Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

Adenosine deaminase (ADA) is an important enzyme related to purine nucleoside metabolism in human serum and various tissues. Abnormal ADA levels are related to a wide variety of diseases such as rheumatoid arthritis, AIDS, anemia, lymphoma, and leukemia and ADA is considered as a useful target for various diseases. Currently, ADA can be divided into open conformation and closed conformation according to the inhibitors of binding. As a consequence, we chose two inhibitors, namely, 6-hydroxy-1,6-dihydro purine nucleoside (PRH) and N-[4,5-bis(4-hydroxyphenyl)-1,3-thiazol-2-yl]hexanamide (FRK) to bind to ADA in the closed conformation or open conformation respectively. In this study, we performed the random acceleration molecular dynamics (RAMD) method, steered molecular dynamics (SMD) simulations and adaptive basing force (ABF) simulation to explore the unbinding tunnels and tunnel characteristics of the two inhibitors in ADA. Our results showed that PRH and FRK escaped from ADA using three main tunnels (namely, T1, T2, and T3). Inhibitors (PRH and FRK) escape through T3 more frequently and more easily. The results from ABF simulations confirm that the free energy barrier in T1 or T2 is larger than that in T3 when inhibitors dissociate from the ADA and have potential mean of force (PMF) depth. Moreover, in the complexes (ADA-PRH, ADA-FRK), we also found that the most active residue that remarkably contributed to the binding affinity is W117 in T3, and the residue played an important role in the unbinding tunnel for inhibitor leaving. Our theoretical study provided insight into the ADA inhibitor passway mechanism and may be a clue for potent ADA inhibitor design.