A Genetically Encoded Allysine for the Synthesis of Proteins with Site‐Specific Lysine Dimethylation

Using the amber suppression approach, N^ϵ‐(4‐azidobenzoxycarbonyl)‐δ,ϵ‐dehydrolysine, an allysine precursor is genetically encoded in E. coli. Its genetic incorporation followed by two sequential biocompatible reactions allows convenient synthesis of proteins with site‐specific lysine dimethylation. Using this approach, dimethyl‐histone H3 and p53 proteins have been synthesized and used to probe functions of epigenetic enzymes including histone demethylase LSD1 and histone acetyltransferase Tip60. We confirmed that LSD1 is catalytically active toward H3K4me2 and H3K9me2 but inert toward H3K36me2, and methylation at p53 K372 directly activates Tip60 for its catalyzed acetylation at p53 K120.     

Histone demethylase KDM4A plays an oncogenic role in nasopharyngeal carcinoma by promoting cell migration and invasion

Compelling evidence has indicated the vital role of lysine-specific demethylase 4 A (KDM4A), hypoxia-inducible factor-1α (HIF1α) and the mechanistic target of rapamycin (mTOR) signaling pathway in nasopharyngeal carcinoma (NPC). Therefore, we aimed to investigate whether KDM4A affects NPC progression by regulating the HIF1α/DDIT4/mTOR signaling pathway. First, NPC and adjacent tissue samples were collected, and KDM4A protein expression was examined by immunohistochemistry. Then, the interactions among KDM4A, HIF1α and DDIT4 were assessed. Gain- and loss-of-function approaches were used to alter KDM4A, HIF1α and DDIT4 expression in NPC cells. The mechanism of KDM4A in NPC was evaluated both in vivo and in vitro via RT-qPCR, Western blot analysis, MTT assay, Transwell assay, flow cytometry and tumor formation experiments. KDM4A, HIF1α, and DDIT4 were highly expressed in NPC tissues and cells. Mechanistically, KDM4A inhibited the enrichment of histone H3 lysine 9 trimethylation (H3K9me3) in the HIF1α promoter region and thus inhibited the methylation of HIF1α to promote HIF1α expression, thus upregulating DDIT4 and activating the mTOR signaling pathway. Overexpression of KDM4A, HIF1α, or DDIT4 or activation of the mTOR signaling pathway promoted SUNE1 cell proliferation, migration, and invasion but inhibited apoptosis. KDM4A silencing blocked the mTOR signaling pathway by inhibiting the HIF1α/DDIT4 axis to inhibit the growth of SUNE1 cells in vivo. Collectively, KDM4A silencing could inhibit NPC progression by blocking the activation of the HIF1α/DDIT4/mTOR signaling pathway by increasing H3K9me3, highlighting a promising therapeutic target for NPC.Subject terms: Oncogenes, Cancer     

Traceless Synthesis of Asymmetrically Modified Bivalent Nucleosomes

Nucleosomes carry extensive post‐translational modifications (PTMs), which results in complex modification patterns that are involved in epigenetic signaling. Although two copies of each histone coexist in a nucleosome, they may not carry the same PTMs and are often differently modified (asymmetric). In bivalent domains, a chromatin signature prevalent in embryonic stem cells (ESCs), namely H3 methylated at lysine 4 (H3K4me3), coexists with H3K27me3 in asymmetric nucleosomes. We report a general, modular, and traceless method for producing asymmetrically modified nucleosomes. We further show that in bivalent nucleosomes, H3K4me3 inhibits the activity of the H3K27‐specific lysine methyltransferase (KMT) polycomb repressive complex 2 (PRC2) solely on the same histone tail, whereas H3K27me3 stimulates PRC2 activity across tails, thereby partially overriding the H3K4me3‐mediated repressive effect. To maintain bivalent domains in ESCs, PRC2 activity must thus be locally restricted or reversed.     

