Screening of a fragment-based library uncovers novel scaffolds for inhibitors of the sodium-coupled neutral amino acid transporter SNAT2

The sodium-coupled neutral amino acid transporter 2 (SNAT2, SLC38A2), responsible for transporting small to medium-sized neutral amino acids, has gained interest due to its potential role in cancer. Despite this, few molecules targeting SNAT2 have been discovered, and its 3D protein structure has yet to be solved experimentally. This hinders drug discovery campaigns aiming to find SNAT2 inhibitors, as no solid starting point exists. Most amino acid transporter inhibitors are based on amino acid scaffolds, but often struggle with selectivity and must compete for the substrate binding site. Hence, the aim was to discover novel non-amino acid inhibitors of SNAT2 by screening a fragment library.
SNAT2 activity was studied through radio-labeled uptake studies of 3H-glycine in hyperosmotically upregulated SNAT2-expressing PC-3 cells. Enamine’s Essential Fragment Library containing 320 compounds was screened at 0.5 mM for their ability to inhibit SNAT2-mediated 3H-glycine uptake and compounds inhibiting by >30% were considered hits.
The fragment library screen yielded 6 hits, and a common scaffold was seen in 1,3-benzothiazole-2-amines and its oxazole equivalent. A simple structure-activity-relationship (SAR) study of these scaffolds revealed that the non-substituted scaffold on its own had no affinity but needed a substituent at the 6 or 7 position of the benzene ring to have an inhibitory effect on SNAT2. The fragments with the greatest inhibition of SNAT2 had their IC50 values determined, which were in the range of 0.6-0.9 mM, comparable to the Km values of SNAT2’s natural amino acid substrates. Furthermore, these fragments did not appear to be competitive inhibitors, thus suggesting that they bind to an allosteric site of SNAT2.
In conclusion, 1,3-benzothiazole-2-amines and 1,3-benzoxazole-2-amines were discovered as novel non-amino acid scaffolds for non-competitive and possibly allosteric SNAT2 inhibitors. Elaborating on these scaffolds and finding analogs with even better potencies could lead to the development of clinically relevant SNAT2 inhibitors, with a possible role in the treatment of cancer.