Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening

Docking-based virtual screening is an established component of structure-based drug discovery. Nev-ertheless, scoring and ranking of computationally docked ligand libraries still suffer from many falsepositives. Identifying optimal docking parameters for a target protein prior to virtual screening canimprove experimental hit rates. Here, we examine protocols for virtual screening against the importantbut challenging class of drug target, protein tyrosine phosphatases. In this study, common interactionfeatures were identified from analysis of protein–ligand binding geometries of more than 50 complexedphosphatase crystal structures. It was found that two interactions were consistently formed across allphosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least oneinteraction with the P-loop backbone amide. In order to investigate the significance of these features onphosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on threephosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine andP-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of thevirtual screen significantly increased in the three studied phosphatases, by up to a factor of two in somecases. Additionally, the use of such pharmacophoric constraints considerably improved the ability ofdocking to predict the inhibitor’s bound pose, decreasing RMSD to the crystallographic geometry by 43%on average. Constrained docking improved enrichment of screens against both open and closed con-formations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found togenerally improve enrichment. The knowledge-based computational strategies explored here can poten-tially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening.