Discovery and preclinical development of LY3473329, a potent small molecule inhibitor of lipoprotein(a) formation

Abstract Background Lipoprotein(a) [Lp(a)] is a lipoprotein particle consisting of a low-density lipoprotein (LDL) particle and apolipoprotein(a) [apo(a)]. Lp(a) is a causal risk factor for cardiovascular disease. The formation of Lp(a) requires an initial interaction of apo(a) Kringle IV Domains 7 and 8 (KIV7, KIV8) with apoB-100 on LDL, followed by formation of a disulfide bond between apo(a) and apoB-100. Blocking the initial apo(a)-apoB interaction is a viable therapeutic approach to reduce circulating levels of Lp(a). The apo(a) protein is encoded by the LPA gene that arose from the plasminogen gene through an evolutionary gene duplication event. Because of sequence conservation between apo(a) and plasminogen, compound selectivity for apo(a) is imperative for clinical development. Purpose We report the discovery and preclinical characterization of LY3473329, a novel selective small molecule inhibitor of Lp(a) formation. Methods Computational and synthetic chemistry approaches coupled with multiple biochemical and biophysical assays were used to create apo(a) KIV7,8 binders. Chemical optimization led to molecules with potent inhibition of in vitro Lp(a) formation. Both apo(a) and plasminogen binding assays were conducted to evaluate compound selectivity. The potential for LY3473329 to lower steady state Lp(a) levels was assessed in human Lp(a) transgenic mice and in cynomolgus monkeys, and its effect on plasminogen activity was assessed in rat and monkey. Results Computational modeling, synthetic chemistry and small molecule library screens identified compounds that bind apo(a) KIV7 and KIV8 domains, and subsequent chemical optimization yielded compounds with sub-micromolar Lp(a) inhibition potency. Exploration of compound multivalency created inhibitors with sub-nanomolar potency, including LY3473329. LY3473329 engages multiple apo(a) KIV motifs, allowing it to potently inhibit Lp(a) formation in vitro. Oral doses of LY3473329 given to human Lp(a) transgenic mice and cynomolgus monkeys caused dose-dependent decreases in plasma Lp(a). The key binding motif for LY3473329 is shared by two KIV domains in rat and monkey plasminogen, but only one KIV domain in human plasminogen. LY3473329 was non-selective for rat and monkey plasminogen, but showed ∼ 50-fold selectivity for human plasminogen in in vitro binding assays. In cynomolgus monkeys and rats, LY3473329 significantly reduced plasminogen activity levels without adverse effects. Given its selectivity against human plasminogen, LY3473329 is expected to lower Lp(a) in human without affecting plasminogen. LY3473329 has been evaluated in a human Phase 1 study and is currently in Phase 2 clinical development. Conclusions LY3473329 is a potent and selective small molecule inhibitor of Lp(a) formation and is the only orally administered Lp(a) investigational therapeutic in clinical development.