Study On The Interaction Between HIV-1 Proetase And Inhibitors Using Molecular Dynamics Simulations

The abnormal expression and activation of proteases are usually related to diseases.Using inhibitors to inhibit the activity of disease-related proteases can treat these diseases.The emergence of drug-resistant virus strains seriously affects the efficacy of drugs.Thus it is urgent to find novel inhibitors that are effective against drug-resistant virus strains.Although the current experimental techniques can reveal the mechanism of the interaction between proteases and inhibitors,there are still limitations in using experimental methods to study the interaction between proteases and inhibitors.For example,it is difficult to obtain information on the dynamic changes of protease structure under physiological conditions.However,molecular dynamics simulation can overcome these limitations,not only can explore the dynamic process of proteases conformational changes,but also obtain energy information during the process of proteases conformational changes.This thesis takes HIV-1(Human Immunodeficiency Virus type 1)protease and its inhibitors Amprenavir(APV),Indiravir(IDV),Ritonavir(RTV),Nelfinavir(NFV),GRL-02031,Darunavial(DRV),CA-p 2and KNI-1657(KNI)as examples to study the interaction mechanism of HIV-1 protease and various inhibitors from the perspective of structure and energy.These results will provide a certain theoretical basis for the design of new anti-HIV drugs.The content mainly included the following parts:1.Theoretical study on the mechanism of cross-resistance of HIV-1 protease inhibitorsThe double mutations G48T/L89 M obviously weaken inhibiting efficiency of several inhibitors on HIV-1 protease.However,the conformational changes of HIV-1 protease caused by the G48T/L89 M mutation and the molecular details and energy information of its interaction with four drug molecules(APV,IDV,RTV and NFV)are still unclear.Based on the complexes of wild type(WT)and G48T/L89 M mutant proteases with APV,IDV,RTV,and NFV,respectively,we used molecular dynamicssimulation methods to investigate the resistance mechanism due to the G48T/L89 M mutations.The simulation results indicate that the G48T/L89 M mutation can cause structural rearrangement of the active site of protease,change the binding conformation of the drug molecule,and decrease the free energy between protease and the drug molecule.2.Theoretical study on the resistance mechanism of mutant HIV-1 protease to its inhibitor GRL-02031The inhibitor GRL-02031 has great advantages in delaying the resistance of HIV-1 protease.However,drug resistance mutations(I47V,L76 V,V82A,N88D)can still reduce the binding force of protease and inhibitor GRL-02031.It is yet unclear why and how these mutations,especially non-active site mutations L76 V and N88 D,reduce inhibitor GRL-02031 binding with HIV-1 protease.To elucidate the binding mechanism of protease with promising inhibitor GRL-02031 and further to probe into the resistance mechanism associated with mutations(I47V,L76 V,V82A,N88D)to the inhibitor,we applied multiple molecular dynamics simulations and(MM-PBSA and SIE)on HIV-1 protease with GRL-02031 complexes.The results indicated that the active site I47 V and V82 A mutations can directly cause changes in the binding pocket of HIV-1 protease,while the L76 V and N88 D mutations located at the distal end of the active site can cause the rearrangement of the active site residues Asp30,Val32,and Ile47 by changing the van der Waals interaction and hydrogen bonding interaction of surrounding residues,which in turn leads to a decrease the binding affinity of HIV-1 protease with inhibitor GRL-02031.3.Theoretical study on the sensitivity of mutant HIV-1 protease PRS17 to its inhibitors DRV and CA-p2PRS17,a mutant of HIV-1 protease,has 17 mutated residues showing high levels of multidrug resistance.The experiments indicate that PRS17 exhibits different sensitivities to inhibitors DRV and CA-p2,but the reason for the difference in sensitivity is still unclear.Focused on the complexes of WT HIV-1 protease and mutant PRS17 with inhibitors DRV and CA-p2,respectively,we performed multiple molecular dynamics simulations combined with binding free energy analyses(MM-PBSA and SIE)to disclose the impact of these mutated residues on the interaction mechanism of HIV-1 protease with these two inhibitors.Our analysis revealed that 17 mutated residues alter the curling degree of the flap tips,the distance between flap regions and catalytic sites,and the volume of inner catalytic site,thereby affecting HIV-1 protease binding to the inhibitors DRV and CA-p2.We also found that the residues near Arg8',Ala28/Ala28',Ile50/Ile50' and Ile84/Ile84' play an important role in the binding of HIV-1 protease and inhibitors.Both van der Waals interaction and electrostatic interaction have important contributions to the binding of HIV-1 protease to inhibitors DRV and CA-p2.Due to mutated residues,the binding conformation of PRS17 and inhibitor DRV is changed,which reduces the binding ability of PRS17 and inhibitor DRV,resulting in decreased sensitivity.During the binding process of PRS17 and the inhibitor CA-p2,the van der Waals interaction and hydrogen bonding interaction between the argnine CA-p2 and the HIV-1 protease are enhanced,which enhances sensitivity to inhibitor CA-p2.4.Theoretical study on the sensitivity of mutant HIV-1 protease to its inhibitors DRV and KNIThe experiments indicate V32I/L33F/I54M/V82 I and V32I/L33F/I54M/I84 V mutations affect the binding of HIV-1 protease to inhibitors DRV and KNI,but the reason for the difference in sensitivity has not been reported yet.Focused on the complexes of WT HIV-1 protease and two mutant HIV-1 proteases(V32I/L33F/I54M/V82 I and V32I/L33F/I54M/I84V)with inhibitors DRV and KNI,respectively,we adopted a research strategy similar to the HIV-1 protease and inhibitor DRV and CA-p2 system,and also investigated the effect of mutated residues on the interaction mechanism of HIV-1 protease with these two inhibitors,and the results were basically similar.The mutated residues alter the curling degree of the flap tips,the distance between flap regions and catalytic sites,and the volume of inner catalytic site,thereby affecting HIV-1 protease binding to the inhibitors DRV and KNI.We also found that the residues near Ala28/Ala28',Ile50/Ile50' and Ile84/Ile84' play an important role in the binding of HIV-1 protease and inhibitors.Both van der Waals interaction and electrostatic interaction also have important contributions to the binding of HIV-1 protease to inhibitors.Due to mutated residues,the binding conformation of the two mutant HIV-1 proteases and inhibitor DRV is changed,which reduces the binding ability between them,resulting in decreased sensitivity.During the binding process of the two mutant HIV-1 proteases and the inhibitor KNI,the van der Waals interaction and hydrogen bonding interaction between the tetrahydrofuranylglycine(Thfg)and 3-amino-2-hydroxy-4-phenylbutyricacid(Apns)groups of KNI and the mutant HIV-1 protease are enhanced,which enhances sensitivity to inhibitor KNI.The above results will provide important reference for the design of more effective HIV-1 protease inhibitors with higher inhibitory activity.