Calcium-dependent Enzyme Research Articles

The Molecular Bases of Anti-Oxidative and Anti-Inflammatory Properties of Paraoxonase 1

The anti-oxidative and anti-inflammatory properties of high-density lipoprotein (HDL) are thought to be mediated by paraoxonase 1 (PON1), a calcium-dependent hydrolytic enzyme carried on a subfraction of HDL that also carries other anti-oxidative and anti-inflammatory proteins. In humans and mice, low PON1 activity is associated with elevated oxidized lipids and homocysteine (Hcy)-thiolactone, as well as proteins that are modified by these metabolites, which can cause oxidative stress and inflammation. PON1-dependent metabolic changes can lead to atherothrombotic cardiovascular disease, Alzheimer’s disease, and cancer. The molecular bases underlying these associations are not fully understood. Biochemical, proteomic, and metabolic studies have significantly expanded our understanding of the mechanisms by which low PON1 leads to disease and high PON1 is protective. The studies discussed in this review highlight the changes in gene expression affecting proteostasis as a cause of the pro-oxidative and pro-inflammatory phenotypes associated with attenuated PON1 activity. Accumulating evidence supports the conclusion that PON1 regulates the expression of anti-oxidative and anti-inflammatory proteins, and that the disruption of these processes leads to disease.

Beyond Inflammation: Role of Pyroptosis Pathway Activation by Gram-Negative Bacteria and Their Outer Membrane Vesicles (OMVs) in the Interaction with the Host Cell

Pyroptosis is a gasdermin-mediated pro-inflammatory programmed cell death that, during microbial infections, aims to restrict the spreading of bacteria. Nevertheless, excessive pyroptosis activation leads to inflammation levels that are detrimental to the host. Pathogen-associated molecular patterns (PAMPs) present in bacteria and outer membrane vesicles (OMVs) can trigger pyroptosis pathways in different cell types with different outcomes. Moreover, some pathogens have evolved virulence factors that directly interfere with pyroptosis pathways, like Yersinia pestis YopM and Shigella flexneri IpaH7.8. Other virulence factors, such as those of Neisseria meningitidis, Neisseria gonorrhoeae, Salmonella enterica, and Helicobacter pylori affect pyroptosis pathways indirectly with important differences between pathogenic and commensal species of the same family. These pathogens deserve special attention because of the increasing antimicrobial resistance of S. flexneri and N. gonorrhoeae, the high prevalence of S. enterica and H. pylori, and the life-threatening diseases caused by N. meningitidis and Y. pestis. While inflammation due to macrophage pyroptosis has been extensively addressed, the effects of activation of pyroptosis pathways on modulation of cell cytoskeleton and cell–cell junctions in epithelia and endothelia and on the bacterial crossing of epithelial and endothelial barriers have only been partly investigated. Another important point is the diverse consequences of pyroptosis pathways on calcium influx, like activation of calcium-dependent enzymes and mitochondria dysregulation. This review will discuss the pyroptotic pathways activated by Gram-negative bacteria and their OMVs, analyzing the differences between pathogens and commensal bacteria. Particular attention will also be paid to the experimental models adopted and the main results obtained in the different models. Finally, strategies adopted by pathogens to modulate these pathways will be discussed with a perspective on the use of pyroptosis inhibitors as adjuvants in the treatment of infections.

Harnessing marine natural products to inhibit PAD4 triple mutant: A structure-based virtual screening approach for rheumatoid arthritis therapy

Peptidylarginine deiminase type4 (PAD4) is a pivotal pro-inflammatory protein within the human immune system, intricately involved in both inflammatory processes and immune responses. Its role extends to the generation of diverse immune cell types, including T cells, B cells, natural killer cells, and dendritic cells. PAD4 has recently garnered attention due to its association with a spectrum of inflammatory and autoimmune disorders, notably rheumatoid arthritis (RA). Mutations in the PAD4 gene, leading to the conversion of arginine to citrulline, have emerged as significant factors in the pathogenesis of RA and related conditions. As a calcium-dependent enzyme, PAD4 is central to the citrullination process, a crucial post-translational modification implicated in disease pathophysiology. Its critical role in autoimmune disorders and inflammation makes PAD4 a prime candidate for therapeutic intervention in RA. Inhibiting PAD4 presents a promising avenue for mitigating inflammatory responses and curtailing joint degradation and impairment. To explore its therapeutic potential, a structure-based virtual screening (SBVS) approach was employed, harnessing an array of marine natural products (MNPs) sourced from databases such as CMNPD, MNPD, and Seaweed. Notably, MNPD10752, CMNPD12680, and CMNPD2751 emerged as potential hit molecules, exhibiting adherence to essential pharmacokinetic properties and favorable toxicity profiles. Quantum mechanics studies using density functional theory (DFT) calculations revealed the inhibitory potential of these identified natural products. Further structural elucidation through molecular dynamics simulations (MDS) and principal component-based free energy landscape (FEL) analysis shed light on the stability of MNP-bound PAD4 complexes. In conclusion, this computational study serves as a stepping stone for further experimental evaluation, aiming to explore the potential of MNPs in addressing PAD4-related human pathologies.

NETosis Drives Blood Pressure Elevation and Vascular Dysfunction in Hypertension.

Neutrophil extracellular traps (NETs) are composed of DNA, enzymes, and citrullinated histones that are expelled by neutrophils in the process of NETosis. NETs accumulate in the aorta and kidneys in hypertension. PAD4 (protein-arginine deiminase-4) is a calcium-dependent enzyme that is essential for NETosis. TRPV4 (transient receptor potential cation channel subfamily V member 4) is a mechanosensitive calcium channel expressed in neutrophils. Thus, we hypothesize that NETosis contributes to hypertension via NET-mediated endothelial cell (EC) dysfunction. NETosis-deficient Padi4-/- mice were treated with Ang II (angiotensin II). Blood pressure was measured by radiotelemetry, and vascular reactivity was measured with wire myography. Neutrophils were cultured with or without ECs and exposed to normotensive or hypertensive uniaxial stretch. NETosis was measured by flow cytometry. ECs were treated with citrullinated histone H3, and gene expression was measured by quantitative reverse transcription PCR. Aortic rings were incubated with citrullinated histone H3, and wire myography was performed to evaluate EC function. Neutrophils were treated with the TRPV4 agonist GSK1016790A. Calcium influx was measured using Fluo-4 dye, and NETosis was measured by immunofluorescence. Padi4-/- mice exhibited attenuated hypertension, reduced aortic inflammation, and improved EC-dependent vascular relaxation in response to Ang II. Coculture of neutrophils with ECs and exposure to hypertensive uniaxial stretch increased NETosis and accumulation of neutrophil citrullinated histone H3. Histone H3 and citrullinated histone H3 exposure attenuates EC-dependent vascular relaxation. Treatment of neutrophils with the TRPV4 agonist GSK1016790A increases intracellular calcium and NETosis. These observations identify a role of NETosis in the pathogenesis of hypertension. Moreover, they define an important role of EC stretch and TRPV4 as initiators of NETosis. Finally, they define a role of citrullinated histones as drivers of EC dysfunction in hypertension.

Citrullination profile analysis reveals peptidylarginine deaminase 3 as an HSV-1 target to dampen the activity of candidate antiviral restriction factors.

Herpes simplex virus 1 (HSV-1) is a neurotropic virus that remains latent in neuronal cell bodies but reactivates throughout an individual's life, causing severe adverse reactions, such as herpes simplex encephalitis (HSE). Recently, it has also been implicated in the etiology of Alzheimer's disease (AD). The absence of an effective vaccine and the emergence of numerous drug-resistant variants have called for the development of new antiviral agents that can tackle HSV-1 infection. Host-targeting antivirals (HTAs) have recently emerged as promising antiviral compounds that act on host-cell factors essential for viral replication. Here we show that a new class of HTAs targeting peptidylarginine deiminases (PADs), a family of calcium-dependent enzymes catalyzing protein citrullination, exhibits a marked inhibitory activity against HSV-1. Furthermore, we show that HSV-1 infection leads to enhanced protein citrullination through transcriptional activation of three PAD isoforms: PAD2, PAD3, and PAD4. Interestingly, PAD3-depletion by specific drugs or siRNAs dramatically inhibits HSV-1 replication. Finally, an analysis of the citrullinome reveals significant changes in the deimination levels of both cellular and viral proteins, with the interferon (IFN)-inducible proteins IFIT1 and IFIT2 being among the most heavily deiminated ones. As genetic depletion of IFIT1 and IFIT2 strongly enhances HSV-1 growth, we propose that viral-induced citrullination of IFIT1 and 2 is a highly efficient HSV-1 evasion mechanism from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection and demonstrate that PAD inhibitors efficiently suppress HSV-1 infection in vitro, which may provide the rationale for their repurposing as HSV-1 antiviral drugs.

