Expression of nitric oxide related enzymes in coronary heart disease

Biochemistry, pharmacology, and in vivo function of arginases

The enzyme arginase catalyzes the hydrolysis of l-arginine into l-ornithine and urea. The 2 existing isoforms Arg1 and Arg2 exhibit different cellular localizations and metabolic functions. Arginase activity is crucial for nitrogen detoxification in the urea cycle, synthesis of polyamines, and control of l-arginine bioavailability and nitric oxide (NO) production. Despite significant progress in the understanding of the biochemistry and function of arginases, several open questions remain. Recent studies have revealed that the regulation and function of Arg1 and Arg2 are cell type-specific, species-specific, and profoundly different in mice and humans. The main differences are in the distribution and function of Arg1 and Arg2 in immune and erythroid cells. Contrary to what was previously thought, Arg1 activity appears to be only partially related to vascular NO signaling under homeostatic conditions in the vascular wall, but its expression is increased under disease conditions and may be targeted by treatment with arginase inhibitors. Arg2 appears to be mainly a catabolic enzyme involved in the synthesis of l-ornithine, polyamine, and l-proline but may play a putative role in blood pressure control, at least in mice. The immunosuppressive role of arginase-mediated arginine depletion is a promising target for cancer treatment. This review critically revises and discusses the biochemistry, pharmacology, and in vivo function of arginases, focusing on the insights gained from the analysis of cell-specific Arg1 and Arg2 knockout mice and human studies using arginase inhibitors or pegylated recombinant arginase. SIGNIFICANCE STATEMENT: Further basic and translational research is needed to deepen our understanding of the regulation of Arg1 and Arg2 in different cell types in consideration of their localization, species-specificity, and multiple biochemical and physiological roles. This will lead to better pharmacological strategies to target arginase activity in liver, cardiovascular, hematological, immune/infectious diseases, and cancer.

Maternal folic acid over-supplementation impairs cardiac function in mice offspring by inhibiting SOD1 expression

AIMS

Folic acid (FA) supplementation during pregnancy aims to protect foetal development. However, maternal over-supplementation of FA has been demonstrated to cause metabolic dysfunction and increase the risk of autism, retinoblastoma, and respiratory illness in the offspring. Moreover, FA supplementation reduces the risk of congenital heart disease. However, little is known about its possible adverse effects on cardiac health resulting from maternal over-supplementation. In this study, we assessed the detrimental effects of maternal FA over-supplementation on the cardiac health of the offspring.

METHODS AND RESULTS

Eight-week-old C57BL/6J pregnant mice were randomly divided into control and over-supplemented groups. The offspring cardiac function was assessed using echocardiography. Cardiac fibrosis was assessed in the left ventricular myocardium by histological analysis. Proteomic, protein, RNA, and DNA methylation analyses were performed by liquid chromatography-tandem mass spectrometry, western blotting, real-time quantitative PCR, and bisulfite sequencing, respectively. We found that maternal periconceptional FA over-supplementation impaired cardiac function with the decreased left ventricular ejection fraction in the offspring. Biochemical indices and tissue staining further confirmed impaired cardiac function in offspring caused by maternal FA over-supplementation. The combined proteomic, RNA expression, and DNA methylation analyses suggested that key genes involved in cardiac function were inhibited at the transcriptional level possibly due to increased DNA methylation. Among these, superoxide dismutase 1 was down-regulated, and reactive oxygen species (ROS) levels increased in the mouse heart. Inhibition of ROS generation using the antioxidant N-acetylcysteine rescued the impaired cardiac function resulting from maternal FA over-supplementation.

CONCLUSIONS

Our study revealed that over-supplementation with FA during mouse pregnancy is detrimental to cardiac function with the decreased left ventricular ejection fraction in the offspring and provides insights into the mechanisms underlying the association between maternal FA status and health outcomes in the offspring.

DeepPRMS: advanced deep learning model to predict protein arginine methylation sites

Protein methylation is a form of post-translational modifications of protein, which is crucial for various cellular processes, including transcription activity and DNA repair. Correctly predicting protein methylation sites is fundamental for research and drug discovery. Some experimental techniques, such as methyl-specific antibodies, chromatin immune precipitation and mass spectrometry, exist for predicting protein methylation sites, but these techniques are time-consuming and costly. The ability to predict methylation sites using in silico techniques may help researchers identify potential candidate sites for future examination and make it easier to carry out site-specific investigations and downstream characterizations. In this research, we proposed a novel deep learning-based predictor, named DeepPRMS, to identify protein methylation sites in primary sequences. The DeepPRMS utilizes the gated recurrent unit (GRU) and convolutional neural network (CNN) algorithms to extract the sequential and spatial information from the primary sequences. GRU is used to extract sequential information, while CNN is used for spatial information. We combined the latent representation of GRU and CNN models to have a better interaction among them. Based on the independent test data set, DeepPRMS obtained an accuracy of 85.32%, a specificity of 84.94%, Matthew's correlation coefficient of 0.71 and a sensitivity of 85.80%. The results indicate that DeepPRMS can predict protein methylation sites with high accuracy and outperform the state-of-the-art models. The DeepPRMS is expected to effectively guide future research experiments for identifying potential methylated protein sites. The web server is available at http://deepprms.nitsri.ac.in/.

Protein Arginine Methyltransferases: Emerging Targets in Cardiovascular and Metabolic Disease

Cardiovascular diseases (CVDs) and metabolic disorders stand as formidable challenges that significantly impact the clinical outcomes and living quality for afflicted individuals. An intricate comprehension of the underlying mechanisms is paramount for the development of efficacious therapeutic strategies. Protein arginine methyltransferases (PRMTs), a class of enzymes responsible for the precise regulation of protein methylation, have ascended to pivotal roles and emerged as crucial regulators within the intrinsic pathophysiology of these diseases. Herein, we review recent advancements in research elucidating on the multifaceted involvements of PRMTs in cardiovascular system and metabolic diseases, contributing significantly to deepen our understanding of the pathogenesis and progression of these maladies. In addition, this review provides a comprehensive analysis to unveil the distinctive roles of PRMTs across diverse cell types implicated in cardiovascular and metabolic disorders, which holds great potential to reveal novel therapeutic interventions targeting PRMTs, thus presenting promising perspectives to effectively address the substantial global burden imposed by CVDs and metabolic disorders.

