Design and Preclinical Characterization Program toward Asundexian (BAY 2433334), an Oral Factor XIa Inhibitor for the Prevention and Treatment of Thromboembolic Disorders

Factor XI/XIa inhibitors: a potential solution to anticoagulation dilemmas

INTRODUCTION

Antithrombotic therapy is the cornerstone of stroke prevention, but standard of care therapies are underutilized and use is limited by bleeding rates, drug interactions, and renal elimination. Factor XI/XIa (FXI/XIa) inhibitors are a novel anticoagulation class that purportedly target thrombosis more than hemostasis, thereby raising the hope of reducing bleeding consequences while maintaining efficacy.

AREAS COVERED

This review covers the mechanistic rationale for FXI/XIa inhibitors, describes the various molecule sub-classes, addresses barriers to current anticoagulation use, and reviews clinical trial data to date for this novel class of anticoagulants.

EXPERT OPINION

FXI/XIa inhibitors offer several advantages over DOACs in stroke prevention such as reduced bleeding, fewer drug interactions, and less renal elimination. However, clinical trials must demonstrate non-inferior efficacy and improved safety compared to DOACs. Additional barriers to use will include cost, inadequacy of antidotes, and overall anticoagulant underutilization. The potential for a small molecule or monoclonal antibody to reach the clinic is very high.

Discovery of potent, highly selective, and orally bioavailable factor XIa inhibitors for anticoagulant therapy

Factor XIa (FXIa) has emerged as a promising target for novel anticoagulant development since inhibiting it can reduce thrombosis without significant bleeding risks. Despite a few FXIa inhibitors entering clinical trials, none have been approved for the market yet. Here, we present highly selective and orally bioavailable FXIa inhibitors derived from compound 1, 4-(5-chloro-2-(1H-tetrazol-1-yl)phenyl)-5-methoxypyridin-2(1H)-one. Structure-activity relationship studies led to the discovery of promising 1-(pyridin-2-ylmethyl)pyridin-2(1H)-one-based FXIa inhibitors 37, 39b, 43, and 46b, which exhibited enhanced FXIa potency and selectivity compared to asundexian, an FXIa inhibitor in phase III clinical trials. Their anticoagulant activity was also comparable to or greater than that of asundexian. Compound 43 significantly reduced thrombosis in both FeCl3-induced mouse and rabbit arterial thrombosis models, demonstrating superior efficacy compared to asundexian. Importantly, 43 did not increase bleeding risks and exhibited a favorable safety profile in mice, suggesting its potential as a promising FXIa inhibitor for the treatment of thrombosis.

Discovery of potent and selective factor XIa inhibitors incorporating triazole-based benzoic acid as novel P2' fragments: Molecular dynamics simulations and anticoagulant activity

Factor XIa (FXIa) has emerged as a novel anticoagulant target with a reduced risk of bleeding. However, due to the nearly identical residues it shares with its closest homologue, plasma kallikrein (PKa), only a few selective FXIa inhibitors have been reported. Herein, we describe the discovery of novel triazole-based pyridone derivatives as potent and selective FXIa inhibitors. Structural optimization identified triazole-based benzoic acids as optimal P2' fragments. The representative compound (S)-10h (IC50 = 0.38 nM for FXIa) was approximately 3-fold more potent than asundexian for FXIa, along with up to 150-fold selectivity over PKa (13-fold for asundexian) and up to 100,000-fold selectivity over FXa and thrombin (5000-fold for asundexian). Extensive molecular dynamics simulations and free energy calculations revealed that electrostatic interactions with varied residues near the binding site, particularly the loop at the bottom of the S2' pocket (IP-loop), are critical factors contributing to the improved selectivity over PKa. Calculations of electrostatic potential (ESP) surfaces illustrated that FXIa forms a more positive ESP than PKa, thrombin, and FXa, which attracts the carboxylic acid group of the designed compounds, enhancing both potency and selectivity. Moreover, compound (S)-10h demonstrated potent in vitro anticoagulant activity with an EC1.5X value of 0.55 μM for aPTT, without interfering with PT up to 100 μM. Thus, compound (S)-10h represents a promising lead for further optimization as a novel anticoagulant agent.

