Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity

Catechol O-methyltransferase (COMT) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. Hydrophobic amino acids near the active site of COMT influence the regioselectivity of this reaction. Our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. Reaction barriers calculated in the gas phase reveal a lower barrier during methylation at the meta- position, suggesting that the observed meta-regioselectivity of COMT can be attributed to the substrate itself, and that COMT has evolved residues to orient the substrate in a manner that increases the rate of catalysis.     

Characterization of Chinese Lacquer in Historical Artwork by On-Line Methylation Pyrolysis-Gas Chromatography/Mass Spectrometry

An effective method for characterizing Chinese lacquer as binding medium in historical artwork has been developed by on-line methylation pyrolysis-gas chromatography–mass spectrometry (pyrolysis GC–MS). The characteristic pyrolytic components of Chinese lacquer were identified in artificially aged pure and pigmented lacquer. Methylation of urushiol (mainly composed of catechol derivatives) was performed by adding tetramethyl ammonium hydroxide to convert phenolic hydroxyl groups into methylated derivatives to improve the resolution of catechol derivatives and urushiol monomers. The mechanism of formation of small molecular components was proposed, and the influence of different mineral pigments (azurite, malachite, ochre, and cinnabar) on the determination of characteristic components was discussed. Aliphatic hydrocarbon components, benzene derivatives, catechol derivatives, and urushiol monomers were proposed as characteristic pyrolytic components. In addition to 3-pentadecene-catechol, 3-pentadecane-catechol, and 3-heptadecene-catechol, 3-pentadecene-phenol was also identified as an urushiol monomer in Chinese lacquer. Four pigments slightly reduced the detection of aliphatic hydrocarbon components, but were unconspicuous for the detection of benzene derivatives. Azurite, malachite, and cinnabar decreased the measurement of urushiol monomers, but ochre significantly increased their relative abundance. The established on-line methylation pyrolysis GC–MS procedure and summarized data were successfully applied to the identification of samples collected from Terra-Cotta Warriors and Horses of Qin Dynasty (221–207 BC), Han Yang Mausoleum of Han Dynasty (206 BC–24 AD), and Dazu Grotto of Tang Dynasty (618–907 AD).     

Bisubstrate inhibitors for the enzyme catechol-O-methyltransferase (COMT): influence of inhibitor preorganisation and linker length between the two substrate moieties on binding affinity

Inhibition of the enzyme catechol-O-methyltransferase (COMT) is an important approach in the treatment of Parkinson's disease. A series of new potent bisubstrate inhibitors for COMT, resulting from X-ray structure-based design and featuring adenosine and catechol moieties have been synthesised. Biological results show a large dependence of binding affinity on inhibitor preorganisation and the length of the linker between nucleoside and catechol moieties. The most potent bisubstrate inhibitor for COMT has an IC50 value of 9 nM. It exhibits competitive kinetics for the SAM and mixed inhibition kinetics for the catechol binding site. Its bisubstrate binding mode was confirmed by X-ray structure analysis of the ternary complex formed by the inhibitor, COMT and a Mg2+ ion.     

Mussel-inspired 3D networks with stiff-irreversible or soft-reversible characteristics - It's all a matter of solvent

Mostly, catechol groups are used as cross-linkers either based on oxidation to make irreversible networks in presence of oxidizing agent or coordination with metal ions to form reversible networks. However, a systematic study of gelation of catecholic polymer by adding oxidizing agent in non-aqueous solvents are scarce. Here, we report a study of gelation of catecholic polymer by adding oxidizing agent in different media to show the effect of media on behavior of catechol groups. When the gelation performed in an aprotic solvent, the copolymer containing catechol units gelates supramolecularly by H-bonding, yielding reversible and self-healing behavior, while in aqueous solvents irreversibly crosslinked not self-healing gels are obtained. As polymer-bound catechol groups are often studied in water, knowledge of the behavior of catecholic polymer in organic solvents is important to create supramolecular structures with more precisely controlled properties.     

