Molecular Modelling of PDE3A Catalytic Domain

Abstract

<p>Recent studies have highlighted the clinical benefits of regulating phosphodiesterase-3 enzymes. Inhibition of PDE3A has proven to aid in preventing and treating cardiovascularrelated disorders and platelet dysfunction. Hypothermia is a condition that can cause cardiac arrest. However, there are no suitable inotropic drugs that are effective for use under hypothermic conditions. Being able to understand the properties and function of the PDE3A enzyme is therefore essential to the development of new drug inhibitors with exceeding potency. The challenge remains unresolved due to the scarcity of PDE3A crystal structure information. <p>In this study, three models of the PDE3A enzyme were created based on homology modelling. The aim of creating homology models of the PDE3A enzyme was to visualize and gather further structural information for future studies related to drug development. The models were constructed by using known 3D structures of evolutionarily related proteins. The PDB IDs of the three chosen templates were 1SO2, 1TAZ and 4NPV. The quality of the models was evaluated using PROCHECK and ERRAT. <p>The three constructed models were all of high quality and fitted well to their corresponding templates. However, the 1SO2-based model proved to be the most reliable and therefore suitable for virtual ligand screening procedure to identify potential binding compounds that can be used as PDE3A inhibitors. The overview of the active site interactions of the models revealed that residues Y751, T844, D950, F972, Q975 and F1004 are highly conserved and presumably essential for enzymatic activity and ligand binding. The structural information of the PDE3A models is a significant asset for the development of PDE3A drug inhibitors that are suitable for use under hypothermic conditions.