Development of New Methoda for Lead Discovery Using Computer

长期以来，我们一直在开发利用计算机进行合理药物设计的新方法。随着蛋白质晶体学技术的发展，许多具有重要生物学功能的蛋白质或蛋白质-配体复合物的三维结构已经或正在被阐明。靶受体的结构信息对于设计具有完全不同结构的新配体以及解释结构-活性关系是最有用的。在这个研究项目中，我们已经开发了从头配体设计的药物先导发现的方法。其中之一是通过受体结合搜索现有化合物的三维结构数据库的方法。利用我们以前开发的自动对接方法实现了三维数据库的构象柔性搜索。如果搜索可用化合物的数据库，则可以获得命中化合物并且不进行合成而进行分析。该方法的实用性被证实的应用到几个酶系统。在二氢叶酸还原酶中，数据库中所有已知的抑制剂都包含在“命中”中。在HIV蛋白酶系统中，50个化合物中有10多个化合物表现出明显的抑制活性。最高效价为20 μ M（Ki）。此外，我们还开发了一种新的方法，该方法结合了结构构建法和数据库搜索法的优点。在该方法中，通过拓扑搜索从2D数据库中非常快速地搜索与从结构构建方法输出的配体结构类似的结构。结构构建法的优点是无论配体结构是否存在，都可以输出与受体腔体相匹配的配体结构。通过这种新方法，可以分析类似的命中化合物，而不是合成具有输出结构的化合物本身。

We have long been developing new methods for rational drug design using computer. With a remarkable progress in techniques of protein crystallography, 3D structures of many proteins or protein-ligand complexes, which have important biological functions, have been elucidated or are being elucidated. Structural information of the target receptor is most useful for designing new ligands with quite different structures as well as for interpreting structure-activity relations. In this research project, we have developed methods for de novo ligand design for drug lead discovery. One of them is a method for searching 3D-structure databases of existing compounds by receptor binding. Conformation-flexible search of 3D-databases was realized by making use of automatic docking method which we have developed previously. Hit compounds can be obtained and assayd without syntheses, if databases of available compounds are searched. The usefulness of the method was confirmed by the application to several enzyme systems. In dihydrofolate reductase, all the known inhibitors in the database were included in the 'hits'. In the HIV protease system, more than ten compounds showed significant inhibitory activity among fifty compounds of 'hits'. The highest potency was 20muM (Ki).Furthermore, we have developed a new method which provides both advantages of structure construction method and database search method. In this method structures analogous to the ligand structures output from the structure construction method are very rapidly searched from 2D-databases by topological search. The advantage of structure construction method is that ligand structure which can well fit to the receptor cavity can be output regardless the structure is existing or nonexisting. By this new method, analogous hit compounds available can be assayd instead of synthesizing compounds with output structures themselves.