A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods

A panel of 92 catechol-O-methyltransferase (COMT) inhibitors was used to examine the molecular interactions affecting their biological activity. COMT inhibitors are used as therapeutic agents in the treatment of Parkinson's disease, but there are limitations in the currently marketed compounds due to adverse side effects. This study combined molecular docking methods with three-dimensional structure-activity relationships (3D QSAR) to analyse possible interactions between COMT and its inhibitors, and to incite the design of new inhibitors. Comparative molecular field analysis (CoMFA) and GRID/GOLPE models were made by using bioactive conformations from docking experiments, which yielded q2 values of 0.594 and 0.636, respectively. The docking results, the COMT X-ray structure, and the 3D QSAR models are in agreement with each other. The models suggest that an interaction between the inhibitor's catechol oxygens and the Mg2+ ion in the COMT active site is important. Both hydrogen bonding with Lys144, Asn170 and Glu199, and hydrophobic contacts with Trp38, Pro174 and Leu198 influence inhibitor binding. Docking suggests that a large R1 substituent of the catechol ring can form hydrophobic contacts with side chains of Val173, Leu198, Met201 and Val203 on the COMT surface. Our models propose that increasing steric volume of e.g. the diethylamine tail of entacapone is favourable for COMT inhibitory activity.     

Structure-based design, synthesis, and in vitro evaluation of bisubstrate inhibitors for catechol O-methyltransferase (COMT)

The enzyme catechol O-methyltransferase (COMT) catalyzes the Me group transfer from the cofactor S-adenosylmethionine (SAM) to the hydroxy group of catechol substrates. Potential bisubstrate inhibitors of COMT were developed by structure-based design and synthesized. The compounds were tested for in vitro inhibitory activity against COMT obtained from rat liver, and the inhibition kinetics were examined with regard to the binding sites of cofactor and substrate. One of the designed molecules was found to be a bisubstrate inhibitor of COMT with an IC50 = 2 microM. It exhibits competitive kinetics for the SAM and noncompetitive kinetics for the catechol binding site. Useful structure-activity relationships were established which provide important guidelines for the design of future generations of bisubstrate inhibitors of COMT.     

Molecular recognition at the active site of catechol-O-methyltransferase (COMT): adenine replacements in bisubstrate inhibitors

L-Dopa, the standard therapeutic for Parkinson's disease, is inactivated by the enzyme catechol-O-methyltransferase (COMT). COMT catalyzes the transfer of an activated methyl group from S-adenosylmethionine (SAM) to its catechol substrates, such as L-dopa, in the presence of magnesium ions. The molecular recognition properties of the SAM-binding site of COMT have been investigated only sparsely. Here, we explore this site by structural alterations of the adenine moiety of bisubstrate inhibitors. The molecular recognition of adenine is of special interest due to the great abundance and importance of this nucleobase in biological systems. Novel bisubstrate inhibitors with adenine replacements were developed by structure-based design and synthesized using a nucleosidation protocol introduced by Vorbrüggen and co-workers. Key interactions of the adenine moiety with COMT were measured with a radiochemical assay. Several bisubstrate inhibitors, most notably the adenine replacements thiopyridine, purine, N-methyladenine, and 6-methylpurine, displayed nanomolar IC(50) values (median inhibitory concentration) for COMT down to 6 nM. A series of six cocrystal structures of the bisubstrate inhibitors in ternary complexes with COMT and Mg(2+) confirm our predicted binding mode of the adenine replacements. The cocrystal structure of an inhibitor bearing no nucleobase can be regarded as an intermediate along the reaction coordinate of bisubstrate inhibitor binding to COMT. Our studies show that solvation varies with the type of adenine replacement, whereas among the adenine derivatives, the nitrogen atom at position 1 is essential for high affinity, while the exocyclic amino group is most efficiently substituted by a methyl group.     

