Sebetralstat (KVD900): A Potent and Selective Small Molecule Plasma Kallikrein Inhibitor Featuring a Novel P1 Group as a Potential Oral On-Demand Treatment for Hereditary Angioedema

Abstract

Hereditary angioedema (HAE) is a rare genetic disorder in which patients experience sudden onset of swelling in various locations of the body. HAE is associated with uncontrolled plasma kallikrein (PKa) enzyme activity and generation of the potent inflammatory mediator, bradykinin, resulting in episodic attacks of angioedema. Herein, we disclose the discovery and optimization of novel small molecule PKa inhibitors. Starting from molecules containing highly basic P1 groups, which typically bind to an aspartic acid residue (Asp189) in the serine protease S1 pocket, we identified novel P1 binding groups likely to have greater potential for oral-drug-like properties. The optimization of P4 and the central core together with the particularly favorable properties of 3-fluoro-4-methoxypyridine P1 led to the development of sebetralstat, a potent, selective, orally bioavailable PKa inhibitor in phase 3 for on-demand treatment of HAE attacks.

Figure 1

Activation of the kallikrein–kinin system. Activation is indicated by black solid arrows, and inhibition is indicated by dashed lines.

Figure 2

Oral small molecule PKa inhibitors with disclosed structures (avoralstat, berotralstat, ATN-249,^, sebetralstat) that have entered clinical trials.

Figure 3

Evolution of our PKa inhibitors resulting in a highly potent scaffold (6) that inspired the design of a neutral P1 library. All PKa IC₅₀ values reported were performed in-house and are the mean values of two or more independent assays. pK_a values denoted with “∗” are calculated values using ACD/Laboratories Percepta software (Toronto, ON, Canada). The pK_a denoted with “#” is a measured value from PION using a UV-metric method over the pH range 1.5–12.5.

Figure 4

Crystal structure of 14w complex with PKa (PDB code 8A3Q). The characteristic U-shaped conformation is stabilized by the movement of Trp215 (“Trp flip”) that enables a network of π-stacking interactions with the ligand: Tyr174/terminal pyridone (face-to-face); Trp215/phenyl linker (face-to-face) and pyrazole core (edge-to-face); His57/pyrazole core (face-to-face). A total of three hydrogen bonds are observed: Gly99 backbone N–H/pyridone carbonyl, Ser214 backbone carbonyl/amide N–H, and Lys192 side chain N–H/amide carbonyl. The pyridine P1 group occupies the S1 subpocket without forming specific polar interactions with any of the amino acids including Asp189. Image created using Maestro (Schrödinger, New York, NY, USA).

Figure 5

(a) P1 group in 14w in relation to the S1 hydrophobic region (yellow volume, calculated with SiteMap). (b) Analysis of predicted water molecules in the unbound form of the S1 pocket (calculated with WaterMap and the relative energy level in a color scale of green (favorable free energy) to red (unfavorable free energy). A high energy water in the proximity of Tyr228 is displaced by the methoxy group upon binding in the S1 pocket.

Figure 6

Green line shows the rapid oral absorption of sebetralstat in healthy volunteers. Blue line shows the effect of sebetralstat on percentage PKa activity. From ref (26). CC BY NC ND.

Scheme 1. Synthesis of Sebetralstat

Reagents and conditions: (a) 2-Hydroxypyridine (1.2 equiv), K₂CO₃ (3.0 equiv), acetone, 50 °C, 18 h, 78%; (b) methanesulfonyl chloride (1.3 equiv), Et₃N, (1.4 equiv), dichloromethane, rt, 18h, 93%; (c) methyl 3-(methoxymethyl)-1H-pyrazole-4-carboxylate (0.83 equiv), K₂CO₃ (2.0 equiv), DMF, 60 °C, 18 h, 54%; (d) NaOH (3.0 equiv), THF-MeOH-H₂O, rt, 18 h, 34%; (e) 22a (1.0 equiv), C-(3-fluoro-4-methoxy-pyridin-2-yl)-methylamine (1.0 equiv), HATU (1.1 equiv), Et₃N (6.0 equiv), dichloromethane, rt, 4 h, 64%.

Figure 7

NMR assignments for 19. NOESY and HMBC crosspeaks shown. NMR spectral analyses are included in the Supporting Information.

Figure 8

NMR assignments for 21a. NOESY crosspeaks shown. NMR spectral analyses are included in the Supporting Information.