Combined QSAR-based virtual screening and fluorescence binding assay to identify natural product mediators of Interferon Regulatory Factor 7 (IRF-7) in pulmonary infection.

Interferon regulatory factor-7 (IRF-7) is involved in pulmonary infection and pneumonia. Here, a synthetic strategy that combined quantitative structure-activity relationship (QSAR)-based virtual screening and in vitro binding assay was described to identify new and potent mediator ligands of IRF-7 from natural products. In the procedure, a QSAR scoring function was developed and validated using Gaussian process (GP) regression and a structure-based set of protein-ligand affinity data. By integrating hotspot pocket prediction, pharmacokinetics profile analysis and molecular docking calculations, the scoring function was successfully applied to virtual screening against a large library of structurally diverse, drug-like natural products. With the method we were able to identify a number of potential hits, from which several compounds were found to have moderate or high affinity to IRF-7 using fluorescence binding assays, with dissociation constants Kd at micromolar level. We have also examined the structural basis and noncovalent interactions of computationally modelled IRF-7 complex with its potent ligands. It is revealed that hydrophobic forces and van der Waals contacts play a central role in stabilization of the complex architecture, while few hydrogen bonds confer additional specificity for the protein-ligand recognition.