Synthesis and Biological Evaluation of Potent Bisubstrate Inhibitors of the Enzyme Catechol O‐Methyltransferase (COMT) Lacking a Nitro Group

Inhibition of the enzyme catechol O‐methyltransferase (COMT) represents a viable strategy for regulation of the catabolism of catecholamine neurotransmitters or their precursors, and is of considerable interest in the therapy of Parkinson's disease. Herein, we report the development of a new generation of potent bisubstrate inhibitors of COMT derived from nitro‐substituted ligand 1 (K_i = 28 nM , Table 1), which achieve high biological activity despite the lack of a NO₂ substituent on the catechol moiety. Their synthesis takes advantage of a convergent approach, in which a series of functionalized catechol intermediates is prepared (Schemes 2–7) and coupled to a common adenosine‐derived allylic amine building block (Scheme 8). Biological activities of the newly synthesized inhibitors, determined by in vitro enzymatic assay and kinetic studies, clearly demonstrate that high inhibitory potency of the bisubstrate inhibitors is not correlated with the pK_a of the catechol OH groups. Aromatic residues, connected to the catechol via a biaryl‐type linkage, were found to maximally benefit from additional favorable hydrophobic interactions with the enzyme and thus to be preferred replacements of the NO₂ group in 1 . A competitive kinetic inhibition mechanism (Fig. 2) with respect to the cofactor binding site was confirmed in all cases, supporting a bisubstrate inhibition mode for inhibitors 2 – 19 .     

How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

A distinct protein lysine methyltransferase (PKMT) only transfers a certain number of methyl group(s) to its target lysine residue in spite of the fact that a lysine residue can be either mono-, di-, or tri-methylated. In order to elucidate how such a remarkable product specificity is achieved, we have carried out ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations on two SET-domain PKMTs: SET7/9 and Rubisco large subunit methyltransferase (LSMT). The results indicate that the methylation state specificity is mainly controlled by the methyl-transfer reaction step, and confirm that SET7/9 is a mono-methyltransferase while LSMT has both mono-and di-methylation activities. It is found that the binding of the methylated lysine substrate in the active site of SET7/ 9 opens up the cofactor AdoMet binding channel so that solvent water molecules get access to the active site. This disrupts the catalytic machinery of SET7/9 for the di-methylation reaction, which leads to a higher activation barrier, whereas for the LSMT, its active site is more spacious than that of SET7/9, so that the methylated lysine substrate can be accommodated without interfering with its catalytic power. These detailed insights take account of protein dynamics and are consistent with available experimental results as well as recent theoretical findings regarding the catalytic power of SET7/9.     

肉桂酰酪胺类似物的合成与抗血小板聚集评价

为了探究肉桂酰酪胺的苯环上甲氧基取代、酪胺上羟基和酰胺上胺基被甲基化对衍生物抗血小板聚集活性的影响,以8种苯甲醛衍生物为原料,经过缩合反应及甲基化等反应制得肉桂酰酪胺类似物,经核磁共振波谱仪(NMR)、质谱(MS)、单晶衍射等技术手段表征了目标化合物结构。 基于变温核磁,探讨了化合物4a~4h中旋转异构及酰胺C-N键双键性质对氢核磁谱的影响。 采用Born比浊法对目标化合物进行活性筛选,9个类似物的活性均强于柄果花椒酰胺,特别是化合物2c、4c、4f在200 μmol/L时显示出强的抑制率,分别为50.03%、60.87%、53.33%。 该类化合物的构效关系是4位甲氧基取代对化合物的抗ADP(二磷酸腺苷)诱导血小板聚集活性最为有利,甲基化B环中的羟基和结构中的酰胺氮原子时,在某种程度上可增强化合物活性。     