High-Affinity Fluorogenic Substrate for Tissue Transglutaminase Reveals Enzymatic Hysteresis.

Transglutaminases (TGases) are a family of calcium-dependent enzymes primarily known for their ability to cross-link proteins. Transglutaminase 2 (TG2) is one isozyme in this family whose role is multifaceted. TG2 can act not only as a typical transamidase through its catalytic core but also as a G-protein via its GTP binding site. These two discrete activities are tightly regulated by both environmental stimuli and redox reactions. Ubiquitously expressed in humans, TG2 has been implicated in numerous disease pathologies that require extensive investigation. The catalytic activity of TG2 can be monitored through various mechanisms, including hydrolysis, transamidation, or cleavage of isopeptide bonds. Activity assays are required to monitor the activity of this isozyme not only for studying its transamidation reaction but also for validation of therapeutics designed to abolish this activity. Herein, we present the design, synthesis, and evaluation of a new TG2 activity substrate based on a previously optimized inhibitor scaffold. The substrate APH7 exhibits excellent affinity, selectivity, and reactivity with TG2 (KM = 3.0 μM). Furthermore, its application also allowed the discovery of unique hysteresis at play within the catalytic activity and inhibition reactivity of TG2.

Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3

Transglutaminase 3 (TG3), the autoantigen of dermatitis herpetiformis (DH), is a calcium dependent enzyme that targets glutamine residues in polypeptides for either transamidation or deamidation modifications. To become catalytically active TG3 requires proteolytic cleavage between the core domain and two C-terminal β-barrels (C1C2). Here, we report four X-ray crystal structures representing inactive and active conformations of human TG3 in complex with a TG3-specific Fab fragment of a DH patient derived antibody. We demonstrate that cleaved TG3, upon binding of a substrate-mimicking inhibitor, undergoes a large conformational change as a β-sheet in the catalytic core domain moves and C1C2 detaches. The unique enzyme-substrate conformation of TG3 without C1C2 is recognized by DH autoantibodies. The findings support a model where B-cell receptors of TG3-specific B cells bind and internalize TG3-gluten enzyme-substrate complexes thereby facilitating gluten-antigen presentation, T-cell help and autoantibody production.

