Lipidomics-based assays coupled with computational approaches can identify novel phospholipase A2 inhibitors.

Phospholipase A2 (PLA2) enzymes play a major role in many diseases including the inflammatory cascade and specific potent small molecule inhibitors could be useful in studying their physiological role as well as for the development of drugs. In order to discover novel small molecule inhibitor platforms for members of the PLA2 superfamily of enzymes, we have applied computational approaches to determine the binding mode of potent inhibitors specific for particular PLA2s to the screening of chemical libraries. This has including the U.S. National Institutes of Health (NIH) National Cancer Institute (NCI) Diversity Set V and the ChemBridge commercial compound libraries. We have then subjected identified inhibitor structures to recently developed lipidomics based screening assays to determine the XI(50) and specificity of the identified compounds for specific PLA2s. Herein we review this approach and report the identity of initial hits for both the Group IVA cytosolic PLA2 and the Group VIA calcium-independent PLA2 that are worthy of further structural modification to develop novel platforms for inhibitor development.

Phospholipase Superfamily: Structure, Functions, and Biotechnological Applications.

Enzymes of the phospholipase superfamily are involved in lipid metabolism, as well as regulation of membrane composition, cell signaling, and inflammation. This review provides an insight into the structure, functional properties, and biotechnological application of phospholipase A2 and phospholipases in general.

Review of four major distinct types of human phospholipase A2.

The phospholipase A2 superfamily of enzymes plays a significant role in the development and progression of numerous inflammatory diseases. Through their catalytic action on membrane phospholipids, phospholipases are the upstream regulators of the eicosanoid pathway releasing free fatty acids for cyclooxygenases, lipoxygenases, and cytochrome P450 enzymes which produce various well-known inflammatory mediators including leukotrienes, thromboxanes and prostaglandins. Elucidating the association of phospholipases A2 with the membrane, the extraction and binding of phospholipid substrates, and their interactions with small-molecule inhibitors is crucial for the development of new anti-inflammatory therapeutics. Studying phospholipases has been challenging because they act on the surface of cellular membranes and micelles. Multidisciplinary approaches including hydrogen/deuterium exchange mass spectrometry, molecular dynamics simulations, and other computer-aided drug design techniques have been successfully employed by our laboratory to study interactions of phospholipases with membranes, phospholipid substrates and inhibitors. This review summarizes the application of these techniques to study four human recombinant phospholipases A2.

Fourier-based classification of protein secondary structures.

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices.

cDNA and gene structures of two phospholipase A2 isoforms, acidic PLA2 PA4 and PLA2 PA3A/PA3B/PA5, in Nemopilema nomurai jellyfish venom.

We have shown that Nemopilema nomurai jellyfish venom (NnV) contains various kinds of proteolytic enzyme activities, including phospholipase (PLA), metalloproteinase (MP) and hyaluronidase activities. In this study, we reported the full-length cDNA and gene sequences of two PLA2 isoforms: acidic PLA2 PA4 and PLA2 PA3A/PA3B/PA5. The full-length cDNA of acidic PLA2 PA4 contains 483 nucleotides (nt), which encode 160 amino acids (and the stop codon), including a signal peptide, six cysteine residues that form disulfide bonds, and metal-binding and catalytic active sites. The gene sequence of the acidic PLA2 PA4 is 1667 base pairs (bp) long and encodes three exons and two introns. The 5' donor (GT) and 3' acceptor (AG) splice sites are highly conserved. The PLA2 PA3A/PA3B/PA5 gene contains 1366 bp, and the 498 nt of the mature mRNA encode 165 amino acids (and the stop codon). The protein includes a signal peptide, six cysteine residues that form disulfide bonds, and metal-binding and catalytic active sites. The three exons and two introns also have highly conserved donor and acceptor splice sites. InterProScan predicted PLA2 activity domains in both isoforms. These results extend our understanding of the PLA2 venom of the N. nomurai jellyfish and will facilitate further research.

Predicting function from sequence in a large multifunctional toxin family.