Protein arginine methyltransferase 4 modulates nitric oxide synthase uncoupling and cerebral blood flow in Alzheimer's disease

Alzheimer's disease (AD) is the leading cause of mortality, disability, and long-term care burden in the United States, with women comprising the majority of AD diagnoses. While AD-related dementia is associated with tau and amyloid beta accumulation, concurrent derangements in cerebral blood flow have been observed alongside these proteinopathies in humans and rodent models. The homeostatic production of nitric oxide synthases (NOS) becomes uncoupled in AD which leads to decreased NO-mediated vasodilation and oxidative stress via the production of peroxynitrite (ONOO-∙) superoxide species. Here, we investigate the role of the novel protein arginine methyltransferase 4 (PRMT4) enzyme function and its downstream product asymmetric dimethyl arginine (ADMA) as it relates to NOS dysregulation and cerebral blood flow in AD. ADMA (type-1 PRMT product) has been shown to bind NOS as a noncanonic ligand causing enzymatic dysfunction. Our results from RT-qPCR and protein analyses suggest that aged (9-12 months) female mice bearing tau- and amyloid beta-producing transgenic mutations (3xTg-AD) express higher levels of PRMT4 in the hippocampus when compared to age- and sex-matched C57BL6/J mice. In addition, we performed studies to quantify the expression and activity of different NOS isoforms. Furthermore, laser speckle contrast imaging analysis was indicative that 3xTg-AD mice have dysfunctional NOS activity, resulting in reduced production of NO metabolites, enhanced production of free-radical ONOO-, and decreased cerebral blood flow. Notably, the aforementioned phenomena can be reversed via pharmacologic PRMT4 inhibition. Together, these findings implicate the potential importance of PRMT4 signaling in the pathogenesis of Alzheimer's-related cerebrovascular derangement.

PRMxAI: protein arginine methylation sites prediction based on amino acid spatial distribution using explainable artificial intelligence

BACKGROUND

Protein methylation, a post-translational modification, is crucial in regulating various cellular functions. Arginine methylation is required to understand crucial biochemical activities and biological functions, like gene regulation, signal transduction, etc. However, some experimental methods, including Chip-Chip, mass spectrometry, and methylation-specific antibodies, exist for the prediction of methylated proteins. These experimental methods are expensive and tedious. As a result, computational methods based on machine learning play an efficient role in predicting arginine methylation sites.

RESULTS

In this research, a novel method called PRMxAI has been proposed to predict arginine methylation sites. The proposed PRMxAI extract sequence-based features, such as dipeptide composition, physicochemical properties, amino acid composition, and information theory-based features (Arimoto, Havrda-Charvat, Renyi, and Shannon entropy), to represent the protein sequences into numerical format. Various machine learning algorithms are implemented to select the better classifier, such as Decision trees, Naive Bayes, Random Forest, Support vector machines, and K-nearest neighbors. The random forest algorithm is selected as the underlying classifier for the PRMxAI model. The performance of PRMxAI is evaluated by employing 10-fold cross-validation, and it yields 87.17% and 90.40% accuracy on mono-methylarginine and di-methylarginine data sets, respectively. This research also examines the impact of various features on both data sets using explainable artificial intelligence.

CONCLUSIONS

The proposed PRMxAI shows the effectiveness of the features for predicting arginine methylation sites. Additionally, the SHapley Additive exPlanation method is used to interpret the predictive mechanism of the proposed model. The results indicate that the proposed PRMxAI model outperforms other state-of-the-art predictors.

PRMT5 knockdown enhances cell viability and suppresses cell apoptosis, oxidative stress, inflammation and endothelial dysfunction in ox-LDL-induced vascular endothelial cells via interacting with PDCD4

Atherosclerosis (AS) is an important pathological basis of cardiovascular disease (CVD). The development of AS commences with endothelial dysfunction due to vascular endothelial cell injury. It is well documented that protein arginine methyltransferase 5 (PRMT5) is highly related to cardiovascular events. BioGRID database analysis indicates that PRMT5 may interact with programmed cell death 4 (PDCD4), which is reported to be involved in AS progression. This present research was formulated to elucidate the biological roles of PRMT5/PDCD4 in vascular endothelial cell injury during AS. In this current work, HUVECs were stimulated with 100 mg/L ox-LDL for 48 h to construct an in vitro AS model. Expression levels of PRMT5 and PDCD4 were analyzed by performing RT-qPCR and western blot. The viability and apoptosis of HUVECs were determined using CCK-8, flow cytometry and western blot assays. The status of oxidative stress and inflammation was assessed via commercial detection kits and ELISA assay, respectively. Besides, biomarkers of endothelial dysfunction were detected via commercial detection kit and western blot assay. In addition, the interacting relationship between PRMT5 and PDCD4 was verified by Co-IP assay. Highly expressed PRMT5 was observed in ox-LDL-stimulated HUVECs. Knockdown of PRMT5 enhanced the viability and inhibited the apoptosis of ox-LDL-induced HUVECs as well as alleviated ox-LDL-triggered oxidative stress, inflammation and endothelial dysfunction in HUVECs. PRMT5 interacted and bound with PDCD4. Furthermore, the enhancing effect on cell viability as well as the suppressing effects on cell apoptosis, oxidative stress, inflammation and endothelial dysfunction of PRMT5 knockdown in ox-LDL-induced HUVECs were partially abolished upon up-regulation of PDCD4. To conclude, down-regulation of PRMT5 might exert protective effects against vascular endothelial cell injury during AS by suppressing PDCD4 expression.

Protein arginine methyltransferase 3: A crucial regulator in metabolic reprogramming and gene expression in cancers

Post-translational modification (PTM) of proteins increases proteome diversity, which is critical for maintaining cellular homeostasis. The importance of protein methylation in the regulation of diverse biological processes has been highlighted in the past decades. Methylation of the arginine residue on proteins is catalyzed by members of the protein arginine methyltransferase (PRMT) family. PRMTs play indispensable roles in various pathways that regulate cancer development, progression, and drug response. In this review, we discuss the role of PRMT3, a member of the PRMT family, in controlling oncogenic processes. Additionally, the effects of PRMT3 on the methylation of regulatory proteins involved in transcription, post-transcriptional control, ribosomal maturation, translation, biological synthesis, and metabolic signaling are summarized. Moreover, recent progresses in the development of PRMT3 inhibitors are introduced. Overall, this review highlights the importance of PRMT3 in tumorigenesis and discusses the underlying mechanisms by which PRMT3 modulates cellular metabolism and gene expression. These results also provide a molecular basis for therapeutic modalities by targeting PRMT3.

Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer

Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.

The Multiple Faces of Nitric Oxide in Chronic Granulomatous Disease: A Comprehensive Update

Nitric oxide (NO), a signaling molecule, regulates multiple biological functions, including a variety of physiological and pathological processes. In this regard, NO participates in cutaneous inflammations, modulation of mitochondrial functions, vascular diseases, COVID-19, neurologic diseases, and obesity. It also mediates changes in the skeletal muscle function. Chronic granulomatous disease (CGD) is a primary immunodeficiency disorder characterized by the malfunction of phagocytes caused by mutations in some of the genes encoding subunits of the superoxide-generating phagocyte NADPH (NOX). The literature consulted shows that there is a relationship between the production of NO and the NADPH oxidase system, which regulates the persistence of NO in the medium. Nevertheless, the underlying mechanisms of the effects of NO on CGD remain unknown. In this paper, we briefly review the regulatory role of NO in CGD and its potential underlying mechanisms.

Metal-Bridged Graphene-Protein Supraparticles for Analog and Digital Nitric Oxide Sensing

Self-limited nanoassemblies, such as supraparticles (SPs), can be made from virtually any nanoscale components, but SPs from nanocarbons including graphene quantum dots (GQDs), are hardly known because of the weak van der Waals attraction between them. Here it is shown that highly uniform SPs from GQDs can be successfully assembled when the components are bridged by Tb3+ ions supplementing van der Waals interactions. Furthermore, they can be coassembled with superoxide dismutase, which also has weak attraction to GQDs. Tight structural integration of multilevel components into SPs enables efficient transfer of excitonic energy from GQDs and protein to Tb3+ . This mechanism is activated when Cu2+ is reduced to Cu1+ by nitric oxide (NO)-an important biomarker for viral pulmonary infections and Alzheimer's disease. Due to multipronged fluorescence enhancement, the limit of NO detection improves 200 times reaching 10 × 10-12 m. Furthermore, the uniform size of SPs enables digitization of the NO detection using the single particle detection format resulting in confident registration of as few as 600 molecules mL-1 . The practicality of the SP-based assay is demonstrated by the successful monitoring of NO in human breath. The biocompatible SPs combining proteins, carbonaceous nanostructures, and ionic components provide a general path for engineering uniquely sensitive assays for noninvasive tracking of infections and other diseases.

Computational Prediction of Protein Arginine Methylation Based on Composition-Transition-Distribution Features

Arginine methylation is one of the most essential protein post-translational modifications. Identifying the site of arginine methylation is a critical problem in biology research. Unfortunately, biological experiments such as mass spectrometry are expensive and time-consuming. Hence, predicting arginine methylation by machine learning is an alternative fast and efficient way. In this paper, we focus on the systematic characterization of arginine methylation with composition-transition-distribution (CTD) features. The presented framework consists of three stages. In the first stage, we extract CTD features from 1750 samples and exploit decision tree to generate accurate prediction. The accuracy of prediction can reach 96%. In the second stage, the support vector machine can predict the number of arginine methylation sites with 0.36 R-squared. In the third stage, experiments carried out with the updated arginine methylation site data set show that utilizing CTD features and adopting random forest as the classifier outperform previous methods. The accuracy of identification can reach 82.1 and 82.5% in single methylarginine and double methylarginine data sets, respectively. The discovery presented in this paper can be helpful for future research on arginine methylation.

Protein Arginine Methyltransferases in Cardiovascular and Neuronal Function

The methylation of arginine residues by protein arginine methyltransferases (PRMTs) is a type of post-translational modification which is important for numerous cellular processes, including mRNA splicing, DNA repair, signal transduction, protein interaction, and transport. PRMTs have been extensively associated with various pathologies, including cancer, inflammation, and immunity response. However, the role of PRMTs has not been well described in vascular and neurological function. Aberrant expression of PRMTs can alter its metabolic products, asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). Increased ADMA levels are recognized as an independent risk factor for cardiovascular disease and mortality. Recent studies have provided considerable advances in the development of small-molecule inhibitors of PRMTs to study their function under normal and pathological states. In this review, we aim to elucidate the particular roles of PRMTs in vascular and neuronal function as a potential target for cardiovascular and neurological diseases.

Asymmetrical methyltransferase PRMT3 regulates human mesenchymal stem cell osteogenesis via miR-3648

Histone arginine methylation, which is catalyzed by protein arginine methyltransferases (PRMTs), plays a key regulatory role in various biological processes. Several PRMTs are involved in skeletal development; however, their role in the osteogenic differentiation of mesenchymal stem cells (MSCs) is not completely clear. In this study, we aimed to elucidate the function of PRMT3, a type-I PRMT that catalyzes the formation of ω-mono- or asymmetric dimethyl arginine, in MSCs osteogenesis. We found that PRMT3 promoted MSCs osteogenic commitment and bone remodeling. PRMT3 activated the expression of miR-3648 by enhancing histone H4 arginine 3 asymmetric dimethylation (H4R3me2a) levels at promoter region of the gene. Overexpression of miR-3648 rescued impaired osteogenesis in PRMT3-deficient cells. Moreover, administration of Prmt3 shRNA or a chemical inhibitor of PRMT3 (SGC707) caused an osteopenia phenotype in mice. These results indicate that PRMT3 is a potential therapeutic target for the treatment of bone regeneration and osteopenia disorders.

