Design, synthesis and structure-activity relationship of a series of arginine aldehyde factor Xa inhibitors. Part 1: structures based on the (D)-Arg-Gly-Arg tripeptide sequence

Pharmacodynamics of Rivaroxaban and Dabigatran in Adults with Diffuse Large B-Cell Lymphoma Receiving R-CHOP Immunochemotherapy

Background/Objectives: Rivaroxaban and dabigatran are commonly used for thromboembolic disease management in active cancer patients. However, limited research explores the impact of concurrent chemotherapy on the pharmacodynamics of direct oral anticoagulants (DOAC). The aim of our study was to evaluate the impact of combined chemotherapy with rivaroxaban and dabigatran on the pharmacodynamics in patients with diffuse large B-cell lymphoma (DLBCL).; Methods: This was a prospective, pharmacodynamic study. Eligible subjects were ≥18 years old, diagnosed with DLBCL and initiating R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) immunochemotherapy. The enrolled adults received either rivaroxaban (10 mg once daily) or dabigatran etixalate (110 mg twice daily). Plasma anti-factor Xa (FXa) in participants on rivaroxaban and diluted thrombin time (dTT) in participants on dabigatran were assessed over the dosing interval before and after R-CHOP administration. Pharmacodynamic parameters of rivaroxaban and dabigatran were determined using a non-compartmental analysis.; Results: Twenty-six adults participated, with twelve in the rivaroxaban group and fourteen in the dabigatran group. The mean age was 59 ± 14.4 years. In the rivaroxaban group, the AUEC of FXa inhibition showed no significant change after R-CHOP (mean difference 3.8 ng·h/mL, 95% confidence interval (CI) -155.4 to 163.0, p = 0.96). Similarly, in the dabigatran group, the AUEC of dTT remained unchanged post R-CHOP (mean difference 54.41 ng·h/mL, 95% CI -99.09 to 207.9 ng/mL, p = 0.46). However, the median time-to-peak dTT was significantly faster with R-CHOP (3 h, [min-max, 1.5-8] compared to without it (4 h, [min-max, 3-8], p = 0.04); Conclusions: Concurrent R-CHOP chemotherapy did not significantly impact FXa inhibition by rivaroxaban or dTT by dabigatran. The time-to-peak dTT was faster when dabigatran was administered with R-CHOP.

Protein Hydrolysates and Biopeptides: Production, Biological Activities, and Applications in Foods and Health Benefits. A Review

In recent years, a great deal of interest has been expressed regarding the production, characterization, and applications of protein hydrolysates and food-derived biopeptides due to their numerous beneficial health effects. In this regard, research is mainly focused on investigating the therapeutic potential of these natural compounds. Based on their amino acids composition, sequences, hydrophobicity, and length, peptides released from food proteins, beyond their nutritional properties, can exhibit various biological activities including antihypertensive, antioxidative, antithrombotic, hypoglycemic, hypocholesterolemic, and antibacterial activities among others. Protein hydrolysates are essentially produced by enzymatic hydrolysis of whole protein sources by appropriate proteolytic enzymes under controlled conditions, followed by posthydrolysis processing to isolate desired and potent bioactive peptides from a complex mixture of active and inactive peptides. Therefore, because of their human health potential and safety profiles, protein hydrolysates and biopeptides may be used as ingredients in functional foods and pharmaceuticals to improve human health and prevent diseases. In this review, we have focused on the major variables influencing the enzymatic process of protein hydrolysates production. The biological properties of protein hydrolysates will be described as well as their applications in foods and health benefits.

Factor Xa active site substrate specificity with substrate phage display and computational molecular modeling

Structural origin of substrate-enzyme recognition remains incompletely understood. In the model enzyme system of serine protease, canonical anti-parallel beta-structure substrate-enzyme complex is the predominant hypothesis for the substrate-enzyme interaction at the atomic level. We used factor Xa (fXa), a key serine protease of the coagulation system, as a model enzyme to test the canonical conformation hypothesis. More than 160 fXa-cleavable substrate phage variants were experimentally selected from three designed substrate phage display libraries. These substrate phage variants were sequenced and their specificities to the model enzyme were quantified with quantitative enzyme-linked immunosorbent assay for substrate phage-enzyme reaction kinetics. At least three substrate-enzyme recognition modes emerged from the experimental data as necessary to account for the sequence-dependent specificity of the model enzyme. Computational molecular models were constructed, with both energetics and pharmacophore criteria, for the substrate-enzyme complexes of several of the representative substrate peptide sequences. In contrast to the canonical conformation hypothesis, the binding modes of the substrates to the model enzyme varied according to the substrate peptide sequence, indicating that an ensemble of binding modes underlay the observed specificity of the model serine protease.

