基于KRAS蛋白结构的药学研究——生物化学课程教育教学改革研究与实践

Pharmaceutical Research Based on the Structure of KRAS Protein—Research and Practice on Teaching Reform of Biochemistry Course

摘要: 目的：本项目通过将生物化学领域里的结构生物学知识应用于药学研究，拓展了基于结构的药物分子分析与设计的理论与技术。通过对药物靶点蛋白结构的统计与分析，研究了KRAS相关蛋白质结构与功能之间的关系，以及药物分子靶向目标蛋白质的分子机制，完成其结构与功能之间关系的分析，指导化合物的合成，为新药设计奠定基础。方法：主要通过PDB、PDBePISA、UniProt等数据库和网络服务器以及Chem3D、UCSF Chimera、PyMol、Origin等软件对于KRAS相关蛋白质的一系列重要参数进行检索、计算和绘图等，收集、整理、分析KRAS蛋白质分子的结构域功能信息，研究药物分子靶向目标蛋白质的分子机制。结果：KRAS蛋白与其配体化合物的结合面积与化合物的分子量呈正相关(除少部分外)。此外，KRAS蛋白与其配体化合物的结合为非共价结合时，化合物的摩尔折射率和分配系数都对其理论结合能影响不大，几乎维持在−5 kcal/mol到5 kcal/mol之间，而且配体化合物通常结合在Switch-II Pocket (S-IIP)附近。而当KRAS蛋白与其配体化合物的结合为共价结合时，突变体的结合能几乎都为负值，绝对值显著增大，而非突变体的结合能变化不大，依旧维持在−5 kcal/mol到5 kcal/mol之间，且配体化合物往往结合于第12位的甘氨酸突变产生的半胱氨酸附近。结论：靶向KRAS的药物分子若能够与蛋白质中由第12位的甘氨酸突变产生的半胱氨酸形成共价结合，且分子量较大，则其与蛋白质的结合面积相对较大、结合较为牢固、特异性更强，或者药物分子可以以非共价结合的方式结合于S-IIP附近，可以增强对KRAS的抑制效应。

Abstract: Aim: To explore the application of structural biology technology in the medicinal research area, structures of KRAS-compound complexes are analyzed for the design of novel potent drugs. This project studies the relationship between the structure and function of KRAS gene-related proteins and the molecular mechanism of inhibitors targeting KRAS protein through structural and statistical analysis; so as to analyze the relationship between the structure and function, guide the synthesis of compounds, and lay the foundation for the design of new drugs. Methods: Searching, calculation and figure representation are carried out by using mainly PDB, UniProt, PDBePISA and some other websites or software, such as Chem3D, UCSF Chimera, PyMol, Origin, etc., for series of important parameters of the related proteins of the KRAS gene. To study the molecular mechanism of inhibitors targeting the KRAS protein molecule, information regarding the biophysical properties of compounds and domain function of protein of interest is collected, analyzed and summarized. Results: Except for a few, the interface areas between KRAS protein and its ligand compounds are positively correlated with the molecular weights of the compounds. In addition, when the binding of KRAS protein and its ligand compounds is non-covalent, the ClogP (molar refractivity or partition coefficient) value of the compounds has little effect on the theoretical binding energy, which almost remains between −5 and 5 kcal/mol. The ligand compound is often bound to the vicinity of Switch-II Pocket (S-lP). However, when the binding of KRAS protein and its ligand compound is covalent binding, the binding energy of the mutants was almost all negative and the absolute value increased significantly, while the binding energy of the non-mutants did not change significantly, still maintaining between −5 and 5 kcal/mol, and the ligand compounds tended to bind to the cysteine produced by glycine 12 mutation. Conclusion: If the drug molecule targeting KRAS can form covalent binding with cysteine produced by glycine 12 mutation in protein, and the molecular weight is large, the binding area with protein is relatively large, the binding is relatively firm, and the selectivity and specificity are stronger. Or, drug molecules can be bound to the vicinity of S-IIP in a non-covalently binding manner, which can enhance the inhibitory effect on KRAS.