Fast Prediction of Protein Methylation Sites Using a Sequence-Based Feature Selection Technique

Protein methylation, an important post-translational modification, plays crucial roles in many cellular processes. The accurate prediction of protein methylation sites is fundamentally important for revealing the molecular mechanisms undergoing methylation. In recent years, computational prediction based on machine learning algorithms has emerged as a powerful and robust approach for identifying methylation sites, and much progress has been made in predictive performance improvement. However, the predictive performance of existing methods is not satisfactory in terms of overall accuracy. Motivated by this, we propose a novel random-forest-based predictor called MePred-RF, integrating several discriminative sequence-based feature descriptors and improving feature representation capability using a powerful feature selection technique. Importantly, unlike other methods based on multiple, complex information inputs, our proposed MePred-RF is based on sequence information alone. Comparative studies on benchmark datasets via vigorous jackknife tests indicate that our proposed MePred-RF method remarkably outperforms other state-of-the-art predictors, leading by a 4.5 percent average in terms of overall accuracy. A user-friendly webserver that implements the proposed method has been established for researchers' convenience, and is now freely available for public use through http://server.malab.cn/MePred-RF. We anticipate our research tool to be useful for the large-scale prediction and analysis of protein methylation sites.

iMethylK_pseAAC: Improving Accuracy of Lysine Methylation Sites Identification by Incorporating Statistical Moments and Position Relative Features into General PseAAC via Chou's 5-steps Rule

BACKGROUND

Methylation is one of the most important post-translational modifications in the human body which usually arises on lysine among the most intensely modified residues. It performs a dynamic role in numerous biological procedures, such as regulation of gene expression, regulation of protein function and RNA processing. Therefore, to identify lysine methylation sites is an important challenge as some experimental procedures are time-consuming.

OBJECTIVE

Herein, we propose a computational predictor named iMethylK_pseAAC to identify lysine methylation sites.

METHODS

Firstly, we constructed feature vectors based on PseAAC using position and composition rel-ative features and statistical moments. A neural network is trained based on the extracted features. The performance of the proposed method is then validated using cross-validation and jackknife testing.

RESULTS

The objective evaluation of the predictor showed accuracy of 96.7% for self-consistency, 91.61% for 10-fold cross-validation and 93.42% for jackknife testing.

CONCLUSION

It is concluded that iMethylK_pseAAC outperforms the counterparts to identify lysine methylation sites such as iMethyl_pseACC, BPB_pPMS and PMeS.

Inhibition of PRMT3 activity reduces hepatic steatosis without altering atherosclerosis susceptibility in apoE knockout mice

The nuclear receptor liver X receptor (LXR) impacts on cholesterol metabolism as well as hepatic lipogenesis via transcriptional regulation. It is proposed that inhibition of the protein arginine methyltransferase 3 (PRMT3) uncouples these two transcriptional pathways in vivo by acting as a specific lipogenic coactivator of LXR. Here we validated the hypothesis that treatment with the allosteric PRMT3 inhibitor SGC707 will diminish the hepatic steatosis extent, while leaving global cholesterol metabolism, important in cholesterol-driven pathologies like atherosclerosis, untouched. For this purpose, 12-week old hyperlipidemic apolipoprotein E knockout mice were fed a Western-type diet for six weeks to induce both hepatic steatosis and atherosclerosis. The mice received 3 intraperitoneal injections with SGC707 or solvent control per week. Mice chronically treated with SGC707 developed less severe hepatic steatosis as exemplified by the 51% reduced (P < 0.05) liver triglyceride levels. In contrast, the extent of in vivo macrophage foam cell formation and aortic root atherosclerosis was not affected by SGC707 treatment. Interestingly, SGC707-treated mice gained 94% less body weight (P < 0.05), which was paralleled by changes in white adipose tissue morphology, i.e. reduction in adipocyte size and browning. In conclusion, we have shown that through PRMT3 inhibitor treatment specific functions of LXR involved in respectively the development of fatty liver disease and atherosclerosis can be uncoupled, resulting in an overall diminished hepatic steatosis extent without a negative impact on atherosclerosis susceptibility. As such, our studies highlight that PRMT3 inhibition may constitute a novel therapeutic approach to limit the development of fatty liver disease in humans.

PRMT1 Deficiency in Mouse Juvenile Heart Induces Dilated Cardiomyopathy and Reveals Cryptic Alternative Splicing Products

Protein arginine methyltransferase 1 (PRMT1) catalyzes the asymmetric dimethylation of arginine residues in proteins and methylation of various RNA-binding proteins and is associated with alternative splicing in vitro. Although PRMT1 has essential in vivo roles in embryonic development, CNS development, and skeletal muscle regeneration, the functional importance of PRMT1 in the heart remains to be elucidated. Here, we report that juvenile cardiomyocyte-specific PRMT1-deficient mice develop severe dilated cardiomyopathy and exhibit aberrant cardiac alternative splicing. Furthermore, we identified previously undefined cardiac alternative splicing isoforms of four genes (Asb2, Fbxo40, Nrap, and Eif4a2) in PRMT1-cKO mice and revealed that eIF4A2 protein isoforms translated from alternatively spliced mRNA were differentially ubiquitinated and degraded by the ubiquitin-proteasome system. These findings highlight the essential roles of PRMT1 in cardiac homeostasis and alternative splicing regulation.

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PRMT1 deficiency in cardiomyocytes causes dilated cardiomyopathy in juvenile mice

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PRMT1-deficient heart shows abnormal alternative splicing patterns

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Previously undefined cardiac splicing events are revealed by transcriptome analysis

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eIF4A2 isoforms are differentially ubiquitinated and degraded

Intake of glucosinolates and risk of coronary heart disease in three large prospective cohorts of US men and women

Importance

Glucosinolates, a group of phytochemicals abundant in cruciferous vegetables, may have cardioprotective properties. However, no prospective study has evaluated the association of intake of glucosinolates with the risk of coronary heart disease (CHD).

Objective

The objective of the study was to evaluate the association between the intake of glucosinolates and incident CHD in US men and women.

Design

Prospective longitudinal cohort study.

Setting

Health professionals in the USA.

Participants

We followed 74,241 women in the Nurses’ Health Study (NHS; 1984–2012), 94,163 women in the NHSII (1991–2013), and 42,170 men in the Health Professionals Follow-Up Study (1986–2012), who were free of cardiovascular disease and cancer at baseline.

Exposure

Glucosinolate intake was assessed using validated semi-quantitative food frequency questionnaires at baseline and updated every 2–4 years during follow-up.

Main outcome measures

Incident cases of CHD were confirmed by medical record review.

