Synthesis and Validation of Substrates for PRMT1 using Plate-Based Screening Assay

PRMT (Protein Arginine Methyltransferase) is a mammalian enzyme that catalyzes methylation of arginine residues in a polypeptide chain. PRMT is categorized as 3 different types. The methylation can occur as asymmetric dimethylation (ADMA, PRMT 1, 2, 3, 4, 6, and 8), symmetric dimethylation (SDMA, PRMT 7, 5 and 9) or monomethylation (MMA, PRMT 7), Type I, II and III respectively. PRMT1 generates ADMA on arginine residues of the Histone H4 N-terminal tail, which can lead to transcription of cancer-related genes. Alternatively, PRMT5 can modify the same arginine residue to produce SDMA, which represses the development of those same cancer-related genes. A better understanding of the substrate specificity of these enzymes can assist in the development of novel isozyme-specific pharmaceuticals.1 To identify these differences, we synthesized a 96-well plate of peptides based on the Histone H4 N-terminal tail, screened them against PRMT1 using a screening method previously developed in the Knuckley lab.2 This medium-throughput screen identified 7 “hit” peptide sequences and consensus sequences based on the “hit” peptides were synthesized by solid-phase peptide synthesis. Each of these consensus sequences varied at the N-terminus, while retaining the more distal positive charges of H4-16 peptide. The peptides were validated using a MTase-GloTM Methyltransferase Assay to determine if they were indeed substrates for PRMT1. The kinetic values indicate their efficiency as PRMT1 substrates and further investigations are being conducted to identify the differences in the substrate specificity regarding PRMT4 and PRMT5. These continued efforts will help us gain a better understanding of the role PRMT isozymes play in the onset of cancer, while assisting in the design of novel pharmaceuticals to battle this disease

Investigating the Substrate Specificity of PRMT1 using a Plate Based Screening Method

Enzymes are biological catalysts that speed up the rate of a reaction by lowering the activation energy and converting substrate (reactant) to product more expeditiously. Enzymes have a high degree of specificity and will only catalyze selective reactions by targeting particular substrates. In mammals, there exists a family of 11 enzymes, PRMT’s (Protein Arginine Methyl transferase), that target protein arginine for post translational methylation on the guanidino nitrogen of the residue. They occur naturally as Type I, II and III and can administer asymmetric di-methylation (ADMA), symmetric dimethylation (SDMA) and monomethylation, respectively. The focal point of this project is to determine the substrate specificity of PRMT1 (Type I), PRMT 4, (Type I) and PRMT5 (Type II) on arginine residues in histone tails. Histones are eukaryotic proteins. The “tails” of the histones (polypeptide chains) are projected out from the protein and are often targets of various post translational modifications (PTM’s). Overexpression of PRMT 1 and PRMT 4 results in increased enzyme activity leading to ADMA on the histones arginine’s. This modification recruit’s transcription factors to the histone tails and induces the transcription of cancerous genes (colon, breast, prostate cancer, etc.). Meanwhile, PRMT 5 is repressive of these developments by leading to SDMA on the arginine, which blocks the enzyme activity and recruitment of these same transcription factors.  By synthesizing the histone H4 tail in this experiment and varying different regions using high-throughput libraries, a screening of PRMT1, 4 and 5 can be completed

Identification of Histone H4-Based Peptoids as Inhibitors of PRMT1

Protein Arginine Methyltransferases (PRMTs) are a family of 11 mammalian enzymes characterized by the post-translational methylation of arginine residues in the histone tail. The majority of the 11 members of the PRMT family are divided into two main types, Type I and Type II. PRMT1, the major Type I isozyme, catalyzes the formation of asymmetrically dimethylated arginine (ADMA). PRMT1 activates transcription of cancer genes. Peptoids, or poly-N-substituted glycine’s are a class of oligomers whose side chains are appended to the nitrogen atom of the peptide backbone rather than the alpha carbon. Kinetic parameters were conducted for both peptide and peptoid sequences. The Kcat/Km and IC50 values determined that peptoids show inhibition activity. The specificity and location of these interactions are currently being determined by altering the residues of a known peptoid sequence that has these interactions

Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening

<p>Abstract</p> <p>Background</p> <p>Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deiminase type 4 (PAD4) is the enzyme responsible for catalyzing the conversion of peptidylarginine into peptidylcitrulline. PAD4 is a new therapeutic target for RA treatment. In order to search for inhibitors of PAD4, structure-based virtual screening was performed using LIDAEUS (Ligand discovery at Edinburgh university). Potential inhibitors were screened experimentally by inhibition assays.</p> <p>Results</p> <p>Twenty two of the top-ranked water-soluble compounds were selected for inhibitory screening against PAD4. Three compounds showed significant inhibition of PAD4 and their IC₅₀values were investigated. The structures of the three compounds show no resemblance with previously discovered PAD4 inhibitors, nor with existing drugs for RA treatment.</p> <p>Conclusion</p> <p>Three compounds were discovered as potential inhibitors of PAD4 by virtual screening. The compounds are commercially available and can be used as scaffolds to design more potent inhibitors against PAD4.</p

Neutrophil extracellular traps enhance early inflammatory response in Sendai virus-induced asthma phenotype

Paramyxoviral infection in childhood has been linked to a significant increased rate of asthma development. In mice, paramyxoviral infection with the mouse parainfluenza virus type I, Sendai virus (Sev), causes a limited bronchiolitis followed by persistent asthma traits. We have previously shown that the absence of cysteine protease dipeptidyl peptidase I (DPPI) dampened the acute lung inflammatory response and the subsequent asthma phenotype induced by Sev. Adoptive transfer of wild type neutrophils into DPPI-deficient mice restored leukocyte influx, the acute cytokine response, and the subsequent mucous cell metaplasia that accompanied Sev-induced asthma phenotype. However, the exact mechanism by which DPPI-sufficient neutrophils promote asthma development following Sev infection is still unknown. We hypothesize that neutrophils recruited to the alveolar space following Sev infection elaborate neutrophil extracellular traps (NETs) that propagate the inflammatory cascade, culminating in the eventual asthma phenotype. Indeed, we found that Sev infection was associated with NET formation in the lung and release of cell-free DNA complexed to myeloperoxidase (MPO) in the alveolar space and plasma that peaked on day 2-post infection. Absence of DPPI significantly attenuated Sev-induced NET formation in vivo and in vitro. Furthermore, concomitant administration of DNase 1, which dismantled NETs, or inhibition of peptidylarginine deiminase 4 (PAD4), an essential mediator of NET formation, suppressed the early inflammatory responses to Sev infection. Lastly, NETs primed bone marrow derived cells to release cytokines that can amplify the inflammatory cascade

Novel furan-containing peptide-based inhibitors of protein arginine deiminase type IV (PAD4)

Protein arginine deiminase type IV (PAD4) is responsible for the posttranslational conversion of peptidylarginine to peptidylcitrulline. Citrullinated protein is the autoantigen in rheumatoid arthritis, and therefore, PAD4 is currently a promising therapeutic target for the disease. Recently, we reported the importance of the furan ring in the structure of PAD4 inhibitors. In this study, the furan ring was incorporated into peptides to act as the “warhead” of the inhibitors for PAD4. IC50 studies showed that the furan-containing peptide-based inhibitors were able to inhibit PAD4 to a better extent than the furan-containing small molecules that were previously reported. The best peptide-based inhibitor inhibited PAD4 reversibly and competitively with an IC50 value of 243.2 ± 2.4 μm. NMR spectroscopy and NMR-restrained molecular dynamic simulations revealed that the peptide-based inhibitor had a random structure. Molecular docking studies showed that the peptide-based inhibitor entered the binding site and interacted with the essential amino acids involved in the catalytic activity. The peptide-based inhibitor could be further developed into a therapeutic drug for rheumatoid arthritis

