Identification of Direct Activator of Adenosine Monophosphate-Activated Protein Kinase (AMPK) by Structure-Based Virtual Screening and Molecular Docking Approach

Effect of Yeast-Derived Peptides on Skeletal Muscle Function and Exercise-Induced Fatigue in C2C12 Myotube Cells and ICR Mice

In our previous study, the antioxidant peptides (XHY69AP, AP-D, YPLP, and AGPL) were obtained from potential probiotic yeast (Yamadazyma triangularis XHY69), which was selected by our lab from dry-cured ham. This work aimed to explore the effects of yeast-derived peptides on skeletal muscle function and muscle fatigue. Results showed that yeast-derived peptides up-regulated slow-twitch fiber expression and down-regulated fast-twitch fiber expression in C2C12 cells (p < 0.05). The peptides improved mitochondrial membrane potential, adenosine triphosphate generation, and expression of cytochrome-relative genes, thus promoting mitochondrial function. Among these peptides, YPLP up-regulated the relative gene expression of the AMP-activated protein kinase (AMPK) pathway and activated AMPK by phosphorylation. Moreover, YPLP could prolong treadmill time, increase muscle and liver glycogen contents, reduce lactic acid and urea nitrogen contents, and alleviate muscle tissue injury in ICR exercise mice. These results demonstrate that yeast-derived peptides could change the muscle fiber composition, improve muscle function, and relieve muscle fatigue.

Quercetin activates the Sestrin2/AMPK/SIRT1 axis to improve amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a chronic neurodegenerative disease with poor prognosis. The intricacies surrounding its pathophysiology could partly account for the lack of effective treatment for ALS. Sestrin2 has been reported to improve metabolic, cardiovascular and neurodegenerative diseases, and is involved in the direct and indirect activation of the adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK)/silent information regulator 1 (SIRT1) axis. Quercetin, as a phytochemical, has considerable biological activities, such as anti-oxidation, anti-inflammation, anti-tumorigenicity, and neuroprotection. Interestingly, quercetin can activate the AMPK/SIRT1 signaling pathway to reduce endoplasmic reticulum stress, and alleviate apoptosis and inflammation. This report examines the molecular relationship between Sestrin2 and AMPK/SIRT1 axis, as well as the main biological functions and research progress of quercetin, together with the correlation between quercetin and Sestrin2/AMPK/SIRT1 axis in neurodegenerative diseases.

In Silico and In Vitro Approach to Assess Direct Allosteric AMPK Activators from Nature

The 5'-adenosine monophosphate-activated protein kinase (AMPK) is an important metabolic regulator. Its allosteric drug and metabolite binding (ADaM) site was identified as an attractive target for direct AMPK activation and holds promise as a novel mechanism for the treatment of metabolic diseases. With the exception of lusianthridin and salicylic acid, no natural product (NP) is reported so far to directly target the ADaM site. For the streamlined assessment of direct AMPK activators from the pool of NPs, an integrated workflow using in silico and in vitro methods was applied. Virtual screening combining a 3D shape-based approach and docking identified 21 NPs and NP-like molecules that could potentially activate AMPK. The compounds were purchased and tested in an in vitro AMPK α 1 β 1 γ 1 kinase assay. Two NP-like virtual hits were identified, which, at 30 µM concentration, caused a 1.65-fold (± 0.24) and a 1.58-fold (± 0.17) activation of AMPK, respectively. Intriguingly, using two different evaluation methods, we could not confirm the bioactivity of the supposed AMPK activator lusianthridin, which rebuts earlier reports.

Synthesis and biological evaluation of 4-phenoxy-phenyl isoxazoles as novel acetyl-CoA carboxylase inhibitors

Acetyl-CoA carboxylase (ACC) is a crucial enzyme in fatty acid metabolism, which plays a major role in the occurrence and development of certain tumours. Herein, one potential ACC inhibitor (6a) was identified through high-throughput virtual screening (HTVS), and a series of 4-phenoxy-phenyl isoxazoles were synthesised for structure-activity relationship (SAR) studies. Among these compounds, 6g exhibited the most potent ACC inhibitory activity (IC₅₀=99.8 nM), which was comparable to that of CP-640186. Moreover, the antiproliferation assay revealed that compound 6l exhibited the strongest cytotoxicity, with IC₅₀ values of 0.22 µM (A549), 0.26 µM (HepG2), and 0.21 µM (MDA-MB-231), respectively. The preliminary mechanistic studies on 6g and 6l suggested that the compounds decreased the malonyl-CoA levels, arrested the cell cycle at the G0/G1 phase, and induced apoptosis in MDA-MB-231 cells. Overall, these results indicated that the 4-phenoxy-phenyl isoxazoles are potential for further study in cancer therapeutics as ACC inhibitors.

