Selective and orally bioavailable phenylglycine tissue factor/factor VIIa inhibitors

Screening of a Library for Factor VIIa Inhibitors

Background:

As an alternative to the anticoagulant’s strategy using direct or indirect anti-Xa drugs, considering other targets upstream in the coagulation cascade such as anti-Factor VIIa could represent an effective and safer strategy in coagulation and pathological angiogenesis.

Objective:

The objective of the study was to assess a high technology methodology composed of virtual screening, anticoagulant, and anti-angiogenesis assays to identify potent small-molecule FVIIa inhibitors.

Methods:

Chemical databanks were screened to select molecules bearing functional groups that could fit into the active site of FVIIa, which were then tested. Ligands assigned with the lowest scores were retained and then biologically assessed.

Results:

From the 500 molecules considered, 8 chemical structures revealed to be effective compounds in vitro and to inhibit angiogenesis in the chick chorioallantoic membrane (CAM) model.

Conclusion:

New potent small-molecule FVIIa inhibitors have been identified; further biochemical and chemical developments would be investigated directly from the selected scaffolds.

Cooperative copper-squaramide catalysis for the enantioselective N-H insertion reaction with sulfoxonium ylides

The first examples of a highly efficient and enantioselective carbene-mediated insertion reaction, from a sulfur ylide, are described. By way of a catalytic asymmetric insertion reaction into N-H bonds from carbonyl sulfoxonium ylides and anilines, using a copper-bifunctional squaramide cooperative catalysis approach, thirty-seven α-arylglycine esters were synthesized in enantiomeric ratios up to 92 : 8 (99 : 1 after a single recrystallization) and reaction yields ranging between 49-96%. Furthermore, the protocol benefits from quick reaction times and is conducted in a straightforward manner.

TfOH-Catalyzed N-H Insertion of α-Substituted-α-Diazoesters with Anilines Provides Access to Unnatural α-Amino Esters

A time-economical TfOH-catalyzed N-H insertion between anilines and α-alkyl and α-aryl-α-diazoacetates provides a straightforward approach to access unnatural α-amino esters, which readily undergo various transformations and can thus be used for the synthesis of pharmaceutically relevant molecules. The α-amino esters were obtained in moderate to excellent yields.

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations

Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguishing active from decoy ligands in a directory of useful decoy-enhanced (DUD-E) dataset. MD trajectories are processed by evaluating ligand-binding stability using root-mean-square deviations. We select 56 protein targets (of 7 different protein classes) and 560 ligands (280 actives, 280 decoys) and show 22% improvement in ROC AUC (area under the curve, receiver operating characteristics curve), from an initial value of 0.68 (AutoDock Vina) to a final value of 0.83. The MD simulation demonstrates a robust performance across all seven different protein classes. In addition, some predicted ligand-binding modes are moderately refined during MD simulations. These results systematically validate the reliability of a physics-based approach to evaluate protein-ligand binding interactions.

Design and Synthesis of Novel Meta-Linked Phenylglycine Macrocyclic FVIIa Inhibitors

Two novel series of meta-linked phenylglycine-based macrocyclic FVIIa inhibitors have been designed to improve the rodent metabolic stability and PK observed with the precursor para-linked phenylglycine macrocycles. Through iterative structure-based design and optimization, the TF/FVIIa K_i was improved to subnanomolar levels with good clotting activity, metabolic stability, and permeability.

Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors

On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.

Discovery methodology for the development of direct factor VIIa inhibitors

INTRODUCTION

Heparin and warfarin have historically been the only antithrombotics available. Recently, however, newer anticoagulants have been developed. Factor VIIa (fVIIa) inhibitors represent one of the new and potentially exciting classes of anticoagulants currently under development. Indeed, several methodologies have been used to develop fVIIa inhibitors.

AREAS COVERED

The authors highlight some of the methologies applied for the discovery of fVIIa inhibitors including phage display, isolation of endogenous peptides from hematophagous animals and the use of the 1,5-benzothiazepine molecular scaffolds and screens of large chemical libraries previously used to identify other serine protease inhibitors. Although these screens were intended to identify thrombin and factor Xa inhibitors, the compounds often had concomitant fVIIa activity. The authors also discuss the utilization of medical chemistry techniques for the discovery of these compounds.

EXPERT OPINION

FVIIa inhibitors represent a viable option for the development of new anticoagulants. There are theoretical advantages that fVIIa inhibitors may possess over existing anticoagulants and highly specific inhibitors that possess oral bioavailability and low bleeding risk may succeed.

