A computational study to identify the key residues of peroxisome proliferator-activated receptor gamma in the interactions with its antagonists

Computational Approaches for PPARγ Inhibitor Development: Recent Advances and Perspectives

The development of peroxisome proliferator-activated receptor gamma (PPARγ) inhibitors has attracted significant interest for treating metabolic disorders, cancer, and inflammatory diseases. This review highlights the crucial role of computational modelling in advancing PPARγ inhibitor development, emphasizing how these techniques streamline the identification, optimization, and evaluation of new drug candidates. Key methods include molecular docking, QSAR, and molecular dynamics simulations, which enhance the efficiency and accuracy of inhibitor design. Computational modelling has deepened our understanding of PPARγ binding mechanisms and conformational dynamics, allowing researchers to predict and optimize ligand-receptor complex stability. Despite these advancements, challenges remain, such as improving predictions of pharmacokinetic properties (ADME) to evaluate drug-like qualities. In conclusion, computational modelling has significantly enhanced PPARγ inhibitor discovery and development, offering new opportunities to address complex diseases. Continued refinement of these models, combined with experimental validation and emerging technologies, is crucial for overcoming current limitations and achieving successful clinical outcomes.

Mechanisms of Nelumbinis folium targeting PPARγ for weight management: A molecular docking and molecular dynamics simulations study

The lotus leaf, Nelumbinis folium (NF), has frequently appeared in obesity clinical trials as an intervention to promote weight loss and improve metabolic profiles. However, the molecular mechanisms by which it interacts with important obesity targets and pathways, such as the peroxisome proliferator-activated receptor gamma (PPARγ) within the PPAR signalling pathway, were not well understood. This study aims to screen for candidate compounds from NF with desirable pharmacokinetic properties and examine their binding feasibility at the PPARγ ligand-binding domain (LBD). Ligand- and structure-based screening of NF compounds were performed, and a consensus approach has been applied to identify druggable candidates. By examining the pharmacokinetic profiles, a large proportion of NF compounds exhibited favourable drug-likeness and oral bioavailability properties. Furthermore, the binding affinity scores and poses provided new insights on the distinctive binding behaviours of NF compounds at the LBD of PPARγ in its inactive form. Several NF compounds could bind strongly to PPARγ at sub-pockets where partial agonists and antagonists were found to bind and may induce conformational changes that influence co-repressor binding, trans-repression, and gene expression inhibition. Subsequent molecular dynamics simulations of a candidate compound (NF129 narcissin) bound to PPARγ revealed conformational stability, residue fluctuation, and binding behaviours comparable to that of the known inhibitor, SR1664. Therefore, it can be proposed that narcissin exhibits characteristics of a PPARγ antagonist. Further experimental validation to support the development of NF129 as a future anti-obesity agent is warranted.

Protective Effect of Hydroxytyrosol on LPS-Induced Inflammation and Oxidative Stress in Bovine Endometrial Epithelial Cell Line

Bovine endometritis is a serious pathogen-induced infectious disease that affects the physiological processes of estrus, pregnancy and the postpartum condition. The inflamed endometrium responds by activating an inflammatory intracellular signaling cascade that leads to increased expression of proinflammatory cytokines and reactive oxygen species (ROS). Oxidative stress is closely related to several pathological conditions in perinatal dairy cows and play a key role in tissue damage. Hydroxytyrosol (HT), a natural phenolic alcohol with a strong antioxidant activity, displayed a wide range of biological effect. The aim of this study was to evaluate the protective effects of HT in an in vitro model of lipopolysaccharide (LPS)-induced inflammation in bovine uterine endometrial cells. Our results showed that HT had a significant protective effect in LPS-induced inflammation and oxidative stress. HT was also able to increase the capacity of endogenous antioxidant systems through the up-regulation of the NRF2 pathway. Furthermore, HT restored the tight junction protein expressions. In conclusion, our results showed the protective effects of HT in LPS-stimulated BEND cells. Therefore, the results of this study suggest an important protective role of HT in the treatment and prevention of uterine pathologies in dairy cows.

To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations

Chiglitazar is a promising new-generation insulin sensitizer with low reverse effects for the treatment of type II diabetes mellitus (T2DM) and has shown activity as a nonselective pan-agonist to the human peroxisome proliferator-activated receptors (PPARs) (i.e., full activation of PPARγ and a partial activation of PPARα and PPARβ/δ). Yet, it has no high-resolution complex structure with PPARs and its detailed interactions and activation mechanism remain unclear. In this study, we docked chiglitazar into three experimentally resolved crystal structures of hPPAR subtypes, PPARα, PPARβ/δ, and PPARγ, followed by 3 μs molecular dynamics simulations for each system. Our MM-GBSA binding energy calculation revealed that chiglitazar most favorably bound to hPPARγ (-144.6 kcal/mol), followed by hPPARα (-138.0 kcal/mol) and hPPARβ (-135.9 kcal/mol), and the order is consistent with the experimental data. Through the decomposition of the MM-GBSA binding energy by residue and the use of two-dimensional interaction diagrams, key residues involved in the binding of chiglitazar were identified and characterized for each complex system. Additionally, our detailed dynamics analyses support that the conformation and dynamics of helix 12 play a critical role in determining the activities of the different types of ligands (e.g., full agonist vs. partial agonist). Rather than being bent fully in the direction of the agonist versus antagonist conformation, a partial agonist can adopt a more linear conformation and have a lower degree of flexibility. Our finding may aid in further development of this new generation of medication.

Agonism activities of lyso-phosphatidylcholines (LPC) Ligands binding to peroxisome proliferator-activated receptor gamma (PPARγ)

PPARγ is an isoform of peroxisome proliferator-activated receptor (PPAR) belonging to a super family of nuclear receptors and is a primary target of the effective drug to treat the type II diabetes. The experiments found that Lyso-phosphatidylcholines (LPC) could bind to PPARγ, but the binding modes remain unknown. We used the Molecular Docking and Molecular Dynamic (MD) simulations to study the binding of four LPC ligands (LPC16:0, LPC18:0, LPC18:1-1 and LPC18:1-2) to PPARγ. The two-step MD simulations were employed to determine the final binding modes. The 20 ns MD simulations for four final LPC-PPARγ complexes were performed to analyze their structures, the binding key residues, and agonism activities. The results reveal that three LPC ligands (LPC16:0, LPC18:0 and LPC18:1-1) bind to Arm II and III regions of the Ligand Binding Domain (LBD) pocket, whereas they do not interact with Tyr473 of Helix 12 (H12). In contrast, LPC18:1-2 can form the hydrogen bonds with Tyr473 and bind into Arm I and II regions. Comparing with the paradigm systems of the full agonist (Rosiglitazone-PPARγ) and the partial agonist (MRL24-PPARγ), our results indicate that LPC16:0, LPC18:0 and LPC18:1-1 could be the potential partial agonists and LPC18:1-2 could be a full agonist. The in-depth analysis of the residue fluctuations and structure alignment confirm the present prediction of the LPC agonism activities.Communicated by Ramaswamy H. Sarma.