IDs: 4G2L and 4G2J) [166].…”