Therapeutic effect of oxyberberine on obese non-alcoholic fatty liver disease rats

BACKGROUND

Berberine (BBR) has been widely used to treat non-alcoholic fatty liver disease (NAFLD). The metabolites of BBR were believed to contribute significantly to its pharmacological effects. Oxyberberine (OBB), a gut microbiota-mediated oxidative metabolite of BBR, has been firstly identified in our recent work.

PURPOSE

Here, we aimed to comparatively investigate the anti-NAFLD properties of OBB and BBR.

METHODS

The anti-NAFLD effect was evaluated in high-fat diet-induced obese NAFLD rats with biochemical/ELISA tests and histological staining. The related gene and protein expressions were detected by qRT-PCR and Western blotting respectively. Molecular docking and dynamic simulation were also performed to provide further insight.

RESULTS

Results indicated OBB remarkably and dose-dependently attenuated the clinical manifestations of NAFLD, which (100 mg/kg) achieved similar therapeutic effect to metformin (300 mg/kg) and was superior to BBR of the same dose. OBB significantly inhibited aberrant phosphorylation of IRS-1 and up-regulated the downstream protein expression and phosphorylation (PI3K, p-Akt/Akt and p-GSK-3β/GSK-3β) to improve hepatic insulin signal transduction. Meanwhile, OBB treatment remarkably alleviated inflammation via down-regulating the mRNA expression of MCP-1, Cd68, Nos2, Cd11c, while enhancing Arg1 mRNA expression in white adipose tissue. Moreover, OBB exhibited closer affinity with AMPK in silicon and superior hyperphosphorylation of AMPK in vivo, leading to increased ACC mRNA expression in liver and UCP-1 protein expression in adipose tissue.

CONCLUSION

Taken together, compared with BBR, OBB was more capable of maintaining lipid homeostasis between liver and WAT via attenuating hepatic insulin pathway and adipocyte inflammation, which was associated with its property of superior AMPK activator.

Docking-based virtual screening of TβR1 inhibitors: evaluation of pose prediction and scoring functions

To improve the reliability of virtual screening for transforming growth factor-beta type 1 receptor (TβR1) inhibitors, 2 docking methods and 11 scoring functions in Discovery Studio software were evaluated and validated in this study. LibDock and CDOCKER protocols were performed on a test set of 24 TβR1 protein-ligand complexes. Based on the root-mean-square deviation (RMSD) values (in Å) between the docking poses and co-crystal conformations, the CDOCKER protocol can be efficiently applied to obtain more accurate dockings in medium-size virtual screening experiments of TβR1, with a successful docking rate of 95%. A dataset including 281 known active and 8677 inactive ligands was used to determine the best scoring function. The receiver operating characteristic (ROC) curves were used to compare the performance of scoring functions in attributing best scores to active than inactive ligands. The results show that Ludi 1, PMF, Ludi 2, Ludi 3, PMF04, PLP1, PLP2, LigScore2, Jain and LigScore1 are better scoring functions than the random distribution model, with AUC of 0.864, 0.856, 0.842, 0.812, 0.776, 0.774, 0.769, 0.762, 0.697 and 0.660, respectively. Based on the pairwise comparison of ROC curves, Ludi 1 and PMF were chosen as the best scoring functions for virtual screening of TβR1 inhibitors. Further enrichment factors (EF) analysis also supports PMF and Ludi 1 as the top two scoring functions.