LSD1: more than demethylation of histone lysine residues

Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer.Subject terms: Epigenetics, Histone post-translational modifications     

Alkali Metal and Alkaline Earth Metal Complexes with the Bis(borane‐diphenylphosphanyl)amido Ligand – Synthesis,Structures, and Catalysis for Ring‐Opening Polymerization of ϵ‐Caprolactone

The syntheses of lithium and alkaline earth metal complexes with the bis(borane‐diphenylphosphanyl)amido ligand ( 1 ‐ H ) of molecular formulas [{κ²‐N(PPh₂(BH₃))₂}Li(THF)₂] ( 2 ) and [{κ³‐N(PPh₂(BH₃))₂}₂M(THF)₂] [(M = Ca ( 3 ), Sr ( 4 ), Ba ( 5 )] are reported. The lithium complex 2 was obtained by treatment of bis(borane‐diphenylphosphanyl)amine ( 1 ‐ H ) with lithium bis(trimethylsilyl)amide in a 1:1 molar ratio via the silylamine elimination method. The corresponding homoleptic alkaline earth metal complexes 3 – 5 were prepared by two synthetic routes – first, the treatment of metal bis(trimethylsilyl)amide and protio ligand 1 ‐ H via the elimination of silylamine, and second, through salt metathesis reaction involving respective metal diiodides and lithium salt 2 . The molecular structures of lithium complex 2 and barium complex 5 were established by single‐crystal X‐ray diffraction analysis. In the solid‐state structure of 2 , the lithium ion is ligated by amido nitrogen atoms and hydrogen atoms of the BH₃ group in κ²‐coordination of the ligand 1 resulting in a distorted tetrahedral geometry around the lithium ion. However, in complex 5 , κ³‐coordination of the ligand 1 was observed, and the barium ion adopted a distorted octahedral arrangement. The metal complex 5 was tested as catalyst for the ring opening polymerization of ?‐caprolactone. High activity for the barium complex 5 towards ring opening polymerization (ROP) of ?‐caprolactone with a narrow polydispersity index was observed. Additionally, first‐principle calculations to investigate the structure and coordination properties of alkaline earth metal complexes 3 – 5 as a comparative study between the experimental and theoretical findings were described.     

Discovery of a Highly Selective Cell‐Active Inhibitor of the Histone Lysine Demethylases KDM2/7

Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell‐permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure–activity relationships, leading to the development of a small molecule with around 75‐fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.     

Direct Synthesis of 5‐Aryl Barbituric Acids by Rhodium(II)‐Catalyzed Reactions of Arenes with Diazo Compounds

A commercially available rhodium(II) complex catalyzes the direct arylation of 5‐diazobarbituric acids with arenes, allowing straightforward access to 5‐aryl barbituric acids. Free N? H groups are tolerated on the barbituric acid, with no complications arising from N? H insertion processes. This method was applied to the concise synthesis of a potent matrix metalloproteinase (MMP) inhibitor.     

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 , K_D=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.     

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 , K_D=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.     

Synthesis and Herbicidal Activity of 5‐Alkyl(aryl)‐3‐[(3‐trifluoromethyl)anilino]‐4,5‐dihydro‐1H‐pyrazolo[4,3‐d]pyrimidin‐4‐imines

A series of novel 5‐alkyl(aryl)‐3‐[(3‐trifluoromethyl)anilino]‐4,5‐dihydro‐1H‐pyrazolo[4,3‐d]pyrimidin‐4‐imines were designed and synthesized by the multistep reactions. 1 reacted with 3‐(trifluoromethyl)aniline to obtain N,S‐acetals 2 in the presence of 10 mol% DBU. 2 reacted with hydrazine to form 5‐amino‐3‐[(3‐trifluoromethyl)anilino]‐1H‐pyrazol‐4‐ nitrile 3 , the target compounds 5a , 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i , 5j , 5k , 5l , 5m were obtained by the reaction of 3 with triethyl orthoformate followed by the cyclization of 4 with various amines. Their structures were confirmed by IR, ¹H NMR, EI‐MS, and elemental analyses. The preliminary bioassay indicated that some of them displayed moderate herbicidal activity against dicotyledonous weed Brassica campestris L at the concentration of 100 mg/L. For example, compounds 5f , 5g , 5h , and 5j possessed 60.1%, 63.4%, 67.1%, and 61.3% inhibition against Brassica campestris L at the concentration of 100 mg/L.     