Results

During 4,824,001 person-years of follow-up, 8,010 cases of CHD were identified in the three cohorts. After adjustment for major lifestyle and dietary risk factors of CHD, weak but significantly positive associations were observed for glucosinolates with CHD risk when comparing the top with bottom quintiles (hazard ratio [HR]:1.09; 95% CI: 1.01, 1.17; P_trend<0.001). Higher intakes of three major subtypes of glucosinolates were consistently associated with a higher CHD risk, although the association for indolylglucosinolate did not achieve statistical significance. Regarding cruciferous vegetable intake, participants who consumed one or more servings per week of Brussels sprouts (HR: 1.16; 95% CI: 1.06, 1.26; P<0.001) and cabbage (HR: 1.09; 95% CI: 1.02, 1.17; P=0.009) had a significantly higher CHD risk than those who consumed these cruciferous vegetables less than once per month.

Conclusion and relevance

In these three prospective cohort studies, dietary glucosinolate intake was associated with a slightly higher risk of CHD in US adults. These results warrant replications in further studies including biomarker-based studies. Further studies are needed to confirm these findings and elucidate mechanistic pathways that may underlie these associations.

Discovery of Potent and Selective Allosteric Inhibitors of Protein Arginine Methyltransferase 3 (PRMT3)

PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is crucial for maturation of ribosomes and has been implicated in several diseases. We recently disclosed a highly potent, selective, and cell-active allosteric inhibitor of PRMT3, compound 4. Here, we report comprehensive structure-activity relationship studies that target the allosteric binding site of PRMT3. We conducted design, synthesis, and evaluation of novel compounds in biochemical, selectivity, and cellular assays that culminated in the discovery of 4 and other highly potent (IC₅₀ values: ∼10-36 nM), selective, and cell-active allosteric inhibitors of PRMT3 (compounds 29, 30, 36, and 37). In addition, we generated compounds that are very close analogs of these potent inhibitors but displayed drastically reduced potency as negative controls (compounds 49-51). These inhibitors and negative controls are valuable chemical tools for the biomedical community to further investigate biological functions and disease associations of PRMT3.

Allosteric regulation of epigenetic modifying enzymes

Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings.

Admixture Mapping of Subclinical Atherosclerosis and Subsequent Clinical Events Among African Americans in 2 Large Cohort Studies

BACKGROUND

Local ancestry may contribute to the disproportionate burden of subclinical and clinical cardiovascular disease among admixed African Americans compared with other populations, suggesting a rationale for admixture mapping.

METHODS AND RESULTS

We estimated local European ancestry (LEA) using Local Ancestry inference in adMixed Populations using Linkage Disequilibrium method (LAMP-LD) and evaluated the association with common carotid artery intima-media thickness (cCIMT) using multivariable linear regression analysis among 1554 African Americans from MESA (Multi-Ethnic Study of Atherosclerosis). We conducted secondary analysis to examine the significant cCIMT-LEA associations with clinical cardiovascular disease events. We observed genome-wide significance in relation to cCIMT association with the SERGEF gene (secretion-regulating guanine nucleotide exchange factor; β=0.0137; P=2.98×10-4), also associated with higher odds of stroke (odds ratio=1.71; P=0.02). Several regions, in particular CADPS gene (Ca2+-dependent secretion activator 1) region identified in MESA, were also replicated in the ARIC cohort (Atherosclerosis Risk in Communities). We observed other cCIMT-LEA regions associated with other clinical events, most notably the regions harboring CKMT2 gene (creatine kinase, mitochondrial 2) and RASGRF2 gene (Ras protein-specific guanine nucleotide-releasing factor 2) with all clinical events except stroke, the LRRC3B gene (leucine-rich repeat containing 3B) with myocardial infarction, the PRMT3 gene (protein arginine methyltransferase 3) with stroke, and the LHFPL2 gene (lipoma high mobility group protein I-C fusion partner-like 2) with hard and all coronary heart disease.

CONCLUSIONS

We identified several novel LEA regions, in addition to previously identified genetic variations, associated with cCIMT and cardiovascular disease events among African Americans.

Protein post-translational modifications: In silico prediction tools and molecular modeling

Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.

Inhibitors of Protein Methyltransferases and Demethylases

Post-translational modifications of histones by protein methyltransferases (PMTs) and histone demethylases (KDMs) play an important role in the regulation of gene expression and transcription and are implicated in cancer and many other diseases. Many of these enzymes also target various nonhistone proteins impacting numerous crucial biological pathways. Given their key biological functions and implications in human diseases, there has been a growing interest in assessing these enzymes as potential therapeutic targets. Consequently, discovering and developing inhibitors of these enzymes has become a very active and fast-growing research area over the past decade. In this review, we cover the discovery, characterization, and biological application of inhibitors of PMTs and KDMs with emphasis on key advancements in the field. We also discuss challenges, opportunities, and future directions in this emerging, exciting research field.

Small Molecule Inhibitors of Protein Arginine Methyltransferases

INTRODUCTION

Arginine methylation is an abundant posttranslational modification occurring in mammalian cells and catalyzed by protein arginine methyltransferases (PRMTs). Misregulation and aberrant expression of PRMTs are associated with various disease states, notably cancer. PRMTs are prominent therapeutic targets in drug discovery.

AREAS COVERED

The authors provide an updated review of the research on the development of chemical modulators for PRMTs. Great efforts are seen in screening and designing potent and selective PRMT inhibitors, and a number of micromolar and submicromolar inhibitors have been obtained for key PRMT enzymes such as PRMT1, CARM1, and PRMT5. The authors provide a focus on their chemical structures, mechanism of action, and pharmacological activities. Pros and cons of each type of inhibitors are also discussed.

EXPERT OPINION

Several key challenging issues exist in PRMT inhibitor discovery. Structural mechanisms of many PRMT inhibitors remain unclear. There lacks consistency in potency data due to divergence of assay methods and conditions. Physiologically relevant cellular assays are warranted. Substantial engagements are needed to investigate pharmacodynamics and pharmacokinetics of the new PRMT inhibitors in pertinent disease models. Discovery and evaluation of potent, isoform-selective, cell-permeable and in vivo-active PRMT modulators will continue to be an active arena of research in years ahead.

