A First-in-class, Highly Selective and Cell-active Allosteric Inhibitor of Protein Arginine Methyltransferase 6 (PRMT6)

2020 ◽  
Author(s):  
Yudao Shen ◽  
Fengling Li ◽  
Magdalena M. Szewczyk ◽  
Levon Halebelian ◽  
Irene Chau ◽  
...  
Keyword(s):  
Kinetic Studies ◽  
Negative Control ◽  
Biological Processes ◽  
Methyltransferase Activity ◽  
Allosteric Inhibitors ◽  
Allosteric Inhibitor ◽  
Arginine Residues ◽  
Health And Disease ◽  
Protein Methyltransferases

AbstractPRMT6 catalyzes monomethylation and asymmetric dimethylation of arginine residues in various proteins, plays important roles in biological processes and is associated with multiple cancers. While there are several reported PRMT6 inhibitors, a highly selective PRMT6 inhibitor has not been reported to date. Furthermore, allosteric inhibitors of protein methyltransferases are rare. Here we report the discovery and characterization of a first-in-class, highly selective allosteric inhibitor of PRMT6, SGC6870. SGC6870 is a potent PRMT6 inhibitor (IC50 = 77 ± 6 nM) with outstanding selectivity for PRMT6 over a broad panel of other methyltransferases and non-epigenetic targets. Notably, the crystal structure of the PRMT6–SGC6870 complex and kinetic studies revealed SGC6870 binds a unique, induced allosteric pocket. Additionally, SGC6870 engages PRMT6 and potently inhibits its methyltransferase activity in cells. Moreover, SGC6870’s enantiomer, SGC6870N, is inactive against PRMT6 and can be utilized as a negative control. Collectively, SGC6870 is a well-characterized PRMT6 chemical probe and valuable tool for further investigating PRMT6 functions in health and disease.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

Open Biology ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 180241 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Budding Yeast ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes (BP). To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences. We use a simple yet powerful metric based on Gene Ontology BP terms to define characterized and uncharacterized proteins for human, budding yeast and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe , and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalogue of proteins’ biological roles.

Review of Progress in Predicting Protein Methylation Sites

2019 ◽  
Vol 23 (15) ◽  
pp. 1663-1670 ◽  
Author(s):  
Chunyan Ao ◽  
Shunshan Jin ◽  
Yuan Lin ◽  
Quan Zou
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Transcriptional Activity ◽  
Regulation Of Gene Expression ◽  
Protein Methylation ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Regulatory Enzymes ◽  
Lysine Residues ◽  
Arginine Residues

Protein methylation is an important and reversible post-translational modification that regulates many biological processes in cells. It occurs mainly on lysine and arginine residues and involves many important biological processes, including transcriptional activity, signal transduction, and the regulation of gene expression. Protein methylation and its regulatory enzymes are related to a variety of human diseases, so improved identification of methylation sites is useful for designing drugs for a variety of related diseases. In this review, we systematically summarize and analyze the tools used for the prediction of protein methylation sites on arginine and lysine residues over the last decade.

Neurochemistry of L-Glutamate Transport in the CNS: A Review of Thirty Years of Progress

2001 ◽  
Vol 66 (9) ◽  
pp. 1315-1340 ◽  
Author(s):  
Vladimir J. Balcar ◽  
Akiko Takamoto ◽  
Yukio Yoneda
Keyword(s):  
Molecular Biology ◽  
Glutamate Transport ◽  
Mammalian Brain ◽  
Activity Data ◽  
System A ◽  
Recent Developments ◽  
The Central Nervous System ◽  
Health And Disease ◽  
Disease Analysis