Purification of enzymatically inactive peptidylarginine deiminase type 6 from mouse ovary that reveals hexameric structure different from other dimeric isoforms

The murine peptidylarginine deiminase (PAD) has five isoforms encoded by different genes and partici- pates in a variety of cellular functions through the citrullination of target proteins. The crystal structure of human PAD4 with a dimeric form was previously solved because of the enzyme’s relevance to rheuma- toid arthritis. PAD6, abundant in mouse oocytes and eggs, is believed to take part in early events of embryogenesis, but its biochemical properties are little understood. Here we have purified and charac- terized a recombinant PAD6. A PAD6 cDNA was cloned from mouse ovary RNA and expressed in Escherichia coli through pET29 and pGEX vectors. When benzoyl-L-arginine ethyl ester was used as a substrate, no appreciable activity was detected with a cell homogenate under conditions where a human PAD4 cDNA caused significant activity. Both pro- teins were affinity-purified to near homogeneity. The circular dichroism spectra of PAD6 and human PAD4 were similar in the far ultraviolet region. On molecular sieving, PAD6 was eluted faster than human PAD4. The cross-linking of PAD6 with dime- thyl suberimidate clearly showed six bands on an sodium dodecyl sulfate-polyacrylamide gel. These results indicate that PAD6 can constitute a hexameric structure. The purified PAD6 still showed no enzy- matic activity. This unique structure and loss in enzymatic activity is strongly suggested to favor the formation of egg cytoplasmic sheets as the architectu- ral protein

Functional Role of Dimerization of Human Peptidylarginine Deiminase 4 (PAD4)

Peptidylarginine deiminase 4 (PAD4) is a homodimeric enzyme that catalyzes Ca2+-dependent protein citrullination, which results in the conversion of arginine to citrulline. This paper demonstrates the functional role of dimerization in the regulation of PAD4 activity. To address this question, we created a series of dimer interface mutants of PAD4. The residues Arg8, Tyr237, Asp273, Glu281, Tyr435, Arg544 and Asp547, which are located at the dimer interface, were mutated to disturb the dimer organization of PAD4. Sedimentation velocity experiments were performed to investigate the changes in the quaternary structures and the dissociation constants (Kd) between wild-type and mutant PAD4 monomers and dimers. The kinetic data indicated that disrupting the dimer interface of the enzyme decreases its enzymatic activity and calcium-binding cooperativity. The Kd values of some PAD4 mutants were much higher than that of the wild-type (WT) protein (0.45 µM) and were concomitant with lower kcat values than that of WT (13.4 s−1). The Kd values of the monomeric PAD4 mutants ranged from 16.8 to 45.6 µM, and the kcat values of the monomeric mutants ranged from 3.3 to 7.3 s−1. The kcat values of these interface mutants decreased as the Kd values increased, which suggests that the dissociation of dimers to monomers considerably influences the activity of the enzyme. Although dissociation of the enzyme reduces the activity of the enzyme, monomeric PAD4 is still active but does not display cooperative calcium binding. The ionic interaction between Arg8 and Asp547 and the Tyr435-mediated hydrophobic interaction are determinants of PAD4 dimer formation

Peptidylarginine deiminases as drug targets in neonatal hypoxic-ischemic encephalopathy

Oxygen deprivation and infection are major causes of perinatal brain injury leading to cerebral palsy and other neurological disabilities. The identification of novel key factors mediating white and grey matter damage are crucial to allow better understanding of the specific contribution of different cell types to the injury processes and pathways for clinical intervention. Recent studies in the Rice-Vannucci mouse model of neonatal hypoxic ischaemia (HI) have highlighted novel roles for calcium-regulated peptidylarginine deiminases (PADs) and demonstrated neuro-protective effects of pharmacological PAD inhibition following HI and synergistic infection mimicked by LPS stimulation