Molecular Dynamics Simulation For Several Important Proteins And Improvement Of Their Inhibitors

Today, along with the development of the relative theories and the advancement of computer technology, the molecular simulations of protein have been an important research field in biology science. Homology modeling, molecular docking and molecular dynamics methods can be used to theoretically construct the three dimension structure of protein and to study the interaction between ligand and receptor. On this basis, the obtained results can give the explanation of the experimental phenomenon and provide the theoretical guidance for the inhibitor design of the special protein and the development of the new drug for the related diseases. In the thesis, these methods were used to study three kinds of important proteins. The main results are summarized as follows:1. Dynamic interaction between human pulmonary surfactant protein D (hSP-D) and monosaccharidesHuman pulmonary surfactant protein D (hSP-D) is a kind of important protein in human lung innate immune system. It binds to surface carbohydrates on all kinds of inhaled pathogens and particles, facilitating their uptake and clearance by other innate immune cell. Hence the protein is involved in many diseases, including influenza and HIV etc. The latest researches show that the dynamic interaction between the protein and monosacchrides is different from the quality in the stable state. The cause is unclear.Molecular docking, conventional molecular dynamics and steered molecular dynamics were used to study the dissociation of three monosaccharides from hSP-D and analyze the special dynamic interaction during the process. Then the adaptive biasing force (ABF) method was used to compute the free energy profile of dissociation. The results show that three monosacchrides have the different transition state energy values in the dissociation, resulting to their different energy barrier. The check in the atomic level gives the different conformation in the transition state. The residues Glu321, Asn323, Asp325, Glu329 and Arg343 are responsible for the non-equilibrium nature. The different directions of OH groups in the monosaccharides result in their different dynamic interaction with hSP-D. The OH groups in C3 and C4 carbon atoms of glucose form H-bonds with Glu321, Asn323 and Glu329. But the other OH groups have little influence on the non-equilibrium affinity. The different binding mode of galactose is different from the other two monosaccharides, attributing to its non-equilibrium quality. The monosaccharide forms H-bonds with thre residue Glu321 by the OH groups in its C1 and C2 carbon atoms. Because C1 carbon atom is its anomeric carbon atom, its anomer influences its non-equilibrium quality. Mannose and glucose have the similar binding mode. Their differences are caused by the H-bond between Asp325 and the OH group in the C2 atom of mannose during the unbinding process. The H-bond pulls mannose forward Glu329 and Arg343, forming another three H-bonds by the OH groups in the C3, C4 and C6 carbon atoms, increasing the energy barrier. The result is that the monosaccharide shows the different dissociation quality. This work could provide the more penetrating understanding of hSP-D physiological functions.2. Homology Modeling of Human Extracellular Signal-regulated Kinase 1 (hERK 1) and Docking and Reconstitution of its InhibitorsThe extracellular signal-regulated kinases are the important componet of the Ras/Raf/MEK/ERK signal transduction pathway, which is highly preserved in all the eukaryotic cells and controls a variety of fundamental cellular processes including cell survival, proliferation, motility, differentiation and metabolism. Hence it is involved in the development of new drug for cancer and inflammatory diseases.The three dimensional structure of hERK1 was modeled and refined using homology modeling and molecular dynamics simulations. Then docking and reconstruction of the inhibitors were carried out. The MM/PBSA approach and two kinds of docking interaction energies were used to evaluate the potency of the inhibitors. The results show that the two inhibitors share the same binding pattern, interacting with Lys36 and Gln87 by H-bonds. Their different substituent groups lead to the different affinities with hERK1. Based on the analysis, the modification for one inhibitor was carried out by the addition of new groups. The new inhibitor reserves the H-bonds at the same time to form four H-bonds with Asp93, Lys96 and Ser135, significantly increasing the interaction with hERK1. The two docking energies significantly decrease, even the binding free energy of MM/PBSA decreases to be the negative value, proving the raise of inhibiting capacity. This work provided the theoretical guidance for the inhibitor design of hERK1 and the development of the new drug for the related diseases.3. Theoretical design of the specific inhibitor of human carbonic anhydrase VIIIn mammals, carbonic anhydrases (CAs) are ubiquitous zinc-metalloenzymes that catalyze a very simple but important physiological reaction, the interconversion between carbon dioxide and the bicarbonate ion. Hence these zinc enzymes are involved in a number of important physiological processes such as respiration and gas exchange, pH homeostasis, cell proliferation and differentiation, etc. The very different distribution of all kinds of isoforms in various tissues and organs as well as quite diverse catalytic properties may be the most prominent reason for unwanted side effects resulting from systemic administration of many nonspecific broad spectrum CA inhibitors. Hence the design of tissue-selective and isozyme-specific inhibitors becomes a critical solution in the chemistry and biology of the carbonic anhydrases.The selectivity of a known inhibitor for hCA II and hCA VII was studied by homology modeling, molecular docking and molecular dynamics methods. The modification for the inhibitor was performed. The MM/PBSA approach was used to evaluate the potency of the inhibitors. The results show that the selectivity of the inhibitor for two isozymes is due to the different side chain length between Asn67 of hCA II and Gln64 of hCA VII. One more methene group in the side chain of Gln64 of hCA VII makes it possible to form H-bond with the bromide atom in the inhibitor. Such the H-bond doesn't exist between hCA II and the kown inhibitor because of the longer distance. On the basis of the analysis, the modification was carried out by the addition of the hydroxypropyl group. The complex conformations of the new inhibitor and two isozymes designate the formation of the H-bond between the newly-added group and Gln64 of hCA VII but not Asn67 of hCA II. The results obtained from the MM/PBSA approach show the binding free energy between the new inhibitor and hCA II has the minor change but that for hCA VII decrease, which increase the selectivity of the new inhibitor for two isoforms. The work will help the design of the isozyme-specific inhibitors of hCA VII.