Scaffold topologies. 2. Analysis of chemical databases

We have systematically enumerated graph representations of scaffold topologies for up to eight-ring molecules and four-valence atoms, thus providing coverage of the lower portion of the chemical space of small molecules (Pollock et al. J. Chem. Inf. Model., this issue). Here, we examine scaffold topology distributions for several databases: ChemNavigator and PubChem for commercially available chemicals, the Dictionary of Natural Products, a set of 2742 launched drugs, WOMBAT, a database of medicinal chemistry compounds, and two subsets of PubChem, "actives" and DSSTox comprising toxic substances. We also examined a virtual database of exhaustively enumerated small organic molecules, GDB (Fink et al. Angew. Chem., Int. Ed. 2005, 44, 1504-1508), and we contrast the scaffold topology distribution from these collections to the complete coverage of up to eight-ring molecules. For reasons related, perhaps, to synthetic accessibility and complexity, scaffolds exhibiting six rings or more are poorly represented. Among all collections examined, PubChem has the greatest scaffold topological diversity, whereas GDB is the most limited. More than 50% of all entries (13 000 000+ actual and 13 000 000+ virtual compounds) exhibit only eight distinct topologies, one of which is the nonscaffold topology that represents all treelike structures. However, most of the topologies are represented by a single or very small number of examples. Within topologies, we found that three-way scaffold connections (3-nodes) are much more frequent compared to four-way (4-node) connections. Fused rings have a slightly higher frequency in biologically oriented databases. Scaffold topologies can be the first step toward an efficient coarse-grained classification scheme of the molecules found in chemical databases.     

Scaffold topologies. 1. Exhaustive enumeration up to eight rings

Mapping the chemical space of small organic molecules is approached from a theoretical graph theory viewpoint, in an effort to begin the systematic exploration of molecular topologies. We present an algorithm for exhaustive generation of scaffold topologies with up to eight rings and an efficient comparison method for graphs within this class. This method uses the return index, a topological invariant derived from the adjacency matrix of the graph. Furthermore, we describe an algorithm that verifies the adequacy of the comparison method. Applications of this method for chemical space exploration in the context of drug discovery are discussed. The key result is a unique characterization of scaffold topologies, which may lead to more efficient ways to query large chemical databases.     

聚丙烯酸酯的玻璃化温度的定量结构性质相关研究

提出了高分子的侧基顺拉模型 ,认为侧基的空间效应主要来源于侧基的轴向横截面积 .与侧基的轴向横截面积密切相关的是侧基的碳链分支数 .直接采用侧基碳链分支数作为侧基的空间效应参数 ,对 13种聚丙烯酸酯和 9种聚甲基丙烯酸酯的玻璃化温度进行了定量结构 性质相关研究 ,得到了良好的三参数模型 ,对聚丙烯酸酯和聚甲基丙烯酸酯的玻璃化温度分别进行回归分析 ,相关系数R2 =0 989(s =3 8K)和R2 =0 993 (s =4 8K) .该模型对 2 2种聚丙烯酸酯和聚甲基丙烯酸酯的合并计算的结果是R2 =0 980 (s =8 3K) .建立的模型参数计算简便 ,模型的稳定性和适应性较好 ,所有模型的标准误差均小于或接近实验误差 .