A Novel Paradigm Defines Functional Molecule Clusters for an Anti-Alzheimer’s Disease Recipe from Traditional Chinese Medicine

Traditional Chinese Medicine (TCM) prescriptions are organically composed of compatible herbs according to the TCM theory. The complex ingredients of TCM could act on multiple targets through various pathways simultaneously to exert pharmacological effects, making TCM an unrivaled gem in the medical world. However, due to a lack of comprehensive and standard study methods, the research of TCM products has been quite limited. A novel paradigm that could aid in the discovery of the material basis and fully clarify the mechanism of TCM prescriptions is urgently needed. In this study, a similarity analysis based on molecular fingerprints was adopted to explore the representative molecules of the Tiaoxin recipe, a Chinese patent formula approved by the National Medical Products Administration (NMPA) for the treatment of mild-to-moderate Alzheimer’s disease (AD), and 38 out of 1047 chemicals were finally screened out. Next, we tried to define a new concept of a “functional molecule cluster” for chemicals with similar pharmacological effects to elucidate how the chemical mixture from TCMs produce their therapeutic effects. Four anti-AD functional molecule clusters from the Tiaoxin recipe were identified: an anti-inflammatory cluster, an anti-ROS cluster, an anti-AChE activity cluster, and an anti-A[Formula: see text] aggregation cluster. Furthermore, the chemicals from the anti-inflammatory cluster and anti-ROS cluster were proved to display their multi-target and multi-pathway roles partially or mainly through molecules of the TLR4-MYD88-NF-[Formula: see text]B and Keap1-Nrf2-ARE pathways. The functional molecule clusters may be vital to the explanation of the efficacy of the Tiaoxin recipe, which could give us a more profound understanding of TCM prescriptions. Our paradigm may open a novel path for TCM research.