A combined shape-, 2D-fingerprint-and pharmacophore-based virtual screening for the identification of dual inhibitors targeting HIV-1 reverse transcriptase.

Background. The human immunodeficiency virus type 1 (HIV-1) Reverse transcriptase (RT) with its two associated catalytic functions, DNA polymerase and ribonuclease H (RNase H), is still one of the most attractive targets in the design of new antiviral agents. Even though several inhibitors of the RT-associated DNA polymerase function are known, only very few inhibitors targeting the RNase H function have been identified so far. We report the first application of virtual screening (VS) methods for discovering new inhibitors of this innovative target. The overall VS campaign consisted of two consecutive screening processes, each of them resulting in a hit list of compounds which were tested experimentally. Methods. The Rapid Overlay of Chemical Structures (ROCS) was first utilized as a virtual screening platform to perform in silico shape-based similarity screening, in which an hydrazone derivative, previously shown to inhibit the HIV-1 RNase H, was chosen as a query. Results. Accordingly, the most active molecules identified in the first VS were selected as queries for a parallel VS which combined three different LB methods: shape-based, 2D-fingerprint, 3D-pharmacophore VS. The effect of the VS selected molecules on the HIV-1 RT-associated activities were tested in biochemical assays. Conclusions. Overall, a set of molecules characterized by different scaffolds were identified as new inhibitors of both RT-associated activities, showing IC50 values that were in the low micromolar range.