Venoms contain active substances with highly specific physiological effects and are increasingly being used as sources of novel diagnostic, research and treatment tools for human disease. Experimental characterisation of individual toxin activities is a severe rate-limiting step in the discovery process, and in-silico tools which allow function to be predicted from sequence information are essential. Toxins are typically members of large multifunctional families of structurally similar proteins that can have different biological activities, and minor sequence divergence can have significant consequences. Thus, existing predictive tools tend to have low accuracy. We investigated a classification model based on physico-chemical attributes that can easily be calculated from amino-acid sequences, using over 250 (mostly novel) viperid phospholipase A2 toxins. We also clustered proteins by sequence profiles, and carried out in-vitro tests for four major activities on a selection of isolated novel toxins, or crude venoms known to contain them. The majority of detected activities were consistent with predictions, in contrast to poor performance of a number of tested existing predictive methods. Our results provide a framework for comparison of active sites among different functional sub-groups of toxins that will allow a more targeted approach for identification of potential drug leads in the future.

Structural characteristics and evolution of the Protobothrops elegans pancreatic phospholipase A2 gene in contrast with those of Protobothrops genus venom phospholipase A2 genes.

The nucleotide sequence of the gene encoding Protobothrops elegans (Crotalinae) pancreatic phospholipase A(2) (PLA(2)), abbreviated PePancPLA(2), was determined by means of inverted PCR techniques. Since its deduced amino acid sequence contains a pancreatic loop and shows high similarity to that of Laticauda semifasciata (Elapinae) group IB pancreatic PLA(2), PePancPLA(2) is classified into group IB PLA(2). The nucleotide sequences of the PePancPLA(2) gene, the L. semifasciata group IB pancreatic PLA(2) gene, and the L. semifasciata group IA venom PLA(2) gene are similar to one another but greatly dissimilar to those of Protobothrops genus (Crotalinae) group II venom PLA(2) genes, suggesting that the Elapinae group IB PLA(2) gene and the group IA PLA(2) gene appeared after Elapinae was established, and that the Crotalinae group II venom PLA(2) genes came into existence before Elapinae and Crotalinae diverged. A phylogenetic analysis of their amino acid sequences confirms this.

Ovarian steroid regulation of endometrial phospholipase A2 isoforms in horses.

Real-time PCR was used to investigate the role of progesterone (P4) and oestradiol (E2) in regulation of endometrial cytosolic, secretory and calcium-independent phospholipase A2 (PLA2G4A, PLA2G2A and PLA2G6, respectively) gene expression. Ovariectomized mares underwent 6 days of E2 pre-treatment followed by 14 days of P4 supplementation. At the start of P4 treatment (Day 1), mares were assigned in a 2 × 2 factorial design to receive either E2 or vehicle starting on Day 11 and endometrial biopsy collection on either Day 14 when P4 concentrations remained high (>4 ng/ml) or Day 16 when P4 concentrations had declined (0.5-2 ng/ml). Additional biopsies were collected from ovariectomized mares on Day 8, which served as control. Blood samples were collected for P4 determination. PLA2G4A expression was higher (p < 0.05) on Day 14 compared with Day 8. In contrast, PLA2G2A did not change significantly (p < 0.12). PLA2G4A and PLA2G2A gene expression increased (p < 0.05), as P4 concentration dropped, on Day 16. In contrast, PLA2G6 gene expression did not show differences between days. Treatment with oestradiol did not increase PLA2 isoforms expression when compared to treatment with the vehicle. PLA2G4A and PLA2G2A were positively correlated with each other and negatively correlated with P4 concentrations. In conclusion, P4 withdrawal upregulated PLA2G4A and PLA2G2A gene expression, and this was not affected by E2. PLA2G4A and PLA2G2A but not PLA2G6 gene expression may be involved in controlling prostaglandin F2 alpha synthesis and luteolysis.

Plant phospholipases: an overview.

Plant phospholipases can be grouped into four major types, phospholipase D, phospholipase C, phospholipase A1 (PLA(1)), and phospholipase A2 (PLA(2)), that hydrolyze glycerophospholipids at different ester bonds. Within each type, there are different families or subfamilies of enzymes that can differ in substrate specificity, cofactor requirement, and/or reaction conditions. These differences provide insights into determining the cellular function of specific phospholipases in plants, and they can be explored for different industrial applications.

Conserved domains and evolution of secreted phospholipases A(2).

