Recent advances in DDAH1 inhibitor design and discovery: insights from structure-activity relationships and X-ray crystal structures.

Nitric oxide (NO) is an important signalling molecule which modulates several biological and pathological processes. Dimethylarginine dimethylaminohydrolase 1 (DDAH1) plays a key role indirectly regulating NO concentrations in the body. It has been shown that DDAH1 inhibition may be an effective therapeutic strategy in certain pathological states in which excessive NO is produced. In recent years, specific DDAH1 inhibitors have shown promise in suppressing abnormal neovascularization in cancer. However, the available DDAH1 inhibitors lack potency and selectivity and are mostly arginine-based. Further, these inhibitors display unfavourable pharmacokinetics and have not been tested in humans. Thus, the development of potent, selective, and chemically diverse DDAH1 inhibitors is essential. In this review, we examine the structure activity relationships (SARs) and X-ray crystal structures of known DDAH1 inhibitors. Then, we discuss current challenges in the design and development of novel DDAH1 inhibitors and provide future directions for developing potent and chemically diverse compounds.

3-Methoxy-2-phenylimidazo[1,2-b]pyridazines highly active against Mycobacterium tuberculosis and Mycobacterium marinum.

A series of 3-methoxy-2-phenylimidazo[1,2-b]pyridazine derivatives which were highly active against autoluminescent Mycobacterium tuberculosis (Mtb) and Mycobacterium marinum (Mm) in an in vitro assay were identified. SAR analysis showed that the most active compounds, which included a phenyl group bearing fluoro substituent(s) at C2, a methoxy function at C3, and a benzyl-heteroatom moiety at C6, exhibited in vitro MIC90 values generally around 0.63-1.26 µM against Mtb and Mm. However, these compounds were inactive against Mtb in vivo (mice), and investigations revealed very short metabolic half-lives (<10 min) when incubated with mouse liver microsomes. Multiple observations of side products produced from oxidative cleavage of the imidazole moiety during the chemical synthesis work suggested that this is a likely metabolic pathway leading to the lack of observed activity in vivo.

Electrochemical Synthesis of Poly(trisulfides).

With increasing interest in high sulfur content polymers, there is a need to develop new methods for their synthesis that feature improved safety and control of structure. In this report, electrochemically initiated ring-opening polymerization of norbornene-based cyclic trisulfide monomers delivered well-defined, linear poly(trisulfides), which were solution processable. Electrochemistry provided a controlled initiation step that obviates the need for hazardous chemical initiators. The high temperatures required for inverse vulcanization are also avoided resulting in an improved safety profile. Density functional theory calculations revealed a reversible "self-correcting" mechanism that ensures trisulfide linkages between monomer units. This control over sulfur rank is a new benchmark for high sulfur content polymers and creates opportunities to better understand the effects of sulfur rank on polymer properties. Thermogravimetric analysis coupled with mass spectrometry revealed the ability to recycle the polymer to the cyclic trisulfide monomer by thermal depolymerization. The featured poly(trisulfide) is an effective gold sorbent, with potential applications in mining and electronic waste recycling. A water-soluble poly(trisulfide) containing a carboxylic acid group was also produced and found to be effective in the binding and recovery of copper from aqueous media.

Chemical similarities and differences among inhibitors of nitric oxide synthase, arginase and dimethylarginine dimethylaminohydrolase-1: Implications for the design of novel enzyme inhibitors modulating the nitric oxide pathway.

Nitric oxide (NO) is a signalling molecule that controls a multitude of regulatory functions including neurotransmission, vascular tone, immune response, and angiogenesis. Regulating NO concentrations in cells using small molecules is an active area of research in the treatment of several pathologies such as cardiovascular disease, cancer, and inflammatory conditions. Small molecule-inhibition of critical NO regulatory enzymes, NO synthase (NOS), arginase, and dimethylarginine dimethyaminohydrolase-1 (DDAH1), has shown therapeutic benefits as well as limitations and is a focus of current research.In recent years, DDAH1 has been explored as a potential target to indirectly regulate NO in diseases characterized by excessive NO production. This review discusses the biological and pathophysiological role of the NO pathway, the existing inhibitors of NOS, arginase and DDAH1, and the conventional and structure-guided structure-activity relationship studies involved in their discovery. The key structural elements of amino acid-derived inhibitors responsible for selective inhibition of each enzyme, and the chemical features responsible for dual enzyme inhibition are also discussed. Finally, a synthetic scheme for developing both selective and dual inhibitors using common starting materials is provided, offering unique insights in the quest for the rational design of novel NO pathway inhibitors.

