Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5)

Neuroprotection by B355252 against Glutamate-Induced Cytotoxicity in Murine Hippocampal HT-22 Cells Is Associated with Activation of ERK3 Signaling Pathway

Glutamate differentially affects the levels extracellular signal-regulated kinase (ERK)1/2 and ERK3 and the protective effect of B355252, an aryl thiophene compound, 4-chloro-N-(naphthalen-1-ylmethyl)-5-(3-(piperazin-1-yl)phenoxy)thiophene-2-sulfonamide, is associated with suppression of ERK1/2. The objectives of this study were to further investigate the impact of B355252 on ERK3 and its downstream signaling pathways affected by glutamate exposure in the mouse hippocampal HT-22 neuronal cells. Murine hippocampal HT22 cells were incubated with glutamate and treated with B355252. Cell viability was assessed, protein levels of pERK3, ERK3, mitogen-activated protein kinase-activated protein kinase-5 (MAPKAPK-5), steroid receptor coactivator 3 (SRC-3), p-S6 and S6 were measured using Western blotting, and immunoreactivity of p-S6 was determined by immunocytochemistry. The results reveal that glutamate markedly diminished the protein levels of p-ERK3 and its downstream targets MK-5 and SRC-3 and increased p-S6, an indicator for mechanistic target of rapamycin (mTOR) activation. Conversely, treatment with B355252 protected the cells from glutamate-induced damage and prevented the glutamate-caused declines of p-ERK3, MK-5 and SRC-3 and increase of p-S6. Our study demonstrates that one of the mechanisms that glutamate mediates its cytotoxicity is through suppression of ERK3 and that B355252 rescues the cells from glutamate toxicity by reverting ERK3 level.

Allosteric MAPKAPK2 inhibitors improve plaque stability in advanced atherosclerosis

Atherosclerotic vascular disease resulting from unstable plaques is the leading cause of morbidity and mortality in subjects with type 2 diabetes (T2D), and thus a major therapeutic goal is to discover T2D drugs that can also promote atherosclerotic plaque stability. Genetic or pharmacologic inhibition of mitogen-activated protein kinase-activated protein kinase-2 (MAPKAPK2 or MK2) in obese mice improves glucose homeostasis and enhances insulin sensitivity. We developed two novel orally active small-molecule inhibitors of MK2, TBX-1 and TBX-2, and tested their effects on metabolism and atherosclerosis in high-fat Western diet (WD)-fed Ldlr-/- mice. Ldlr-/- mice were first fed the WD to allow atherosclerotic lesions to become established, and the mice were then treated with TBX-1 or TBX-2. Both compounds improved glucose metabolism and lowered plasma cholesterol and triglyceride, without an effect on body weight. Most importantly, the compounds decreased lesion area, lessened plaque necrosis, and increased fibrous cap thickness in the aortic root lesions of the mice. Thus, in a preclinical model of high-fat feeding and established atherosclerosis, MK2 inhibitors improved metabolism and also enhanced atherosclerotic plaque stability, suggesting potential for further clinical development to address the epidemic of T2D associated with atherosclerotic vascular disease.

Analyses on the binding interaction between rice glutelin and conjugated linoleic acid by multi-spectroscopy and computational docking simulation

It is an interesting topic to elucidate the interaction among plant proteins and bioactive lipid components. However, there is a shortage of understanding regarding the nature of the interaction between rice protein and conjugated linoleic acid (CLA). In this study, the intrinsic fluorescence intensity of rice glutelin (RG) was quenched upon increasing concentrations of CLA, indicating the occurrence of an interaction between them. Thermodynamic analysis showed that the RG-CLA binding process occurred spontaneously and hydrogen bonds were the primary driving force. Moreover, only one binding site was calculated between RG and CLA by the intrinsic fluorescence data. The surface hydrophobicity of RG was reduced with increasing CLA. Circular dichroism and synchronous fluorescence spectroscopy showed conformational and microenvironmental changes around the chromophores of RG. The α-helical content increased and β-sheet content declined after the binding reaction. The computational docking program displayed the target site in which CLA and amino acid residues of RG might be linked together. This study provides valuable insights into the nature of the interactions between plant proteins and fatty acids.