Abstract 1256: Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma

Abstract Cutaneous melanoma is the most fatal skin cancer; resistance to targeted therapies contributes to poor prognosis. In some cases, resistance arises from pre-existing tumor heterogeneity, which allows subpopulations of drug-tolerant cells with distinct transcriptional states to survive in the presence of drug. The loss of SOX10, a lineage-specific transcription factor, is known to drive melanoma phenotype switching from a proliferative to an invasive drug-tolerant state. Here, we found that knocking out SOX10 in human and mouse melanoma cell lines leads to the upregulation of transglutaminase-2 (TGM2), a calcium-dependent cross-linking enzyme. Analysis of publicly available bulk and single-cell RNA-sequencing data showed that TGM2 is highly expressed in the invasive cell state in melanoma cell lines and patient-derived melanoma cultures, respectively. Furthermore, knockdown of SOX10 in patient-derived melanoma cultures increases TGM2 mRNA expression. 3D spheroid assays and extracellular matrix production/remodeling assays showed that knockdown of TGM2 has no effect on the invasiveness of SOX10-deficient cells. However, we found that TGM2 is secreted by SOX10-deficient cells and hypothesized that it could modulate the tumor immune microenvironment (TIME) given that TGM2 has been associated with increased immune infiltration in melanoma patient samples. To investigate the effect of TGM2 on the TIME, we stably overexpressed TGM2/Tgm2 in syngeneic mouse melanoma cell lines and allowed tumors to grow in immune-competent C57BL/6 mice. As compared to empty vector, TGM2/Tgm2-overexpression led to an increase in the percentage and number of CD4+ T cells and B cells, and a decrease in the number of myeloid cells, in the tumor immune compartment by flow cytometry analysis. Future studies will assess which subsets of CD4+ T cells and B cells infiltrate TGM2/Tgm2-overexpressing tumors, how these changes to the TIME affect melanoma invasiveness, and if TGM2 expression affects response to targeted therapy in vivo. Overall, our data suggest that TGM2 is highly expressed in the invasive melanoma cell state, is regulated by the SOX10 transcription factor, and can modulate adaptive immune cells in the TIME. Citation Format: Signe Caksa, Nicole A. Wilski, Erica L. Kitterman, McKenna Q. Glasheen, Jacob S. Heilizer, Timothy J. Purwin, Claudia Capparelli, Andrew E. Aplin. Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1256.

Cinnamic acid derivatives as potential matrix metalloproteinase-9 inhibitors: molecular docking and dynamics simulations.

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer's disease, autoimmune diseases, cardiovascular diseases, and dental caries. Therefore, MMP-9 inhibition is recommended as a therapeutic strategy for combating various diseases. Cinnamic acid derivatives have shown therapeutic effects in different cancers, Alzheimer's disease, cardiovascular diseases, and dental caries. A computational drug discovery approach was performed to evaluate the binding affinity of selected cinnamic acid derivatives to the MMP-9 active site. The stability of docked poses for top-ranked compounds was also examined. Twelve herbal cinnamic acid derivatives were tested for possible MMP-9 inhibition using the AutoDock 4.0 tool. The stability of the docked poses for the most potent MMP-9 inhibitors was assessed by molecular dynamics (MD) in 10 nanosecond simulations. Interactions between the best MMP-9 inhibitors in this study and residues incorporated in the MMP-9 active site were studied before and after MD simulations. Cynarin, chlorogenic acid, and rosmarinic acid revealed a considerable binding affinity to the MMP-9 catalytic domain (ΔGbinding < -10 kcal/ mol). The inhibition constant value for cynarin and chlorogenic acid were calculated at the picomolar scale and assigned as the most potent MMP-9 inhibitor from the cinnamic acid derivatives. The root-mean-square deviations for cynarin and chlorogenic acid were below 2 Å in the 10 ns simulation. Cynarin, chlorogenic acid, and rosmarinic acid might be considered drug candidates for MMP-9 inhibition.

18F-labeling and initial in vivo evaluation of a Hitomi peptide for imaging tissue transglutaminase 2

IntroductionTissue transglutaminase 2 (TG2) is a calcium-dependent enzyme which cross-links proteins. It is overexpressed in many diseases and plays a key role in tissue remodeling, including cell adhesion and migration. Overexpression of TG2 in breast cancer is a marker for patients at risk of recurrence. Non-invasive imaging of TG2 can therefore play an important role in patient management. TG2 probes labeled with the positron emitters 11C and 18F have thus far not found widespread application due to purity and metabolism issues. Our approach was to radiolabel a TG2 selective, 13-mer amino acid peptide, which was modified with a 5-azidopentanoic acid group at the N-terminus via a copper free click chemistry approach. MethodsRadiochemistry was performed and fully automated using an iPhase FlexLab module. We produced the radiolabeling synthon [18F]FBz-DBCO from [18F]SFB and DBCO-amine. After HPLC purification, [18F]FBz-DBCO was reacted with the modified peptide and the putative radiotracer purified by HPLC.In vivo imaging using the radiolabeled amine was performed in mice bearing either TG2 expressing MDA-MB-231 or non-TG2 expressing MCF-7 xenografts as negative control. Expression of the target was confirmed using immunohistochemistry and western blot techniques. ResultsWe obtained 9 ± 2 GBq of the radiolabeled peptide from 55 ± 5 GBq of fluorine-18 in an overall synthesis time of 160 min from end of bombardment (EOB), including HPLC purification and reformulation.Small animal PET/MR imaging showed that visualization of MDA-MB-231 tumors using the radiolabeled peptide could only be achieved due to differences in clearance between tumor and surrounding tissue. In the MCF-7 xenograft model, radiotracer clearance from tumor and surrounding tissue occurred at a similar rate, thus making it impossible to visualize MCF-7 tumors. The presence of TG2 in MDA-MB-231 tumors and absence in MCF-7 tumors was confirmed by immunohistochemistry staining and western blot analysis. ConclusionA fully automated synthesis of a TG2 selective, 13-amino-acid peptide modified with 5-azido pentynoic acid at the N-terminal was established using [18F]FBzDBCO as a prosthetic group.Although our results show that radiolabeled peptides have potential as imaging agents for TG2, more research needs to be performed to improve radiotracer kinetics.