Divalent manganese,cobalt, copper and cadmium complexes of (Z)‐N‐benzoyl‐N′‐(1H‐1,2,4‐triazol‐3‐yl)carbamimidothioic acid: Preparation,characterization, computational and biological studies

In this work, (Z)‐N‐benzoyl‐N′‐(1H‐1,2,4‐triazol‐3‐yl)carbamimidothioic acid and its Mn(II), Co(II), Cu(II) and Cd(II) complexes were introduced for the first time. This carbonyl thiourea ligand was prepared by the reaction of 1H‐1,2,4‐triazol‐3‐amine with benzoyl isothiocyanate. The structural elucidation of these compounds was performed using elemental analysis and spectral and magnetic measurements. Octahedral structures of all complexes, except Cd(II) complex with a tetrahedral geometry, were confirmed by applying DFT structural optimization. The thermal decomposition behaviour of metal complexes of carbonyl thiourea ligand is discussed. The calculation of kinetic parameters for prepared complexes (E_a, A, ΔH*, ΔS* and ΔG*) of all thermal degradation stages has been evaluated using two comparable approaches. Antimicrobial and ABTS‐antioxidant studies indicated potent activity of Cd(II) complex compared with the other investigated compounds. The cytotoxic activity of the prepared compounds was investigated in vitro. The results indicated potent activity of Mn(II) complex against both HePG2 (liver carcinoma) and MCF‐7 (breast carcinoma) cancer cells.     

New Rh(III) complexes of 5‐methyl‐5‐(pyridyl)‐2,4‐imidazolidenedione: Synthesis,X‐ray structure,electrochemical study and catalytic behaviour for hydrogenation of ketones

We describe the reaction of anion [RhCl₆]³⁻ with a series of hydantoin ligands (HL1, HL2 and HL3 = 5‐methyl‐5‐(2‐, 3‐ and 4‐pyridyl)‐2,4‐imidazolidenedione, respectively). Based on spectroscopic, cyclic voltammetric, elemental and MS analyses, the complexes have the general formula K[RhCl₂(L1)₂] ( 1 ), cis ‐ and trans ‐K[RhCl₄(HL2)₂] ( 2a and 2b ) and cis ‐ and trans ‐K[RhCl₄(HL3)₂] ( 3a and 3b ). Complexes 2a , 2b , 3a and 3b were characterized successfully using infrared, ¹H NMR and ¹³C NMR spectral analyses. Dissolution of complex 1 in dimethylsulfoxide (DMSO) led to elimination of one KL1 ligand and coordination of two DMSO molecules as ligands and transformation of this complex to cis ‐ and trans ‐[RhCl₂L1(DMSO)₂] ( 1a and 1b ). Recrystallization led to separation and isolation of crystals of 1a from the initial mixture. X‐ray analysis results showed that this complex was crystallized as solvated complex cis ‐[RhCl₂L1(DMSO)₂]DMSO. The catalytic activity of these complexes was then evaluated for the hydrogenation of various ketones.     

A Heteroleptic Ferrous Complex with Mesoionic Bis(1,2,3‐triazol‐5‐ylidene) Ligands: Taming the MLCT Excited State of Iron(II)

