Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry

AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is essential in regulating energy metabolism in all eukaryotic cells. It is a heterotrimeric protein complex composed of a catalytic subunit (α) and two regulatory subunits (β and γ). C-terminal truncation of AMPKα at residue 312 yielded a protein that is active upon phosphorylation of Thr172 in the absence of β and γ subunits, which is refered to as the AMPK catalytic domain and commonly used to substitute for the AMPK heterotrimeric complex in in vitro kinase assays. However, a comprehensive characterization of the AMPK catalytic domain is lacking. Herein, we expressed a His-tagged human AMPK catalytic domin (denoted as AMPK^Δ) in E. coli, comprehensively characterized AMPK^Δ in its basal state and after in vitro phosphorylation using top-down mass spectrometry (MS), and assessed how phosphorylation of AMPK^Δ affects its activity. Unexpectedly, we found that bacterially-expressed AMPK^Δ was basally phosphorylated and localized the phosphorylation site to the His-tag. We found that AMPK^Δ had noticeable basal activity and was capable of phosphorylating itself and its substrates without activating phosphorylation at Thr172. Moreover, our data suggested that Thr172 is the only site phosphorylated by its upstream kinase, liver kinase B1, and that this phosphorylation dramatically increases the kinase activity of AMPK^Δ. Importantly, we demonstrated that top-down MS in conjunction with in vitro phosphorylation assay is a powerful approach for monitoring phosphorylation reaction and determining sequential order of phosphorylation events in kinase-substrate systems.

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Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases

Protein kinases are key enzymes that catalyze the covalent phosphorylation of substrates via the transfer of the γ-phosphate of ATP, playing a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. Due to their pivotal cellular role, the aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Decades of intense development of protein kinase inhibitors (PKIs) resulted in 71 FDA-approved PKI drugs that target dozens of protein kinases for the treatment of various diseases. How do FDA-approved protein kinase inhibitor PKI drugs compete with ATP in their own binding pocket? This is the central question we attempt to address in this work. Based on modes of non-bonded interactions and their calculated interaction strengths by means of the advanced double hybrid DFT method B2PLYP, the molecular recognition of PKI drugs in the ATP-binding pockets was systematically analyzed. It was found that (1) all the FDA-approved PKI drugs studied here form one or more hydrogen bond(s) with the backbone amide N, O atoms in the hinge region of the ATP binding site, mimicking the adenine base; (2) all the FDA-approved PKI drugs feature two or more aromatic rings. The latter reach far and deep into the hydrophobic regions I and II, forming multiple CH-π interactions with aliphatic residues L(3), V(11), A(15), V(36), G(51), L(77) and π-π stacking interactions with aromatic residues F(47) and F(82), but ATP itself does not utilize these regions extensively; (3) all FDA-approved PKI drugs studied here have one thing in common, i.e., they frequently formed non-bonded interactions with a total of 12 residues L(3),V(11), A(15), K(17), E(24),V(36),T(45), F(47), G(51), L(77), D(81) and F(82) in the ATP binding. Many of those 12 commonly involved residues are highly conserved residues with important structural and catalytic functional roles. K(17) and E(24) are the two highly conserved residues crucial for the catalytic function of kinases. D(81) and F(82) belong to the DFG motif; T(45) was dubbed the gate keeper residue. F(47) is located on the hinge region and G(51) sits on the linker that connects the hinge to the αD-helix. It is this targeting of highly conserved residues in protein kinases that led to promiscuous PKI drugs that lack selectivity. Although the formation of hydrogen bond(s) with the backbone of the hinge gives PKI drugs the added binding affinity and the much-needed directionality, selectivity is sacrificed. That is why so many FDA-approved PKI drugs are known to have multiple targets. Moreover, off-target-mediated toxicity caused by a lack of selectivity was one of the major challenges facing the PKI drug discovery community. This work suggests a road map for future PKI drug design, i.e., targeting non-conserved residues in the ATP binding pocket to gain better selectivity so as to avoid off-target-mediated toxicity.     

