How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for De Novo siRNA Guide Strand Surrogate Selection

The Argonaute-2 protein is part of the RNA-induced silencing complex (RISC) and anchors the guide strand of the small interfering RNA (siRNA). The 3’ end of the RNA contains two unpaired nucleotides (3’-overhang) that interact with the PAZ (PIWI-Argonaute-Zwille) domain of the protein. Theoretical and experimental evidence points towards a direct connection between the PAZ/3’-overhang binding affinity and siRNA’s potency and specificity. Among the challenges to overcome when deploying siRNA molecules as therapeutics are their ready degradation under physiological conditions, and off-target effects. It has been demonstrated that nuclease resistance can be improved via replacement of the dinucleotide overhang by small molecules which retain the interactions of the RNA guide strand with the PAZ domain. Most commonly, nucleotide analogues are used to substitute the siRNA overhang. However, in this study we adopt a de novo approach to its modification. The X-ray structure of human Argonaute-2 PAZ domain served...