3,6-Disubstituted Coumarins as Mechanism-Based Inhibitors of Thrombin and Factor Xa

In this work, coumarins were screened on thrombin (THR) and factor Xa (FXa), two of the most promising targets for the development of anticoagulant drugs. This allowed us to highlight compound 30, characterized by a 2,5-dichlorophenyl ester in the 3-position and a chloromethyl moiety in the 6-position, as a very potent THR inhibitor (ki/KI= 37,000 M(-1) s(-1)). Moreover, this compound exhibits good selectivity over FXa (168-fold) and trypsin (54-fold). The mechanism of inactivation was investigated in this series and significantly differs from that previously observed with alpha-chymotrypsin. Indeed, the addition of hydrazine on the THR-inhibitor complex promotes a partial induced THR reactivation. This reactivation, confirmed by LC/MS, showed the resurgence of the native THR and a new dihydrazide complex. Docking experiments were then efficiently used to explain the trends observed in the enzymatic assays as well as to corroborate the postulated inhibition mechanism. Finally, the cell permeability of our derivatives was estimated using a computational approach.

Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling

The flexibility of activated factor X (fXa) binding site was assessed employing ligand-based pharmacophor modeling combined with genetic algorithm (GA)-based QSAR modeling. Four training subsets of wide structural diversity were selected from a total of 199 direct fXa inhibitors and were employed to generate different fXa pharmacophoric hypotheses using CATALYST software over two subsequent stages. In the first stage, high quality binding models (hypotheses) were identified. However, in the second stage, these models were refined by applying variable feature weight analysis to assess the relative significance of their features in the ligand-target affinity. The binding models were validated according to their coverage (capacity as a three-dimensional (3D) database search queries) and predictive potential as three-dimensional quantitative structure-activity relationship (3D-QSAR) models. Subsequently, GA and multiple linear regression (MLR) analysis were employed to construct different QSAR models from high quality pharmacophores and explore the statistical significance of combination models in explaining bioactivity variations across 199 fXa inhibitors. Three orthogonal pharmacophoric models emerged in the optimal QSAR equation suggesting they represent three binding modes accessible to ligands in the binding pocket within fXa.

Fuzzy Pharmacophore Models from Molecular Alignments for Correlation-Vector-Based Virtual Screening

A pharmacophore-based approach for compiling focused screening libraries is presented. It integrates information from three-dimensional molecular alignments into correlation vector-based database screening. The pharmacophore model is represented by a number of spheres of Gaussian-distributed feature densities. Different degrees of "fuzziness" can be introduced to influence the model's resolution. Transformation of this pharmacophore representation into a correlation vector results in a vector of feature probabilities which can be utilized for rapid virtual screening of compound databases or virtual libraries. The approach was validated by retrospective screening for cyclooxygenase 2 (COX-2) and thrombin ligands. A variety of models with different degrees of fuzziness were calculated and tested for both classes of molecules. Best performance was obtained with pharmacophore models reflecting an intermediate degree of fuzziness, yielding an enrichment factor of up to 39 for the first 1% of the ranked database. Appropriately weighted fuzzy pharmacophore models performed better in retrospective screening than similarity searching using only a single query molecule. The new pharmacophore method was shown to complement existing approaches.

SVM-Based Feature Selection for Characterization of Focused Compound Collections

Artificial neural networks, the support vector machine (SVM), and other machine learning methods for the classification of molecules are often considered as a "black box", since the molecular features that are most relevant for a given classifier are usually not presented in a human-interpretable form. We report on an SVM-based algorithm for the selection of relevant molecular features from a trained classifier that might be important for an understanding of ligand-receptor interactions. The original SVM approach was extended to allow for feature selection. The method was applied to characterize focused libraries of enzyme inhibitors. A comparison with classical Kolmogorov-Smirnov (KS)-based feature selection was performed. In most of the applications the SVM method showed sustained classification accuracy, thereby relying on a smaller number of molecular features than KS-based classifiers. In one case both methods produced comparable results. Limiting the calculation of descriptors to only the most relevant ones for a certain biological activity can also be used to speed up high-throughput virtual screening.

Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa

A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.

Solid-phase optimisation of achiral amidinobenzyl indoles as potent and selective factor Xa inhibitors

Starting from the achiral and potent factor Xa inhibitor 1, a new and flexible solid-phase optimisation strategy is described to reduce its cationic character. By replacing one positively charged side chain by a lipophilic substituent, a novel series of highly potent and selective achiral factor Xa inhibitors was discovered. The identified lipophilic replacements in the S4 pocket might be valuable for other approaches towards fXa inhibitors.

Novel, potent and selective chimeric FXa inhibitors featuring hydrophobic P1-ketoamide moieties

Judicious combination of P-region sequences of highly potent anticoagulant proteins including NAP5, NAP6, Ecotin, and Antistasin with SAR from small molecule FXa inhibitors led to a series of chimeric inhibitors of formula 1a-j. We report herein the design, synthesis, and biological activity of this novel family of FXa inhibitors that express both high in vitro potency and superb selectivity against related serine proteases.

New advances in the discovery of thrombin and factor Xa inhibitors

The search for the ideal anticoagulant has spanned decades and has resulted in several strategies including the clinical use of heparin, low molecular weight heparins, and the vitamin K antagonist warfarin. Over the past five years, many groups have reported preclinical results with direct-acting thrombin inhibitors and several of these are now moving into clinical trials. In addition, many groups have disclosed the discovery of potent, orally bioavailable factor Xa inhibitors. Several of these compounds are now in early clinical trials and the results are forthcoming.