Drug Repurposing and De Novo Drug Discovery of Protein Kinase Inhibitors as New Drugs against Schistosomiasis

Schistosomiasis is a neglected tropical disease affecting more than 200 million people worldwide. Chemotherapy relies on one single drug, praziquantel, which is safe but ineffective at killing larval stages of this parasite. Furthermore, concerns have been expressed about the rise in resistance against this drug. In the absence of an antischistosomal vaccine, it is, therefore, necessary to develop new drugs against the different species of schistosomes. Protein kinases are important molecules involved in key cellular processes such as signaling, growth, and differentiation. The kinome of schistosomes has been studied and the suitability of schistosomal protein kinases as targets demonstrated by RNA interference studies. Although protein kinase inhibitors are mostly used in cancer therapy, e.g., for the treatment of chronic myeloid leukemia or melanoma, they are now being increasingly explored for the treatment of non-oncological conditions, including schistosomiasis. Here, we discuss the various approaches including screening of natural and synthetic compounds, de novo drug development, and drug repurposing in the context of the search for protein kinase inhibitors against schistosomiasis. We discuss the status quo of the development of kinase inhibitors against schistosomal serine/threonine kinases such as polo-like kinases (PLKs) and mitogen-activated protein kinases (MAP kinases), as well as protein tyrosine kinases (PTKs).     

PKA酶及其抑制剂balanol的计算化学

蛋白激酶通过磷酸化蛋白底物来调节细胞内的信号转导途径,是重要的药物设计靶标。蛋白激酶A（PKA）是最早获得催化结构域X衍射晶体结构的激酶,是蛋白激酶家族中代表性结构。本文综述了PKA在计算化学领域的研究进展,包括PKA全酶以及它的催化（C）亚基和调节(R)亚基在水溶液中的分子动力学模拟研究,磷酰基转移机理和C亚基与其抑制剂balanol的结合自由能预测、柔性对接。分子动力学、分子对接、同源模建、QM/MM等计算机辅助设计方法在该体系中得到运用。     

Angelica gigas NAKAI and Its Active Compound,Decursin, Inhibit Cellular Injury as an Antioxidant by the Regulation of AMP-Activated Protein Kinase and YAP Signaling

Natural products and medicinal herbs have been used to treat various human diseases by regulating cellular functions and metabolic pathways. Angelica gigas NAKAI (AG) helps regulate pathological processes in some medical fields, including gastroenterology, gynecology, and neuropsychiatry. Although some papers have reported its diverse indications, the effects of AG against arachidonic acid (AA)+ iron and carbon tetrachloride (CCl₄) have not been reported. In HepG2 cells, AA+ iron induced cellular apoptosis and mitochondrial damage, as assessed by mitochondrial membrane permeability (MMP) and the expression of apoptosis-related proteins. On the other hand, AG markedly inhibited these detrimental phenomena and reactive oxygen species (ROS) production induced by AA+ iron. AG activated the liver kinase B1 (LKB1)-dependent AMP-activated protein kinase (AMPK), which affected oxidative stress in the cells. Moreover, AG also regulated the expression of yes-associated protein (YAP) signaling as mediated by the AMPK pathways. In mice, an oral treatment of AG protected against liver toxicity induced by CCl₄, as indicated by the plasma and histochemical parameters. Among the compounds in AG, decursin had antioxidant activity and affected the AMPK pathway. In conclusion, AG has antioxidant effects in vivo and in vitro, indicating that natural products such as AG could be potential candidate for the nutraceuticals to treat various disorders by regulating mitochondrial dysfunction and cellular metabolic pathways.     

Beer: An Ancient Yet Modern Biotechnology

The brewing of beer is a complex process that draws on a diversity of sciences and technology, of which chemistry is but one. This paper focuses on the chemistry of the brewing process and of the finished product. It examines each of the main classes of molecule found in beer, considers their contribution to quality and their origins in the brewing process. The study of beer and its production provides an excellent illustrative example for teaching how raw materials and the manner by which they are processed determine the acceptability of a product. Beer, whilst 90%+ water, contains a wide range of chemical species which establish its properties. Apart from ethanol (the common denominator amongst all alcoholic beverages), beer contains substances that determine its flavor, foam, and color. The flavorsome components of beer include the bitter iso-a-acids and aromatic essential oils from hops, along with esters, acids, sulfur-containing compounds and vicinal diketones from yeast. The foaminess of beer depends on the presence of carbon dioxide but also of surface-active materials like amphipathic polypeptides from malt and the bitter substances from hops. The color is due to Maillard reaction products generated largely during the kilning of malt. The malting and brewing processes (which are briefly described) are designed to maximize the extraction and digestion of barley starch and protein, yielding highly fermentable wort. The processes are also designed to eliminate materials that can have an adverse effect on beer quality, such as the haze-forming polyphenol from barley and hops and the lipids and oxygen that, together, can cause beer to stale.     

