Aldose reductase (AKR1B1) has been considered as a significant target for designing drugs to counteract the development of diabetic complications. In the present study, molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to make sure which tautomer is the preferred one among three tautomeric forms (Mtia1, Mtia2, and Mtia3) of 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid (Mtia) for binding to AKR1B1. The overall structural features and the results of calculated binding free energies indicate that Mtia1 and Mtia2 have more superiority than Mtia3 in terms of binding to AKR1B1. Furtherly, the local active site conformational characteristics and non-covalent interaction analysis were identified. The results indicate that the combination of Mtia2 and AKR1B1 is more stable than that of Mtia1. Furthermore, two extra hydrogen bonds between AKR1B1 and Mtia2 are found with respect to Mtia1. In addition, Mtia2 makes slightly stronger electrostatic interaction with the positively charged nicotinamide group of NADP+ than Mtia1. Based on the results above, Mtia2 is the preferred tautomeric form among the three tautomers. Our study can provide an insight into the details of the interaction between AKR1B1 and Mtia at the atomic level, and will be helpful for the further design of AKR1B1 inhibitors.
Keywords: AKR1B1, Aldose Reductase; ARI, aldose reductase inhibitor; FEL, free energy landscape; MD, molecular dynamics; MM-GB/SA calculation; MM-GB/SA, molecular mechanics generalized Born surface area; Mtia, 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid; PCA, principal component analysis; Three AKR1B1-Mtia complex systems: AKR1B1-Mtia1, AKR1B1-Mtia2, and AKR1B1-Mtia3; Three tautomeric forms of Mtia: Mtia1, Mtia2, and Mtia3; aldose reductase; inhibitor; molecular dynamics; tautomer.