Precise recognition of benzonitrile derivatives with supramolecular macrocycle of phosphorylated cavitand by co-crystallization method

• Published in: Nature communications Vol. 15; no. 1; pp. 5315 - 9
• Main Authors: Li, Heng, Li, Zhijin, Lin, Chen, Jiang, Juli, Wang, Leyong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.06.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 639/301/923/966; 639/638/298/923/3931; 639/638/541/961; Benzonitrile; Cocrystallization; Computer applications; Crystallization; Dermatitis; Drug development; Humanities and Social Sciences; Molecular docking; multidisciplinary; Recognition; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49540-2

The importance of molecular docking in drug discovery lies in the precise recognition between potential drug compounds and their target receptors, which is generally based on the computational method. However, it will become quite interesting if the rigid cavity structure of supramolecular macrocycles can precisely recognize a series of guests with specific fragments by mimicking molecular docking through co-crystallization experiments. Herein, we report a phenylphosphine oxide-bridged aromatic supramolecular macrocycle, F[3]A1-[P(O)Ph] 3 , which precisely recognizes benzonitrile derivatives through non-covalent interactions to form key-lock complexes by co-crystallization method. A total of 15 various benzonitrile derivatives as guest molecules are specifically bound by F[3]A1-[P(O)Ph] 3 in co-crystal structures, respectively. Notably, among them, crisaborole (anti-dermatitis) and alectinib (anti-cancer) with the benzonitrile fragment, which are two commercial drug molecules approved by the U.S. Food and Drug Administration (FDA), could also form a key-lock complex with F[3]A1-[P(O)Ph] 3 in the crystal state, respectively. While establishing specific lock-and-key recognition for structure-based drug design is typically based on the computational method, co-crystallization could mimic molecular docking. Herein, the authors report a supramolecular macrocycle that can precisely recognize benzonitrile derivatives through non-covalent interactions.