The review highlights the landmark studies leading from the discovery and initial characterization of the Na+-dependent "high affinity" uptake in the mammalian brain to the cloning of individual transporters and the subsequent expansion of the field into the realm of molecular biology. When the data and hypotheses from 1970's are confronted with the recent developments in the field, we can conclude that the suggestions made nearly thirty years ago were essentially correct: the uptake, mediated by an active transport into neurons and glial cells, serves to control the extracellular concentrations of L-glutamate and prevents the neurotoxicity. The modern techniques of molecular biology may have provided additional data on the nature and location of the transporters but the classical neurochemical approach, using structural analogues of glutamate designed as specific inhibitors or substrates for glutamate transport, has been crucial for the investigations of particular roles that glutamate transport might play in health and disease. Analysis of recent structure/activity data presented in this review has yielded a novel insight into the pharmacological characteristics of L-glutamate transport, suggesting existence of additional heterogeneity in the system, beyond that so far discovered by molecular genetics. More compounds that specifically interact with individual glutamate transporters are urgently needed for more detailed investigations of neurochemical characteristics of glutamatergic transport and its integration into the glutamatergic synapses in the central nervous system. A review with 162 references.

scholarly journals Plasma proteomics of green turtles (Chelonia mydas) reveals pathway shifts and potential biomarker candidates associated with health and disease

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David P Marancik ◽  
Justin R Perrault ◽  
Lisa M Komoroske ◽  
Jamie A Stoll ◽  
Kristina N Kelley ◽  
...  
Keyword(s):  
Chelonia Mydas ◽  
Sea Turtle ◽  
Protein Abundance ◽  
Plasma Samples ◽  
Important Species ◽  
Green Turtles ◽  
Rehabilitation Programs ◽  
Potential Biomarker ◽  
Health And Disease

Abstract Evaluating sea turtle health can be challenging due to an incomplete understanding of pathophysiologic responses in these species. Proteome characterization of clinical plasma samples can provide insights into disease progression and prospective biomarker targets. A TMT-10-plex-LC–MS/MS platform was used to characterize the plasma proteome of five, juvenile, green turtles (Chelonia mydas) and compare qualitative and quantitative protein changes during moribund and recovered states. The 10 plasma samples yielded a total of 670 unique proteins. Using ≥1.2-fold change in protein abundance as a benchmark for physiologic upregulation or downregulation, 233 (34.8%) were differentially regulated in at least one turtle between moribund and recovered states. Forty-six proteins (6.9%) were differentially regulated in all five turtles with two proteins (0.3%) demonstrating a statistically significant change. A principle component analysis showed protein abundance loosely clustered between moribund samples or recovered samples and for turtles that presented with trauma (n = 3) or as intestinal floaters (n = 2). Gene Ontology terms demonstrated that moribund samples were represented by a higher number of proteins associated with blood coagulation, adaptive immune responses and acute phase response, while recovered turtle samples included a relatively higher number of proteins associated with metabolic processes and response to nutrients. Abundance levels of 48 proteins (7.2%) in moribund samples significantly correlated with total protein, albumin and/or globulin levels quantified by biochemical analysis. Differentially regulated proteins identified with immunologic and physiologic functions are discussed for their possible role in the green turtle pathophysiologic response and for their potential use as diagnostic biomarkers. These findings enhance our ability to interpret sea turtle health and further progress conservation, research and rehabilitation programs for these ecologically important species.

scholarly journals Biochar Chemistry in a Weathered Tropical Soil: Kinetics of Phosphorus Sorption

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 295
Author(s):  
Marina Moura Morales ◽  
Nicholas Brian Comerford ◽  
Maurel Behling ◽  
Daniel Carneiro de Abreu ◽  
Iraê Amaral Guerrini
Keyword(s):  
Mineral Soil ◽  
Soil Surface ◽  
Kinetic Studies ◽  
Inorganic Phosphorus ◽  
Initial Reaction ◽  
Phosphorus Sorption ◽  
P Sorption ◽  
Published Research ◽  
Kinetics Of

