Molecular Mechanism Study On Activity And Drug Resistance Changes Of Hiv-1 Integrase Caused By Mutations

Acquired immune deficiency syndrome(AIDS) is a serious infectious disease caused by the human immunodeficiency virus(HIV). Since the first case of AIDS was reported in the United States in July 1981, AIDS has led to 25 million people around the world lost their lives to date, and AIDS can not be cured yet. HIV-1 integrase(IN) is a key enzyme necessary for the integration of the viral c DNA into the host genome. Inhibiting IN activity can effectively block the virus replication in host cells. At the same time, because of no IN functional analogues in the normal human host cells, the inhibitor could have fewer side effects on the human body. Therefore, IN is considered to be an ideal target for the research and development of anti- HIV target drugs. The progess of integration catalyzed by IN can be mainly divided into two reactions in vivo, 3 ’- processing and strand transfer.At present, a variety of IN inhibitors(INIs) have been developed, the diketo acids(DKA) and its analogues, which targeting inhibition of strand transfer reaction, are the most potent and successful drugs by far. Among the drugs of this class, Raltegravir, Elvitegravir and Dolutegravir have been approved by FDA. But as a result of high error rate of the HIV-1 reverse transcription, viruses are prone to mutations and the majority of mutations were related to drug resistance. Drug resistance is a main cause of treatment failure in AIDS patients. Therefore, it is urgent to develop new drugs. The complete HIV-1 IN crystal structure has not been obtained yet, which greatly hindered the research on drug-resistant mechanism and the progress of new drugs discovery and development. In this thesis, six dimeric models of the wild type and mutant full- length HIV-1 IN-v/hDNA complexes were built, respectively. Then inhibitor Raltegravir was docked to the active site of the IN-v/hDNA complexes using molecular docking method. Finally, the molecular mechanism of activity and drug resisitance changes of HIV-1 IN caused by mutaitons were explored using molecular dynamics(MD) simulation method. It will be helpful for drug development.The results show that the molecular mechanisms of IN activity changes caused by mutations are:(1) Mutations result in the changes of the interaction network in IN active site, and then affect IN catalytic activity by changing the distance and the relative position between the two magnesiums;(2) Mutations result in the reduction of IN Loop140-143 flexibility, and then reduce the IN catalytic activity;(3) Mutations result in the changes of binding mode between IN and v/hDNA, and then affect IN catalytic activity;(4) Mutations result in the changes of IN residues correlation. These changes affect the stabilities of IN-v/hDNA complexes and then affect IN catalytic activity. The molecular mechanisms of drug resistance caused by mutations are :(1) Mutations result in the changes of binding mode between IN-v/hDNA and RAL. These changes weaken the inhibitory effect of RAL and then cause drug resistance;(2) Mutations result in the changes of the interaction network in IN active site, which influence the combination of IN-v/hDN A and RAL, and then reduce the stability of IN-DNA_RAL complexes, furthermore, affect the inhibitory effect of RAL;(3) Mutations result in the changes of IN residues correlation. These changes affect the binding pattern of RAL and IN-v/hDN A, and then cause drug resistance.This study will help us to comprehend the molecular mechanism of the activity and drug resistance changes of HIV-1 caused by mutations, and will provide some meaningful information for lead optimization and anti- IN drug discovery.