Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics Approaches

Abstract

Tissue-nonspecific alkaline phosphatase (TNAP) is known to be involved in the degradation of extracellular ATP via the hydrolysis of pyrophosphate (PPi). We investigated, using three different computational methods, namely molecular docking, thermodynamic integration (TI) and conventional molecular dynamics (MD), whether TNAP may also be involved in the utilization of β,γ-modified ATP analogues. For that, we analyzed the interaction of bisphosphonates with this enzyme and evaluated the obtained structures using in silico studies. Complexes formed between pyrophosphate, hypophosphate, imidodiphosphate, methylenediphosphonic acid monothiopyrophosphate, alendronate, pamidronate and zoledronate with TNAP were generated and analyzed based on ligand docking, molecular dynamics and thermodynamic integration. The obtained results indicate that all selected ligands show high affinity toward this enzyme. The forming complexes are stabilized through hydrogen bonds, electrostatic interactions and van der Waals forces. Short- and middle-term molecular dynamics simulations yielded very similar affinity results and confirmed the stability of the protein and its complexes. The results suggest that certain effectors may have a significant impact on the enzyme, changing its properties.

Substrate Specificity of T7 RNA Polymerase toward Hypophosphoric Analogues of ATP

“…Whereas a slight decrease of the in vitro transcription activity with a higher concentration of pyrophosphoric acid has been previously reported, and this was observed in our studies (Figure S23), the inhibitory activity of hypodiphosphoric acid toward T7 RNA polymerase has never been demonstrated. Hypodiphosphoric acid has been considered to interact with placental alkaline phosphatase (PLAP) and tissue-nonspecific alkaline phosphatase (TNAP) and was demonstrated to be a substrate of pyrophosphorolysis catalyzed by HIV-1 reverse transcriptase; however, to date, little is known about the other biological properties of this molecule . Thus, the obtained results make a significant contribution toward the knowledge about this molecule and the potential activity of its derivatives.…”

Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking.

“…Nowadays, computational tools are widely used to provide much information both in chemistry and biological activity of existing and potential drugs [18]. Molecular docking plays a major role in understanding the drug-receptor interactions and is widely used as an important tool in the process of establishing potential applications of a given drug, its affinity and activity to the target protein [18][19][20] and has therefore become an indispensable part of modern drug discovery process [21].…”

Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation

“…In particular, we have conducted a systematic analysis of a number of single-point mutants of the flavodoxin from Clostridium Beijerinckii , for which redox potentials were already experimentally measured, with the aim of evaluating and validating this approach in the calculation of relative redox potential in flavoproteins, comparing results with similar investigations carried out using different methodological approaches. Non-equilibrium TI protocols have already been used to investigate other processes, such as docking of ligands to proteins and redox processes [ 32 , 33 , 34 , 35 ]. However, to the best of our knowledge, this is the first report about the evaluation of a non-equilibrium thermodynamic integration study for the prediction of the relative redox potential of biological macromolecules.…”