Chinese herbal medicines for the management of obesity: systematic reviews and in silico identification of potential antio-besity phytochemical compounds
Creators: name: Wong, Ann Rann
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 420803
subject: Traditional Chinese medicine and treatments

description: Background
The rising pandemic of obesity worldwide poses a significant burden to individual patients and the public health system, as obesity (BMI ≥ 30 kg/m2) and its co-morbidities heavily affect physical, mental and social wellbeing. Currently, a few FDA-approved anti-obesity drugs are available, and these typically act on the central nervous system to modulate hunger and satiety, often resulting in specific adverse events such as insomnia and irritability. Therefore, research efforts on peripheral-acting anti-obesity agents have been emerging. As the development of anti-obesity drugs continues, large-scale pharmacologic screenings of herbs offer a reasonable basis for identifying candidate compounds. Historically, many conventional medications have originated from medicinal herbs, such as aspirin (from Salix alba) and morphine (from Papaver somniferum). To date, computational studies in search of novel bioactive phytochemicals for obesity have not received wide attention, highlighting the need for further research in this area.

Aims
This study aimed to identify herbs with anti-obesity properties, examine their interactions with common obesity targets and pathways, and propose specific drug-like phytochemicals with adipose inhibition and lipid-modulating effects.

Phase 1: Identification of highly prescribed medicinal herbs from obesity trials.
Two prospectively registered systematic reviews and meta-analyses examining the effects and safety of Chinese herbal medicine (CHM) on obesity presented in Chapter 4 and Chapter 5 of this thesis have been published. The first meta-analysis involving 39 randomised controlled trials (RCTs) reported significant adjunctive effects of CHM treatments to lifestyle interventions (LI) with or without Western medication (WM). To further probe into the lipid-modulating properties of herbs, another systematic review and meta-analysis was carried out on blood lipid profile outcomes among obese participants. The findings revealed that CHM formulations could improve triglycerides and high-density lipoprotein cholesterol (HDL-c) levels over a median of 12 weeks, with greater interventional effects on participants who were overweight and had higher triglyceride concentrations at baseline. Ten highly prescribed herbs were identified among these two systematic reviews:  Coptidis rhizoma (CC, 黄连, n = 16), Crataegi fructus (CF, 山楂, n = 15), Poria cocos (PC, 茯苓, n = 14),  Nelumbinis folium (NF, 荷叶, n = 13), Alismatis rhizoma (AR, 泽泻, n = 12), Glycyrrhizae radix (GR, 甘草, n = 12), Pinelliae rhizoma (PR, 半夏, n = 11), Citri reticulatae pericarpium (CR, 陈皮, n = 11), Atractylodes lancea (AL, 苍术, n = 11) and Atractylodis macrocephala (AM, 白术, n = 10). As Glycyrrhizae radix is a heavily studied herb presented in nearly every Chinese herbal formulation, it has been excluded from further studies to screen for specific anti-obesity properties.

Phase 2: Identification of top interacting herbs involved in peripheral pathways in obesity and the implementation of a pilot computational study to evaluate binding properties of candidate compounds.
Molecular docking and network pharmacology studies were performed on eligible phytochemicals from nine herbs and obesity-related targets (Chapter 7). A total of 816 phytochemicals from 9 herbs were systematically retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Traditional Chinese Medicine Information Database (TCM-ID). Phytochemicals of these herbs were docked with 26 obesity-related targets obtained from disease-association databases yielding 21,216 binding affinity results. Most phytochemicals exhibited drug-like properties (91.3%) and had favourable affinities to all 26 targets (99.93%). By examining the relative binding affinities in a herb-target-pathway network, 3 herbs (NF, PC, and CF) were identified as the main contributors to weight reduction. These herbs were proposed to act via significant KEGG pathways such as the PPAR signalling pathway, responsible for adipocyte differentiation, lipid metabolism and energy modulation in the periphery. 

