Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach

Abstract

The serine protease factor XI (FXI) is a prominent drug target as it holds promise to deliver efficacious anticoagulation without an enhanced risk of major bleeds. Several efforts have been described targeting the active form of the enzyme, FXIa. Herein, we disclose our efforts to identify potent, selective, and orally bioavailable inhibitors of FXIa. Compound 1, identified from a diverse library of internal serine protease inhibitors, was originally designed as a complement factor D inhibitor and exhibited submicromolar FXIa activity and an encouraging absorption, distribution, metabolism, and excretion (ADME) profile while being devoid of a peptidomimetic architecture. Optimization of interactions in the S1, S1β, and S1′ pockets of FXIa through a combination of structure-based drug design and traditional medicinal chemistry led to the discovery of compound 23 with subnanomolar potency on FXIa, enhanced selectivity over other coagulation proteases, and a preclinical pharmacokinetics (PK) profile consistent with bid dosing in patients.

Discovery and Optimization of Novel SUCNR1 Inhibitors: Design of Zwitterionic Derivatives with a Salt Bridge for the Improvement of Oral Exposure

“…A second FD inhibitor, the nonamide analog 9 (Table 2), lost SUCNR1 potency completely (>100 μM), while it was highly potent against FD 28 and also factor XIa (FXIa). 29 Rather surprisingly, an additional chlorine atom in the para-position in the C-ring of 8 (10) could rescue the SUCNR1 potency, whereas it completely prevented binding of such analogs to FD but not to FXIa (Table 2).…”

“…Although beneficial in the para -position, as demonstrated by the potency of 7 and its X-ray structure showing a direct interaction of the adjacent piperazine nitrogen with E18 1.31 , the basic amine in the meta -position of the C-ring ( 8 ) proved much less potent (27 μM) compared to 7 (0.025 μM) or even compound 5 (1.3 μM) missing the basic amine (Table ). A second FD inhibitor, the nonamide analog 9 (Table ), lost SUCNR1 potency completely (>100 μM), while it was highly potent against FD and also factor XIa (FXIa) . Rather surprisingly, an additional chlorine atom in the para -position in the C-ring of 8 ( 10 ) could rescue the SUCNR1 potency, whereas it completely prevented binding of such analogs to FD but not to FXIa (Table ).…”

“… a IC 50 determined as a mean ( n ≥ 3) in the [ 35 S]­GTPγS assay run with membranes prepared from stably transfected SUCNR1 in human CHEM-1 cells. b IC 50 ( n ≥ 2) determined by the recombinant human complement factor D time-resolved fluorescence resonance energy transfer (TR-FRET) assay c IC 50 ( n ≥ 2) determined by the human factor XIa TR-FRET assay …”

“…Gratifyingly, compound 10 also showed improved potency against SUCNR1 compared to the simple chloro-analog 5 , thus indicating a synergistic effect of these two substituents for inhibition of SUCNR1. The meta -benzylamine in FD- and FXIa-inhibitors was shown to be crucial for these serine proteases , as it participates in an interaction with an essential aspartate . Therefore, our strategy to avoid cross-reactivity with these proteases was to keep the potency-boosting chlorine atom in the para -position as well as to probe larger substituents in the meta -position varying the position of the basic amine.…”

“…lan-2-yl)benzamido)phenyl)acetate (29). According to the general procedure for the preparation of boron esters, the reaction of methyl 2-(2-(3-bromobenzamido)-5-fluorophenyl)acetate (25, 700 mg, 1.9 mmol) and bis(pinacolato)diboron (534 mg, 2.1 mmol) provided the title product after column chromatography (0−60% ethyl acetate in cyclohexane) as a beige solid in 612 mg (77%) yield.…”