| The enzyme plays an important role in the life activities.Enzymes can catalyze reactions under mild conditions.Abnormal expression and activation of the enzyme is often related to some diseases.The use of inhibitors to regulate the activity of enzymes which are involved in these diseases has become one of the scientific research topics.Exploring the interactions between enzymes and inhibitors could provide theoretical support for drug modification and new drug design.At present,experimental method could generally reveal the interaction mechanism between enzymes and inhibitors,but there are still some limitations.For instance,it is impossible to obtain dynamic information of protein structure in physiological condition.However,molecular dynamics simulation could overcome these obstacles.It could not only explore protein conformation changes,but also obtain the energy information in the dynamic process.With the development of computer hardware and the improvement of software,the molecular dynamics simulation method has achieved unprecedented development in terms of calculation scale,precision and breadth.Molecular dynamics simulation has been paid more and more attention by researchers.It has become an important technology in the fields of biochemistry and materials science.In this dissertation,molecular dynamics simulations were used to explore the interaction mechanism of non-receptor tyrosine kinases(focal adhesion kinase and BCR-ABL)and aldose reductase with respective inhibitors,which will be useful for the development of cancer and diabetes drugs.The main contents are as follows:1.Exploring the interactions between focal adhesion kinase(FAK)and inhibitors by molecular dynamics simulationsFAK is a non-receptor tyrosine kinase of the FAK subfamily,which mainly locates in the cell adhesion site.Since this enzyme plays an important role in the progression for tumors transforming into the malignant invasion phenotype,it is considered as a therapeutic target for cancer treatment.Molecular dynamics simulations and molecular mechanics generalized Born surface area(MM-GB/SA)calculation were performed to explore the interactions between FAK and three inhibitors(PHM16,TAE226,and 7PY).The results show that Glu500 and Cys502 are two crucial residues for the three inhibitors binding to FAK: they could form hydrogen bonds with the middle part of each inhibitor,anchoring the position of the inhibitors.Asp564 can form a hydrogen bond with the acylamino tail of PHM16 and TAE226,decreasing the distance between the inhibitor and the residues around Asp564,and enhancing the interaction between the inhibitor and these residues.Arg426 can form electrostatic interactions with the meta-position methoxy groups on 3,4,5-trimethoxyaniline group of PHM16 and 7PY,while the electrostatic interaction with the ortho-position methoxy on the 2-ortho-methoxyaniline group of TAE226 is relatively weak.Besides,Ile428,Val436,Ala452,Val484,Leu501,Glu505,Glu506,Leu553,Gly563,Leu567,and Ser568 can form hydrophobic interactions with the inhibitors.In conclusion,these results could be usefull for further inhibitor design of FAK and also give a new perspective for further research of cancer.2.The Molecular Mechanism of BCR-ABL Mutants Affecting Inhibitor BindingBCR-ABL is a non-receptor tyrosine kinase generated by the fusion of the gene encoding breakpoint cluster region(BCR)on chromosome 22 and the gene encoding cell Abelson tyrosine kinase(c-ABL)on chromosome 9.Due to the structural features,BCR-ABL is in constitutive active state,leading to the generation of chronic myeloid leukemia(CML).Thus,BCR-ABL has been regarded as a therapeutic target for treating CML.Asciminib is a highly selective non-ATP competitive inhibitor of BCR-ABL.However,several resistant mutations(I502L and V468F)around myristoyl site have been found.In order to investigate the molecular mechanism of Asciminib resistance induced by the two mutants,molecular dynamics simulations and MM-GB/SA calculations were performed.The obtained results indicate that the mutations have adverse influence on the binding of Asciminib to BCR-ABL,as the nonpolar contributions decline in the two mutants.In addition,I502 L mutation causes ?-helix I'(?I')to shift away from the helical bundle composed of ?E,?F,and ?H,making the distance between ?I' and Asciminib increasing.For V468 F mutant,the side chain of Phe468 occupies the bottom of the myristoyl pocket(MP),which drives Asciminib to shift toward the outside of MP.These results provide the molecular insights of Asciminib resistance mechanism in BCR-ABL mutants,which could provide theoretical information for the design of new inhibitors against BCR-ABL resistance in the future.3.Molecular dynamics simulation on the interactional details between AKR1B1 and 3-mercapto-5-hydro-1,2,4-triazin[5,6-b] indole-5-acetic acid(Mtia)In the human body,aldose reductase(AKR1B1)can transform glucose into sorbitol.At hyperglycemia,aldose reductase is overexpressed,leading to the accumulation of sorbitol and the consumption of NADPH,which causes diabetic complications or cancers,threatening human life.Fortunately,aldose reductase inhibitors could effectively alleviate these symptoms.Recently,an inhibitor,Mtia,has been reported that it has three tautomeric forms(Mtia1,Mtia2,and Mtia3)in aqueous solution.However,the preferred form for binding to AKR1B1 is not clear.In this study,molecular dynamics(MD)simulations and MM-GB/SA calculations were performed to make sure which tautomer is the preferred one.The overall structural features and the results of binding free energies indicate that Mtia1 and Mtia2 have more superiority than Mtia3 in terms of binding to AKR1B1.Furtherly,the results of free energy landscapes,local active site conformational characteristics,and non-covalent interaction analyses indicate that the combination of Mtia2 and AKR1B1 is more stable than Mtia1.Our study can provide insights into the details of the interaction between AKR1B1 and Mtia at the atomic level,and will be helpful for the further design of AKR1B1 inhibitors. |
PDF Full Text Request