Reaction of [18F]Fluoride at Heteroatoms and Metals for Imaging of Peptides and Proteins by Positron Emission Tomography.

The ability to radiolabel proteins with [18F]fluoride enables the use of positron emission tomography (PET) for the early detection, staging and diagnosis of disease. The direct fluorination of native proteins through C-F bond formation is, however, a difficult task. The aqueous environments required by proteins severely hampers fluorination yields while the dry, organic solvents that promote nucleophilic fluorination can denature proteins. To circumvent these issues, indirect fluorination methods making use of prosthetic groups that are first fluorinated and then conjugated to a protein have become commonplace. But, when it comes to the radiofluorination of proteins, these indirect methods are not always suited to the short half-life of the fluorine-18 radionuclide (110 min). This review explores radiofluorination through bond formation with fluoride at boron, metal complexes, silicon, phosphorus and sulfur. The potential for these techniques to be used for the direct, aqueous radiolabeling of proteins with [18F]fluoride is discussed.

Proteome-Wide Survey of Cysteine Oxidation by Using a Norbornene Probe.

Rapid detection of cysteine oxidation in living cells is critical in advancing our understanding of responses to reactive oxygen species (ROS) and oxidative stress. Accordingly, there is a need to develop chemical probes that facilitate proteome-wide detection of cysteine's many oxidation states. Herein, we report the first whole-cell proteomics analysis using a norbornene probe to detect the initial product of cysteine oxidation: cysteine sulfenic acid. The oxidised proteins identified in the HeLa cell model represent the first targets of the ROS hydrogen peroxide. The panel of protein hits provides new and important information about the targets of oxidative stress, including 148 new protein members of the sulfenome. These findings provide new leads for the study and understanding of redox signalling and diseases associated with oxidative stress.

Norbornene Probes for the Detection of Cysteine Sulfenic Acid in Cells.

Norbornene derivatives were validated as probes for cysteine sulfenic acid on proteins and in live cells. Trapping sulfenic acids with norbornene probes is highly selective and revealed a different reactivity profile than the traditional dimedone reagent. The norbornene probe also revealed a superior chemoselectivity when compared to a commonly used dimedone probe. Together, these results advance the study of cysteine oxidation in biological systems.

Sulfur polymer composites as controlled-release fertilisers.

Sulfur polymer composites were prepared by the reaction of canola oil and elemental sulfur in the presence of the NPK fertiliser components ammonium sulfate, calcium hydrogen phosphate, and potassium chloride. These composites released nutrients in a controlled fashion, resulting in less wasted fertiliser and better health for potted tomato plants when compared to free NPK.

Total synthesis and structural elucidation of spongosoritin A.

Two putative structures of spongosoritin A, with syn (6R,8R) and anti (6S,8R) configurations, were each synthesised in a total of 11 linear steps with only 8 purification procedures. The key steps in our strategy included Evans alkylation and olefin dihydroxylation to install the C8 and C6 stereocentres, a transacetalisation/dehydration cascade to construct the furanylidene core, and chromatographic separation of 9E- and 9Z-isomers of the final compounds with silver nitrate impregnated silica. Comparison of the 1H and 13C NMR data for the synthetic syn- and anti-isomers to that reported for the natural product revealed that the relative configuration of spongosoritin A is syn. The absolute stereochemistry was also confirmed as 6R,8R based on optical rotation measurements where the synthetic syn (6R,8R) and natural product had the same sign of optical rotation (negative).

Chemical methods for mapping cysteine oxidation.

Cysteine residues in proteins are subject to diverse redox chemistry. Oxidation of cysteine to S-nitrosocysteine, cysteine sulfenic and sulfinic acids, disulfides and persulfides are a few prominent examples of these oxidative post-translational modifications. In living organisms, these modifications often play key roles in cell signalling and protein function, but a full account of this biochemistry is far from complete. It is therefore an important goal in chemical biology to identify what proteins are subjected to these modifications and understand their physiological function. This review provides an overview of these modifications, how they can be detected and quantified using chemical probes, and how this information provides insight into their role in biology. This survey also highlights future opportunities in the study of cysteine redox chemistry, the challenges that await chemists and biologists in this area of study, and how meeting such challenges might reveal valuable information for biomedical science.