Intracellular Calcium Localization Mediates the Activity of Venetoclax in Targeting Acute Myeloid Leukemia Stem Cells

Venetoclax (BCL2 inhibitor) based regimens have significantly improved outcomes for elderly patients with acute myeloid leukemia (AML). While most patients initially respond to venetoclax-based regimens, upfront resistance or relapse on therapy occurs in many. Therefore, elucidating the mechanistic link between BCL2 inhibition and AML cell death is crucial to finding novel therapeutic strategies to combat venetoclax resistance and to discover predictors of venetoclax response. Previous studies have shown BCL2 has a non-canonical function in modulating oxidative phosphorylation (OXPHOS) activity of AML stem cells (LSCs). However, the mechanistic link between BCL2 and OXPHOS has not yet been established. BCL2 has been shown to regulate intracellular calcium localization by modulating the activity of calcium channels at the ER and mitochondria. Optimal mitochondrial calcium concentrations are crucial for cell metabolism as calcium overload or decrease can inhibit OXPHOS activity. In preliminary studies, we established venetoclax increases mitochondrial calcium levels (Fig. 1A) leading to a subsequent decrease in OXPHOS activity and changes in the activity of key calcium dependent TCA cycle enzymes in primary human AML LSCs. Genetic inhibition of BCL2 in LSCs phenocopied the effects of venetoclax treatment. Based on these data, we hypothesized that BCL2 exerts its effect on LSC metabolism by modulating calcium localization between the ER and mitochondria. Furthermore, we sought to explore whether dysregulation of calcium localization by venetoclax is a mechanistic component of drug activity that leads to suppression of OXPHOS. To determine how BCL2 may be influencing mitochondrial calcium levels, we assessed the relationship between BCL2 and SERCA3, a key ion channel responsible for calcium uptake into the ER. Venetoclax disrupted the physical interaction between BCL2 and SERCA3. Mechanistically, venetoclax perturbed this interaction by decreasing SERCA3 protein levels. These findings were recapitulated by genetic inhibition of BCL2 in LSCs. Functional analysis of SERCA3 via siRNA-mediated knock-down in primary AML specimens demonstrated increased mitochondrial calcium levels, decreased OXPHOS activity and decreased engraftment of immune deficient NSG-S mice. Based on these data, we propose a model in which venetoclax disrupts SERCA function leading to less calcium uptake at the ER and more calcium sequestered into the mitochondria leading to overload, decreased OXPHOS activity and decreased LSC function. Next, we evaluated how calcium pathways were impacted in venetoclax resistant AML patient specimens. Intriguingly, venetoclax did not affect mitochondrial calcium levels (Fig. 1B) or the relationship between BCL2 and SERCA3. Therefore, we tested whether inhibiting the activity of MCU, the channel responsible for calcium uptake into the mitochondrial matrix, would target venetoclax resistant LSCs as it was overexpressed in this population. MCU inhibition led to decreased mitochondrial calcium levels, decreased OXPHOS activity and decreased LSC engraftment. These data indicate that venetoclax-resistant AML cells are no longer subject to changes in calcium localization induced by drug treatment but do retain an overall reliance on calcium regulation for LSC function/survival. Finally, we assessed whether our findings could be leveraged to predict venetoclax sensitivity. Analysis of single cell RNA-seq data from venetoclax sensitive versus resistant AML patient specimens (n=19) revealed multiple calcium pathway gene sets were enriched in venetoclax resistant LSCs. Additionally, levels of certain genes including SERCA3 and MCU were differentially expressed in primitive versus monocytic clusters between sensitive and resistant specimens. Taken together, our data demonstrate an unexpected and critical link between BCL2 and calcium signaling in human LSCs. A surprising aspect of our work is that venetoclax, a BH3 mimetic, acts to modulate the interaction with SERCA3. Lastly, our findings suggest that targeting intracellular calcium dynamics may represent a novel therapeutic strategy in the context of venetoclax resistant AML. In addition, we show that there are significant differences in calcium gene signatures between venetoclax sensitive vs resistant AML specimens that may be useful in predicting patient response to venetoclax based regimens. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Molecular characterization of transesterification activity of novel lipase family I.1.

