Compound I of nitric oxide synthase: the active site protonation state

A quantum mechanical/molecular mechanical (QM/MM) study of the formation of the elusive active species Compound I (Cpd I) of nitric oxide synthase (NOS) from the oxyferrous intermediate shows that two protons have to be provided to produce a reaction that is reasonably exothermic and that leads to the appearance of a radical on the tetrahydrobiopterin cofactor. Molecular dynamics and energy considerations show that a possible source of proton is the water H-bond chain formed from the surface to the active site, but that a water molecule by itself cannot be the source of the proton; an H3O+ species that is propagated along the chain is more likely. The QM/MM calculations demonstrate that Cpd I and H2O are formed from the ferric-hydrogen peroxide complex in a unique heterolytic O-O cleavage mechanism. The properties of the so-formed Cpd I are compared with those of the known species of chloroperoxidase, and the geometry and spin densities are found to be compatible. The M?ssbauer parameters are calculated and may serve as experimental probes in attempts to characterize NOS Cpd I.     

C6-substituted analogues of 8-azanebularine: probes of an RNA-editing enzyme active site

[reaction: see text] We describe the synthesis of derivatives of 8-azanebularine, a known inhibitor of adenosine deaminases including the RNA-editing enzyme ADAR2. 6-Methyl, 6-hydroxymethyl, 6-cyano, and 6-mercapto derivatives were obtained from 6-bromo precursors using different cross-coupling or substitution reactions. The C6-methyl derivative was incorporated into an RNA substrate for ADAR2 via the phosphoramidite. Quantitative gel mobility shift experiments with the resulting RNA indicate that methylation at C6 dramatically reduces the affinity of 8-azanebularine for ADAR2.     

Suppression of inducible nitric oxide synthase expression by yakuchinones and their analogues

Analogues of yakuchinones were synthesized as inhibitors of nitric oxide production in lipopolysaccharide-activated macrophage cell line, RAW 264.7 cells. We prepared stronger inhibitors than the original natural molecules, yakuchinones A and B reported from Alpinia oxyphylla. From the limited structural activity relation study of analogues, we concluded that the optimal length of linker between two aryl groups and the presence of enone moiety in the linker were identified as essential for the activity. The IC50 value of the most potent structure was 0.92 microM. The active analogues suppressed the expression of inducible nitric oxide synthase protein and mRNA.     

Stereoselective synthesis of novel uracil polyoxin C conjugates as substrate analogues of chitin synthase

Stereoselective syntheses of both the natural (C5'- S) and unnatural (C5'- R) diastereoisomers of uracil polyoxin C methyl ester have been developed. The key stereocontrolled step involves nucleophilic addition of trimethylsilyl cyanide to the appropriate chiral sulfinimine derived from 2',3'-protected 5'-formyluridine and (S)-(-)-tert-butanesulfinamide or (R)-(+)-tert-butanesulfinamide, respectively. A variety of substrate mimics designed to function as inhibitors of chitin synthase have been synthesized by conjugation of the methyl ester of uracil polyoxin C (UPOC) with activated isoxazole carboxylic acids. Amide bond formation was accomplished via coupling of the amino functionality of UPOC methyl ester with a free isoxazole acid using HBTU or alternatively an isoxazole pentafluorophenyl ester. The substrate mimics incorporate features of the nucleoside-peptide antibiotics, the polyoxins and the nikkomycins, as well as features of the transition state structure expected during polymerization of the natural chitin synthase substrate uridine diphosphoryl-N-acetylglucosamine (UDP-GlcNAc), namely, a metal-binding site and glycosyl oxocarbenium ion mimic.     

Quantum chemical calculations of the NHA bound nitric oxide synthase active site: O2 binding and implications for the catalytic mechanism

Density functional theory has been employed to model the binding of the intermediate substrate NHA, by nitric oxide synthases. In particular, the orientation and interactions of possibly catalytically important substrate hydrogens, with and without molecular oxygen bound to the active site heme group, are considered. Without O(2), three possible conformers have been found, with the energetically most favored structure being that in which both protons of the -NHOH moiety of NHA are directed toward the heme group. With oxygen bound, four different structures were found. The energetically lowest structure is again found to have both hydrogens of the -NHOH group pointing toward the heme group, thus forming hydrogen bonds between -NH- and the terminal oxygen, and between -OH and the inner oxygen of the heme-O(2) group. In addition, unprotonated structures of the substrate bound to the active site are considered and the proton affinity calculated.     

l-Arginine and nitric oxide synthesis in the cells with inducible NO synthase

Russian Chemical Bulletin - The effect of citrulline and ammonium chloride on the nitric oxide formation by peritoneal macrophages and liver tissue cells was studied using ESR spectroscopy. In ex...     

