Theoretical And Computational Study On The Binding And Dissociation Properties Of HIV-1 Intasome And Small Molecule Inhibitors

Acquired immunodeficiency syndrome,also known as AIDS,is a serious global disease.It is mainly caused by human immunodeficiency virus type 1（HIV-1）which belongs to the family Retroviridae.At present,antiretroviral drugs targeting the key enzymes in virus replication process were widely used for the treatment of AIDS.Among them,integrase（IN）,which catalyzes the integration of virally derived DNA into the host cell DNA in the nucleus,has become an attractive target for the development of antiretroviral drugs due to its least resemblance to any human protein.At present,for this target,a number of IN inhibitors have been approved for the treatment of AIDS.However,the occurrence of drug resistance seriously declined the therapeutic effect of IN inhibitors.Therefore,the design of new IN inhibitors is necessary.In this thesis,through molecular simulation and energy calculation methods,we systematically studied the mechanism of action of integrase inhibitors and the dissociation of integrase inhibitors.Besides,the mechanism of accessory drug resistance leading to high level drug resistance were also explored.At last,the binding mode of HIV-1 IN and ribonuclease H（RNase H）dual inhibitor 6f were explored.The results will be beneficial for the design of new anti-HIV-1 drugs with high affinity and high barrier to drug resistance.1.The study on the mechanism of HIV-1 IN inhibitor.Based on 6 HIV-1 integrase inhibitors（RAL,EVG,DTG,BIC,CAB and MK-2048）,we used molecular dynamics simulation and energy calculation explored the mechanism of action of integrase inhibitors.The results showed that the mechanism of action of the six integrase inhibitors has some similarities:firstly,all of them could chelate with the"DDE"motif and Mg²⁺in the active site,which related to the affinity of the inhibitors;secondly,the halogenated benzene ring can formπ-πinteractions with G4,C16 and A17 of v DNA.2.The study on the dissociation mechanism of HIV-1 integrase inhibitors.Based on RAL,EVG and DTG,the dissociation mechanism of integrase inhibitors was explored through RAMD and SMD.Firstly,the results of RAMD showed that the dissociation path of RAL,EVG and DTG were different.Secondly,the dissociation mechanism of was explore through SMD,including the force during the dissociation process and the interaction between receptor-inhibitor.It was found that DTG binded tightly with the active site than RAL and EVG,while RAL bind tightly than EVG,which is corresponds to the affinity of the three inhibitors,indicating that our results were reliable.Besides,it was also found that hydrogen bonding andπ-πinteraction played a key role in the dissociation process of the three inhibitors.Finally,the average power potential（PMF）and?G_off of each system were calculated and indicated that our simulation results were reliable.3.The study on the mechanism of accessory drug resistance（L74M and T97A）leading to high level drug resistance to DTG.Based on 6 mutant type HIV-1 intasome（L74M,T97A,G140A-Q148R,Y143R-N155H,L74M-G140A-Q148 and T97A-Y143R-N155H）,we used molecular dynamics simulation to explore the mechanism of L74M and T97A leading to high level drug resistance to DTG.The results showed that with the increase of mutations,the chelation interaction between DTG and Mg²⁺gradually weakened.Compared with the wild type,the conformation of DTG changes little when only accessory mutations exist,while the conformation changes a lot when accessory mutations existed with major mutations.Theɑ2 helix of the CCD region untwisted,which forced DTG deviate from the binding site,resulting theπ-πinteraction between DTG and G4,C16 of v DNA weakened or even disappeared.4.The study on the mechanism of HIV-1 integrase and RNase H dual inhibitors and prediction of drug resistance.Based on HIV-1 IN and RNase H dual inhibitor 6f,the mechanism of diketo acid dual HIV-1 IN and RNase H dual inhibitor was studied by molecular dynamics simulation and energy calculation methods.The results showed that the binding modes of 6f with the two targets shared two similarities:（1）The diketo acid groups of 6f could chelate with the“DDE”or“DDDE”motifs and Mg²⁺in the active site（2）The pyrrole substituents of 6f stretched into the cavities constituted by hydrophobic amino acids.Besides,the results of drug resistance prediction by molecular dynamics method showed that three IN mutations（Y143C,Q148R and N155H）caused different degrees declines of binding affinity of 6f and two RNase H mutations（Y501R and Y501W）caused declines of binding affinity of 6f,indicated that these mutations may cause drug resistance to 6f.Our theoretical results provided a molecular insight on the mechanism of action of integrase inhibitors and the mechanism of action of accessory drug resistance mutations,provides an important theoretical guiding significance for the design of new IN inhibitors with high affinity and high barrier to drug resistance.