Polyphyllin I activates AMPK to suppress the growth of non-small-cell lung cancer via induction of autophagy

Polyphyllin I (PPI), a bioactive constituent extracted from the rhizomes of Paris polyphylla, is cytotoxic to several cancer types. This study was designed to explore whether PPI prevents non-small-cell lung cancer (NSCLC) growth and to investigate the molecular mechanism. AMP-activated protein kinase (AMPK) has been implicated in the activation of autophagy in distinct tissues. In cultured human NSCLC cell lines, PPI induces autophagy by activating AMPK and then inhibiting mTOR signaling in a concentration-dependent manner. Furthermore, the activation of autophagy induced by PPI was reversed by the AMPK inhibitor compound C. Computational docking showed that PPI directly interacted with the allosteric drug and metabolite site of AMPK to stabilize its activation. Microscale thermophoresis and Drug Affinity Responsive Targeting Stability (DARTS) assay further confirmed the high affinity between PPI and AMPK. In vivo studies indicated that PPI suppressed the growth of NSCLC and increased the levels of LC3-II and phosphorylated AMPK in tumors isolated from a xenograft model of NSCLC in mice. Moreover, PPI exhibited favorable pharmacokinetics in rats. In summary, PPI conclusively acts as a direct AMPK activator to induce cell autophagy which inhibits the growth of NSCLC cells. In the future, PPI therapy should be applied to treat patients with NSCLC.

Ethoxysanguinarine, a Novel Direct Activator of AMP-Activated Protein Kinase, Induces Autophagy and Exhibits Therapeutic Potential in Breast Cancer Cells

Ethoxysanguinarine (Eth) is a benzophenanthridine alkaloid extracted from Macleaya cordata (Willd) R. Br. It possesses antibacterial and antiviral activities and offers therapeutic benefits for the treatment of respiratory syndrome virus-induced cytopathic effects. However, the effect of Eth on human tumors and its pharmacological effects remain to be elucidated, together with its cellular target. Here, we examined the effects of Eth on breast cancer (BC) cells. We found that at low doses, Eth strongly inhibited the viability of BC cell lines and induced autophagy. Mechanistic studies showed that Eth induced autophagy by upregulating the activity of the AMP-activated protein kinase (AMPK). The AMPK inhibitor compound C significantly attenuated Eth-induced autophagy and inhibited proliferation. Meanwhile, the AMPK activator metformin significantly enhanced Eth-induced autophagy and inhibited proliferation. Computational docking and affinity assays showed that Eth directly interacted with the allosteric drug and metabolite site of AMPK to stabilize its activation. AMPK was less activated in tumor samples compared to normal breast tissues and was inversely associated with the prognosis of the patients. Moreover, Eth exhibited potent anti-BC activity in nude mice and favorable pharmacokinetics in rats. These characteristics render Eth as a promising candidate drug for further development and for designing new effective AMPK activators.

All-Trans-Retinoic Acid Suppresses Neointimal Hyperplasia and Inhibits Vascular Smooth Muscle Cell Proliferation and Migration via Activation of AMPK Signaling Pathway

The proliferation and migration of vascular smooth muscle cells (VSMC) is extensively involved in pathogenesis of neointimal hyperplasia. All-trans-retinoic acid (ATRA) is a natural metabolite of vitamin A. Here, we investigated the involvement of AMP-activated protein kinase (AMPK) in the anti-neointimal hyperplasia effects of ATRA. We found that treatment with ATRA significantly reduced neointimal hyperplasia in the left common carotid artery ligation mouse model. ATRA reduced the proliferation and migration of VSMC, A7r5 and HASMC cell lines. Our results also demonstrated that ATRA altered the expression of proliferation-related proteins, including CyclinD1, CyclinD3, CyclinA2, CDK2, CDK4, and CDK6 in VSMC. ATRA dose-dependently enhanced the phosphorylation level of AMPKα (Thr172) in the left common carotid artery of experimental mice. Also, the phosphorylation level of AMPKα in A7r5 and HASMC was significantly increased. In addition, ATRA dose-dependently reduced the phosphorylation levels of mTOR and mTOR target proteins p70 S6 kinase (p70S6K) and 4E-binding protein 1 (4EBP1) in A7r5 and HASMC. Notably, the inhibition of AMPKα by AMPK inhibitor (compound C) negated the protective effect of ATRA on VSMC proliferation in A7r5. Also, knockdown of AMPKα by siRNA partly abolished the anti-proliferative and anti-migratory effects of ATRA in HASMC. Molecular docking analysis showed that ATRA could dock to the agonist binding site of AMPK, and the binding energy between AMPK and ATRA was -7.91 kcal/mol. Molecular dynamics simulations showed that the binding of AMPK-ATRA was stable. These data demonstrated that ATRA might inhibit neointimal hyperplasia and suppress VSMC proliferation and migration by direct activation of AMPK and inhibition of mTOR signaling.