Position-specific prediction of methylation sites from sequence conservation based on information theory

Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

A metabolite of Danshen formulae attenuates cardiac fibrosis induced by isoprenaline, via a NOX2/ROS/p38 pathway

BACKGROUND AND PURPOSE

Cardiac fibrosis is a common feature of advanced coronary heart disease and is characteristic of heart disease. However, currently available drugs against cardiac fibrosis are still very limited. Here, we have assessed the role of isopropyl 3-(3,4-dihydroxyphenyl)-2-hydroxylpropanoate (IDHP), a new metabolite of Danshen Dripping Pills, in cardiac fibrosis mediated by the β-adrenoceptor agonist, isoprenaline, and its underlying mechanisms.

EXPERIMENTAL APPROACH

Identification of IDHP was identified by mass spectrometry, and proton and carbon nuclear magnetic resonance spectra. Myocardial collagen was quantitatively assessed with Picrosirius Red staining. Expression of mRNA for collagen was evaluated with real-time PCR. Phosphorylated and total p38 MAPK, NADPH oxidase (NOX) and superoxide dismutase (SOD) were analysed by Western blot. Generation of reactive oxygen species (ROS) generation was evaluated by dihydroethidium (DHE) fluorescent staining. NOX2 was knocked down using specific siRNA.

KEY RESULTS

IDHP attenuated β-adrenoceptor mediated cardiac fibrosis in vivo and inhibited isoprenaline-induced proliferation of neonatal rat cardiac fibroblasts (NRCFs) and collagen I synthesis in vitro. Phosphorylation of p38 MAPK, which is an important mediator in the pathogenesis of isoprenaline-induced cardiac fibrosis, was inhibited by IDHP. This inhibition of phospho-p38 by IDHP was dependent on decreased generation of ROS. These effects of IDHP were abolished in NRCFs treated with siRNA for NOX2.

CONCLUSIONS AND IMPLICATIONS

IDHP attenuated the cardiac fibrosis induced by isoprenaline through a NOX2/ROS/p38 pathway. These novel findings suggest that IDHP is a potential pharmacological candidate for the treatment of cardiac fibrosis, induced by β-adrenoceptor agonists.

Redox Control of Protein Arginine Methyltransferase 1 (PRMT1) Activity

Elevated levels of asymmetric dimethylarginine (ADMA) correlate with risk factors for cardiovascular disease. ADMA is generated by the catabolism of proteins methylated on arginine residues by protein arginine methyltransferases (PRMTs) and is degraded by dimethylarginine dimethylaminohydrolase. Reports have shown that dimethylarginine dimethylaminohydrolase activity is down-regulated and PRMT1 protein expression is up-regulated under oxidative stress conditions, leading many to conclude that ADMA accumulation occurs via increased synthesis by PRMTs and decreased degradation. However, we now report that the methyltransferase activity of PRMT1, the major PRMT isoform in humans, is impaired under oxidative conditions. Oxidized PRMT1 displays decreased activity, which can be rescued by reduction. This oxidation event involves one or more cysteine residues that become oxidized to sulfenic acid (-SOH). We demonstrate a hydrogen peroxide concentration-dependent inhibition of PRMT1 activity that is readily reversed under physiological H2O2 concentrations. Our results challenge the unilateral view that increased PRMT1 expression necessarily results in increased ADMA synthesis and demonstrate that enzymatic activity can be regulated in a redox-sensitive manner.

A potent, selective and cell-active allosteric inhibitor of protein arginine methyltransferase 3 (PRMT3)

PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is essential for maturation of ribosomes, may have a role in lipogenesis, and is implicated in several diseases. A potent, selective, and cell-active PRMT3 inhibitor would be a valuable tool for further investigating PRMT3 biology. Here we report the discovery of the first PRMT3 chemical probe, SGC707, by structure-based optimization of the allosteric PRMT3 inhibitors we reported previously, and thorough characterization of this probe in biochemical, biophysical, and cellular assays. SGC707 is a potent PRMT3 inhibitor (IC50 =31±2 nM, KD =53±2 nM) with outstanding selectivity (selective against 31 other methyltransferases and more than 250 non-epigenetic targets). The mechanism of action studies and crystal structure of the PRMT3-SGC707 complex confirm the allosteric inhibition mode. Importantly, SGC707 engages PRMT3 and potently inhibits its methyltransferase activity in cells. It is also bioavailable and suitable for animal studies. This well-characterized chemical probe is an excellent tool to further study the role of PRMT3 in health and disease.

No evidence for mosaic pathogenic copy number variations in cardiac tissue from patients with congenital heart malformations

The aim of this study was to investigate if pathogenic copy number variations (CNVs) are present in mosaic form in patients with congenital heart malformations. We have collected cardiac tissue and blood samples from 23 patients with congenital heart malformations that underwent cardiac surgery and screened for mosaic gene dose alterations restricted to cardiac tissue using array comparative genomic hybridization (array CGH). We did not find evidence of CNVs in mosaic form after array CGH analysis. Pathogenic CNVs that were present in both cardiac tissue and blood were detected in 2/23 patients (9%), and in addition we found several constitutional CNVs of unclear clinical significance. This is the first study investigating mosaicism for CNVs in heart tissue compared to peripheral blood and the results do not indicate that pathogenic mosaic copy number changes are common in patients with heart malformations. Importantly, in line with previous studies, our results show that constitutional pathogenic CNVs are important factors contributing to congenital heart malformations.

Selective inhibitors of protein methyltransferases

Mounting evidence suggests that protein methyltransferases (PMTs), which catalyze methylation of histone and nonhistone proteins, play a crucial role in diverse biological processes and human diseases. In particular, PMTs have been recognized as major players in regulating gene expression and chromatin state. PMTs are divided into two categories: protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs). There has been a steadily growing interest in these enzymes as potential therapeutic targets and therefore discovery of PMT inhibitors has also been pursued increasingly over the past decade. Here, we present a perspective on selective, small-molecule inhibitors of PMTs with an emphasis on their discovery, characterization, and applicability as chemical tools for deciphering the target PMTs' physiological functions and involvement in human diseases. We highlight the current state of PMT inhibitors and discuss future directions and opportunities for PMT inhibitor discovery.

iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach

Before becoming the native proteins during the biosynthesis, their polypeptide chains created by ribosome's translating mRNA will undergo a series of “product-forming” steps, such as cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs is the Arg- or Lys-methylation that occurs on arginine or lysine, respectively. Given a protein, which site of its Arg (or Lys) can be methylated, and which site cannot? This is the first important problem for understanding the methylation mechanism and drug development in depth. With the avalanche of protein sequences generated in the postgenomic age, its urgency has become self-evident. To address this problem, we proposed a new predictor, called iMethyl-PseAAC. In the prediction system, a peptide sample was formulated by a 346-dimensional vector, formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form of pseudo amino acid composition. It was observed by the rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior to any of the existing predictors in this area.

