In silico design of hERG non-blocker compounds with retained pharmacological activity using multi-scale molecular modeling applications

hERG K + ion channels are responsible in the regulation process of the action potential of human ventricular myocyte by contributing the rapid component of delayed rectifier K + current (I Kr ) component of the cardiac action potential. The direct inhibition of hERG channels/current raises cardiac diseases, i.e., serious life- threatening arrhythmias further leading to Torsades de pointes (TdP) and long QT syndrome (LQTS). Various drugs have been withdrawn from the drug markets such as terfenadine, cisapride, astemizol or restricted in their use icluding thioridazine, haloperidol, sertindole, and pimozide due to hERG-related life-threatening cardiac arrhythmias. In this thesis, molecular interactions between human ether-à-go-go-related gene (hERG) blocker compounds and pore domains of hERG1 K + ion channels (in its voltage driven open and open-inactivated conformational states) together with their target proteins were investigated using computational modeling methods. In silico drug rehabilitation studies were conducted for the selected compounds (i.e., some phosphodiesterase 5-type enzyme (PDE5) inhibitors) as well with an aim of reducing their hERG1 blocking affinity while keeping their principal enzymes' activity. Using computational approaches such as homology modeling, protein-ligand docking, Alanine mutagenesis studies, E-pharmacophore modeling, structure- and ligand- based virtual screening strategies (such as rapid screening of drug-like molecular database with molecular similarity approaches and fragment based in silico design of novel compounds using fragment libraries), molecular dynamics (MD) simulations, post-MD analyses via considering the detailed analysis of the trajectories-especially conformational behaviours of both the apo and holo systems-and post-MD computations ((e.g., Molecular Mechanics Poisson-Boltzmann Surface Area and Molecular Mechanics Generalized Born Surface Area (MM-PBSA and MM-GBSA, respectively)) for evaluating the binding energies of the studied ligands towards the hERG channels and also towards PDE enzymes have enabled to get insight into the important blocking elements of hERG channels in terms of drug association with its central inner cavities. Additionally, some drug-like hits (with reduced hERG blocking affinity and kept principal target activity) were presented in the consequence of the multi-step virtual screening protocols. Hence, the consequences of the derived outcomes from this thesis may be helpful in the effort for designing novel and safe drugs. The studied drugs, herein, (e.g., sildenafil-Viagra TM ,vardenafil-Levitra TM , tadalafil- Cialis TM and vesnarinone) are all PDE5 inhibitors used in the treatment of erectyle dysfunction except for vesnarinone which is used as a PDE3 inhibitor). Phosphodiesterase (PDE) type enzymes are important biological elements of human organisms and found in many tissues and organs. Their biological function in human organism is to regulate the cytoplasmic concentration levels of intracellular second messengers, 3',5'-cyclic guanosine monophosphate (cGMP) and/or 3',5'-cyclic adenosine monophosphate (cAMP) via catalytic degradation reactions occuring in their substrate pockets. At the end of the applied multi-scale modeling applications, tadalafil and sildenafil-like molecules having drug-like properties (tested using pharmacokinetic modeling applications) have been identified and proposed as novel and safe potential PDE5 inhibitors. In addition to the hERG direct blocking investigations, selectivity of tadalafil-like hits has also been tested against PDE6 and PDE11 isoenzymes which have been identified as the causes of the side-effects of the used PDE5 inhibitor drugs in the market. In summary, through the duration of this thesis, various computational modeling tools have been utilized and applied in the investigation of novel and safe drugs (with reduced side-effects towards hERG channels and also towards the related PDE- isoenzymes) whilst keeping their principal target activities. Besides, the critical protein-ligand interactions have been illuminated at the molecular level along with the dynamics of the studied drugs and their target proteins. This thesis comprises of three chapters that present three scientific articles that have been published at peer-reviewed journals. In the first article (Chapter 2), various computer aided drug-designing and computational molecular modeling techniques were used for the investigation of the action mechanisms of the FDA approved drugs, sildenafil-Viagra TM , vardenafil- LevitraTM and tadalafil-Cialis TM with their target protein, PDE5 and also hERG1 channels. In addition, fragment-based virtual screening strategy was employed in order to obtain potent and safe sildenafil-like molecules. Second article (Chapter 3) focuses on the development of potent tadalafil-like molecules via combination of ligand-based screening and structure-based modeling protocols. hERG1 binding affinities of the selected compounds together with tadalafil were evaluated via flexible molecular docking computations. In addition, PDE5/PDE6 & PDE5/PDE11 selectivities of the compounds were studied and important structural binding patterns such as the critical residue-ligand interactions were highlighted. Third article (Chapter 4) deals with vesnarinone (used a PDE3 inhibitor agent)-hERG complex systems and time-dependent dynamical behaviour of vesnarinone at the pore domains of hERG channels in its open and open-inactivated states. By the use of molecular docking, MD simulations and detailed post-MD analysis computations, possible binding modes of vesnarinone within the central cavities of the channels were proposed. Also, crucial hERG residues in terms of vesnarinone binding were further highlighted which may help to design safe and novel drug-like molecules. In Chapter 5, overall interpretation of the results and potential further works are briefly presented.