Thalidomide as a nitric oxide synthase inhibitor and its structural development

Thalidomide has been found to exhibit weak nitric oxide synthase (NOS)-inhibitory activity. Structural development studies of thalidomide showed that some N-2,6-dimethylphenylhomophthalimide analogs possess NOS-inhibiting activity.     

Improved synthesis of V-PYRRO/NO, a liver-selective nitric oxide prodrug, and analogues

The reported synthesis of O²-vinyl 1-(pyrrolidin-1-yl)diazen-1-ium-1,2-diolate (V-PYRRO/NO), a hepatoprotective agent, was cumbersome and limited by a poor overall yield of 4% from sodium 1-(pyrrolidin-1-yl)diazen-1-ium-1,2-diolate (PYRRO/NO). We report an improved synthesis of V-PYRRO/NO in two steps with a significantly higher overall yield of 40% from PYRRO/NO. Using this protocol, a number of structural analogues of V-PYRRO/NO were prepared in good yields.     

An efficient and convenient route for the synthesis of thiophene-2-carboxamidines as potential inhibitors of nitric oxide synthase (NOS)

A mild and efficient synthesis of substituted thiophene-2-carboxamidines which are potent inhibitors of nitric oxide synthase (NOS) is reported herein. The key step involves reaction of a BOC-protected imidazolyl thiophene-2-carboxamidine reactive intermediate with various primary amines to form BOC-thiophene-2-carboxamidines which could be readily deprotected using TFA to furnish free carboxamidines. The method is very mild and tolerates diverse substituents including sensitive peptide and amino acid fragments. This new methodology represents a substantial improvement to the literature method owing to its simplicity and hassle-free purification procedures.     

Synthesis and biological evaluation of 2,4-diaminopteridine derivatives as nitric oxide synthase inhibitor

A series of novel 2,4-diamino-pteridines(9a-1)were synthesized and evaluated as inhibitors of inducible nitric oxide synthase (iNOS)in vitro.It was found that 9a,9d,9e,9h,9i and 91 showed potent inhibitory activities similar to that of methotrexate(MTX),while the activities of 9b,9c,9f,9g,9j and 9k ale stronger than MTX.     

Azalysine analogues as probes for protein lysine deacetylation and demethylation

Reversible lysine acetylation and methylation regulate the function of a wide variety of proteins, including histones. Here, we have synthesized azalysine-containing peptides in acetylated and unacetylated forms as chemical probes of the histone deacetylases (HDAC8, Sir2Tm, and SIRT1) and the histone demethylase, LSD1. We have shown that the acetyl-azalysine modification is a fairly efficient substrate for the sirtuins, but a weaker substrate for HDAC8, a classical HDAC. In addition to deacetylation by sirtuins, the acetyl-azalysine analogue generates a novel ADP-ribose adduct that was characterized by mass spectrometry, Western blot analysis, and nuclear magnetic resonance spectroscopy. This peptide-ADP-ribose adduct is proposed to correspond to a derailed reaction intermediate, providing unique evidence for the direct 2'-hydroxyl attack on the O-alkylimidate intermediate that is formed in the course of sirtuin catalyzed deacetylation. An unacetylated azalysine-containing H3 peptide proved to be a potent inhibitor of the LSD1 demethylase, forming an FAD adduct characteristic of previously reported related structures, providing a new chemical probe for mechanistic analysis.     

Structure-activity relationships of 2-aminothiazole derivatives as inducible nitric oxide synthase inhibitor

Nitric oxide synthase (NOS) has been divided into two major sub-enzymes, i.e. inducible NOS (iNOS) and constitutive NOS (cNOS). Although nitric oxide (NO) plays an important role as host defense mediator, excessive production of NO by iNOS has been involved in the pathology of many inflammatory diseases. Recently, we reported that the 2-imino-1,3-oxazolidine (1a) weakly inhibits iNOS and that introduction of an alkyl moiety on the oxazolidine ring of 1a enhances the inhibitory activity and selectivity for iNOS. In our search for better iNOS inhibitors, we focused our efforts on the 2-aminothiazole scaffold 3 as it possesses a ring similar to that of 1a. In this study, we evaluated the inhibitory activity of a series of 2-aminothiazole derivatives against both iNOS and neuronal NOS (nNOS). Our results show that introduction of appropriately-sized substituents at the 4- and 5-position of the 2-aminothiazole ring improves the inhibitory activity and selectivity for iNOS. We also found that the selectivity of 5a [5-(1-methyl)ethyl-4-methylthiazol-2-ylamine] and 5b [5-(1,1-dimethyl)ethyl-4-methylthiazol-2-ylamine] for iNOS was similar to that of oxazolidine derivative 1b (4-methyl-5-propyl-2-imino-1,3-oxazolidine) and much higher than that of L-NAME. However, we could not enhance the inhibitory activity against iNOS by introducing an alkyl substituent into the 2-aminothiazole ring as we could in the case of oxazolidine one. On the other hand, introduction of bulky or hydrophilic substituent at any position of the 2-aminothiazole ring remarkably decreased or even abolished the inhibitory activity against NOS.     

