The inhibition of adenylate kinase by 2,4-thiazolidinedione evaluated by protein-ligand docking

Abstract

Due to its crucial role in nucleotide metabolism, adenylate kinase deserves a special attention in screening of potential inhibitors. Herein, we report the assessment of the relative orientation of the ligand 2,4-thiazolidinedione to adenylate kinase crystallized in closed conformation. Protein-ligand docking was performed to estimate the binding energy and inhibition constant of 2,4-thiazolidinedione to the adenylate kinases’ active sites from different organisms. Our results revealed the best orientation of 2,4-thiazolidinedione is with Gram-positive and acid fast bacteria adenylate kinase – K_i = 0.76±0.1 mM and binding energy -4.26±0.08 kcal/mol. Human adenylate kinases display unfavourable interactions, the binding affinity fluctuating among K_i=0.84 mM and 8.8 mM (3.88±3.51); the energy binding -3.56±0.57. From the three human adenylate kinases analysed, only isoenzyme 2 shows a binding conformation similar to its counterpart from E. coli. Adenylate kinase - this small enzyme needed for survival of every organisms - interacts differently with 2,4-thiazolidinedione, this selectivity being the most important evidence of the present study.