Secreted phospholipases A(2) (sPLA(2) s) are lipolytic enzymes present in organisms ranging from prokaryotes to eukaryotes but their origin and emergence are poorly understood. We identified and compared the conserved domains of 333 sPLA(2) s and proposed a model for their evolution. The conserved domains were grouped into seven categories according to the in silico annotated conserved domain collections of 'cd00618: PLA(2) _like' and 'pfam00068: Phospholip_A2_1'. PLA(2) s containing the conserved domain cd04706 (plant-specific PLA(2) ) are present in bacteria and plants. Metazoan PLA(2) s of the group (G) I/II/V/X PLA(2) collection exclusively contain the conserved domain cd00125. GIII PLA(2) s of both vertebrates and invertebrates contain the conserved domain cd04704 (bee venom-like PLA(2) ), and mammalian GIII PLA(2) s also contain the conserved domain cd04705 (similar to human GIII PLA(2) ). The sPLA(2) s of bacteria, fungi and marine invertebrates contain the conserved domain pfam09056 (prokaryotic PLA(2) ) that is the only conserved domain identified in fungal sPLA(2) s. Pfam06951 (GXII PLA(2) ) is present in bacteria and is widely distributed in eukaryotes. All conserved domains were present across mammalian sPLA(2) s, with the exception of cd04706 and pfam09056. Notably, no sPLA(2) s were found in Archaea. Phylogenetic analysis of sPLA(2) conserved domains reveals that two main clades, the cd- and the pfam-collection, exist, and that they have evolved via gene-duplication and gene-deletion events. These observations are consistent with the hypothesis that sPLA(2) s in eukaryotes shared common origins with two types of bacterial sPLA(2) s, and their persistence during evolution may be related to their role in phospholipid metabolism, which is fundamental for survival.

Phospholipase A2 superfamily members play divergent roles after spinal cord injury.

Spinal cord injury (SCI) results in permanent loss of motor functions. A significant aspect of the tissue damage and functional loss may be preventable as it occurs, secondary to the trauma. We show that the phospholipase A(2) (PLA(2)) superfamily plays important roles in SCI. PLA(2) enzymes hydrolyze membrane glycerophospholipids to yield a free fatty acid and lysophospholipid. Some free fatty acids (arachidonic acid) give rise to eicosanoids that promote inflammation, while some lysophospholipids (lysophosphatidylcholine) cause demyelination. We show in a mouse model of SCI that two cytosolic forms [calcium-dependent PLA(2) group IVA (cPLA(2) GIVA) and calcium-independent PLA(2) group VIA (iPLA(2) GVIA)], and a secreted form [secreted PLA(2) group IIA (sPLA(2) GIIA)] are up-regulated. Using selective inhibitors and null mice, we show that these PLA(2)s play differing roles. cPLA(2) GIVA mediates protection, whereas sPLA(2) GIIA and, to a lesser extent, iPLA(2) GVIA are detrimental. Furthermore, completely blocking all three PLA(2)s worsens outcome, while the most beneficial effects are seen by partial inhibition of all three. The partial inhibitor enhances expression of cPLA(2) and mediates its beneficial effects via the prostaglandin EP1 receptor. These findings indicate that drugs that inhibit detrimental forms of PLA(2) (sPLA(2) and iPLA2) and up-regulate the protective form (cPLA2) may be useful for the treatment of SCI.

Secreted phospholipase A2 revisited.

Phospholipase A(2) (PLA(2)) catalyses the hydrolysis of the sn-2 position of glycerophospholipids to yield fatty acids and lysophospholipids. So far, more than 30 enzymes that possess PLA(2) or related activity have been identified in mammals. About one third of these enzymes belong to the secreted PLA(2) (sPLA(2)) family, which comprises low molecular weight, Ca(2+) requiring, secreted enzymes with a His/Asp catalytic dyad. Individual sPLA(2)s display distinct localizations and enzymatic properties, suggesting their specialized biological roles. However, in contrast to intracellular PLA(2)s, whose roles in signal transduction and membrane homoeostasis have been well documented, the biological roles of sPLA(2)s in vivo have remained obscure until recently. Over the past decade, information fuelled by studies employing knockout and transgenic mice as well as specific inhibitors, in combination with lipidomics, has clarified when and where the different sPLA(2) isoforms are expressed, which isoforms are involved in what types of pathophysiology, and how they exhibit their specific functions. In this review, we highlight recent advances in PLA(2) research, focusing mainly on the physiological functions of sPLA(2)s and their modes of action on 'extracellular' phospholipid targets versus lipid mediator production.

Phospholipase A2 subclasses in acute respiratory distress syndrome.