Strongly σ‐donating N‐heterocyclic carbenes (NHCs) have revived research interest in the catalytic chemistry of iron, and are now also starting to bring the photochemistry and photophysics of this abundant element into a new era. In this work, a heteroleptic Fe^II complex ( 1 ) was synthesized based on sequentially furnishing the Fe^II center with the benchmark 2,2′‐bipyridine (bpy) ligand and the more strongly σ‐donating mesoionic ligand, 4,4′‐bis(1,2,3‐triazol‐5‐ylidene) (btz). Complex 1 was comprehensively characterized by electrochemistry, static and ultrafast spectroscopy, and quantum chemical calculations and compared to [Fe(bpy)₃](PF₆)₂ and (TBA)₂[Fe(bpy)(CN)₄]. Heteroleptic complex 1 extends the absorption spectrum towards longer wavelengths compared to a previously synthesized homoleptic Fe^II NHC complex. The combination of the mesoionic nature of btz and the heteroleptic structure effectively destabilizes the metal‐centered (MC) states relative to the triplet metal‐to‐ligand charge transfer (³MLCT) state in 1 , rendering it a lifetime of 13 ps, the longest to date of a photochemically stable Fe^II complex. Deactivation of the ³MLCT state is proposed to proceed via the ³MC state that strongly couples with the singlet ground state.     

Synthesis,Characterization and X‐ray Structures of AMTT‐Type Schiff bases and two CuI Complexes (AMTT= 4‐amino‐5‐methyl‐2H‐1,2,4‐triazole‐3(4H)‐thione)

The reaction of 4‐amino‐5‐methyl‐2H‐1,2,4‐triazole‐3(4H)‐thione (AMTT) with 4‐methylbenzaldehyde and 4‐methoxybenzaldehyde in ethanol led to the iminic derivatives ‐4‐(4‐methylbenzylideneamino)‐5‐methyl‐2H‐1,2,4‐triazole‐3(4H)thione ( L1 ) and 4‐(4‐methoxybenzyl‐ideneamino)‐5‐methyl‐2H‐1,2,4‐triazole‐3(4H)‐thione ( L2 ). The reaction of L1 with CuCl in the presence of triphenylphosphane as co‐ligand in methanol/chloroform solution gave the Cu^I complex containing L1 , [Cu( L1 )(PPh₃)₂Cl]·0.5CH₃OH·0.25CHCl₃ ( 1 ). Treatment of L2 with the same metal salt in a molar ratio of 1:1 in methanol and further addition of a solution of PPh₃ in chloroform led to the complex [Cu( L2 )(PPh₃)₂Cl]·2.5CHCl₃ ( 2 ). The complexes and L1 were characterized by IR and NMR spectroscopy as well as by X‐ray diffraction studies. In both complexes, the Schiff base ligand is coordinated to the copper ion through its sulfur atom. The other coordination sites around the copper ion are occupied by two triphenylphosphane molecules and one chloride ion. Therefore, each Cu^I ion is in a distorted tetrahedral environment. Crystal data for L1 at ?100 °C: space group P2₁/n with a = 720.5(1), b = 1140.6(1), c = 1426.3(2) pm, β = 91.25(1)°, Z = 4, R₁ = 0.03, for 1 at ?120 °C : space group with a = 1286.3(1), b = 1740.3(1), c = 2060.2(1) pm, α = 79.085(6), β = 83.827(5), γ = 76.688(6)°, Z = 4, R₁ = 0.0649 and for 2 at ?80 °C : space group with a = 1183.7(2), b = 1370.1(2), c = 1812.1(3) pm, α = 85.69(2), β = 88.52(2), γ = 64.89(2)°, Z = 2, R₁ = 0.0488.     

Synthesis,characterization and biological evaluation of a cobalt(II) complex with 5‐chloro‐8‐hydroxyquinoline as anticancer agent