蛋白类药物口服药剂的设计与稳定性研究

口服给药具有方便、安全、患者依存性强等优势,是理想的给药途径,但蛋白类药物在口服过程中易被胃酸及蛋白酶分解而失活,导致生物利用度较低.本实验设计了一种药物载体,用于蛋白类药物口服给药,解决了蛋白类药物在胃肠道中易失活的问题.以葡萄糖氧化酶为蛋白药物模型,通过在蛋白质表面原位自由基聚合反应制备葡萄糖氧化酶纳米微囊,低温干...     

N-acetylgalactosamine Kinase: A Naturally Promiscuous Small Molecule Kinase

N-acetylgalactosamine kinase is a member of the GHMP family of small molecule kinases which catalyses the ATP-dependent phosphorylation of N-acetylgalactosamine. It is highly similar in structure and sequence to galactokinase. Alteration of galactokinase at a key tyrosine residue (Tyr-379 in the human enzyme) has been shown to dramatically enhance the substrate range of this enzyme. Here, we investigated the substrate specificity of the wild type N-acetylgalactosamine kinase and demonstrated that it can also catalyse the phosphorylation of N-acetylglucosamine and N-acetylmannosamine. In human N-acetylgalactosamine kinase, the equivalent residue to Tyr-379 in galactokinase is Phe-444. Alteration of this residue did not result in dramatic changes to the specificity of the enzyme. The more relaxed substrate specificity of N-acetylgalactosamine kinase, compared to galactokinase, can be explained by the greater flexibility of a glycine rich loop in the active site of the enzyme. These results suggest that N-acetylgalactosamine kinase is a potential biocatalyst for the phosphorylation of N-acetyl sugars. However, it is unlikely that it will be possible to further broaden the substrate range by alteration of Phe-444.     

Protein Phosphorylation and Cellular Information Transfer: Signaling by MAP Kinase Cascades

Summary. Living cells, unicellular organisms as well as cells of multicellular organisms, are permanently exposed to a multitude of signals. Cells have to transform these external stimuli into physiological intelligible signals that are transduced from outside of the cell into the cell to induce a proper cellular response. Extracellular stimuli are perceived and internalised by various cellular receptors. Subsequently, signals are transduced by one of many protein kinase signaling cascades. Mitogen-activated protein kinases (MAPKs) belong to the evolutionary most conserved class of such molecular switches. MAPKs can change the activity of target proteins and thereby bring about physiological responses to external signals. This review discusses the basic principles of MAPK pathways in the context of cellular information processing: Cellular bioinformatics is an increasingly important interdisciplinary field with important implications for basic and applied sciences.Received February 24, 2003; accepted March 28, 2003 Published online August 18, 2003     

泉生热袍菌结构基因组的选靶研究

对泉生热袍菌进行了结构基因组的选靶研究，从泉生热袍菌的蛋白组中挑选了20个蛋白质作为第一批进行结构测定的目标，以发现新的蛋白质折叠模式. 选靶研究主要使用了BLAST搜索， PSI-BLAST搜索和ProtoNet数据库搜索等方法. 另外，还用PredictProtein程序对选中的蛋白质进行了二级结构和外形预测. 选中的20个蛋白质中有8个被克隆、表达和纯化，其中2个得到了单晶并收集了X衍射数据. 实验结果和最近一些文献报道的结果表明，挑选的一些蛋白质具有新的折叠模式，表明了这种选靶策略的有效性.     

Long‐Wavelength Fluorescent Reporters for Monitoring Protein Kinase Activity

In vivo optical imaging must contend with the limitations imposed by the optical window of tissue (600–1000 nm). Although a wide array of fluorophores are available that are visualized in the red and near‐IR region of the spectrum, with the exception of proteases, there are few long wavelength probes for enzymes. This situation poses a particular challenge for studying the intracellular biochemistry of erythrocytes, the high hemoglobin content of which optically obscures subcellular monitoring at wavelengths less than 600 nm. To address this, tunable fluorescent reporters for protein kinase activity were developed. The probing wavelength is preprogrammed by using readily available fluorophores, thereby enabling detection within the optical window of tissue, specifically in the far‐red and near‐IR region. These agents were used to monitor endogenous cAMP‐dependent protein kinase activity in erythrocyte lysates and in intact erythrocytes when using a light‐activatable reporter.     