Phospholipases A2 (PLA2) catalyse the cleavage of fatty acids esterified at the sn-2 position of glycerophospholipids. In acute lung injury-acute respiratory distress syndrome (ALI-ARDS) several distinct isoenzymes appear in lung cells and fluid. Some are capable to trigger molecular events leading to enhanced inflammation and lung damage and others have a role in lung surfactant recycling preserving lung function: Secreted forms (groups sPLA2-IIA, -V, -X) can directly hydrolyze surfactant phospholipids. Cytosolic PLA2 (cPLA2-IVA) requiring Ca2+ has a preference for arachidonate, the precursor of eicosanoids which participate in the inflammatory response in the lung. Ca(2+)-independent intracellular PLA2s (iPLA2) take part in surfactant phospholipids turnover within alveolar cells. Acidic Ca(2+)-independent PLA2 (aiPLA2), of lysosomal origin, has additionally antioxidant properties, (peroxiredoxin VI activity), and participates in the formation of dipalmitoyl-phosphatidylcholine in lung surfactant. PAF-AH degrades PAF, a potent mediator of inflammation, and oxidatively fragmented phospholipids but also leads to toxic metabolites. Therefore, the regulation of PLA2 isoforms could be a valuable approach for ARDS treatment.

A novel phospholipase A2 from Agkistrodon blomhoffii ussurensis venom: purification, proteomic, functional and structural characterizations.

A phospholipase A(2) was isolated from the snake venom of Chinese Agkistrodon blomhoffii Ussurensis by column chromatography using DEAE Sephadex A-50 ion-exchange chromatography, Sephadex G-75 gel filtration chromatography and Mono Q ion-exchange chromatography, and designated as Akbu-PLA(2). It showed an average molecular mass of 13,980+/-3 amu determined by MALDI TOF mass spectrometry. Protein identification results from HPLC-nESI-MS/MS analysis indicated that the Akbu-PLA(2) was a new snake venom acidic PLA(2). Seven peptides were sequenced from Akbu-PLA(2) by HPLC-nESI-MS/MS analysis. Sequencing alignment indicated that Akbu-PLA(2) shared homolog peptides of phospholipases A(2) from the venoms of Gloydius ussurensis, Gloydius halys, Gloydius halys (halys viper), Deinagkistrodon acutus and Agkistrodon halys Pallas. Akbu-PLA(2) has an optimum hydrolytic activity temperature of approximately 45 degrees C. The intrinsic fluorescences of Tyr and Trp residues of Akbu-PLA(2) showed emission wavelengths red-shifted by 13.6 and 1.6 nm from those of free Tyr and Trp, respectively. Akbu-PLA(2) was shown to contain one Ca(2+) per monomer by ICP-AES measurement. The Ca(2+) ion was found to be critical for both the hydrolytic activity and the structure of Akbu-PLA(2). Ca(2+) increased the emission fluorescence intensity and the hydrophobicity of the environment of Akbu-PLA(2). The hydrolytic activity of Akbu-PLA(2) was accelerated due to the addition of Ca(2+) ion by enhancing the substrate binding. However, a protein component with the molecular weight two-fold relative to that of Akbu-PLA(2) was found to be difficult to eliminate for the purification of Akbu-PLA(2). HPLC-nESI-MS/MS detected the same peptides from it as from Abku-PLA(2), which indicated that it should be a homodimer of Akbu-PLA(2). A proteomic approach, 2D SDS-PAGE coupled to HPLC-nESI-MS/MS, supported the co-existence of the Akbu-PLA(2) monomer and dimer in the crude snake venom. Results from the combination of phosphoprotein and glycoprotein specific stains combined with the HPLC-nESI-MS/MS method indicated that both the Akbu-PLA(2) monomer and dimer were both phosphorylated and glycosylated. The addition of exogenous Ca(2+) ion was found to be able to promote the dimer formation of Akbu-PLA(2). We conclude that a novel PLA(2) was successfully obtained. The systemically biochemical, proteomic, structural and functional characterization results from Akbu-PLA(2) reveal new threads and provide valuable inputs for the study of snake venom phospholipases A(2).

Signal-activated phospholipase regulation of leukocyte chemotaxis.