Diamidine compounds for selective inhibition of protein arginine methyltransferase 1

Protein arginine methylation is a posttranslational modification critical for a variety of biological processes. Misregulation of protein arginine methyltransferases (PRMTs) has been linked to many pathological conditions. Most current PRMT inhibitors display limited specificity and selectivity, indiscriminately targeting many methyltransferase enzymes that use S-adenosyl-l-methionine as a cofactor. Here we report diamidine compounds for specific inhibition of PRMT1, the primary type I enzyme. Docking, molecular dynamics, and MM/PBSA analysis together with biochemical assays were conducted to understand the binding modes of these inhibitors and the molecular basis of selective inhibition for PRMT1. Our data suggest that 2,5-bis(4-amidinophenyl)furan (1, furamidine, DB75), one leading inhibitor, targets the enzyme active site and is primarily competitive with the substrate and noncompetitive toward the cofactor. Furthermore, cellular studies revealed that 1 is cell membrane permeable and effectively inhibits intracellular PRMT1 activity and blocks cell proliferation in leukemia cell lines with different genetic lesions.

Profiling substrates of protein arginine N-methyltransferase 3 with S-adenosyl-L-methionine analogues

Protein arginine N-methyltransferase 3 (PRMT3) belongs to the family of type I PRMTs and harbors the activity to use S-adenosyl-l-methionine (SAM) as a methyl-donor cofactor for protein arginine labeling. However, PRMT3's functions remain elusive with the lacked knowledge of its target scope in cellular settings. Inspired by the emerging Bioorthogonal Profiling of Protein Methylation (BPPM) using engineered methyltransferases and SAM analogues for target identification, the current work documents the endeavor to systematically explore the SAM-binding pocket of PRMT3 and identify suitable PRMT3 variants for BPPM. The M233G single point mutation transforms PRMT3 into a promiscuous alkyltransferase using sp(2)-β-sulfonium-containing SAM analogues as cofactor surrogates. Here the conserved methionine was defined as a hot spot that can be engineered alone or in combination with nearby residues to render cofactor promiscuity of multiple type I PRMTs. With this promiscuous variant and the matched 4-propargyloxy-but-2-enyl (Pob)-SAM analogue as the BPPM reagents, more than 80 novel proteins were readily uncovered as potential targets of PRMT3 in the cellular context. Subsequent target validation and functional analysis correlated the PRMT3 methylation to several biological processes such as cytoskeleton dynamics, whose roles might be compensated by other PRMTs. These BPPM-revealed substrates are primarily localized but not restricted in cytoplasm, the preferred site of PRMT3. The broad localization pattern may implicate the diverse roles of PRMT3 in the cellular setting. The revelation of PRMT3 targets and the transformative character of BPPM for other PRMTs present unprecedented pathways toward elucidating physiological and pathological roles of diverse PRMTs.

Design of small molecule epigenetic modulators

The field of epigenetics has expanded rapidly to reveal multiple new targets for drug discovery. The functional elements of the epigenomic machinery can be categorized as writers, erasers and readers, and together these elements control cellular gene expression and homeostasis. It is increasingly clear that aberrations in the epigenome can underly a variety of diseases, and thus discovery of small molecules that modulate the epigenome in a specific manner is a viable approach to the discovery of new therapeutic agents. In this Digest, the components of epigenetic control of gene expression will be briefly summarized, and efforts to identify small molecules that modulate epigenetic processes will be described.

Selective up-regulation of arginase-1 in coronary arteries of diabetic patients

Coronary artery disease (CAD) remains the leading cause of death in the Western societies. Diabetes mellitus (DM) is one of the highly prevalent diseases, which remarkably accelerates the development of CAD. Experimental evidence indicates that decreased bioavailability of coronary endothelial nitric oxide (NO) contributes to the development of CAD in DM. There are recent studies showing that a selective impairment of NO synthesis occurs in coronary arteries of DM patients, which is mainly due to the limited availability of endothelial NO synthase (eNOS) precursor, l-arginine. Importantly, these studies demonstrated that DM, independent of the presence of CAD, leads to selective up-regulation of arginase-1. Arginase-1 seems to play an important role in limiting l-arginine availability in the close proximity of eNOS in vessels of DM patients. This brief review examines recent clinical studies demonstrating the pathological role of vascular arginase-1 in human diabetes. Whether arginase-1, which is crucial in the synthesis of various fundamental polyamines in the body, will represent a potent therapeutic target for prevention of DM-associated CAD is still debated.

Exercise intensity modulates nitric oxide and blood pressure responses in hypertensive older women

BACKGROUND AND AIMS

Whether intensity or other characteristics of physical activity can better promote the release of nitric oxide (NO) and reduction of blood pressure in hypertensive older-adults is still unknown. In this study, the post-exercise blood pressure (BP) response and NO release after different intensities of aerobic exercise in elderly women were analyzed.

METHODS

Blood pressure response and NO were analyzed in 23 elderly mildly hypertensive women. Participants underwent (1) high-intensity incremental exercise (IT); (2) moderate-intensity 20 min exercise at 90% of the anaerobic threshold (AT), and (3) control (CONT) session. BP was measured before and after interventions; volunteers remained seated for 1 h. NO estimates were made through NO2- analyses.

RESULTS

After CONT session, both diastolic BP and mean arterial pressure (MAP) were significantly higher than during pre-exercise resting. Post-exercise hypotension (PEH) was observed after exercise at IT and 90% of AT. Although exercise in both sessions lowered SBP and MAP compared with CONT, exercise at the highest intensity (IT) was more effective on lowering systolic BP after exercise. In comparison with pre-exercise resting, NO2- increased significantly only after IT, but both exercise sessions caused NO2- to increase compared with CONT.

