Molecular Modeling Of Pyrimidine Nucleoside Phosphorylase, Squamous Cell Carcinoma Antigen And Methylenetetrahydrofolate

In recent years, along with the development of calculator technique and software, the development of molecular mechanics, molecular dynamics, and quantum chemistry theories, via molecular modeling can build the three-dimensional structure of the macromolecules, to research the structure characteristics of the macromolecules, analyze the interaction between the receptor and ligand, describe the catalyst mechanism of the enzyme, and perform drug design and sieving, thus molecular modeling has already become a main research means in the fields of biology and medical science. The complex structure of protein and ligand is important for clarifying the function and action mechanisms of protein and useful for drug design. Up to date, X-ray diffraction or NMR techniques have been the most valuable tools for elucidating structure-function relationships of biological molecules. Although the application of these experimental methods is continually growing, they remain time-consuming and show limited applicability due to the difficulties of obtaining accurate experimental data. Molecular modeling can not only overcome the limiting of experimental tools effectively, but also guide the experiment. Molecular modeling has been applied in scientific research widely, its significance and advantage have been acknowledged. The application of molecular modeling to studying the interaction between small drug molecules and their target proteins can afford theoretical guide for drug design or the structure modification of protein. In this thesis, we used the new molecular modeling technology to study three target proteins that have significant medical value. The main results of the thesis are as follows: [1] Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. PYNP of Bacillus subtilis shares 40% sequence of amino-acid identical with human TP, which has been implicated as a growth factor of some tumors. Potent inhibitors of TP might have significant therapeutic value in various chemotherapeutic strategies. The models of PYNP should provide a valuable insight into the rational design of such inhibitors. We used the docking, molecular dynamics and a hybrid quantum-mechanical/molecular-mechanical (QM/MM) approach to build the model of the three-dimensional structure of pyrimidined the nucleoside phosphorylase (PYNP) from Bacillus subtilis, and determine mechanism of catalysis by PYNP and the role of each residue in the catalysis at active site. Based on the structural information of PYNP-substrate system from this work, a probable mechanism of pyrimidine phosphorolysis, which is similar to that of the SN1-type reaction is proposed for PYNP. The results indicate that the functions of histidine 82, arginine169 and lysine188 are to stabilize the uridine that at high-energy conformation by means electrostaticinteraction and involved in the catalysis. In addition, the function of aspartate 162 is likely to activate lysine 188 for phosphorolysis catalysis via polarization effects. [2] The squamous cell carcinoma antigen (SCCA) serves as a serological marker for more advanced squamous cell tumors of the cervix, lung, and oropharynx. SCCA is not specific for malignant tissues, and the functional role of SCCA in both normal and malignant cells has not been elucidated. SCCA is serine proteinase inhibitor (serpin), and in mammals, inhibitorytype serpins regulate serine proteinases involved in, for example, coagulation, fibrinolysis, inflammation, cell migration, and extracellular matrix remodeling. Thus to study the interactions between SCCA and serpins is important for biology and medical science. An attempt has been made to build up a three-dimensional model of squamous cell carcinoma antigen 2 (SCCA2) by means of the homology module of Insight II, and SCCA2 contains the stressed and relaxed forms, i.e. SCCA2(S) and SCCA2(R). The docking of SCCA2(S) with two different target serine proteinases, which are cathepsin G (Cat G) and the human mast cell chymase (HMC), is studied theoretically to give two different complexes, respectively. It is shown, from the molecular surface electricity potential, that in the formation of two complexes SCCA2(S)–Cat G and SCCA2(S)–HMC, the electrostatic interaction may play an important role. Since HMC possesses a loop to produce spatial anti-effect, complex SCCA2 (S)–HMC is less stable than the complex SCCA2 (S)–Cat G. [3] Because 5,10-methylene-H4folate and 10-formyl-H4folate are...