Lipase’s thermostability and organic solvent tolerance are two crucial properties that enable it to function as a biocatalyst. The present study examined the characteristics of two recombinant thermostable lipases (Lk2, Lk3) based on transesterification activity. Conversion of C12-C18 methyl ester with paranitrophenol was investigated in various organic solvent. Both lipases exhibited activity on difference carbon chain length (C12 - C18, C18:1, C18:2) of substrates. The activity of Lk2 was higher in each of substrate compared with that of Lk3. Experimental findings showed that the best substrates for Lk2 and Lk3 are C18:1 and C18:2 respectively, in agreement with the computational analysis. The activity of both enzymes prefers on nonpolar solvent. On nonpolar solvent the enzymes are able to keep its native folding shown by the value of radius gyration, solvent–enzyme interaction and orientation of triad catalytic residues. Lk3 appeared to be more thermostable, with maximum activity at 55°C. The presence of Fe3+ increased the activity of Lk2 and Lk3. However, the activity of both enzymes were dramatically decreased by the present of Ca2+ despite of the enzymes belong to family I.1 lipase known as calcium dependent enzyme. Molecular analysis on His loop of Lk2 and Lk3 on the present of Ca2+ showed that there were shifting on the orientation of catalytic triad residues. All the data suggest that Lk2 and Lk3 are novel lipase on the family I.1 and both lipase available as a biocatalyst candidate.

Identification of Novel GTP Analogs as Potent and Specific Reversible Inhibitors for Transglutaminase 2

ABSTRACT Transglutaminase 2 (TG2) is a calcium-dependent enzyme that catalyzes the N-ϵ-(γ-glutamyl) lysine bonds between side chains of glutamine and lysine residues resulting in proteolytically resistant cross-links. Increased TG2 activity and levels are involved in the pathophysiology of various diseases, including liver injury, cystic fibrosis, celiac sprue, metastatic cancers, and several neurodegenerative conditions. Inhibiting TG2 activity is considered a potential strategy to combat these diseases. Although guanine nucleotide (GTP) could inhibit TG2, its inhibitory activity decreased with increased calcium concentration. Search for GTP analogs that could strongly bind and inhibit TG2 activity is intense. This study screened the PubChem database for about two thousand GTP-like compounds for TG2. Using docking and molecular dynamics simulations we identified three compounds (C4959, C4215, and C9560) that could selectively interact with TG2. These three compounds have less affinity for several other intracellular and extracellular GTP-binding proteins suggesting selectivity for TG2. Interestingly, C9560 showed stronger interactions and better binding energy with TG2 than C4959 and C4215, suggesting that C9560 can form a more stable complex with TG2. Our study indicates that C9560, a GTP analog, could be exploited as a promising candidate to inhibit TG2-mediated fibrotic conditions.