CONCLUSION

Exercise intensity and NO release may exert a role in eliciting PEH in mildly hypertensive elderly women.

Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors

Protein arginine methyltransferases (PRMTs) play an important role in diverse biological processes. Among the nine known human PRMTs, PRMT3 has been implicated in ribosomal biosynthesis via asymmetric dimethylation of the 40S ribosomal protein S2 and in cancer via interaction with the DAL-1 tumor suppressor protein. However, few selective inhibitors of PRMTs have been discovered. We recently disclosed the first selective PRMT3 inhibitor, which occupies a novel allosteric binding site and is noncompetitive with both the peptide substrate and cofactor. Here we report comprehensive structure-activity relationship studies of this series, which resulted in the discovery of multiple PRMT3 inhibitors with submicromolar potencies. An X-ray crystal structure of compound 14u in complex with PRMT3 confirmed that this inhibitor occupied the same allosteric binding site as our initial lead compound. These studies provide the first experimental evidence that potent and selective inhibitors can be created by exploiting the allosteric binding site of PRMT3.

Identification of small-molecule enhancers of arginine methylation catalyzed by coactivator-associated arginine methyltransferase 1

Arginine methylation is a common post-translational modification that is crucial in modulating gene expression at multiple critical levels. The arginine methyltransferases (PRMTs) are envisaged as promising druggable targets, but their role in physiological and pathological pathways is far from being clear due to the limited number of modulators reported to date. In this effort, enzyme activators can be invaluable tools useful as gain-of-function reagents to interrogate the biological roles in cells and in vivo of PRMTs. Yet the identification of such molecules is rarely pursued. Herein we describe a series of aryl ureido acetamido indole carboxylates (dubbed "uracandolates"), able to increase the methylation of histone (H3) or nonhistone (polyadenylate-binding protein 1, PABP1) substrates induced by coactivator-associated arginine methyltransferase 1 (CARM1), both in in vitro and cellular settings. To the best of our knowledge, this is the first report of compounds acting as CARM1 activators.

Association study of dimethylarginine dimethylaminohydrolase 2 gene polymorphisms and coronary heart disease

While a number of genetic and environmental risk factors for coronary heart disease (CHD) have been identified, the list of potential risk factors remains long. One candidate is dimethylarginine dimethylaminohydrolase (DDAH2), which is known to be polymorphic in humans. The gene product indirectly increases the endogenous production of nitric oxide, an anti-atherogenic molecule. Therefore, alterations in DDAH2 activity may indirectly result in an increased risk of CHD. We studied allele and genotype distributions for two polymorphic loci of DDAH2, rs805305 and rs2272592, in 180 patients with CHD and 180 healthy controls. Disease history and other clinical data were recorded. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine the genotype at rs805305, and ligase detection reaction (LDR) was used to determine the genotype at rs2272592. Systolic blood pressure and blood triglyceride and glucose levels were higher, and history of hypertension, diabetes, smoking and alcohol use was more common in the patients with CHD (P<0.05). However, the genotype and allele frequencies at the two polymorphic loci of DDAH2 were not statistically different between the two groups. Therefore, no association was observed between the DDAH2 polymorphisms at rs805305 and rs2272592 and CHD.

An allosteric inhibitor of protein arginine methyltransferase 3

PRMT3, a protein arginine methyltransferase, has been shown to influence ribosomal biosynthesis by catalyzing the dimethylation of the 40S ribosomal protein S2. Although PRMT3 has been reported to be a cytosolic protein, it has been shown to methylate histone H4 peptide (H4 1-24) in vitro. Here, we report the identification of a PRMT3 inhibitor (1-(benzo[d][1,2,3]thiadiazol-6-yl)-3-(2-cyclohexenylethyl)urea; compound 1) with IC50 value of 2.5 μM by screening a library of 16,000 compounds using H4 (1-24) peptide as a substrate. The crystal structure of PRMT3 in complex with compound 1 as well as kinetic analysis reveals an allosteric mechanism of inhibition. Mutating PRMT3 residues within the allosteric site or using compound 1 analogs that disrupt interactions with allosteric site residues both abrogated binding and inhibitory activity. These data demonstrate an allosteric mechanism for inhibition of protein arginine methyltransferases, an emerging class of therapeutic targets.

PMeS: prediction of methylation sites based on enhanced feature encoding scheme

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx.

Role of dimethylarginine dimethylaminohydrolase activity in regulation of tissue and plasma concentrations of asymmetric dimethylarginine in an animal model of prolonged critical illness

High plasma concentrations of asymmetric dimethylarginine (ADMA), an endogenous nitric oxide synthase inhibitor, are associated with adverse outcome in critically ill patients. Asymmetric dimethylarginine is released within cells during proteolysis of methylated proteins and is either degraded by dimethylarginine dimethylaminohydrolase (DDAH) or exported to the circulation via cationic amino acid transporters. We aimed to establish the role of DDAH activity in the regulation of tissue and plasma concentrations of ADMA. In 33 critically ill rabbits, we measured DDAH activity in kidney, liver, heart, and skeletal muscle and related these values to concentrations of ADMA in these tissues and in the circulation. Both DDAH activity and ADMA concentration were highest in kidney and lowest in skeletal muscle, with intermediate values for liver and heart. Whereas ADMA content was significantly correlated between tissues (r = 0.40-0.78), DDAH activity was not. Significant inverse associations between DDAH activity and ADMA content were only observed in heart and liver. Plasma ADMA was significantly associated with ADMA in the liver (r = 0.41), but not in the other tissues. In a multivariable regression model, DDAH activities in muscle, kidney, and liver, but not in heart, were negatively associated with plasma ADMA concentration, together explaining approximately 50% of its variation. In critical illness, plasma ADMA poorly reflects intracellular ADMA. Furthermore, tissue DDAH activity is a stronger predictor of plasma ADMA than of intracellular ADMA, indicating that, compared with DDAH activity, generation of ADMA and cationic amino acid transporter-mediated exchange may be more important regulators of intracellular ADMA.