Optimized Virtual Screening Workflow: Towards Target-Based Polynomial Scoring Functions for HIV-1 Protease.

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One key step in the development of inhibitors for an enzyme is the application of computational methodologies to predict protein-ligand interactions. The abundance of structural and ligand-binding information for HIV-1 protease opens up the possibility to apply computational methods to develop scoring functions targeted to this enzyme. Our goal here is to develop an integrated molecular docking approach to investigate protein-ligand interactions with a focus on the HIV-1 protease. In addition, with this methodology, we intend to build target-based scoring functions to predict inhibition constant (Ki) for ligands against the HIV-1 protease system. Here, we described a computational methodology to build datasets with decoys and actives directly taken from crystallographic structures to be applied in evaluation of docking performance using the program SAnDReS. Furthermore, we built a novel function using as terms MolDock and PLANTS scoring functions to predict binding affinity. To build a scoring function targeted to the HIV-1 protease, we have used machine-learning techniques. The integrated approach reported here has been tested against a dataset comprised of 71 crystallographic structures of HIV protease, to our knowledge the largest HIV-1 protease dataset tested so far. Comparison of our docking simulations with benchmarks indicated that the present approach is able to generate results with improved accuracy. We developed a scoring function with performance higher than previously published benchmarks for HIV-1 protease. Taken together, we believe that the approach here described has the potential to improve docking accuracy in drug design projects focused on HIV-1 protease.