Increased lysine N-methylation of a 23-kDa protein during hepatic regeneration

The methylation of a 23-kDa nuclear protein increased after partial hepatectomy and methylation returned to basal levels after the initial stage of regeneration. The methylating enzyme was partially purified from rat liver by ammonium sulfate precipitation, DEAE-anion exchange chromatography and Butyl-Sepharose chromatography. The 23-kDa protein was purified from a nuclear fraction of liver tissue with SP-Sepharose. When the 23-kDa protein was methylated with the partially purified methyltransferase and analyzed on C(18) high performance liquid chromatography (HPLC), the methylated acceptor amino acid was monomethyl lysine (MML). Previously, only arginine N-methylation of specific substrate proteins has been reported during liver regeneration. However, in this report, we found that lysine N-methylation increased during early hepatic regeneration, suggesting that lysine N-methylation of the 23-kDa nuclear protein may play a functional role in hepatic regeneration. The methyltransferase did not methylate other proteins such as histones, hnRNPA1, or cytochrome C, suggesting the enzyme is a 23-kDa nuclear protein- specific lysine N-methyltransferase.     

The assignment of IR absorption bands due to free hydroxyl groups in cellulose

Interpretation of the IR hydroxyl absorption bands in cellulose has been limited to the inter- and intramolecularly hydrogen-bonded hydroxyl groups in the crystalline form. This paper attempts to assign IR frequencies due to ‘free‘ or non-hydrogen bonded hydroxyl groups by using a curve fitting method. The almost completely methylated cellulose derivatives of tritylcellulose (previously used in related studies) exhibited small IR bands due to hydroxyl groups. The IR bands were assumed to appear under stereohindered conditions and thus resulted in a mixture of bands which included the contribution of free hydroxyl groups. The curve fitting method deconvoluted the IR bands into three bands in the OH stretching region: they were interpreted in terms of free or hydrogen bonded hydroxyl groups. The assignments were confirmed by comparison of an almost completely methylated derivative with partially methylated derivatives having different degrees of substitution. In addition, intramolecular hydrogen bonds involving OH at the C-3, C-2 and C-6 positions were shown to be easily formed, even between extremely small numbers of unsubstituted hydroxyl groups present, and thus cause perturbation of the specific deconvoluted band. This revised version was published online in August 2006 with corrections to the Cover Date.     

A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants

The core histones, H2A, H2B, H3 and H4, undergo post‐translational modifications (PTMs) including lysine acetylation, methylation and ubiquitylation, arginine methylation and serine phosphorylation. Lysine residues may be mono‐, di‐ and trimethylated, the latter resulting in an addition of mass to the protein that differs from acetylation by only 0.03639 Da, but that can be distinguished either on high‐performance mass spectrometers with sufficient mass accuracy and mass resolution or via retention times. Here we describe the use of chemical derivatization to quantify methylated and acetylated histone isoforms by forming deuteroacetylated histone derivatives prior to tryptic digestion and bottom‐up liquid chromatography‐mass spectrometric analysis. The deuteroacetylation of unmodified or mono‐methylated lysine residues produces a chemically identical set of tryptic peptides when comparing the unmodified and modified versions of a protein, making it possible to directly quantify lysine acetylation. In this work, the deuteroacetylation technique is used to examine a single histone H3 peptide with methyl and acetyl modifications at different lysine residues and to quantify the relative abundance of each modification in different deacetylase and methylase knockout yeast strains. This application demonstrates the use of the deuteroacetylation technique to characterize modification ‘cross‐talk’ by correlating different PTMs on the same histone tail. Copyright © 2013 John Wiley & Sons, Ltd.     

