8K4H

Crystal structure of PDE4D complexed with benzbromarone

Summary for 8K4H

• Entry DOI: 10.2210/pdb8k4h/pdb
• Descriptor: cAMP-specific 3',5'-cyclic phosphodiesterase 4D, ZINC ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: pde4d, complex, benzbromarone, inhibitor, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 81344.44

Authors

Liu, J.Y.,Li, M.J.,Xu, Y.C. (deposition date: 2023-07-18, release date: 2023-11-22)

Primary citation

Liu, J.,Zhang, X.,Chen, G.,Shao, Q.,Zou, Y.,Li, Z.,Su, H.,Li, M.,Xu, Y.
Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors.
Eur.J.Med.Chem., 262:115893-115893, 2023

PubMed Abstract: Phosphodiesterase-4 (PDE4) and PDE5 responsible for the hydrolysis of intracellular cAMP and cGMP, respectively, are promising targets for therapeutic intervention in a wide variety of diseases. Here, we report the discovery of novel, drug-like PDE4 inhibitors by performing a high-throughput drug repurposing screening of 2560 approved drugs and drug candidates in clinical trial studies. It allowed us to identify eight potent PDE4 inhibitors with IC values ranging from 0.41 to 2.46 μM. Crystal structures of PDE4 in complex with four compounds, namely ethaverine hydrochloride (EH), benzbromarone (BBR), CX-4945, and CVT-313, were further solved to elucidate molecular mechanisms of action of these new inhibitors, providing a solid foundation for optimizing the inhibitors to improve their potency as well as selectivity. Unexpectedly, selectivity profiling of other PDE subfamilies followed by crystal structure determination revealed that CVT-313 was also a potent PDE5 inhibitor with a binding mode similar to that of tadalafil, a marketed PDE5 inhibitor, but distinctively different from the binding mode of CVT-313 with PDE4. Structure-guided modification of CVT-313 led to the discovery of a new inhibitor, compound 2, with significantly improved inhibitory activity as well as selectivity towards PDE5 over PDE4. Together, these results highlight the utility of the drug repurposing in combination with structure-based drug design in identifying novel inhibitors of PDE4 and PDE5, which provides a prime example for efficient discovery of drug-like hits towards a given target protein.

PubMed: 37918035
DOI: 10.1016/j.ejmech.2023.115893

Experimental method

X-RAY DIFFRACTION (1.95 Å)