Identification of berberine as a direct thrombin inhibitor from traditional Chinese medicine through structural, functional and binding studies

Abstract

Thrombin acts as a key enzyme in the blood coagulation cascade and represents a potential drug target for the treatment of several cardiovascular diseases. The aim of this study was to identify small-molecule direct thrombin inhibitors from herbs used in traditional Chinese medicine (TCM). A pharmacophore model and molecular docking were utilized to virtually screen a library of chemicals contained in compositions of traditional Chinese herbs, and these analyses were followed by in vitro bioassay validation and binding studies. Berberine (BBR) was first confirmed as a thrombin inhibitor using an enzymatic assay. The BBR IC50 value for thrombin inhibition was 2.92 μM. Direct binding studies using surface plasmon resonance demonstrated that BBR directly interacted with thrombin with a KD value of 16.39 μM. Competitive binding assay indicated that BBR could bind to the same argartroban/thrombin interaction site. A platelet aggregation assay demonstrated that BBR had the ability to inhibit thrombin-induced platelet aggregation in washed platelets samples. This study proved that BBR is a direct thrombin inhibitor that has activity in inhibiting thrombin-induced platelet aggregation. BBR may be a potential candidate for the development of safe and effective thrombin-inhibiting drugs.

Study on Structure Activity Relationship of Natural Flavonoids against Thrombin by Molecular Docking Virtual Screening Combined with Activity Evaluation In Vitro

“…Molecular docking technology, an algorithm that predicts the putative geometry of a protein-ligand complex has been successfully applied in the studies of SAR of compounds and TCM as well as predicting binding affinities of ligands [18][19][20][21][22]. Irrespective of these gains, there also exist disadvantages such as low accuracy and high false positive rate.…”

Identification of a specific agonist of human TAS2R14 from Radix Bupleuri through virtual screening, functional evaluation and binding studies

“…Natural products have been considered a valuable source for small-molecule drug discovery 14 , 15 . Radix Bupleuri , a common Chinese herbal medicine designated as “bitter taste” according to Chinese medicine theory, displays anti-asthmatic and antitussive effects in clinical use 16 .…”

Influence of Chelidonium majus Water Extract onto Cancer Cells and Platelets

“…Thus, we suggested that this effect must be caused by chelerythrine or berberine precursors and berberine-like alkaloids content of the extract. This is an opposite effect, that shown for pure berberine [10][11][12][13][14]. We thought, that we got precursors of main alkaloids not because of degradation them during extraction, but because of harvesting young flowering plants, where main alkaloids has not been synthesized yet.…”

“…In particular, it has been established that the chelidonin interacts with tubulin causing the termination of the mitosis phase [5] chelidonine has several pharmacological effects [6,7]. Heliterrin, sanguinarine, berberine and coptisin affect the processes of respiration in mitochondria, berberine affects platelet activation [8], berberine is a reversible inhibitor of acetylcholinesterase [9] and pure berberin is the trombin inhibitor and inhibitor of platelets aggregation [10]. It was steadied in case of cardiovascular and thrombotic deceases [11], but FDA declined it in clinical trials, because of risk cytotoxicity [12].…”