Polymer-assisted solution-phase synthesis of 2'-amido-2'-deoxyadenosine derivatives targeted at the NAD(+)-binding sites of parasite enzymes

A polymer-assisted solution-phase (PASP) synthesis of lead structure analogues ready for biological testing without the demand for chromatographic purification is described. Carboxylic acids are coupled to the Kenner or Ellman safety catch linker, respectively, activated by methylation or cyanomethylation and subsequently transferred to the 2'-amino group of the 2'-amino-2'-deoxyadenosine scaffold (5). The chemoselective attack of weakly nucleophilic amino groups on the N-alkylated N-acyl sulfonamide linker allows for the synthesis of amides 6 in high yields without the need for protection of primary and secondary hydroxyl functions. Thus, the use of 4-sulfamylbenzoylaminomethyl polystyrene is reported for the construction of chemoselective polymer-supported acylating reagents instead of its known use as linker in solid-phase peptide or organic synthesis. This approach is demonstrated to be well suited to obtain 2'-amido-2'-deoxyadenosine derivatives 6 in parallel format. Biological evaluation of all compounds reported revealed no improvement over known lead structures.     

Unconventional methyl galactan synthesized via the thexyldimethylsilyl intermediate: preparation, characterization, and properties

Reaction of a beta-(1 --> 4) linked galactan with TDMS chloride followed by methylation and desilylation yields methyl galactans with unconventional functionalization patterns. The products were characterized via FTIR and NMR of the intact polymer and by CE after controlled depolymerization. A TDMS-derivatized methyl galactan contains differently methylated secondary hydroxyl groups. SEC and analytical ultracentrifugation showed a consistent decrease in the molecular weight after the consecutive reaction steps. Biological studies revealed that the methyl galactans are less active in complement fixation assays as compared with a 3-O-methyl galactan-enriched polysaccharide fraction isolated from Acanthus ebracteatus.     

Polyhydroxylated bicyclic isoureas and guanidines are potent glucocerebrosidase inhibitors and nanomolar enzyme activity enhancers in Gaucher cells

Four diastereomeric series of N-alkylated [6+5] bicyclic isoureas having hydroxyl substituents mimicking glucose hydroxyl groups have been synthesized as potential β-glucocerebrosidase (GCase) inhibitors with the aim of developing pharmacological chaperones for enzyme deficiency in Gaucher disease (GD). The bicyclic compounds differ either by the configuration of the ring fusion carbon atoms or by the nature of the N-alkyl substituents. When assayed for effects on GCase activity, the isoureas displayed selective inhibition of GCase with low micromolar to nanomolar IC(50)'s in isolated enzyme experiments. One of the series of isoureas, a family having a specific cis ring fusion, exhibited strong inhibition of recombinant GCase activity with K(i) values in the 2-42 nM range. In addition, the [6+5] bicyclic guanidine derivatives with a substitution pattern analogous to the most active isoureas were also found to be potent inhibitors of GCase with K(i) values between 3 and 10 nM. Interestingly, the active bicyclic isoureas and guanidines also behaved as GCase inhibitors in wild-type human fibroblasts at nanomolar concentrations. The potential of these compounds as pharmaceutical chaperones was determined by analyzing their capacity for increasing GCase activity in GD lymphoblasts derived from N370S and L444P variants, two of the most prevalent Gaucher mutations. Six compounds were selected from the different bicyclic isoureas and guanidines obtained that increased GCase activity by 40-110% in N370S and 10-50% in L444P cells at low micromolar to nanomolar concentrations following a 3 day incubation. These results describe a promising series of potent GCase ligands having the cellular properties required for pharmacological chaperones.     

An evaluation of the utility of in vacuo methylation for mass-spectrometry-based analyses of peptides

In vacuo trimethylation of the N-terminus of a lyophilized peptide with methyl iodide was previously reported to enhance the peptide's signal in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and to suppress alkali adduct formation in electrospray ionization mass spectrometry (ESI-MS). Both the signal enhancement and alkali adduct suppression observed for methylated peptides are believed to be due to the permanent positive charge on the N-terminus of the peptide resulting from the formation of a quaternary ammonium moiety. The present work evaluates the general utility of the in vacuo methylation procedure for the MS analysis of peptides, and specifically addresses the issue of whether the methylation of nucleophilic sites other than the N-terminal amine affects the MALDI signal of modified peptides. This work establishes that, although certain side-chain modifications are inevitable using present reaction conditions, the derivatization leads to significant MALDI-MS signal improvement. The experimental results demonstrate that the N-terminal trimethylammonium derivatives of peptides exhibit MALDI signals comparable to or exceeding those of arginine-containing standards such as angiotensin I. The advantages and limitations of the in vacuo methylation procedure are discussed.     

Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry

Arginine and lysine methylation are widespread protein post-translational modifications. Peptides containing these modifications are difficult to retain using traditional reversed-phase liquid chromatography because they are intrinsically basic/hydrophilic and often fragment poorly during collision induced fragmentation (CID). Therefore, they are difficult to analyze using standard proteomic workflows. To overcome these caveats, we performed peptide separations at neutral pH, resulting in increased retention of the hydrophilic/basic methylated peptides before identification using MS/MS. Alternatively trifluoroacetic acid (TFA) was used for increased trapping of methylated peptides. Electron-transfer dissociation (ETD) mass spectrometry was then used to identify and characterize methylated residues. In contrast to previous reports utilizing ETD for arginine methylation, we observed significant amount of side-chain fragmentation. Using heavy methyl stable isotope labeling with amino acids in cell culture it was shown that, similar to CID, a loss of monomethylamine or dimethylamine from the arginine methylated side-chain during ETD can be used as a diagnostic to determine the type of arginine methylation. CID of lysine methylated peptides does not lead to significant neutral losses, but ETD is still beneficial because of the high charge states of such peptides. The developed LC MS/MS methods were successfully applied to tryptic digests of a number of methylated proteins, including splicing factor proline-glutamine-rich protein (SFPQ), RNA and export factor-binding protein 2 (REF2-I) and Sul7D, demonstrating significant advantages over traditional LC MS/MS approaches.     

Homology Modeling and Molecular Docking Studies of (S)‐Scoulerine 9‐O‐Methyltransferase from Coptis chinensis

(S)‐Scoulerine 9‐O‐methyltransferase (SMT), belonging to the S‐adenosyl‐L‐methionine (SAM)‐dependent O‐methyltransferase family, is an essential enzyme in the berberine biosynthetic pathways. In order to study the interactions of SMT with its substrate and further to understand the catalytic mechanism and substrate specificity, a three dimensional model of SMT from Coptis chinensis was constructed by homology modeling using the crystal structure of caffeic acid/5‐hydroxyferulic acid 3/5‐O‐methyltransferase (COMT) as a template. The three dimensional structure of SMT, which was mainly composed of α‐helices and some β‐sheets, was similar to that of COMT. In contrast with COMT, the non‐conserved residues in the substrate binding pocket of SMT might be responsible for their differences in the substrate specificity. Val119 and Asp254 in SMT were the key residues for orienting substrate for methylation as both residues had H‐bonds with (S)‐scoulerine. The methylation of (S)‐scoulerine involved deprotonation of the 9‐hydroxyl group by His253 and Asp254 in SMT followed by a nucleophilic attack on the SAM‐methyl resulting in the product, (S)‐tetrahydrocolumbamine.     

Inhibition of prostaglandin and leukotriene biosynthesis by gingerols and diarylheptanoids.

The rhizomes of Zingiber officinale (ginger) and Alpinia officinarum contain potent inhibitors against prostaglandin biosynthesizing enzyme (PG synthetase). Gingerols and diarylhepatanoids were identified as active compounds. Their possible mechanism of action which was deduced from the structures of active compounds indicated that the inhibitors would also be active against arachidonate 5-lipoxygenase, an enzyme of leukotriene (LT) biosynthesis. This was verified by testing their inhibitory effects on 5-lipoxygenase prepared from RBL-1 cells. A diarylheptanoid with catechol group was the most active compound against 5-lipoxygenase, while yakuchinone A was the most active against PG synthetase.