Tissue factor-fVIIa inhibition: update on an unfinished quest for a novel oral antithrombotic

The tissue factor-coagulation factor VIIa complex (TF-fVIIa) is a well-validated biological target and has been the focus of extensive research directed toward the discovery of novel oral antithrombotics. This review briefly summarizes the key antithrombotic target validation data and provides an update on recent advances in small molecule TF-fVIIa inhibitors.

Structural biology of factor VIIa/tissue factor initiated coagulation

Factor VII (FVII) consists of an N-terminal gamma-carboxyglutamic acid domain followed by two epidermal growth factor-like (EGF1 and EGF2) domains and the C-terminal protease domain. Activation of FVII results in a two-chain FVIIa molecule consisting of a light chain (Gla-EGF1-EGF2 domains) and a heavy chain (protease domain) held together by a single disulfide bond. During coagulation, the complex of tissue factor (TF, a transmembrane glycoprotein) and FVIIa activates factor IX (FIX) and factor X (FX). FVIIa is structurally "zymogen-like" and when bound to TF, it is more "active enzyme-like." FIX and FX share structural homology with FVII. Three structural biology aspects of FVIIa/TF are presented in this review. One, regions in soluble TF (sTF) that interact with FVIIa as well as mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in FVIIa and their functions; two, modeled interactive regions of Gla and EGF1 domains of FXa and FIXa with FVIIa/sTF; and three, incompletely formed oxyanion hole in FVIIa/sTF and its induction by substrate/inhibitor. Finally, an overview of the recognition elements in TF pathway inhibitor is provided.

Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.

Design and synthesis of peptidomimetic factor VIIa inhibitors

Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is regarded as a promising target for developing new anticoagulant drugs. In previous reports, we described a S3 subsite found in the X-ray crystal structure of compound 2 that bound to FVIIa/soluble tissue factor (sTF). Based on the X-ray crystal structure information and with the aim of improving the inhibition activity for FVIIa/TF and selectivity against other serine proteases, we synthesized derivatives by introducing substituents at position 5 of the indole ring of compound 2. Among them, compound 16 showed high selectivity against other serine proteases. Contrary to our expectations, compound 16 did not occupy the S3-subsite; X-ray structure analysis revealed that compound 16 improved selectivity by forming hydrogen bonds with Gln217, Thr99 and Asn100.

Activation loop 3 and the 170 loop interact in the active conformation of coagulation factor VIIa

The initiation of blood coagulation involves tissue factor (TF)-induced allosteric activation of factor VIIa (FVIIa), which circulates in a zymogen-like state. In addition, the (most) active conformation of FVIIa presumably relies on a number of intramolecular interactions. We have characterized the role of Gly372(223) in FVIIa, which is the sole residue in activation loop 3 that is capable of forming backbone hydrogen bonds with the unusually long 170 loop and with activation loop 2, by studying the effects of replacement with Ala [G372(223)A]. G372A-FVIIa, both in the free and TF-bound form, exhibited reduced cleavage of factor X (FX) and of peptidyl substrates, and had increased K(m) values compared with wild-type FVIIa. Inhibition of G372A-FVIIa.sTF by p-aminobenzamidine was characterized by a seven-fold higher K(i) than obtained with FVIIa.sTF. Crystallographic and modelling data suggest that the most active conformation of FVIIa depends on the backbone hydrogen bond between Gly372(223) and Arg315(170C) in the 170 loop. Despite the reduced activity and inhibitor susceptibility, native and active site-inhibited G372A-FVIIa bound sTF with the same affinity as the corresponding forms of FVIIa, and burial of the N-terminus of the protease domain increased similarly upon sTF binding to G372A-FVIIa and FVIIa. Thus Gly372(223) in FVIIa appears to play a critical role in maturation of the S1 pocket and adjacent subsites, but does not appear to be of importance for TF binding and the ensuing allostery.

Advancement in antithrombotics for stroke prevention in atrial fibrillation

The focus of this review is the evolving field of antithrombotic drug therapy for stroke prevention in patients with atrial fibrillation (AF). The current standard of therapy includes warfarin, acenocoumarol and phenprocoumon which have proven efficacy by reducing stroke by 68% against placebo. However, a narrow therapeutic index, wide variation in metabolism, and numerous food and drug interactions have limited their clinical application to only 50% of the indicated population. Newer agents such as direct thrombin inhibitors, factor Xa inhibitors, factor IX inhibitors, tissue factor inhibitors and a novel vitamin K antagonist are being developed to overcome the limitations of current agents. The direct thrombin inhibitor dabigatran is farthest along in development. Further clinical trial testing, and eventual incorporation into clinical practice will depend on safety, efficacy and cost. Development of a novel vitamin K antagonist with better INR control will challenge the newer mechanistic agents in their quest to replace the existing vitamin K antagonists. Till then, the large unfilled gap to replace conventional agents remains open. This review will assess all these agents, and compare their mechanism of action, stage of development and pharmacologic profile.

