Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-Based Inhibitors

Abstract

Inhibition of the insulin-regulated aminopeptidase (IRAP) improves memory and cognition in animal models. The enzyme has recently been crystallized and several series of inhibitors reported. We herein focused on one series of benzopyran-based inhibitors of IRAP known as the HFI series, with unresolved binding mode to IRAP, and developed a robust computational model to explain the structure-activity relationship (SAR) and potentially guide their further optimization. The binding model here proposed places the benzopyran ring in the catalytic binding site, coordinating the Zn2+ ion through the oxygen in position 3, in contrast to previous hypothesis. The whole series of HFI compounds was then systematically simulated, starting from this binding mode, using molecular dynamics and binding affinity estimated with the linear interaction energy (LIE) method. The agreement with experimental affinities supports the binding mode proposed, which was further challenged by rigorous free energy perturbation (FEP) calculations. Here, we found excellent correlation between experimental and calculated binding affinity differences, both between selected compound pairs and also for recently reported experimental data concerning the site directed mutagenesis of residue Phe544. The computationally derived structure-activity relationship of the HFI series and the understanding of the involvement of Phe544 in the binding of this scaffold provide valuable information for further lead optimization of novel IRAP inhibitors.

Synthesis of Spirooxindoles and Study of their Self‐Assembly features; Hirshfeld Surface, Energy Framework andIn Silicoanalysis

“…It also associates with glucose metabolism and fibrosis i. e., the control of fibrotic responses in the heart and kidney [26–31] . Further, it also regulates production of vasopressin and oxytocin levels in the brain [32] . Therefore, effective IRAP inhibitors may one day form a new class of possible cognitive enhancers, besides they may also function as drugs that are helpful for controlling immunological responses.…”

“…[26][27][28][29][30][31] Further, it also regulates production of vasopressin and oxytocin levels in the brain. [32] Therefore, effective IRAP inhibitors may one day form a new class of possible cognitive enhancers, besides they may also function as drugs that are helpful for controlling immunological responses.…”

Mapping Structural Drivers of Insulin Analogs Using Molecular Dynamics and Free Energy Calculations at Insulin Receptor

“…2,2,18,28,29,45 In this study, we used MD simulations along with an adaptation of the powerful free energy perturbation (FEP) method to perform in silico mutagenesis, in order to map and understand the contribution of different residues and domains on receptor binding and activation. 46 FEP has been widely used to compute relative protein-ligand binding affinities for small-molecules and mapping the effect of mutating receptor residues, 46 however, to the best of our knowledge this is the first use of the method for assessing mutations in bound polypeptide ligands, such as insulin. [47][48][49] Unlike, with other faster free energy estimation methods, the use of FEP allows for deconvolution of the energy contributions of individual residues and can shed light on the role of waters due to the use of explicit solvation.…”