Design and synthesis of activity probes for glycosidases

[structure: see text] A new synthetic route was developed for the preparation of activity probe 1 for beta-glucosidase in this study. The key glycosidation step begins with benzyl p-hydroxyphenylacetate. Benzylic functionalization for the construction of the trapping device was achieved at later stages. Probe 1 was shown to be able to label the target enzyme. This cassette-like design offers great flexibility for future alterations. It would allow the synthetic scheme to expand to other glycosidase probes with different linker/reporter combinations.     

Substrate- and isoform-specific dioxygen complexes of nitric oxide synthase

Nitric oxide synthase (NOS) catalyzes the formation of NO via a consecutive two-step reaction. In the first step, L-arginine (Arg) is converted to N-hydroxy-L-arginine (NOHA). In the second step, NOHA is further converted to citrulline and nitric oxide (NO). To assess the mechanistic differences between the two steps of the reaction, we have used resonance Raman spectroscopy combined with a homemade continuous-flow rapid solution mixer to study the structural properties of the metastable dioxygen-bound complexes of the oxygenase domain of inducible NOS (iNOSoxy). We identified the O-O stretching frequency of the substrate-free enzyme at 1133 cm-1. This frequency is insensitive to the presence of tetrahydrobiopterin, but it shifts to 1126 cm-1 upon binding of Arg, which we attribute to H-bonding interactions to the terminal oxygen atom of the heme iron-bound dioxygen. In contrast, the addition of NOHA to the enzyme did not bring about a shift in the frequency of the O-O stretching mode, because, unlike Arg, there is no H-bond associated with the terminal oxygen atom of the dioxygen. The substrate-specific H-bonding interactions play a critical role in determining the fate of the key peroxy intermediate. In the first step of the reaction, the H-bonds facilitate the rupture of the O-O bond, leading to the formation of the active ferryl species, which is essential for the oxidation of the Arg. On the other hand, in the second step of the reaction, the absence of the H-bonds prevents the premature O-O bond cleavage, such that the peroxy intermediate can perform a nucleophilic addition reaction to the substrate, NOHA.     

Design, synthesis and evaluation of nitric oxide releasing derivatives of 3-n-butylphthalide as antiplatelet and antithrombotic agents

Novel nitric oxide (NO) releasing derivatives (7a-7l) of 3-n-butylphthalide (NBP) were designed and synthesized. Compound 7e inhibited the adenosine diphosphate (ADP), thrombin (TH) and arachidonic acid (AA)-induced in vitro platelet aggregation, superior to NBP and aspirin, released moderate levels of NO, and improved aqueous solubility relative to NBP. Furthermore, 7e exhibited greater antithrombotic activity than NBP and aspirin in rats, and protected against collagen and adrenaline-induced thrombosis in mice. Therefore, NO-releasing NBP derivatives possessed potent antiplatelet aggregation and antithrombotic activity. Our findings may aid in the design of new therapeutic agents for the treatment of thrombosis-related ischemic stroke.     

Design and synthesis of chitin synthase inhibitors as potent fungicides

Chitin is a structural component of fungal cell walls but is absent in vertebrates,mammals,and humans.Chitin synthase is thus an attractive molecular target for developing fungicides.Based on the structure of its donor substrate,UDP-N-acetyl-glucosamine,as well as the modelled structure of the bacterial chitin synthase NodC,we designed a novel scaffold which was then further optimized into a series of chitin synthase inhibitors.The most potent inhibitor,compound 13,exhibited high chitin synthase inhibitory activity with an IC_(50) value of 64.5 μmol/L All of the inhibitors exhibited antifungal activities against the growth of agriculturally-destructive fungi,Fusarium graminearum,Botrytis cinerea.and Colletotrichum lagenarium.This work presents a new scaffold which can be used for the development of novel fungicides.     

Synthesis of nitric oxide reductase active site models bearing key components at both distal and proximal sites

Porphyrins 1ab and 2ab were successfully synthesized from cis-alpha2-bisimidazole-beta-imidazole-tail porphyrins and two newly synthesized imidazole pickets containing an aliphatic ester chain following a [2+1] approach. The four compounds possess a distal trisimidazole set, a distal carboxylic acid, and a proximal imidazole, which constitute all the key features of the coordination environment of the active site in Bacterial Nitric Oxide Reductase (NOR) and make them the closest synthetic NOR model ligands to date.