Molecular Mechanism Of Recognition In Several Protein-Ligand Interactions By Theoretical Calculations

It is well known that the dynamic behavior of the protein spatial structure and the interaction between protein and ligand, are closely related to the biological function. An accurate estimation of binding free energy between protein and ligand, is one of the most important issues in the drug discovery process. Recently, theoretical calculation has already become an attractive method in the fields of biochemistry. In this thesis, homology modeling, molecular dynamics, quantum mechanics methods, and binding free energy calculation were used to theoretically study on understanding the role of an amino acid residue with the metal ion-dependent adhesion site playing in integrin-RGD binding affinity, the molecular mechanism of potency and selectivity inhibitors of the Aurora A, the role of bivalent cations in structural stabilities of vaccinia-related kinases(VRK), and the impacts of eight various atomic net charge models on Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) binding free energy profiles. The main results are summarized as follows:1、Variation in One Residue Associated with the Metal Ion-Dependent Adhesion Site Regulates αⅡbβ3Integrin Ligand Binding AffinityIn this study, a mutation was introduced in the intergrin αⅡbβ3to convert the MIDAS associated Ala252to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding affinity through molecular dynamics simulations and free energy calculations estimations. We found that the ability of ligand binding was reduced when this MIDAS residue Ala252was mutated to Asp252in integrin αⅡbβ3, whereas was increased when paired with mutations of one ADMIDAS residue and was nearly abolished when combined this mutant with mutations of two ADMIDAS residues. Our results suggest that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins.2、Understanding the Molecular Mechanism of Binding Modes of Aurora A and Inhibitors by Long Time Scale GPU DynamicsIn this study, the binding mechanisms of two different inhibitors with a contrasting binding affinity to Aurora A were investigated by long time scale GPU molecular dynamics simulations coupled with MM/PB(Generalized Born, GB)SA method. The results showed that the predicted binding free energies of these two complexes were consistent with the experimental data. Through analyzing the individual energy components of binding free energy, we found that the van der Waals contribution was the main force to drive the inhibitor-protein binding. The structural analysis demonstrated that the inhibitor HPM could produce more hydrophobic interaction contacts with Aurora A than that of2JZ, and the loss of key hydrogen bonds between the inhibitor and residue Argl37of Aurora A was another important reason for the weaker binding affinity of2JZ to Aurora A. This study sheds more light on the development of the efficient inhibitors targeting the Aurora A.3^Role of Bivalent Cations in Structural Stabilities of New Drug Targets-Vaccinia-related Kinases (VRK) from Molecular Dynamics SimulationsTo study the underlying molecular mechanisms, molecular dynamics simulations were performed to investigate the role of divalent cations Mg2+and Mn2+in the structural stabilities and dynamical behaviors of vaccinia related kinase3(VRK3), which was the first solved crystal structure of the pseudokinase, and that of its closest active relatives VRK1and VRK2. The results suggested that the binding of Mg+in the active site played a key structural role in the stabilization of VRK1and VRK2, and Mn2+was slightly required for VRK2. By contrast, the pseudokinase VRK3was well ordered with lower RMSD values indicating it was rigid and very stable regardless of whether the bivalent cations were bound or not. The present study provided evidence for the role of bivalent cations in stabilizing the structure of VRKs and the modeling results were supported by available experimental data.4、Binding Free Energy Estimation for Protein-Ligand Complex Based on MM/PBSA with Various Partial Charge ModelsIn this study, the impacts of eight various atomic net charge models were considered, and their effects on binding free energy profiles also were investigated. The methods were tested on:the30structurally diverse ligands of diverse protein complexes, the14structurally diverse ligands of the Protein Kinase B(PKB) and the10structurally diverse ligands of the Cyclin-Dependent Kinases2(CDK2) with measured affinities. The tested charges were calculated based on AM1(Austin Method, version1)-BCC(Bond Charge Correction), MNDO (Modified Neglect of Diatomic Differential Overlay), PM5(Parameterisation Model, version5), MUL(Mulliken), CM2(Charge Model2), CM3(Charge Model3), RESP(Restrained Electrostatic Potential) and QM/MM(Quantum Mechanics/Molecular Mechanics) models. Our findings showed that the MNDO charge model was best propitious for PKB and QM/MM for CDK2, whereas none of any given models was suited for the diverse ligands of diverse protein complexes. The trends of MM/PBSA binding free energies using all charge models were in good accord with experimental results for CDK2but not for PKB in most cases.