The Molecular Simulation Study On The Drug Resistance Mechanism Of Mycobacterium Tuberculosis To Anti-TB Drugs

Tuberculosis (TB) is a chronic infectious disease that can harm people’s health seriously. TB is caused mainly by mycobacterium tuberculosis. So far, the main effective therapy for patients infected by mycobacterium tuberculosis is the combination use of anti-tuberculosis drugs. However, the emergence of multidrug-resistant mycobacterium tuberculosis strains weakens the effectiveness of drug treatment and blocks the treatment of patients with tuberculosis seriously. Understanding the drug-target interactions and the molecular mechanisms of drug resistance can provide important guidance for designing and finding new and effective anti-tuberculosis drugs. In this paper, we explored the resistance mechanisms of mycobacterium tuberculosis to anti-tuberculosis drugs rifampicin and isoniazid by using the molecular dynamics simulation and binding free energy calculation methods.The first part of the thesis is to explore the drug resistance mechanisms of mycobacterium tuberculosis RNA polymerase β-subunit with His526Asp、His526Tyr、His526Arg、Ser531Trp and Ser531Leu mutations to rifampicin by using molecular dynamics simulation combined with MM-GBSA free energy calculation. By comparing the calculated binding free energies, the resistant rank order:His526Arg> Ser531Leu> His526Tyr> His526Asp. The loss of nonpolar interaction between amino acid residues and rifampicin molecule is the main factor to cause the reduced binding ability of RNA polymerase to rifampicin. In addition, for the Ser531Leu and His526Arg mutants, the electrostatic interaction energy in gas phase is also decreased significantly. By the analysis of the hydrogen bonding and hydrophobic interactions at binding pocket of complexes, we find that the mutations can influence the size and properties of binding pocket, also can cause the displacement of the ligand molecule. Thereby the hydrogen bonding and hydrophobic interactions are affected partly after mutations of the526th histidine and531th leucine residues.The second part of the thesis is to explain the reasons why Ser94Ala、Ile194Thr and Ser94Ala/Ile194Thr mutants of mycobacterium tuberculosis enoyc-Acp reductase have resistance to isoniazid (INH). Isoniazid that has entered into bacteria can be oxidized into the active form——INH-NAD, which combined with Nicotinamide Adenine Dinucleotide (NAD). For all the complexes of INH-NAD binding to wild type and mutant reductase, according to the size of bnding free energy, the ability of INH-NAD binding to enoyc-Acp reductase rank as below:WT> Ile194Thr> Ser94Ala> Ser94Ala/Ile194Thr. When we try to explore the main reasons of mutations causing the weaker binding ability, we find the mutations can cause the reduction of the electrostatic interaction energy from polar interaction energy and nonpolar interaction energy, and the loss of nonpolar interaction is the most critical factor leading to the loss of binding free energy, In addition, the decrease of the polar interaction energy has a close relationship with the weak or disappeared hydrogen bonding interaction. From the structural comparison, the mutations Ile194Thr, Ser94Ala and Ser94Ala/Ile194Thr can cause the change of INH-NAD binding pocket, furthermore can affect the original hydrogen bonding and van der Waals interactions between enoyc-Acp reductase and INH-NAD. As result, the binding affinity reduced.The main aim of this thesis is to explore the interaction mechanism between anti-TB drugs and their target, and the drug resistance mechanism from the molecular level. The obtained results will provide the valuable information for the design and discovery of the effective anti-TB drugs for drug-resistant tuberculosis.