Protein-polyphenol interactions enhance the antioxidant capacity of phenolics: analysis of rice glutelin-procyanidin dimer interactions

Rice glutelin and procyanidins are often used in functional foods as sources of plant-based proteins and polyphenols, respectively, but little is currently known about the interactions between them. In our research, the interaction between rice glutelin and the B-type procyanidin dimer (PB2) was investigated. The presence of the PB2 decreased the α-helix and random coil structure of the rice protein and reduced its surface hydrophobicity. However, the PB2 did not adversely affect the functional performance of RG in emulsions. Conversely, the antioxidant capacity of the PB2 was enhanced in the presence of the rice protein. Fluorescence spectroscopy confirmed that the protein and PB2 formed molecular complexes, which were primarily the result of hydrophobic attractive forces. Molecular docking analysis provides insights into the nature of the interaction between the rice protein and PB2. This study provides valuable insights into the nature of the interactions between plant proteins and polyphenolic nutraceuticals.

Investigation on the binding interaction between rice glutelin and epigallocatechin-3-gallate using spectroscopic and molecular docking simulation

The interaction between plant protein and polyphenol is a topic of considerable interest. However, there is relatively little understanding about the interaction between rice protein and epigallocatechin-3-gallate (EGCG). The spectroscopy and computational docking program were used to investigate the potential interaction between rice glutelin (RG) and EGCG. It was found that the intrinsic fluorescence of RG could be quenched by EGCG, which indicated interaction occurred between them. Thermodynamic analysis elucidated that the interaction process between RG and EGCG happened spontaneously with hydrogen bond as the primary driving force. The ANS-fluorescence indicated that the surface hydrophobicity of RG reduced with the increasing of EGCG. Circular dichroism spectra and synchronous fluorescence gave further information for the conformational and microenvironmental changes of RG. Particularly, the α-helix structure reduced and random coil structure increased after the binding interaction. Furthermore, the computational docking program exhibited target sites in which the amino acid residues of RG and EGCG might be bound together.

Triazolo[4,5-d]pyrimidines as Validated General Control Nonderepressible 2 (GCN2) Protein Kinase Inhibitors Reduce Growth of Leukemia Cells

Cellular stress signals activate adaptive signaling pathways of the mammalian integrated stress response (ISR), of which the unfolded protein response (UPR) is a subset. These pathways converge at the phosporylation of eIF2α. Drug-like, potent and selective chemical inhibitors (valid chemical probes) targeting major ISR kinases have been previously identified, with the exception of GCN2. We synthesized and evaluated a series of GCN2 inhibitors based on a triazolo[4,5-d]pyrimidine scaffold. Several compounds potently inhibited GCN2 in vitro and displayed good selectivity over the related kinases PERK, HRI, and IRE1. The compounds inhibited phosporylation of eIF2α in HEK293T cells with an IC₅₀ < 150 nM, validating them as chemical probes for cellular studies. These probes were screened against the National Cancer Institute NCI-60 human cancer cell line panel. Uniform growth inhibition was observed in the leukemia group of cell lines. Growth inhibition in the most sensitive cell lines coincided with high GCN2 mRNA expression levels. Oncomine analysis revealed high GCN2 expression accompanied by lower asparagine synthetase (ASNS) expression in patient-derived acute lymphoblastic leukemias with B-Cell origins (B-ALL) as well. Notably, asparaginase, which depletes amino acids and triggers GCN2 activity, is a licensed, first-line B-ALL treatment. Thus, we hypothesize that leukemias exhibiting high GCN2 expression and low ASNS expression may be susceptible to pharmacologic GCN2 inhibition.

MK5: A novel regulator of cardiac fibroblast function?

MAP kinase-activated protein kinases (MKs), protein serine/threonine kinases downstream of the MAPKs, regulate a number of biological functions. MK5 was initially identified as a substrate for p38 MAPK but subsequent studies revealed that MK5 activity is regulated by atypical MAPKs ERK3 and ERK4. However, the roles of these MAPKs in activating MK5 remain controversial. The interactome and physiological function of MK5 are just beginning to be understood. Here, we provide an overview of the structure-function of MK5 including recent progress in determining its role in cardiac structure and function. The cardiac phenotype of MK5 haplodeficient mice, and the effect of reduced MK5 expression on cardiac remodeling, is also discussed. © 2017 IUBMB Life, 69(10):785-794, 2017.

