title: In silico design of novel hERG-neutral sildenafil-like PDE5 inhibitors.
abstract: Cyclic nucleotide phosphodiesterase enzymes (PDEs) have functions in regulating the levels of intracellular second messengers, 3', 5'-cyclic adenosine monophosphate (cAMP) and 3', 5'-cyclic guanosine monophosphate (cGMP), via hydrolysis and decomposing mechanisms in cells. They take essential roles in modulating various cellular activities such as memory and smooth muscle functions. PDE type 5 (PDE5) inhibitors enhance the vasodilatory effects of cGMP in the corpus cavernosum and they are used to treat erectile dysfunction. Patch clamp experiments showed that the IC50values of the human ether-à-go-go-related gene (hERG1) potassium (K) ion channel blocking affinity of PDE5 inhibitors sildenafil, vardenafil, and tadalafil as 33, 12, and 100 μM, respectively. hERG1 channel is responsible for the regulation of the action potential of human ventricular myocyte by contributing the rapid component of delayed rectifier K+current (IKr) component of the cardiac action potential. In this work, interaction patterns and binding affinity predictions of selected PDE5 inhibitors against the hERG1 channel are studied. It is attempted to develop PDE5 inhibitor analogs with lower binding affinity to hERG1 ion channel while keeping their pharmacological activity against their principal target PDE5 using in silico methods. Based on detailed analyses of docking poses and predicted interaction energies, novel analogs of PDE5 inhibitors with lower predicted binding affinity to hERG1 channels without loosing their principal target activity were proposed. Moreover, molecular dynamics (MD) simulations and post-processing MD analyses (i.e. Molecular Mechanics/Generalized Born Surface Area calculations) were performed. Detailed analysis of molecular simulations helped us to better understand the PDE5 inhibitor-target binding interactions in the atomic level. Results of this study can be useful for designing of novel and safe PDE5 inhibitors with enhanced activity and other tailored properties.
authors: a Department of Chemistry , Istanbul Technical University , Istanbul 34469 , Turkey.
authors: Gülru
authors: G
authors: Kayık
authors: a Department of Chemistry , Istanbul Technical University , Istanbul 34469 , Turkey.
authors: Nurcan Ş
authors: NŞ
authors: Tüzün
authors: b Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.
authors: Serdar
authors: S
authors: Durdagi
mesh_terms: D000200:Action Potentials / Q000187:drug effects; D000596:Amino Acids / Q000378:metabolism; D020134:Catalytic Domain / Q000502:physiology; D000242:Cyclic AMP / Q000378:metabolism; D006152:Cyclic GMP / Q000737:chemistry; D000072237:ERG1 Potassium Channel / Q000037:antagonists & inhibitors*; D006801:Humans; D056004:Molecular Dynamics Simulation; D032342:Muscle Cells / Q000187:drug effects / Q000378:metabolism; D058986:Phosphodiesterase 5 Inhibitors / Q000737:chemistry*; D000068677:Sildenafil Citrate / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D000072237:ERG1 Potassium Channel; D058986:Phosphodiesterase 5 Inhibitors; D000068677:Sildenafil Citrate; D000242:Cyclic AMP; D006152:Cyclic GMP
keywords: De Novo design; MM/GBSA calculations; PDE5 inhibitors; hERG1 channel; molecular docking; molecular dynamics; virtual screening