A chemical proteomics based enrichment technique targeting the interactome of the PDE5 inhibitor PF-4540124.
The starting point for the discovery and development of new drugs is the design of molecules that bind to their target proteins with high specificity. Here we describe a systematic chemical proteomics based approach, whereby we use a novel PDE5 inhibitor as bait in mice lung tissue. The compound N-(6-aminohexyl)-3-(1-ethyl-3-methyl-7-oxo-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)-4-propoxybenzenesulfonamide (or PF-4540124), which binds to phosphodiesterase-5 (PDE5) with high affinity, was therefore immobilized on an affinity support. Initial affinity enrichment revealed the binding of hundreds of proteins to this immobilized PDE5 inhibitor. Therefore, selective pre-clearing and elution protocols were designed and used in combination with differential stable-isotope labeling to discriminate between the specific binding of low abundant proteins and less specific binding of high abundant proteins. The optimized method allowed us to selectively analyze the "interactome" of the PDE5 inhibitor PF-4540124 and enabled us to identify different isoforms of PDE5 present in mouse lung. Additionally, we enriched for the prenyl binding protein PrBP, which is also known as PDE6delta. Further analysis, applying in vitro binding assays allowed us to verify PrBP as a novel interactor of PF-4540124. The presented method provides a generic highly-specific chemical proteomics based enrichment technique for analyzing drug-protein interactions in mammalian tissue lysates.
Dadvar
Poupak
P
Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands.
O'Flaherty
Martina
M
Scholten
Arjen
A
Rumpel
Klaus
K
Heck
Albert J R
AJ
D000818:Animals; D054706:Cyclic Nucleotide Phosphodiesterases, Type 5 / Q000737:chemistry / Q000378:metabolism; D051379:Mice; D008807:Mice, Inbred BALB C; D058986:Phosphodiesterase 5 Inhibitors; D010726:Phosphodiesterase Inhibitors / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D011744:Pyrimidinones / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D013449:Sulfonamides / Q000737:chemistry* / Q000378:metabolism; D000096926:Benzenesulfonamides
D054706:Cyclic Nucleotide Phosphodiesterases, Type 5; D058986:Phosphodiesterase 5 Inhibitors; D010726:Phosphodiesterase Inhibitors; D011744:Pyrimidinones; D013449:Sulfonamides; C542240:N-(6-aminohexyl)-3-(1-ethyl-3-methyl-7-oxo-6,7-dihydro-1H-pyrazolo(4,3-d)pyrimidin-5-yl)-4-propoxybenzenesulfonamide; D000096926:Benzenesulfonamides