Construction of Protein Probe with a His-tag and an Electron-transfer Peptide for a Target Protein Sensing

A protein probe with an electron-transfer peptide and a His-tag was designed to electrochemically sense a target protein. We selected tyrosine-rich (Y₄C) and tryptophan-rich (W₄C) peptides for use as electron-transfer agents. The peak for oxidation was based on the oxidations of the phenolic hydroxy groups in Y₄C and on the indole rings in W₄C. Asialofetuin (ASF) with galactose residues was the protein probe, and a galactose recognition protein, soybean agglutinin (SBA), was the target protein. A protein probe composed of an amino acid and carbohydrate residue was expected to be biocompatible. When voltammetric measurements were performed using a glassy carbon electrode, the oxidation peaks of H₆Y₄C and ASF-H₆Y₄C appeared at the same potential. The peak current of ASF-H₆Y₄C was 4-fold that of H₆Y₄C because of the stronger adsorption of ASF-H₆Y₄C onto the electrode. The electrode response of ASF-H₆Y₄C with SBA was half that of ASF-H₆Y₄C alone. By contrast, the peak current of ASF-Y₄CH₆ was higher than that of ASF-H₆Y₄C, which was the result of a greater degree of contact between the Y₄C moieties and an electrode. On the other hand, the voltammetric behaviors of ASF with W₄C and a His-tag were similar to those with Y₄C and a His-tag. The sensitivity of SBA using ASF-Y₄CH₆ was at the 10⁻¹³ M level. To confirm the function of the sensing system, measurements were performed in human serum with SBA and ASF-Y₄CH₆. When SBA was added, the serum had a concentration that ranged between 5.0×10⁻¹³ and 4.0×10⁻¹² M, and the amount of SBA that could be recovered ranged from 97 to 101%. Consequently, this system could be applied to the detection of SBA in serum.     

Modern Synthetic Methods for Fluorine‐Substituted Target Molecules

Fluorine has come to be recognized as a key element in materials science: in heat‐transfer agents, liquid crystals, dyes, surfactants, plastics, elastomers, membranes, and other materials. Furthermore, many fluorine‐containing biologically active agents are finding applications as pharmaceuticals and agrochemicals. Progress in synthetic fluorine chemistry has been critical to the development of these fields and has led to the invention of many novel fluorinated molecules as future drugs and materials. As a result of the electronic effects of fluorine substituents, fluorinated substrates and reagents often exhibit unusual and unique chemical properties, which often make them incompatible with established synthetic methods. Thus, the problem of how to control the unusual properties of compounds with fluorine substituents deserves much attention, so as to promote the design of facile, efficient, and environmentally benign methods for the synthesis of valuable organofluorine targets.     

丙酮酸脱氢酶系：除草剂品种的新靶标

丙酮酸脱氢酶系抑制剂;综述;丙酮酸脱氢酶系：除草剂品种的新靶标     

DNA Replication Is the Target for the Antibacterial Effects of Nonsteroidal Anti-Inflammatory Drugs

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Yuanhuacin A Is a Selective Antagonist of Phorbol Ester Receptor in Protein Kinase C

Protein kinase C with a molecular weight of 82 kD has been purified to electrophoresis homogenous from rat brain through a series of chromatography columns including DE-52, Sepharose G-200 and phenyl-Sepharose. The enzyme possessed autophosphorylation activity. Yuanhuacin A inhibited the ~3H-phorbol-12, 13-dibutyrate (~3H-PdBu) binding of PKC with an IC_(50) value of 1.48±0.28×10~(-8) mol/L when the concentration of ~3H-PdBu was 1.5×10~(-9) mol/L (K_i=1.2×10~(-8) mol/L). Yuanhuacin A inhibited the PdBu-stimulated PKC activity in the catalysis of the phosphorylation of Histone Ⅲ-S with an IC_(50) of 2.82±0.37×10~(-9) mol/L (PdBu=10~(-6) mol/L), while it had no effect on the basal and Ca~(2+)-stimulated PKC activity in the same assay system. This result suggests that Yuanhuacin A is a selective antagonist of the phorbol ester receptor in protein kinase C.