To address this issue, synthetic community has been developing many DOS-based approaches for the generation of compound libraries embodying core scaffolds of natural products or its mimetics7,8,9,10,11. pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetaseCRagD proteinCprotein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets. The molecular diversity and complexity in a screening collection of drug-like small molecules is a paramount breakthrough in the discovery of novel small-molecule modulators for currently undruggable’ targets, including proteinCprotein interactions (PPIs) and proteinCnucleic acid interactions1,2,3. Towards this end, a strategy termed diversity-oriented synthesis (DOS) was devised, which seeks to populate the vast area of new chemical space made up of diverse and three-dimensional (3D) complex drug-like compounds4,5,6. Although DOS has emerged as an indispensable tool to promote the unbiased screening of compounds and their interactions with diverse biological targets, one of the key challenges in this field is the identification of appropriate chemical structures that will exhibit improved biological relevance and high molecular diversity. To address this issue, synthetic community has been developing many DOS-based approaches for the generation of compound libraries embodying core scaffolds of natural products or its mimetics7,8,9,10,11. Natural products have inherent bioactivity and high bioavailability; thus, the natural product-inspired DOS libraries with biological relevance could be of great value for the identification of bioactive compounds12,13,14. With the goal of targeting unexplored biologically relevant chemical space, we postulated that privileged structures could also serve as chemical navigators’ and therefore reported a privileged substructure-based DOS (pDOS) strategy, which targets the synthesis of diverse polyheterocyclic skeletons containing privileged substructures through complexity-generating reactions in order to maximize the unbiased coverage of bioactive space15,16,17. By incorporating privileged substructures into a rigid core skeleton, we envisioned Pico145 that the resulting compounds would exhibit enhanced interactions with various biomacromolecules including proteins and DNA/RNA. Consequently, we demonstrated the importance of pDOS strategy through the discovery of new bioactive small molecules that interact with a wide range of biological targets18,19. As a continuation of our previous work, we identified pyrimidine as a new privileged substructure that could be used to navigate through bioactive chemical space. The pyrimidine moiety is commonly present in Pico145 various bioactive small molecules, and it plays a critical role as a nucleoside analogue in various kinase inhibitors or adenosine receptor modulators due to its hydrogen bonding ability (Fig. 1a)20,21,22. Therefore, many synthetic efforts towards pyrimidine-containing species have been focused on aromatic monocyclic or bicyclic skeletons, which limits the structural diversity of the pyrimidine-containing core skeletons. In addition, the 3D structural complexity of the core skeletons becomes important because planar frameworks less frequently comprise FDA (Food and Drug Administration) -approved chemical entities, especially in regard to undruggable’ targets23,24,25. Open in a separate window Figure 1 Diversity-oriented synthetic strategy with pyrimidine as a privileged structure.(a) Pyrimidine-containing bioactive compounds. (b) 3D chemical space of pyrimidine and the comparison between pyrimidine-containing tricyclic 6/6/6 and 6/7/6 systems in terms of 3D diversity and complexity by overlaying energy-minimized conformers aligned along the pyrimidine substructure. (c) Synthetic strategy for diversity-oriented synthesis of pyrimidodiazepine- or pyrimidine-containing polyheterocycles through divergent pairing pathways. To expand the molecular diversity beyond monocyclic and bicyclic pyrimidine skeletons, we develop a new pDOS strategy towards the divergent synthesis of natural product-like polyheterocycles containing pyrimidodiazepine or pyrimidine. Diazepine is also often found in complex natural products that exhibit a wide range of biological activities, and is known to be a prominent privileged structure that can improve the bioavailability and bioactivity of compounds26,27. In addition, seven-membered rings that are fused to aromatic rings generally have higher conformational flexibility and a greater number of reactive sites than six- or five-membered fused ring systems, as confirmed by the direct comparison of pyrimidine-embedded tricyclic 6/6/6 and 6/7/6 systems by overlaying the energy-minimized conformers aligned along the pyrimidine substructure (Fig. 1b). Thus, pyrimidodiazepine can serve as a versatile intermediate to access highly diverse Mouse monoclonal to KSHV ORF26 and complex polyheterocycles through the incorporation of additional ring systems, which forms the basis of a new pyrimidodiazepine-based pDOS pathway. To establish the pDOS pathway, we first design and synthesize highly functionalized pyrimidodiazepine intermediates 1 containing five reactive sites (ACE). Pico145 In our pDOS strategy, intermediates 1 can.