TXNIP mediated the oxidative stress response in glomerular mesangial cells partially through AMPK pathway

BACKGROUND

Thioredoxin-interacting protein (TXNIP) plays an important role in the development of diabetic nephropathy. In the present study, we investigated role of TXNIP on oxidative stress in glomerular mesangial cells (GMCs) cultured in high glucose or normal glucose, and explored the potential mechanism related to TXNIP as well.

METHODS

Oxidative stress in GMCs under high or normal glucose was detected. TXNIP knockdown by specific siRNA or over expression by pcDNA3.0-TXNIP vector was performed to evaluate the role of TXNIP on injury of GMCs caused by oxidative stress. Activator of AMPK AICAR and AMPK inhibitor Compound C were treated the GMCs. Reactive oxygen species (ROS) and mitochondrial membrane potential were detected by flow cytometry. Activities of superoxide dismutase (SOD) and superoxide dismutase (CAT) were measured by ELISA. Activity of thioredoxin (Trx) was determined using Trx activity assay kit. mRNA expression of AMPK, TXNIP, Trx1 and Trx2 were tested by qRT-PCR. Expressions of P-AMPK, TXNIP and fibronectin proteins were detected by Western blotting.

RESULTS

High glucose induced the increase of ROS level, activation of TXNIP, but restricted mitochondrial membrane potential and activities of p-AMPK, SOD and CAT, and Trx. TXNIP siRNA and AICAR inhibited high glucose-induced oxidative stress response in GMCs and fibronectin expression, but promoted cell viability. In contrast, pcDNA3.0-TXNIP and Compound C increased oxidative stress response in normal glucose cultured GMCs, but decreased cell viability. The combined effect of TXNIP siRNA and AICAR on the inhibition of oxidative stress was obviously stronger than that of single use of TXNIP siRNA.

CONCLUSION

TXNIP facilitates the oxidative stress response in GMCs partially through AMPK pathway, which may provide potential therapeutic target for diabetic nephropathy treatment.

Special Protein Molecules Computational Identification

Computational identification of special protein molecules is a key issue in understanding protein function. It can guide molecular experiments and help to save costs. I assessed 18 papers published in the special issue of Int. J. Mol. Sci., and also discussed the related works. The computational methods employed in this special issue focused on machine learning, network analysis, and molecular docking. New methods and new topics were also proposed. There were in addition several wet experiments, with proven results showing promise. I hope our special issue will help in protein molecules identification researches.

Special Protein Molecules Computational Identification

Computational identification of special protein molecules is a key issue in understanding protein function. It can guide molecular experiments and help to save costs. I assessed 18 papers published in the special issue of Int. J. Mol. Sci., and also discussed the related works. The computational methods employed in this special issue focused on machine learning, network analysis, and molecular docking. New methods and new topics were also proposed. There were in addition several wet experiments, with proven results showing promise. I hope our special issue will help in protein molecules identification researches.

Promise and challenges for direct small molecule AMPK activators

AMP-activated protein kinase (AMPK) is an evolutionary conserved and ubiquitously expressed serine/threonine kinase playing a central role in the coordination of energy homeostasis. Based on the beneficial outcomes of its activation on metabolism, AMPK has emerged as an attractive target for the treatment of metabolic diseases. Identification of novel downstream targets of AMPK beyond the regulation of energy metabolism has renewed considerable attention in exploiting AMPK signaling for novel therapeutic targeting strategies including treatment of cancer and inflammatory diseases. The complexity of AMPK system with tissue- and species-specific expression of multiple isoform combination regulated by various inputs, post-traductional modifications and subcellular locations presents unique challenges for drug discovery. Here, we review the most recent advances in the understanding of the mechanism(s) of action of direct small molecule AMPK activators and the potential therapeutic opportunities.