Enhancement in the production of recombinant human paraoxonase 1 in Escherichia coli: A comprehensive approach of cellular engineering and optimization of protein folding process in vitro

Human paraoxonase 1(hPON1) belongs to the paraoxonase (PON) family. It is a calcium-dependent enzyme with a size of ∼43 kDa and is composed of 6 bladed beta-barrel structures with two calcium ions in its active site. In humans, it is synthesized in the liver and remains bound with the high-density lipoproteins (HDL) within the blood. It has immense potential to tackle the poisoning associated with the use of organophosphates (OPs) and their derivatives, such as nerve agents, due to role in their degradation. Therefore, hPON1 serves as a potential bio-scavenger that can be used as an antidote or as a surface decontaminating agent in OPs poisoning. However, present systems prove insufficient to produce it in sufficient quantity to make it industrially relevant. Here, our efforts involve producing it recombinantly in an E. coli system with enhanced expression levels by altering cellular and environmental conditions. This has been further improved by the development of in-vitro refolding process for the denatured recombinant hPON1 (rhPON1) protein. This methodology resulted in approximately 200 mg of the enzymatically functional protein from 1 l of E. coli culture. Proper refolding of rhPON1 was confirmed by comparing its enzymatic activity and conformation with serum purified hPON1.

Insights into peptidylarginine deiminase expression and citrullination pathways.

Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate citrullination, an irreversible post-translational modification (PTM). PAD enzymes have received increasing attention in (patho-)physiology since multi-omics analysis accelerated their expression profiling. Here, we provide a comprehensive overview of PAD expression at the RNA and protein levels, and a list of annotated substrates per PAD isozyme. We discuss novel roles of citrullination in cellular growth, epigenetic regulation, tissue remodeling, inflammation, and cancer in mouse models and humans. Additionally, we cluster similar effects of protein deimination to offer a different perspective and improve our understanding of citrullination in health and disease. Citrullination should no longer be considered as a rare PTM, but as an important regulatory mechanism in physiology and pathology.

A Pilot Study on Peptidylarginine Deiminases and Protein Deimination in Animal Cancers across Vertebrate Species.

PADs are a group of calcium-dependent enzymes that play key roles in inflammatory pathologies and have diverse roles in cancers. PADs cause irreversible post-translational modification of arginine to citrulline, leading to changes in protein function in different cellular compartments. PAD isozyme diversity differs throughout phylogeny in chordates, with five PAD isozymes in mammals, three in birds, and one in fish. While the roles for PADs in various human cancers are mounting (both in regards to cancer progression and epigenetic regulation), investigations into animal cancers are scarce. The current pilot-study therefore aimed at assessing PAD isozymes in a range of animal cancers across the phylogeny tree. In addition, the tissue samples were assessed for total protein deimination and histone H3 deimination (CitH3), which is strongly associated with human cancers and also indicative of gene regulatory changes and neutrophil extracellular trap formation (NETosis). Cancers were selected from a range of vertebrate species: horse, cow, reindeer, sheep, pig, dog, cat, rabbit, mink, hamster, parrot, and duck. The cancers chosen included lymphoma, kidney, lung, testicular, neuroendocrine, anaplastic, papilloma, and granulosa cell tumour. Immunohistochemical analysis revealed that CitH3 was strongly detected in all of the cancers assessed, while pan-deimination detection was overall low. Both PAD2 and PAD3 were the most predominantly expressed PADs across all of the cancers assessed, while PAD1, PAD4, and PAD6 were overall expressed at lower, albeit varying, levels. The findings from this pilot study provide novel insights into PAD-mediated roles in different cancers across a range of vertebrate species and may aid in the understanding of cancer heterogeneity and cancer evolution.

Biological evaluation and in silico study of benzohydrazide derivatives as paraoxonase 1 inhibitors.

Serum paraoxonase 1 (PON1) is found in all mammalian species and is a calcium-dependent hydrolytic enzyme. PON1 hydrolyze several substrates, including carbonates, esters, and organophosphates. In the current study, we aimed to investigate the effect of the presynthesized benzohydrazide derivatives (1-9) on PON1 activity. Benzohydrazide compounds moderate inhibited PON1 with thehalf-maximal inhibitory concentration values ranging from 76.04 ± 13.51 to 221.70 ± 13.59 μM and KI values ranging from 38.75 ± 12.21 to 543.50 ± 69.76 μM. Compound 4 (2-amino-4-chlorobenzohydrazide) showed the best inhibition (KI = 38.75 ± 12.21 μM). Molecular docking and ADME-Tox studies of benzohydrazide derivatives were also carried out. In this context, we hope that the results obtained in this study contribute to the determination of the side effects of current and new benzohydrazide-based pharmacological compounds to be developed.