The use of the Ugi four-component condensation

This protocol describes a procedure for the Ugi four-component condensation. It describes the general mechanism as well as the effects of the nature of the components on the Ugi reaction. It also describes the effects of the reaction conditions on the reaction, along with special procedures and workup. The experimental procedure is exemplified by a description of the preparation of N-cyclohexyl 2-[N-(2-chloroacetyl)-N-(4-chlorobenzyl)]amino-2-(4-chlorophenyl)acetamide, a typical Ugi product, that is subsequently used for the synthesis of a 2,5-diketopiperazine, an example of an important type of pharmaceutical compound. The experimental procedure is then extended to the synthesis of a 1,5-disubstituted tetrazole via Ugi four-component condensation. The protocol describes the preparation and characterization of the new 1-cyclohexyl-5-(1-phenylamino-2-methyl)propyltetrazole. The total time for the synthesis and isolation of the two example reactions in parallel is 3 d.

Inhibitors of Factor VIIa/tissue factor

The formation of the proteolytic complex composed of the serine protease Factor VIIa and the cell-associated glycoprotein tissue factor (FVIIa/TF) initiates a cascade of amplified zymogen activation reactions leading to thrombus formation. The critical role of the coagulation cascade in pathological thrombosis has been the basis for significant efforts to design selective inhibitors of the protease components as new anticoagulant alternatives for the treatment of thrombotic diseases. However, for the new generation of anticoagulant drugs in development that primarily target protease complexes distal from FVIIa/TF, the differential between efficacy and safety as defined by bleeding is unresolved. Targeting the FVIIa/TF complex has several theoretical advantages that exploit the amplified nature of the coagulation cascade. However, progress on the development of clinical-stage FVIIa/TF-based anticoagulants has not been as successful to date. This review summarizes recent efforts in the discovery of synthetic inhibitors of FVIIa/TF.

High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor

Factor VIIa (FVIIa) consists of a gamma-carboxyglutamic acid (Gla) domain, two epidermal growth factor-like domains, and a protease domain. FVIIa binds seven Ca(2+) ions in the Gla, one in the EGF1, and one in the protease domain. However, blood contains both Ca(2+) and Mg(2+), and the Ca(2+) sites in FVIIa that could be specifically occupied by Mg(2+) are unknown. Furthermore, FVIIa contains a Na(+) and two Zn(2+) sites, but ligands for these cations are undefined. We obtained p-aminobenzamidine-VIIa/soluble tissue factor (sTF) crystals under conditions containing Ca(2+), Mg(2+), Na(+), and Zn(2+). The crystal diffracted to 1.8A resolution, and the final structure has an R-factor of 19.8%. In this structure, the Gla domain has four Ca(2+) and three bound Mg(2+). The EGF1 domain contains one Ca(2+) site, and the protease domain contains one Ca(2+), one Na(+), and two Zn(2+) sites. (45)Ca(2+) binding in the presence/absence of Mg(2+) to FVIIa, Gla-domainless FVIIa, and prothrombin fragment 1 supports the crystal data. Furthermore, unlike in other serine proteases, the amide N of Gly(193) in FVIIa points away from the oxyanion hole in this structure. Importantly, the oxyanion hole is also absent in the benzamidine-FVIIa/sTF structure at 1.87A resolution. However, soaking benzamidine-FVIIa/sTF crystals with d-Phe-Pro-Arg-chloromethyl ketone results in benzamidine displacement, d-Phe-Pro-Arg incorporation, and oxyanion hole formation by a flip of the 192-193 peptide bond in FVIIa. Thus, it is the substrate and not the TF binding that induces oxyanion hole formation and functional active site geometry in FVIIa. Absence of oxyanion hole is unusual and has biologic implications for FVIIa macromolecular substrate specificity and catalysis.

Dose-dependent antithrombotic activity of an orally active tissue factor/factor VIIa inhibitor without concomitant enhancement of bleeding propensity

The discovery of a highly potent and selective tissue factor/factor VIIa inhibitor is described. Upon oral administration of its double prodrug in the guinea pig, a dose-dependent antithrombotic effect is observed in an established model of arterial thrombosis without prolonging bleeding time. The pharmacodynamic properties of this selective inhibitor are compared to the behaviour of a mixed factor VIIa/factor Xa inhibitor.