Visini Ricardo, Arús-Pous Josep, Awale Mahendra, Reymond Jean-Louis
Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.
J Chem Inf Model. 2017 Nov 27;57(11):2707-2718. doi: 10.1021/acs.jcim.7b00457. Epub 2017 Oct 30.
Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.
在此，我们探索所有虚拟可能的有机分子的化学空间，重点关注环状系统，环状系统是通过去除所有非环状键并将所有剩余原子转化为碳而获得的有机分子的环状核心。这种方法规避了在枚举分子本身时遇到的组合爆炸问题。我们报告了化学宇宙数据库GDB4c，其中包含916130个环状系统，这些环状系统最多有四个饱和或芳香环，最大环尺寸为14个原子，以及GDB4c3D，其中包含相应的6555929个立体异构体。这些环状系统中几乎所有（98.6%）都是未知的，并且代表了含有小环和季中心的手性三维形状大环，让人联想到多环天然产物。我们设想GDB4c可用于选择新的环状系统，从中设计此类天然产物的类似物。该数据库可在www.gdb.unibe.ch上下载，同时还提供交互式可视化和搜索工具，作为分子设计的资源。