Plant Transglutaminases: New Insights in Biochemistry, Genetics, and Physiology.

Transglutaminases (TGases) are calcium-dependent enzymes that catalyse an acyl-transfer reaction between primary amino groups and protein-bound Gln residues. They are widely distributed in nature, being found in vertebrates, invertebrates, microorganisms, and plants. TGases and their functionality have been less studied in plants than humans and animals. TGases are distributed in all plant organs, such as leaves, tubers, roots, flowers, buds, pollen, and various cell compartments, including chloroplasts, the cytoplasm, and the cell wall. Recent molecular, physiological, and biochemical evidence pointing to the role of TGases in plant biology and the mechanisms in which they are involved allows us to consider their role in processes such as photosynthesis, plant fertilisation, responses to biotic and abiotic stresses, and leaf senescence. In the present paper, an in-depth description of the biochemical characteristics and a bioinformatics comparison of plant TGases is provided. We also present the phylogenetic relationship, gene structure, and sequence alignment of TGase proteins in various plant species, not described elsewhere. Currently, our knowledge of these proteins in plants is still insufficient. Further research with the aim of identifying and describing the regulatory components of these enzymes and the processes regulated by them is needed.

Novel antiviral activity of PAD inhibitors against human beta-coronaviruses HCoV-OC43 and SARS-CoV-2

The current SARS-CoV-2 pandemic, along with the likelihood that new coronavirus strains will appear in the nearby future, highlights the urgent need to develop new effective antiviral agents. In this scenario, emerging host-targeting antivirals (HTAs), which act on host-cell factors essential for viral replication, are a promising class of antiviral compounds. Here we show that a new class of HTAs targeting peptidylarginine deiminases (PADs), a family of calcium-dependent enzymes catalyzing protein citrullination, is endowed with a potent inhibitory activity against human beta-coronaviruses (HCoVs). Specifically, we show that infection of human fetal lung fibroblasts with HCoV-OC43 leads to enhanced protein citrullination through transcriptional activation of PAD4, and that inhibition of PAD4-mediated citrullination with either of the two pan-PAD inhibitors Cl-A and BB-Cl or the PAD4-specific inhibitor GSK199 curbs HCoV-OC43 replication. Furthermore, we show that either Cl-A or BB-Cl treatment of African green monkey kidney Vero-E6 cells, a widely used cell system to study beta-CoV replication, potently suppresses HCoV-OC43 and SARS-CoV-2 replication. Overall, our results demonstrate the potential efficacy of PAD inhibitors, in suppressing HCoV infection, which may provide the rationale for the repurposing of this class of inhibitors for the treatment of COVID-19 patients.

A highly alkaline pectate lyase from the Himalayan hot spring metagenome and its bioscouring applications

From the vast enzymatic weaponry encrypted in the metagenomic resource of the Himalayan hot spring, a novel gene encoding pectate lyase (eplM) was identified. Mapping against the nucleotide non-redundant NCBI database could not reveal any match for this gene sequence. At the protein level, it was about 56.86% identical to an uncharacterized sequence from Rheinheimera tangshanensis. The novel gene, eplM, was cloned and expressed in a heterologous host, Escherichia coli. The purified protein, EPLM, was biochemically characterized for pectate lyase activity towards pectin. It exhibited the maximum activity in the alkaline pH range, with optimum activity at 11.0 pH (1524.10 U/mg). The enzyme was functional in the temperature range of 30–50 °C, with the optimum activity at 40 °C. EPLM was found to be a calcium-dependent enzyme that can efficiently act on the methylated pectin obtained from a diverse source of plant biomass. The catalytic utility of EPLM was tested by demonstrating bioscouring of banana pseudostem biomass. The micrographic changes in surface structures of the fibers and release of unsaturated galacturonides endorsed EPLM as a promising biocatalyst for pectin-removal processing applications.