Identification and anticoagulant mechanisms of novel factor XIa inhibitory peptides by virtual screening of a in silico generated deep-sea peptide database

The objective of this study was to identify novel anticoagulant peptides from the deep-sea using multiple in silico methods, and to investigate their inhibitory activity and molecular mechanisms. A deep-sea peptide database was firstly constructed by performing virtual proteolysis on protein sequences from animals inhabiting deep-sea hydrothermal vents and cold seeps. Candidate anticoagulant peptides were identified through molecular docking and binding free energy screening against FXIa as the target. Two novel anticoagulant peptides, PRNIF (IC50 = 0.67 mM) and GNDRCL (IC50 = 1.52 mM), were identified, and their anticoagulant activities were verified in vitro. PRNIF was demonstrated to be a noncompetitive inhibitor of FXIa, and caused significant prolongation of thrombin time (TT) and activated partial thromboplastin time (APTT), whereas GNDRCL markedly prolonged the APTT only. Molecular dynamics simulations demonstrated considerable conformational shifts of both anticoagulant peptides when bound to the active sites of FXIa. The lowest energy binding poses of the FXIa-peptide complexes for PRNIF and GNDRCL exhibited comparable numbers of hydrogen bonds and binding free energies. However, occupancy analysis revealed completely distinct stability characteristics of the hydrogen bond interactions. The conserved residue Asp569 in the S1 pocket of FXIa formed strong and stable hydrogen bonds as well as a salt bridge with the arginine residues of PRNIF, which were not observed in the FXIa-GNDRCL complex. To our knowledge, PRNIF represented the first FXIa inhibitory peptide derived from the deep-sea, which may contribute to the development and utilization of deep-sea peptides resources. Two deep-sea peptides may potentially serve as an alternative food-derived ingredient that could be utilized for thrombosis prevention.

Structure-based design and synthesis of novel FXIa inhibitors targeting the S2' subsite for enhanced antithrombotic efficacy

Factor XIa (FXIa), a key component of the intrinsic coagulation pathway, has recently been recognized as a safe and effective target for antithrombotic therapy. Research indicates that FXIa inhibitors can lower bleeding risk compared to novel oral anticoagulants. In this study, we designed and synthesized a series of novel FXIa inhibitors based on the structure of Asundexian, with a particular focus on optimizing the P2' region to enhance binding to the S2' subsite of FXIa. This strategy led to the discovery of compound F47, which demonstrated significantly greater FXIa inhibition (IC50 = 2.0 nM) compared to Asundexian (IC50 = 5.0 nM). F47 also showed excellent anticoagulant activity in the aPTT assay (EC2x = 0.4 μM), with strong efficacy and minimal impact on the extrinsic coagulation pathway. Additionally, F47 exhibited inhibitory activity against plasma kallikrein (PKal), with selectivity comparable to that of Asundexian. The compound also displayed acceptable stability in human liver microsomal stability assays. Molecular modeling revealed that F47 binds tightly to the S1, S1', and S2' pockets of FXIa while maintaining key interactions; notably, its P2' moiety forms two additional π-π stacking interactions with the crucial amino acid TYR143. Further studies demonstrated that F47 exhibits dose-dependent antithrombotic efficacy in a rat FeCl3-induced thrombosis model. Ongoing research aims to further elucidate the potential of compound F47 as a promising lead in antithrombotic therapy.

Effect of Age, Sex, Renal Impairment and Hepatic Impairment on the Safety, Pharmacokinetics and Pharmacodynamics of Asundexian

INTRODUCTION

Asundexian is a reversible and selective inhibitor of activated factor XI. It is currently under investigation for the prevention of secondary stroke in at-risk patients; these patients are often characterised by advanced age, impaired organ function and comorbidities. This article summarises results from three Phase I studies that investigated the effects of age and sex (study 1), chronic kidney disease including end-stage kidney disease (ESKD) on dialysis and dialysis-free days (study 2) and Child-Pugh A and B liver disease (study 3) on the safety, pharmacokinetics and pharmacodynamics of a single oral dose of asundexian 25 mg.

METHODS

Study 1 was a multicentre, randomised, single-blind, placebo-controlled group-stratification design; study 2 was a single-centre, non-randomised, non-placebo-controlled, non-blinded group-stratification design; and study 3 had a non-randomised, non-blinded, non-placebo-controlled group-stratification design.

RESULTS

Single doses of asundexian 25 mg were generally well tolerated in all three studies, with no asundexian-related bleeding events or treatment-emergent adverse events of special interest. Point estimates (geometric least squares [LS] means) (90% confidence intervals [CIs]) for the total asundexian area under the plasma concentration-time curve (AUC) for participants aged ≥ 65 to < 75 years versus ≥ 18 to < 45 years and ≥ 75 to ≤ 80 years versus ≥ 18 to < 45 years were 1.257 (1.134-1.393) and 1.288 (1.158-1.433), respectively, and for females versus males, it was 1.084 (0.995-1.182). Point estimates (geometric LS means) (90% CIs) for unbound AUC in participants in estimated glomerular filtration rate (eGFR) categories G2 (60-89 mL/min/1.73 m2), G3 (30-59 mL/min/1.73 m2) and G4 (15-29 mL/min/1.73 m2) versus control were 1.003 (0.698-1.443), 0.791 (0.550-1.138) and 0.882 (0.606-1.285), respectively, and in participants with ESKD on dialysis-free day versus control was 0.597 (0.406-0.877). There was no effect of the dialysis procedure on the pharmacokinetics of asundexian. In participants deemed Child-Pugh class A and Child-Pugh class B, geometric LS means (90% CIs) for unbound AUC were 0.834 (0.597-1.164) and 1.143 (0.810-1.612), respectively, when compared to participants with normal liver function. Activated partial thromboplastin time (aPTT) was assessed as a pharmacodynamic variable of interest. Geometric mean maximum aPTT prolongation as a ratio to baseline after administration of asundexian 25 mg ranged from 1.45 to 1.55 in all age and sex groups, 1.49-1.59 in the control and eGFR G2 to G4 groups, 1.38-1.54 in the control and ESKD groups on dialysis and dialysis-free day and 1.38-1.89 in the healthy control and liver impairment groups.

