Docking and Molecular Dynamics Simulations of the Ternary Complexes Between Glycyrrhizin Derivatives and Thrombin, Factor Xa and Trypsin
Caceres, R. A.(1); Guimarães, J. A.(1); de Amorim, H. L. N.(1,2);
(1) Departamento de Química, ULBRA, RS. (2) Centro de Biotecnologia, UFRGS, RS. e-mail: hlnamorim@terra.com.br
Glycyrrhizin (GL), a triterpenoid saponin composed of one residue of glycyrrhetinic acid (GA) and two residues of glucuronic acid (GU) is know for its anti-inflammatory, anti-allergenic, anti-viral and anti-carcinogenic activities. Also, GL was identified by our group as a thrombin inhibitor and, thus, presenting anticoagulant effect. Biochemical and molecular modeling studies pointed for a model where GL binds thrombin at the "anion binding exosite I (ABEI)". However, the inhibition of thrombin by GL was achieved in the micromolar range, suggesting that the interaction thrombin-GL is of low affinity. In this work docking and molecular dynamics (MD) methods were used to evaluate the affinity of six GL derivatives for thrombin. Structural modifications in GL template were based in methoxylation, acylation and sulphatation of the functional groups. Also, ternary complexes of factor Xa (fXa) and trypsin were simulated in order to compare the ligand affinity and selectivity with respect to thrombin. GL derivatives were parameterized using conformational analysis combined with ab initio calculations. Docking of the ligands in the target proteins was carried out interactively and guided by a complementary criteria of electrostatics and geometry. Eighteen molecular dynamics simulations were performed for a time period of 5 ns using GROMOS 43A2 force field, PBC and SPCE water model. GROMACS package modules were used in the analyzes of the MD trajectories. The designed ligands have presented different affinities and selectivity. GL have no affinity for factor Xa. However, methoxylation of GL hydroxyl groups increase the affinity for factor Xa and diminishes the energy interaction with thrombin. Also, sulphatation and methoxylation of GL derivatives increase the affinity for fXa. In conclusion, molecular modeling studies have demonstrated that is possible to modulate the ligand affinity and selectivity by punctual changes of the functional groups of GL. The compounds will be synthesized for characterization of the anticoagulant potential.
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