The phosphorus (P) chemistry of biochar (BC)-amended soils is poorly understood. This statement is based on the lack of published research attempting a comprehensive characterization of biochar’s influence on P sorption. Therefore, this study addressed the kinetic limitations of these processes. This was accomplished using a fast pyrolysis biochar made from a mix of waste materials applied to a highly weathered Latossolo Vermelho distrofico (Oxisol) from São Paulo, Brazil. Standard method (batch method) was used. The sorption kinetic studies indicated that P sorption in both cases, soil (S) and soil-biochar (SBC), had a relatively fast initial reaction between 0 to 5 min. This may have happened because adding biochar to the soil decreased P sorption capacity compared to the mineral soil alone. Presumably, this is a result of: (i) Inorganic phosphorus desorbed from biochar was resorbed onto the mineral soil; (ii) charcoal particles physically covered P sorption locations on soil; or (iii) the pH increased when BC was added SBC and the soil surface became more negatively charged, thus increasing anion repulsion and decreasing P sorption.

scholarly journals Antiangiogenic potential of Jatropha curcas latex in the chick chorioallantoic membrane model

2019 ◽  
Vol 29 (1) ◽  
pp. 32157
Author(s):  
Luciane Madureira Almeida ◽  
Elisa Flávia Luiz Cardoso Bailão ◽  
Illana Reis Pereira ◽  
Fabrício Alves Ferreira ◽  
Patrícia Lima D'Abadia ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Jatropha Curcas ◽  
Physicochemical Characterization ◽  
Chorioallantoic Membrane ◽  
Angiogenesis Inhibitor ◽  
Negative Control ◽  
New Drugs ◽  
Membrane Model ◽  
Chick Chorioallantoic Membrane

AIMS: To perform a physicochemical and phytochemical characterization of Jatropha curcas latex and to investigate its antiangiogenic potential. METHODS: We performed an initial physicochemical characterization of J. curcas latex using thermal gravimetric analyses and Fourier Transform Infrared spectroscopy. After that, phenols, tannins and flavonoids were quantified. Finally, the potential of J. curcas latex to inhibit angiogenesis was evaluated using the chick chorioallantoic membrane model. Five groups of 20 fertilized chicken eggs each had the chorioallantoic membrane exposed to the following solutions: (1) water, negative control; (2) dexamethasone, angiogenesis inhibitor; (3) Regederm®, positive control; (4) 25% J. curcas latex diluted in water; (5) 50% J. curcas latex diluted in water; and (6) J. curcas crude latex. Analysis of the newly-formed vascular net was made through captured images and quantification of the number of pixels. Histological analyses were performed to evaluate the inflammation, neovascularization, and hyperemia parameters. The results were statically analyzed with a significance level set at p ˂0.05.RESULTS: Physicochemical characterization showed that J. curcas latex presented a low amount of cis-1.4-polyisoprene, which reduced its elasticity and thermal stability. Phytochemical analyses of J. curcas latex identified a substantial amount of phenols, tannins, and flavonoids (51.9%, 11.8%, and 0.07% respectively). Using a chick chorioallantoic membrane assay, we demonstrated the antiangiogenic potential of J. curcas latex. The latex induced a decrease in the vascularization of the membranes when compared with neutral and positive controls (water and Regederm®). However, when compared with the negative control (dexamethasone), higher J. curcas latex concentrations showed no significant differences.CONCLUSIONS: J. curcas latex showed low thermal stability, and consisted of phenols, tannins, and flavonoids, but little or no rubber. Moreover, this latex demonstrated a significant antiangiogenic activity on a chick chorioallantoic membrane model. The combination of antimutagenic, cytotoxic, antioxidant and antiangiogenic properties makes J. curcas latex a potential target for the development of new drugs.

