Structure-Guided Discovery of Orally Bioavailable Allosteric SLC6A19 Inhibitors that Promote Urinary Amino Acid Excretion In Vivo

Abstract SLC6A19 is a sodium-dependent transporter that mediates the absorption of neutral amino acids in the intestine and reabsorption of these amino acids in the kidney. Pharmacological inhibition of SLC6A19 may provide therapeutic benefit by normalizing plasma amino acid levels and potentially reducing renal tubular transport burden. Virtual screening against an allosteric binding pocket observed in the cryo-EM structure of SLC6A19/cinromide (1) identified compound 6 as a promising hit. The cryo-EM structure of SLC6A19/CB3 (2) revealed a second, partially overlapping pocket adjacent to the compound 6 binding site. Analogue design merging these two binding pockets followed by optimization led to compound 20, a potent, selective, and orally bioavailable allosteric SLC6A19 inhibitor. While compound 20 demonstrates an approximately 10-fold rightward potency shift against mouse SLC6A19, it retains good potency against non-human primate SLC6A19. Consistent with the SLC6A19 inhibition mechanism, oral dosing of 20 led to increased urinary amino acid excretion in a dose-dependent manner in human SLC6A19 knock-in mice and wild-type non-human primates.