Co-crystal structure of PDE4B with bound inhibitor provides the structural basis for PDE4B inhibitor design.
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A C-terminal helix, designated CR3, regulates PDE4B activity by opening and closing over the active site.
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Small molecule inhibitors of PDE4B engage CR3 in multiple “closed” poses.
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A single residue, Leucine 674, in CR3 determines PDE4B inhibitor selectivity.
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The interchange of PDE4B Leucine and PDE4D Glutamine in CR3 changes inhibitor potency by 70–80 fold.
Abstract
Phosphodiesterase-4B (PDE4B) regulates the pro-inflammatory Toll Receptor –Tumor Necrosis Factor α (TNFα) pathway in monocytes, macrophages and microglial cells. As such, it is an important, although under-exploited molecular target for anti-inflammatory drugs. This is due in part to the difficulty of developing selective PDE4B inhibitors as the amino acid sequence of the PDE4 active site is identical in all PDE4 subtypes (PDE4A-D). We show that highly selective PDE4B inhibitors can be designed by exploiting sequence differences outside the active site. Specifically, PDE4B selectivity can be achieved by capture of a C-terminal regulatory helix, now termed CR3 (Control Region 3), across the active site in a conformation that closes access by cAMP. PDE4B selectivity is driven by a single amino acid polymorphism in CR3 (Leu674 in PDE4B1 versus Gln594 in PDE4D). The reciprocal mutations in PDE4B and PDE4D cause a 70–80 fold shift in selectivity. Our structural studies show that CR3 is flexible and can adopt multiple orientations and multiple registries in the closed conformation. The new co-crystal structure with bound ligand provides a guide map for the design of PDE4B selective anti-inflammatory drugs.