Synthesis and Characterization of Novel PEPPSI type Pd–BICAAC Complexes

2022 ◽  
Author(s):  
Márton Nagyházi ◽  
Balázs Almási ◽  
Ádám Lukács ◽  
Attila Bényei ◽  
Tibor Nagy ◽  
...  
Keyword(s):  
High Activity ◽  
Coupling Reaction ◽  
Kinetic Studies ◽  
Elemental Mercury ◽  
Palladium Complexes ◽  
Synthesis And Characterization ◽  
Heck Coupling ◽  
Moisture Resistant

A series of bicyclic alkylamino carbenes (BICAAC) (where N-aryl = dipp, mes, 2,6-dimethyl-4-(dimethylamino)phenyl, 5a-d) and their novel air- and moisture-resistant pyridine (pyridine, 4 dimethylaminopyridine) containing palladium PEPPSI-type Pd(II) complexes (6a-e) were synthetized and characterized. The new palladium complexes have shown high activity in Mizoroki–Heck coupling reaction even at as low as 100 ppm loading (TON up to 10000). Kinetic studies revealed that reactions carried out in the presence of elemental mercury resulted in decrease in activity. It indicates that the coupling reaction may have both molecular and Pd(0)-mediated catalytic paths.

scholarly journals Evaluation of antipyretic activity of hydroalcoholic extract of Corchorus depressus Linn. in Escherichia coli–induced pyretic rabbits

2018 ◽  
Vol 16 ◽  
pp. 205873921879295
Author(s):  
Saeed Ahmad ◽  
Muhammad Akram ◽  
Syed Muhammad Ali Shah ◽  
Sabira Sultana
Keyword(s):  
Escherichia Coli ◽  
Positive Control ◽  
Negative Control ◽  
The Body ◽  
Hydroalcoholic Extract ◽  
Antipyretic Effect ◽  
E Coli ◽  
Antipyretic Activity ◽  
Experimental Treatments

This study was conducted to investigate the antipyretic effect of the hydroalcoholic extract of Corchorus depressus Linn. against Escherichia coli ( E. coli)-induced pyrexia in rabbits. Hydroalcohalic extracts of C. depressus were given orally at 25, 50, and 100 mg/kg for antipyretic affect in E. coli-induced fever in rabbits. The animals were divided into five groups of five each. Among these five groups, three received various doses of experimental treatments, whereas the fourth one served as positive control and received paracetamol. The fifth group of animals served as negative control and received no treatment. The body temperature of the rabbits was measured rectally over a period of 5 h. C. depressus exhibited better effects at dose rate of 25, 50, and 100 mg/kg. The hydroalcoholic extract of C. depressus has significant antipyretic effect. These results lend support to the popular use of C. depressus in traditional medicine as a remedy for pyrexia and suggest that the characterization of the principles for such activity deserves further investigation.

scholarly journals Impact of spineless cactus cultivation (O. Ficus-indica) on the thermal characteristics of soil

2018 ◽  
Vol 13 (1) ◽  
pp. 1
Author(s):  
Willames De Albuquerque Soares
Keyword(s):  
Heat Capacity ◽  
Thermal Characteristics ◽  
Thermal Characterization ◽  
Biological Processes ◽  
Volumetric Heat Capacity ◽  
Average Value ◽  
Brazilian Semiarid ◽  
Cultivation Techniques ◽  
Soil Changes

Temperature is a fundamentally important factor for understanding the physical, chemical, and biological processes that occur in soil. However, there are few studies in the Brazilian semiarid zone that seek to understand how soil degradation affects its thermal characteristics. The objective of this study was to evaluate the influence of cultivation techniques on the thermal characterization of soil, using the model proposed by Johansen. The study was conducted in the Agreste region of the state of Pernambuco, Brazil on two plots of land, one with native vegetation (Caatinga) and the other with spineless cactus (O. ficus - indica). It was observed that the procedures used to prepare the soil for cultivation of spineless cactus caused a reduction in the capacity to transmit the surface temperature to the interior of the soil. Changes in the physical properties of the soil required for cultivation resulted in a reduction in the average value of the volumetric heat capacity of about 22%; an increase of approximately 5% in the average volumetric heat capacity and a 26% increase in the thermal diffusivity of the soil, as well as a reduction of approximately 50% in the heat flux from the surface of the soil.

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