Ricerc@Sapienza

HIV persistent infection requires a life-long treatment and among the 2.1 million new
HIV infections that occur every year there is an increased rate of transmitted drugresistant
mutations. This fact requires a constant and timely effort in order to identify
and develop new HIV inhibitors endowed with innovative mechanisms. The HIV-1
Reverse Transcriptase (RT) associated Ribonuclease H (RNase H) is the only viral
encoded enzymatic activity that still lacks an efficient inhibitor despite the fact that it
is a well-validated target whose functional abrogation compromises viral infectivity.
Identification of new drugs is a long and expensive process that can be speeded up by
in silico methods. In the present study, a structure-guided screening is coupled with a
similarity-based search on the Specs database to identify a new class of HIV-1 RNase
H inhibitors. Out of 45 compounds selected for experimental testing, 15 of these
inhibited the RNase H function below 100 μM with three hits possessing IC50 values
μM, and possesses Mg-independent mode of inhibition. Site-directed mutagenesis
studies provide valuable insight into the binding mode of newly identified
compounds, for instance, compound AA involves extensive interactions with a
lipophilic pocket formed by Ala502, Lys503, Trp (406, 426 and 535) and polar
interactions with Arg557 and with the highly conserved RNase H primer-grip residue
Asn474. The structural insights obtained from this work provide the bases for further
lead optimization.