Application of\nthe Linear Interaction Energy Method\nto Nitric Oxide Synthase Structure-Based Inhibitor Design

The overproduction of nitric oxide by neuronal nitric\noxide synthase\n(nNOS) is associated with several neuropathological conditions. As\na result, inhibition of nNOS is a desirable therapeutic goal while\navoiding the inhibition of endothelial NOS (eNOS) given its essential\nrole in maintaining cardiovascular tone. Designing inhibitors with\nhigh specificity for nNOS over eNOS is challenging given the close\nsimilarity in the active site structure of all mammalian NOS isoforms.\nComputational methods like free energy perturbation (FEP) and thermodynamic\nintegration (TI) offer attractive avenues for rational drug design,\nbut application of these methods to NOS is hindered by several challenges,\nincluding proper handling of highly charged inhibitors with diverse\nstructures as well as computational expense. To address these issues,\nwe present a simplified approach combining continuum dielectric generalized\nborn (GB) solvent models with linear interaction energy (LIE) calculations.\nOur method demonstrates excellent agreement with experimental data\nfor charged inhibitors targeting mammalian NOS isoforms (mNOS). Our\nresults highlight the utility of the GB-LIE method as a promising\ntool for screening NOS inhibitors and potentially other protein targets\nwith charged active sites and diverse inhibitor structures.