Phase 3: Screening of candidate compounds from ligand-based and structure-based approaches.
A pilot molecular docking and dynamics simulations study (Chapter 8) was performed on the highest binding receptor, the neuropeptide Y1 receptor, and its corresponding herb, PC. Findings from this preliminary computational chapter suggest that the methods of ligand-based screening combined with molecular docking were possible to identify candidate compounds, and molecular dynamics simulations could be performed to examine the feasibility and stability of these candidate compounds compared to protein-only structures and those bound to a known inhibitor. 
Within the PPAR signalling pathway, an in-depth 3D ligand-residue interaction between NF, PC, and CF with receptors PPARγ (Chapter 9.1), PPARδ (Chapter 10.1) and PPARα (Chapter 11.1) were conducted. NF129 Narcissin has been identified as a PPARγ antagonist, as it is found to interact with residues Arg288, Tyr327, and His449, consistent with a known antagonist SR1664. In addition, PC41 Poricoic acid C, was proposed as a putative partial agonist of PPARδ, owing to the binding location it occupies within the ligand-binding domain as well as its hydrogen bonds with Thr256, Leu304, Ala306, and Asn307, none of which were key residues involved in classical agonism. Similarly, CF36 Chlorogenic acid was also found to dock at the location of partial agonists, and form hydrogen bonds with Thr279, Ser280, Thr283, Thr283, and Leu331. As CF36 is positioned close to the phosphorylation sites and far from important residues at the activation function 2 surface domain, it was proposed as a partial agonist of PPARα. These compounds, NF129, PC41, and CF36 had favourable drug-likeness properties and were not predicted with toxicity. Thus, they were selected as candidate compounds for further evaluation of feasibility and stability in molecular dynamics simulations.

Phase 4: Evaluation of the feasibility and stability of candidate compounds in molecular dynamics simulations.
Classical molecular dynamics simulations were performed on high-performance computing facilities for three ligand-protein complexes (NF129 Narcissin-PPARγ, PC41 Poricoic acid C-PPARδ, and CF36 Chlorogenic acid-PPARα), using co-crystalised ligands as controls. Upon analysing time-series data, large-scale conformational changes were absent in the apo-protein or ligand-bound systems, indicating that the stability of ligand binding was maintained throughout the simulation. Furthermore, specific regions of the protein with high RMSD correlated well with the RMS fluctuations, implying that the phosphorylation loop and omega loop in PPARδ and PPARα as well as helix 11 in PPARγ had the greatest displacement from their initial structures. Findings from the principal components analysis revealed three main clusters of stable states consistent across the PPAR subtypes, with ligand-bound structures showing higher delineation while whole apo-proteins covered a larger area of conformational space. Finally, binding free energies were calculated for ligands and their respective controls, and while the ΔGbind of synthetic ligands were higher than that of the candidate compounds, differences between the candidate compounds and synthetic ligands for each protein target were comparable. The stability of conformations and binding characteristics in molecular dynamics simulation studies of these ligand-protein complexes suggest NF129 as a putative PPARγ antagonist, PC41 as a PPARδ partial agonist, and CF36 as a PPARα partial agonist with potential for full agonistic behaviours.

Conclusion
This research project has provided novel insights into the mechanistic behaviours of highly prescribed weight-loss herbs, namely NF, PC and CF on PPARγ, PPARδ and PPARα, three major receptors responsible for cellular metabolic function in humans. High-throughput screening technologies have enabled us to propose a selection of NF, PC and CF compounds with favourable binding affinities and to elucidate the potential mechanisms by which they may achieve favourable lipid-modulating clinical outcomes. Meanwhile, several unique binding sites independent from the orthosteric ligand-binding domain (LBD) have been discovered on PPAR subtypes, offering new avenues for the discovery of allosteric modulators. Further refinement of the physicochemical properties and binding profiles supported by experimental and clinical studies may assist with the future development of NF129 narcissin, PC41 Poricoic acid C, and CF36 Chlorogenic acid as alternatives to anti-obesity agents.