CONCLUSIONS

The effects of the investigated intrinsic factors on the exposure of asundexian were small and not considered clinically relevant. The impact of lower exposure in participants with ESKD requires further investigation. Pharmacodynamics were as expected.

CLINICAL TRIAL REGISTRATION NUMBERS

EudraCT 2022-000196-38 and 2020-000626-25.

Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery

Computational methods constitute efficient strategies for screening and optimizing potential drug molecules. A critical factor in this process is the binding affinity between candidate molecules and targets, quantified as binding free energy. Among various estimation methods, alchemical transformation methods stand out for their theoretical rigor. Despite challenges in force field accuracy and sampling efficiency, advancements in algorithms, software, and hardware have increased the application of free energy perturbation (FEP) calculations in the pharmaceutical industry. Here, we review the practical applications of FEP in drug discovery projects since 2018, covering both ligand-centric and residue-centric transformations. We show that relative binding free energy calculations have steadily achieved chemical accuracy in real-world applications. In addition, we discuss alternative physics-based simulation methods and the incorporation of deep learning into free energy calculations.

A pharmacokinetic and pharmacodynamic evaluation of asundexian: a novel factor XIa inhibitor for stroke prevention

INTRODUCTION

Antithrombotic therapy is the mainstay of ischemic stroke prevention. Current drugs (antiplatelets and oral anticoagulants) lead to increased bleeding risks, and the rates of stroke recurrence, despite antithrombotic therapy, are still elevated. There is a need for novel antithrombotic therapies with superior effectiveness but without increased bleeding risk. Factor XIa inhibitors might cover this gap.

AREAS COVERED

This manuscript examines the pharmacokinetic and pharmacodynamic properties of asundexian and the current clinical evidence regarding its application in preventing ischemic stroke.

EXPERT OPINION

Asundexian shows a very favoring pharmacokinetic profile. Despite asundexian being inferior to apixaban for cardioembolic ischemic stroke, it could be useful in patients with non-cardioembolic ischemic stroke. Although antiplatelet therapy is the recommended treatment to prevent non-cardioembolic ischemic stroke, adding an anticoagulant might have beneficial effects through the dual-pathway inhibition strategy. Due to the potential risk of hemorrhagic transformation, there is hesitation to administer anticoagulants early to patients who have recently had an ischemic stroke, especially if they are also on antiplatelet therapy. However, clinical trials on asundexian confirmed its safety for bleeding, even when used with antiplatelets. A phase 3 trial is currently investigating the efficacy of asundexian in preventing non-cardioembolic ischemic stroke.

Fluorinated Protein-Ligand Complexes: A Computational Perspective

Fluorine is an element renowned for its unique properties. Its powerful capability to modulate molecular properties makes it an attractive substituent for protein binding ligands; however, the rational design of fluorination can be challenging with effects on interactions and binding energies being difficult to predict. In this Perspective, we highlight how computational methods help us to understand the role of fluorine in protein-ligand binding with a focus on molecular simulation. We underline the importance of an accurate force field, present fluoride channels as a showcase for biomolecular interactions with fluorine, and discuss fluorine specific interactions like the ability to form hydrogen bonds and interactions with aryl groups. We put special emphasis on the disruption of water networks and entropic effects.

Design, synthesis and biological evaluation of 6-chloro-quinolin-2-one derivatives as novel FXIa inhibitors

A series of 6-chloro-quinolin-2-one derivatives were designed and synthesized as FXIa inhibitors by exploration of P1, P1 prime and P2 prime groups. Each compound was accessed for inhibitory effect on FXIa and some of them were evaluated in the clotting assay. 14c demonstrated excellent in-vitro potency (FXIa IC50: 15 nM, 2 x aPTT: 6.8 μM) and good in-vivo efficacy (prolonged in-vivo aPTT by more than 1-fold but not PT). Moreover, the pharmacokinetics property of 14c were evaluated following intravenous administration in rats, which indicated that 14c probably will be a clinical candidate for intravenous administration.