Signal-activated phospholipases are a recent focus of the rapidly growing field of lipid signaling. The extent of their impact on the pathways regulating diverse cell functions is beginning to be appreciated. A critical step in inflammation is the attraction of leukocytes to injured or diseased tissue. Chemotaxis of leukocytes, a requisite process for monocyte and neutrophil extravasation from the blood into tissues, is a critical step for initiating and maintaining inflammation in both acute and chronic settings. Recent studies have identified new important and required roles for two signal-activated phospholipases A2 (PLA2) in regulating chemotaxis. The two intracellular phospholipases, cPLA2alpha (Group IVA) and iPLA2beta (Group VIA), act in parallel to provide distinct lipid mediators at different intracellular sites that are both required for leukocytes to migrate toward the chemokine monocyte chemoattractant protein-1. This review will summarize the separate roles of these phospholipases as well as what is currently known about the influence of two other classes of intracellular signal-activated phospholipases, phospholipase C and phospholipase D, in regulating chemotaxis in eukaryotic cells, but particularly in human monocytes. The contributions of these phospholipases to chemotaxis both in vitro and in vivo will be highlighted.

Analysis of several PLA2 mRNA in human meningiomas.

In view of the important oncogenic action of phospholipase A(2)(PLA(2)) we investigated PLA(2) transcripts in human meningiomas. Real-time PCR was used to investigate PLA(2) transcripts in 26 human meningioma tumors. Results indicated that three Ca(2+)-dependent high molecular weight PLA(2) (PLA(2)-IVA, PLA(2)-IVB, PLA(2)-IVC), one Ca(2+)-independent high molecular weight PLA(2) (PLA(2)-VI) and five low molecular weight secreted forms of PLA(2) (PLA(2)-IB, PLA(2)-IIA, PLA(2)-III, PLA(2)-V, and PLA(2)-XII) are expressed with PLA(2)-IVA, PLA(2)-IVB, PLA(2)-VI, and PLA(2)-XIIA as the major expressed forms. PLA(2)-IIE, PLA(2)-IIF, PLA(2)-IVD, and PLA(2)-XIIB are not detected. Plasma (PLA(2)-VIIA) and intracellular (PLA(2)-VIIB) platelet-activating factor acetylhydrolase transcripts are expressed in human meningiomas. However no difference was found for PLA(2) transcript amounts in relation to the tumor grade, the subtype of meningiomas, the presence of inflammatory infiltrated cells, of an associated edema, mitosis, brain invasion, vascularisation or necrosis. In conclusion numerous genes encoding multiples forms of PLA(2) are expressed in meningiomas where they might act on the phospholipid remodeling and on the local eicosanoid and/or cytokine networks.

The emerging role of group VI calcium-independent phospholipase A2 in releasing docosahexaenoic acid from brain phospholipids.

Brain phospholipids are highly enriched in docosahexaenoic acid (DHA; 22:6n-3). Recent advances indicate that 22:6n-3 is released from brain phospholipids via the action of phospholipase A2 (PLA2) in response to several stimuli, including neurotransmission, where it then acts as a secondary messenger. Furthermore, it is now known that released 22:6n-3 is a substrate for several oxygenation enzymes whose products are potent signaling molecules. One emerging candidate PLA2 involved in the release of 22:6n-3 from brain phospholipids is the group VI calcium-independent phospholipase A2 (iPLA2). After a brief review of brain 22:6n-3 metabolism, cell culture and rodent studies facilitating the hypothesis that group VI iPLA2 releases 22:6n-3 from brain phospholipids are discussed. The identification of PLA2s involved in cleaving 22:6n-3 from brain phospholipids could lead to the development of novel therapeutics for brain disorders in which 22:6n-3 signaling is disordered.

The first phospholipase inhibitor from the serum of Vipera ammodytes ammodytes.

Ammodytoxins are neurotoxic secretory phospholipase A(2) molecules, some of the most toxic components of the long-nosed viper (Vipera ammodytes ammodytes) venom. Envenomation by this and by closely related vipers is quite frequent in southern parts of Europe and serotherapy is used in the most severe cases. Because of occasional complications, alternative medical treatment of envenomation is needed. In the present study, ammodytoxin inhibitor was purified from the serum of V. a. ammodytes using two affinity procedures and a gel exclusion chromatography step. The ammodytoxin inhibitor from V. a. ammodytes serum consists of 23- and 25-kDa glycoproteins that form an oligomer, probably a tetramer, of about 100 kDa. N-terminal sequencing and immunological analysis revealed that both types of subunit are very similar to gamma-type secretory phospholipase A(2) inhibitors. The ammodytoxin inhibitor from V. a. ammodytes serum is a potent inhibitor of phospholipase activity and hence probably also the neurotoxicity of ammodytoxins. Discovery of the novel natural inhibitor of these potent secretory phospholipase A(2) toxins opens up prospects for the development of new types of small peptide inhibitors for use in regulating the physiological and pathological activities of secretory phospholipases A(2).