Homology modeling and molecular dynamics simulation of the HIF2α degradation-related HIF2α-VHL complex

BACKGROUND

Hypoxia-inducible factor 2 alpha (HIF2α), prolyl hydroxylase domain protein 2 (PHD2), and the von Hippel Lindau tumor suppressor protein (pVHL) are three principal proteins in the oxygen-sensing pathway. Under normoxic conditions, a conserved proline in HIF2α is hydroxylated by PHD2 in an oxygen-dependent manner, and then pVHL binds and promotes the degradation of HIF2α. However, the crystal structure of the HIF2α-pVHL complex has not yet been established, and this has limited research on the interaction between HIF and pVHL. Here, we constructed a structural model of a 23-residue HIF2α peptide (528-550)-pVHL-ElonginB-ElonginC complex by using homology modeling and molecular dynamics simulations. We also applied these methods to HIF2α mutants (HYP531PRO, F540L, A530 V, A530T, and G537R) to reveal structural defects that explain how these mutations weaken the interaction with pVHL.

METHODS

Homology modeling and molecular dynamics simulations were used to construct a three-dimensional (3D) structural model of the HIF2α-VHL complex. Subsequently, MolProbity, an active validation tool, was used to analyze the reliability of the model. Molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) and solvated interaction energy (SIE) methods were used to calculate the binding free energy between HIF2a and pVHL, and the stability of the simulation system was evaluated by using root mean square deviation (RMSD) analysis. We also determined the secondary structure of the system by using the definition of secondary structure of proteins (DSSP) algorithm. Finally, we investigated the structural significance of specific point mutations known to have clinical implications.

RESULTS

We established a reliable structural model of the HIF2α-pVHL complex, which is similar to the crystal structure of HIF1α in 1LQB. Furthermore, we compared the structural model of the HIF2α-pVHL complex and the HIF2α (HYP531P, F540L, A530V, A530T, and G537R)-pVHL mutants on the basis of RMSD, DSSP, binding free energy, and hydrogen bonding. The experimental data indicate that the stability of the structural model of the HIF2α-pVHL complex is higher than that of the mutants, consistently with clinical observations.

CONCLUSIONS

The structural model of the HIF2α-pVHL complex presented in this study enhances understanding of how HIF2α is captured by pVHL. Moreover, the important contact amino acids that we identified may be useful in the development of drugs to treat HIF2a-related diseases.

Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches

WbpP encoding UDP-GlcNAC C4 epimerase is responsible for the activation of virulence factor in marine pathogen Vibrio vulnificus (V. vulnificus) and it is linked to many aquatic diseases, thus making it a potential therapeutic target. There are few reported compounds that include several natural products and synthetic compounds targeting Vibrio sp, but specific inhibitor targeting WbpP are unavailable. Here, we performed structure-based virtual screening using chemical libraries such as Binding, TOSLab and Maybridge to identify small molecule inhibitors of WbpP with better drug-like properties. Deficient structural information forced to model the structure and the stable protein structure was obtained through 30 ns of MD simulations. Druggability regions are focused for new lead compounds and our screening protocol provides fast docking of entire small molecule library with screening criteria of ADME/Lipinski filter/Docking followed by re-docking of top hits using a method that incorporates both ligand and protein flexibility. Docking conformations of lead molecules interface displays strong H-bond interactions with the key residues Gly101, Ser102, Val195, Tyr165, Arg298, Val209, Ser142, Arg233 and Gln200. Subsequently, the top-ranking compounds were prioritized using the molecular dynamics simulation-based conformation and stability studies. Our study suggests that the proposed compounds may aid as a starting point for the rational design of novel therapeutic agents.

Binding interaction between rice glutelin and amylose: Hydrophobic interaction and conformational changes

The interaction of rice glutelin (RG) with amylose was characterized by spectroscopic and molecular docking studies. The intrinsic fluorescence of RG increased upon the addition of amylose. The binding sites, binding constant and thermodynamic features indicated that binding process was spontaneous and the main driving force of the interaction was hydrophobic interaction. The surface hydrophobicity of RG decreased with increasing amount of amylose. Furthermore, synchronous fluorescence and circular dichroism (CD) spectra provided data concerning conformational and micro-environmental changes of RG. With the concentration of amylose increasing, the polarity around the tyrosine residues increased while the hydrophobicity decreased. Alteration of protein conformation was observed with increasing of α-helix and reducing of β-sheet. Finally, a visual representation of two binding sites located in the amorphous area of RG was presented by molecular modeling studies.

Comparative molecular dynamics simulations of mitogen-activated protein kinase-activated protein kinase 5

The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD) simulations of: (1) MK5 alone; (2) MK5 in complex with an inhibitor; and (3) MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS) calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.