| Literature DB >> 36117662 |
Yuxin Zhang1, Xing Wang2, Binan Lu1, Yanbin Gao2, Yanling Zhang3, Yatong Li2, Hongjuan Niu1, Lu Fan1, Zongran Pang1, Yanjiang Qiao3.
Abstract
Objective: This study was devoted to identifying natural thrombin inhibitors from traditional Chinese medicine (TCM) and evaluating its biological activity in vitro and binding characteristics.Entities:
Keywords: gallic acid; molecular dynamics; natural thrombin inhibitor; platelet aggregation; surface plasmon resonance
Year: 2021 PMID: 36117662 PMCID: PMC9476537 DOI: 10.1016/j.chmed.2021.09.001
Source DB: PubMed Journal: Chin Herb Med ISSN: 1674-6384
Fig. 1Binding mode of ligand MEL (A), argatroban (B) and gallic acid (C) in the inhibitor-binding site of thrombin. The green and red sticks represent the re-docked and co-crystallized conformations of ligand MEL, respectively. The red dotted lines represent the hydrogen bond interactions between the ligand and thrombin. Key residues are shown and the red dotted lines represent the hydrogen bond interactions between the inhibitors and thrombin. Yellow, white, red and blue atoms represent carbon, hydrogen, oxygen and nitrogen atoms, respectively. (D) Dose-response curves of thrombin inhibition for gallic acid and argatroban, respectively.
Fig. 2Gallic acid inhibits thrombin induced platelet aggregation. (A) Platelet aggregation curve of argatroban (0.33 nmol/L) and gallic acid at different concentrations (50.00 μmol/L, 25.00 μmol/L, 12.50 μmol/L) under 1U/mL thrombin stimulation. (B) Gallic acid at 50.0 μmol/L, 25.0 μmol/L and argatroban (0.33 nmol/L) shows statistically significant inhibitory effects on thrombin induced platelet aggregation. *P < 0.05, ***P < 0.001.
Fig. 3SPR-based binding analysis between gallic acid and thrombin. (A) Sensorgram of gallic acid and thrombin. The concentrations of gallic acid were 37.50, 18.75, 9.38, 4.69, 2.34 and 1.17 μmol/L (from top to bottom). (B) Fit curve of thrombin with different concentrations of gallic acid generated by the ‘Affinity’ module in Biacore T200 evaluation software.
Fig. 4(A) RMSD of the backbone atoms of thrombin-gallic acid system. (B) RMSF values of amino acid residues in thrombin-gallic acid system. Key amino acid residues that bind to gallic acid are labelled with dashed lines. (C) MM/GBSA decomposition results of total binding free energies per residue for thrombin-gallic acid system.
Free energies of binding and intermolecular interaction energy components of thrombin-gallic acid obtained by MM/GBSA approach.
| Energy components | Average energy/(kcal·mol−1) | Standard deviation | Standard error of mean |
|---|---|---|---|
| ΔEvdw | −21.55 | 2.65 | 0.08 |
| ΔEele | −16.06 | 11.62 | 0.37 |
| ΔEGB | 26.01 | 9.53 | 0.30 |
| ΔESURF | −3.01 | 0.26 | 0.01 |
| ΔGsol | 23.00 | 9.40 | 0.30 |
| ΔGbind | −14.61 | 3.73 | 0.12 |
Evdw and Eele are the van der waals and coulomb energies. EGB and ESURF are the polar and non-polar solvation contribution calculated by solving the GB equations. Gsol is the total solvation free energy. Gbind is the binding energy between the thrombin protein and ligands. ΔGbind = Gcom − (Gpro + Glig) ≈ ΔEvdw + ΔEele + ΔGsol.