Molecular Modeling Study On The Interactions Bemeen HIV-1Intasome And Drugs

Human immunodeficiency virus type1(HIV-1) integrase (IN) is one of the most important antiretroviral drug targets. During HIV-1life cycle, the integrase catalyzes the viral DNA integrated into the host cell chromosomal DNA, which is essencial for the viral replication. In the process of integration, HIV-1makes important interaction with cell cofactor LEDGF/p75protein. Currently, many specific integrase inhibitors have been developed to inhibit the enzyme functions, including integrase strand transfer integrases (INSTIs) and allosteric inhibitors targeting LEDGF/p75binding site of HIV-1integrase (LEDGINs). The INSTIs have been proven to inhibit HIV-1integrase selectively by targeting the HIV-1intasome, while the LEDGINs binding to the LEDGF/p75binding site of HIV-1integrase and inhibition of viral replication through an allosteric mechanism. In2007,2012and2013, Raltegravir, Elvitegravir, and Dolutegravir were approved by the U.S. FDA as the therapeutic integrase inhibitors, which have validated integrase as an attractive chemotherapeutic target to develop safe and efficacious drugs for the treatment of HIV/AIDS. Nonetheless, the emergence of drug resistant strains of HIV-1represents a major challenge in the treatment of patients who contract the virus. It is therefore unmet medicinal need to the rational design of next-generation integrase inhibitors, especially the INSTIs overcoming resistance and the more potent LEDGINs.In this thesis, we first give a general introduction to HIV-1, the structure and function of HIV-1intasome and its interactions with small molecular drugs, the basic principles of computer aided drug design (CADD) method. On this basis, we focus on the action of INSTIs and LEDGINs and the causes of resistance in HIV-1integrase by using the CADD method.The first part of the thesis is to study the inhibition mechanism of the anti-HIV drug Raltegravir. First, the structures of HIV-1intasome and HIV-1intasome in complexed with Ralltegravir were constructured by using homology modeling and structure alignment methods. Based on the build models, molecular dynamics (MD) simulation and binding free energy calculation were performed to investigate the molecular mechanism of HIV-1integrase-viral DNA interactions and the inhibition action of Raltegravir. The structural analysis showed that Raltegravir did not influence the interaction between viral DNA and HIV-1IN, but rather targeted a special conformation of HIV-1IN to compete with host DNA and block the function of HIV-1IN by forcing the3’-OH of the viral DNA terminal A17nucleotide away from the three catalytic residues (Asp64, Asp116, and Glul52) and two Mg2+ions.The second part of the thesis is to study the most common HIV-1integrase mutations (Y143R, Q148K, N155H, Q148H/G140S, and N155H/E92Q) induced drug resistance mechanism to Raltegravir. The values of the calculated binding free energy follow consistently the experimentally observed ranking of resistance levels. Analyses of the MD simulation result and binding free energy calculation suggested that the five mutations induce the conformational change of the integrase140s loop (Gly140to Glyl49) and viral DNA terminal in HIV-1intasome and further lead to the decrease of the binding free energy contribution from residues Tyr143, G4, and A17.The third part of the thesis is to study the cross-resistance mechanism of HIV-1integrase E138K/Q148K mutation to Raltegravir, Elvitegravir, and Dolutegravir. MD simulation and binding free energy calculation demonstrated that the E138K/Q148K mutation cause the structure rearrangements in HIV-1intasome active site. The active site structure rearrangements alter the two-metal chelating model of Raltegravir and Elvitegravir, due to the unfavorable orientation of oxygen atoms. Remarkably, a limited cross-resistance profile was observed for Dolutegravir, which possesses a less flexible linker region between the metal chelating core and the halogenated phenyl group. In addition, a systematic comparison and analysis of the residue interaction network (RIN) proves that the communications between the residues in the resistance mutant is increased when compared with that of the wild-type HIV-1intasome.The forth part of the thesis is to study the allosteric inhibition mechanism of LEDGFNs BI-1001and CX14442to HIV-1integrase. On the basis of the co-crystal structure of HIV-1integrase with BI-1001, molecular docking was used to obtain the3D structure of the more potent CX14442in complexed with HIV-1integrase. Then, MD simulation and binding free energy calculations were employed to determine the detailed binding mode of the BI-1001, CX14442. and LEDGF/p75. It is demonstrated that CX14442has a tert-butyl group which help it forms better interactions with the highly hydrophobic binding pocket. The result also demonstrated that to design of novel and more potent LEDGINs, a further extension strategy is the stretch of the LEDGF/p75Phe406and Val408binding sites in HIV-1integrase. In addition, we found that binding of BI-1001and CX14442induced the structure rearrangements of HIV-1integrase active site.Our theoretical results provide a molecular insight into the action of integrase inibitors and the mutation induced drug resistance mechanism to integrase strand transfer inhibitors, which is helpful for the further development of more effective integrase inhibitors to treat HIV/AIDS.