Thermodynamic And Kinetic Studies On The Interaction Of Proteins And Small Molecules Based On Enhanced Sampling Molecular Dynamics Simulation

The thermodynamics of proteins and small molecules interaction(such as binding free energy ?Gbind and the equilibrium dissociation constant KD)is an important basis for the characterization of the binding stability of a drug and its target protein,and is also an important index to evaluate the affinity of a drug and its target protein interaction.But in recent years,the binding kinetics between protein and small molecules(such as the dissociation rate constant koff and the residence time),which has been paid more and more attention,is closely related to the pharmacokinetic and toxicity of a drug.Therefore,the binding kinetics should be taking into account in the drug design based on the thermodynamics of target proteins and small molecules interaction.Based on the calculation of thermodynamics and kinetics of proteins and small molecules,and the importance of predicting thermodynamics and kinetics,the main contents of present paper include the following five parts.The first chapter of this paper describes the importance of proteins and small molecules.Starting from the theory model of proteins and small molecules interaction,this chapter introduces the physical and chemical basis of the interaction and the thermodynamics and kinetics between the proteins and small molecules.Then we summed up the calculation methods of thermodynamics and kinetics of proteins and small molecules interaction.For thermodynamics of proteins and small molecules,there are mainly scoring functions based on molecular docking and binding free energy calculations based on molecular dynamic simulations,such as the well-known MM/PB(GB)method and free energy perturbation calculations.While the most mature methods for the calculation of binding kinetics including steered molecular dynamic simulations,the adaptive biasing force simulations and metadynamic simulations.In the second chapter,we studied the dissociation mechanism of two potent inhibitors PLX4720 and TAK-632 of B-RAF kinase and the relationship between the dissociation mechanism and the residence time.Starting from the crystal structures of the two inhibitors with B-RAF complexes,we firstly simulated the equilibrium trajectory of conventional molecular dynamics for energy decomposition,and we found that the energy contribution of the key amino acid residues for binding the two inhibitors is obvious differences,especially in the allosteric site.This shows that the hydrophobic interaction located in the allosteric site is very important to improve the efficacy and prolong the residence time of the B-RAF kinase inhibitors.we then used the random acceleration molecular dynamic simulations with different parameters for multiple equilibrium trajectories carried out statistics,found that the ligand PLX4720 dissociated from the ATP channel,while the ligand TAK-632 has a 1/3 chance to dissociate from the allosteric channel.In order to compare the ease of the two inhibitors dissociation from the different channel,we applied the steered molecular dynamic simulations to study the ligands PLX4720 and TAK-632 dissociate along the ATP channel and the ligand TAK-632 dissociates along the allosteric channel.The results show that TAK-632 dissociating along the allosteric channel is more difficult than that along the ATP channel,so the two ligands both dissociate along the ATP channel,which is agreement with the experimental data koff.In the third chapter,we studied the differences of the four ERK2 kinase inhibitors SCH772984?VTX-11e?FR180204 and 5-iTU dissociating mechanism.Conventional molecular dynamic simulations and energy decomposition were employed to study the binding difference of ERK2 protein and the four ligands,the results show that the maximum difference between the ligand and the other three ligands is the binding of SCH772984 with the ERK2 protein between the P-loop and the ?C helix.Afterwards,the steered molecular dynamic simulations and adaptive biasing force were applied to study the dissociation mechanism of the four ligands,the results show that SCH772984 has different dissociation mechanisms with the other three ligands.VTX-11 e,FR180204 and 5-iTU are only required to overcome the hydrophobic interaction located in ATP binding site in the dissociation course,and SCH772984 needs to overcome the pi-pi interaction in the allosteric site,and then it needs to overcome the hydrophobic interaction in the ATP binding site,which significantly increases the free energy barrier of SCH772984 dissociation.In the fourth chapter,we discussed the influence of chirality of crizotinib on its MTH1 protein inhibitory activity,and our theoretical calculations are well agreement with the experimental values.the results of molecular dynamic simulations and amino acid residues energy decomposition indicate that the difference in(S)-crizotinib/MTH1 and(R)-crizotinib/MTH1 binding is due to the energy contribution of these residues Tyr7?Phe27?Phe72 and Trp117.The adaptive biasing force simulations show that(S)-crizotinib and(R)-crizotinib have the completely different dissociation paths,which makes(S)-crizotinib need to absorb more energy than(R)-crizotinib when dissociating from the MTH1 binding site,that is to say,(S)-crizotinib need to overcome the larger free energy barrier.The fifth chapter also explains the difference in the inhibitory activity of(S)-PFI and(R)-PFI-2 against SETD7 protein.We first obtain the complex structure of(S)-PFI-2 and SETD7 by molecular docking,and the static analysis revealed the two ligands binding SETD7 by completely different conformation.Further molecular dynamic simulations show that the binding of(S)-PFI-2 with SETD7 is very unstable,which is found by monitoring the RMSD of the simulated system.In addition,the results of residues interaction network analysis show that the van del Waal interaction plays a key role in the binding of(R)-PFI-2 with SETD7.we got the average structure of the equilibrium trajectory from conventional molecular dynamic simulations and found that the post-SET loop in the(S)-PFI-2/SETD7 complex move more outward,which makes(S)-PFI-2 more exposed to the solvent and more unstable.Therefore,the adaptive biasing force was employed to study the dissociation behavior of the two ligands.Comparing with the(R)-PFI-2 dissociating along its reaction coordinate,the(S)-PFI-2 dissociates significantly easier along its reaction coordinate.The amplitude of the PMF curve of(S)-PFI-2/SETD7 is not larger than that of(R)-PFI-2/SETD7,so we get the conclusion that the instability of(S)-PFI-2 binding to SETD7 leads to the inhibitory activity of(S)-PFI-2 is less high than that of(R)-PFI-2.The results of these studies directly elucidate the molecular mechanism of the interaction between the four targets and their inhibitors,which will be helpful the development of more efficient and selective anticancer drugs.