We described a prospective application of ligand-based virtual screening program SHAFTS to discover novel inhibitors for p90
ribosomal S6 protein kinase 2 (RSK2). Taking the putative 3D conformations of two weakly binding RSK2 NTKD inhibitors as
query templates, SHAFTS was used to perform 3D similarity based virtual screening because of a lack of crystal structure of RSK2
protein, thus leading to the identification of several novel scaffolds that would have been missed by conventional 2D fingerprint
methods. The most potent hit compounds show low micromolar inhibitory activities against RSK2. In particular, one of the hit
compounds exhibits potent antimigration activity against the MDA-MB-231 tumor cell. The results exemplified SHAFTS’
application in active enrichment and scaffold hopping, which is of general interest for lead identification in drug discovery endeavors
and also provides novel scaffolds that lay the foundation for uncovering new RSK2 regulatory mechanisms.