Phosphodiesterase-4 (PDE4) molecular pharmacology and Alzheimer's disease

Abstract

Between 20% and 25% of patients diagnosed with Alzheimer's disease (AD) do not have amyloid burden as assessed by positron emission tomography imaging. Thus, there is a need for nonamyloid-directed therapies for AD, especially for those patients with non-amyloid AD. The family of phosphodiesterase-4 (PDE4) enzymes are underexploited therapeutic targets for central nervous system indications. While the PDE4A, B, and D subtypes are expressed in brain, the strict amino acid sequence conservation of the active site across the four subtypes of PDE4 has made it difficult to discover subtype inhibitors. The recent elucidation of the structure of the PDE4 N- and C-terminal regulatory domains now makes it possible to design subtype-selective, negative allosteric modulators (PDE4-NAMs). These act through closing the N-terminal UCR2 or C-terminal CR3 regulatory domains, and thereby inhibit the enzyme by blocking access of cyclic adenosine monophosphate (cAMP) to the active site. PDE4B-NAMs have the potential to reduce neuroinflammation by dampening microglia cytokine production triggered by brain amyloid, while PDE4D-NAMs have potent cognitive benefit by augmenting signaling through the cAMP/protein kinase A/cAMP response element-binding protein (CREB) pathway for memory consolidation. The importance of PDE4D for human cognition is underscored by the recent discovery of PDE4D mutations in acrodysostosis (ACRDY2: MIM 600129), an ultra rare disorder associated with intellectual disability. Thus, the family of PDE4 enzymes provides rich opportunities for the development of mechanistically novel drugs to treat neuroinflammation or the cognitive deficits in AD.

Figures

Fig. 1

Burden of amyloid and nonamyloid dementia in patients diagnosed with Alzheimer’s disease (AD). Large human clinical trials incorporating positron emission tomography imaging of amyloid plaque reveal substantial clinical heterogeneity in amyloid burden despite a common diagnosis of AD. Development of disease-modifying therapies focuses on amyloid-β (Aβ) peptide formation and accumulation, tau neuropathy, and prevention of neuroinflammation secondary to formation of amyloid plaque. Patients with nonamyloid dementia show slow progression of cognitive impairment suggesting that cognition enhancers may have sustained benefit in that clinical subgroup

Fig. 2

Binding mode of phosphodiesterase-4 (PDE4)D negative allosteric modulators (NAMs) directed against upstream conserved region (UCR)2. PDE4D NAMs close the UCR2 regulatory domain (green) in trans over the active site of the opposite catalytic domain (cyan) in the PDE4 dimer (only one monomer is shown), thereby preventing access by cyclic adenosine monophosphate and inhibiting the enzyme. A surface view with UCR2 closed over the active site is shown on the left with an inhibitor (purple) bound in the active site. On the right, the bound inhibitor forms a hydrogen bond to an invariant, active-site glutamine (Q610 in PDE4D7), while two arms project outwards towards UCR2. Binding of the inhibitor completes a hydrophobic interaction surface for the closure of UCR2 by displacing water from the active site. The UCR2 shown on the left is taken from a PDE4B structure (PDB ID: 3G45) as more of the regulatory domain is visible in the crystal [21]. The catalytic domain and UCR2 on the right are taken from a PDE4D structure (PDB ID: 3IAD)

Fig. 3

Binding mode of phosphodiesterase-4 (PDE4)B negative allosteric modulators (NAMs) directed against CR3. The CR3 regulatory domain (yellow) is linked to the catalytic domain (cyan) through a short linker (gray), which allows PDE4B allosteric inhibitors to close CR3 in cis across the active site of the same monomer. PDE4B NAMs form a hydrogen bond to the invariant active site glutamine (Q615 in PDE4B3). The inhibitor captures CR3 by hydrogen bonding through a water network to lysine672. Capture of CR3 allows the amine of lysine677 (K677) to hydrogen bond to proline602 (P602) of the catalytic domain. CR3 has flexibility when closing across the PDE4B active site such that the compound selects the registration of the CR3 helix [22]

Fig. 4

Proposed phosphodiesterase-4 (PDE4)D dimer with the location of acrodyostosis (ACRDY2) mutations. Richter and Conti previously showed that a C-terminal helix of upstream conserved region (UCR)1 and an N-terminal helix of UCR2 (neither of which are visible in our co-crystal structures) are needed for dimerization of PDE4D (cartoon, top) [60, 61]. Three views of the proposed PDE4D dimer are shown. The “TOP” and “FACE” views show how UCR2 closes in trans, where the cyan protein’s UCR2 closes over the green protein’s catalytic domain and vice versa. The two active sites face outwards in opposite directions from the dimer. The dimer interface occurs across the crystallographic unit cell, and is supported by the finding of Lee et al. that mutation of aspartate466 to arginine (D466R) and arginine502 to aspartic acid (R502D) disrupt dimerization of the PDE4D catalytic domain (purple) [67]. The ACRDY2 mutations are shown in red. These occur primarily on contact surfaces between UCR2 and the catalytic domain (V268A and I272V on UCR2, which are hidden in the surface view, and G612D, Y616H and I617T on the opposite catalytic domain surface). In addition, there are 4 “hot spots” for ACRDY2 mutations on the top of the PDE4D dimer (red circles, “TOP VIEW”). These occur on a surface parch of the catalytic domain (T526P, M527V/I, and E529A) and at the N-terminus of the second UCR2 helix (M242V and A243V). No ACRDY2 mutations have been discovered in the active site, on the dimerization surface between the catalytic domains (purple), or on the underside of the PDE4D dimer (“BOTTOM VIEW”). The Richter and Conti [60], and Lee et al. [67] dimer proposals are consistent with a crystal structure of the PDE4B dimer that has been obtained by Cedervall and Pandit (personal communication)