A new cobalt(II) complex ( 1 ) of 5‐chloro‐8‐hydroxyquinoline was prepared and structurally characterized using infrared spectroscopy, electrospray ionization mass spectrometry, elemental analysis, single‐crystal X‐ray diffraction as well as powder X‐ray diffraction. Its biological activities including DNA binding and anticancer activity were investigated. The DNA binding study of complex 1 suggested that it interacted with calf thymus DNA mainly via an intercalative binding mode. The in vitro anticancer activity of complex 1 was screened against a series of tumor cell lines as well as the normal liver cell line HL‐7702 using MTT assay. complex 1 showed much higher cytotoxicity than corresponding metal salt and ligand towards the five tested tumor cell lines, in which T‐24 was the most sensitive tumor cell line towards 1, with IC₅₀ value of 7.04 ± 0.06 μM. complex 1 was found to greatly induce cell cycle arrest in T‐24 cells at S phase, and consequently to induce cell apoptosis in a dose‐dependent mode suggested by cell apoptosis analysis via Hoechst 33258 and acridine orange/ethidium bromide staining assays. The cell apoptosis mechanism of 1 was studied targeting the mitochondrion‐mediated pathway, since the apoptotic mechanism in the T‐24 cells treated by 1 was investigated by reactive oxygen species (ROS) detection, intracellular calcium concentration measurement and caspase‐9/3 activity assay. The results suggested that the cell apoptosis induced by 1 was closely related to the loss of mitochondrial membrane potential, ROS production and enhancement of intracellular [Ca²⁺], which would trigger the caspase‐9/3 activation via a mitochondrial dysfunction pathway. Copyright © 2016 John Wiley & Sons, Ltd.     

Binding Modes of Small-Molecule Inhibitors to the EED Pocket of PRC2

Polycomb Polycomb repressive complex 2 (PRC2) plays a key role in silencing epigenetic gene through trimethylation of lysine 27 on histone 3 (H3K27). Dysregulations of PRC2 caused by overexpression and mutations of the core subunits of PRC2 have been implicated in many cancers. The core subunits EZH1/2 are histone-lysine N-methyltransferases that function as the enzymatic component of PRC2. While the core subunit EED is a scaffolding protein to support EZH1/2 and binds JARID2K116me3/H3K27me3 to enhance the enzymatic activity of PRC2 through allosteric activation. Recently, several small molecules that compete with JARI2K116me3 and H3K27me3 have been reported. These molecules selectively bind to the JARID2K116me3/H3K27me3-binding pocket of EED, thereby preventing the allosteric regulation of PRC2. These first-in-class PRC2 inhibitors show robust suppression in DLBCL cell lines, demonstrating anticancer drugs that target the EED subunit of PRC2 are viable. In this study, we used the recently developed MM/GBSA_IE and the alanine scanning method to analyze the hot spots in EED/inhibitor interactions. The analysis of these hot and warm spots helps us to understand the fundamental differences between inhibitors. Our results give a quantitative explanation on why the binding affinities of EED/A-395 interactions are stronger than that of EED/EED226 while their binding modes are similar and provide valuable insights for rational design of novel EED inhibitors.     

Synthesis of 2,6‐diamino‐5‐[(2‐substituted phenylamino)ethyl]pyrimidin‐4(3h)‐one as inhibitors of folate metabolizing enzymes

A series of eleven novel 2,6‐diamino‐5‐[(2‐substituted phenylamino)ethyl]pyrimidin‐4(3H)‐one derivatives were synthesized as potential inhibitors of dihydrofolate reductase (DHFR) and thymidylate synthase (TS). The synthesis of analogues 2a‐f, 3a and 3e was achieved via an improved method. Commercially available anilines 12a‐f were used as starting materials which on reaction with chloroacetaldehyde followed by cyanoacetate and cyclocondensation with guanidine afforded 2,6‐diamino‐5‐[(2‐substituted phenylamino)ethyl]pyrimidin‐4(3H)‐one 2a‐f in three steps. The N‐methyl analogues 3a‐3e were prepared by reductive methylation. These compounds were evaluated against dihydrofolate reductase from Escherichia coli, Toxoplasma gondii, Pneumocystis carinii, human, and rat liver. Few compounds were marginally active against dihydrofolate reductase. The most potent inhibitor, ( 2c ) which has a 1‐naphthyl substituent on the side chain, has an IC₅₀ = 150 μM and 9.1 μM against Escherichia coli and Toxoplasma gondii DHFR, respectively.     

What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C−H or N−H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N−H pathway is ∼10 kcal/mol higher than for the C−H pathway due to the higher bond dissociation energy of the N−H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C−H pathway, by contrast, such EEFs inhibit the N−H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C−H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.