Synthesis and Characterization of Novel Anchorlipids for Tethered Bilayer Lipid Membranes.

Tethered bilayer lipid membranes are versatile solid-supported model membrane systems. Core to these systems is an anchorlipid that covalently links a lipid bilayer to a support. The molecular structure of these lipids can have a significant impact on the properties of the resulting bilayer. Here, the synthesis of anchorlipids containing ester groups in the tethering part is described. The lipids are used to form bilayer membranes, and the resulting structures are compared with membranes formed using conventional anchorlipids or sparsely tethered membranes. All membranes showed good electrical sealing properties; the disulphide-terminated anchorlipids could be used in a sparsely tethered system without significantly reducing the sealing properties of the lipid bilayers. The sparsely tethered systems also allowed for higher ion transport across the membrane, which is in good correlation with higher hydration of the spacer region as seen by neutron scattering.

Total Synthesis of Plakilactones C, B and des-Hydroxyplakilactone B by the Oxidative Cleavage of Gracilioether Furanylidenes.

A chemoselective oxidative cleavage of synthetic gracilioether B, 11-epi-gracilioether C benzoate, and des-hydroxygracilioether C with pyridinium chlorochromate, which proceeds with loss of the furanyl acetate, has enabled total synthesis and stereochemical elucidation of the marine sponge metabolites (4R,6R)-plakilactone C, (4R,6R,9R)-plakilactone B, and (4R,6R)-des-hydroxyplakilactone B. des-Hydroxygracilioether C, the putative biosynthetic precursor to hippolachnin A, was also found to undergo a facile ene cyclization on treatment with SnCl4.

Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges.

Covering: up to early 2016Marine sponges are widely known as a rich source of natural products, especially of polyketide origin, with a wealth of chemical diversity. Within this vast collection, peroxide and peroxide-derived secondary metabolites have attracted significant interest in the fields of natural product isolation and chemical synthesis for their structural distinction and promising in vitro antimicrobial and anticancer properties. In this review, peroxide and peroxide-derived polyketide metabolites isolated from marine sponges in the past 35 years are summarised. Efforts toward their synthesis are detailed with a focus on methods that utilise or attempt to elucidate the complex biosynthetic interrelationships of these compounds beyond enzymatic polyketide synthesis. Recent isolations, advances in synthetic methodology and theories of biogenesis are highlighted and critically evaluated.

New marine natural products from sponges (Porifera) of the order Dictyoceratida (2001 to 2012); a promising source for drug discovery, exploration and future prospects.

The discovery of new drugs can no longer rely primarily on terrestrial resources, as they have been heavily exploited for over a century. During the last few decades marine sources, particularly sponges, have proven to be a most promising source of new natural products for drug discovery. This review considers the order Dictyoceratida in the Phylum Porifera from which the largest number of new marine natural products have been reported over the period 2001-2012. This paper examines all the sponges from the order Dictyoceratida that were reported as new compounds during the time period in a comprehensive manner. The distinctive physical characteristics and the geographical distribution of the different families are presented. The wide structural diversity of the compounds produced and the variety of biological activities they exhibited is highlighted. As a representative of sponges, insights into this order and avenues for future effective natural product discovery are presented. The research institutions associated with the various studies are also highlighted with the aim of facilitating collaborative relationships, as well as to acknowledge the major international contributors to the discovery of novel sponge metabolites. The order Dictyoceratida is a valuable source of novel chemical structures which will continue to contribute to a new era of drug discovery.

Biomimetic total synthesis of gracilioethers B and C.

Total syntheses of the marine polyketide metabolites gracilioethers B and C have been realized in 9 steps (40% overall yield) and 10 steps (34% overall yield), respectively. The [2(5H)-furanylidene]ethanoate (furanylidene) motif was constructed in a transacetalization/dehydration cascade of an advanced ß-ketoester intermediate, which was designed to mimic a postulated biosynthetic precursor to the natural products. The relative and absolute configurations of gracilioethers B and C are confirmed as (6R,8R) and (6R,8R,11S), respectively.

Cross sections for positron impact with 2,2,4-trimethylpentane.

2,2,4-Trimethylpentane (C8H18), a hydrocarbon produced all over the world on a large scale in the processing of crude oil, has long been known and used in the energy sector. It has also recently attracted the attention of the radiation physics and chemistry community, owing to its applications in medical imaging techniques. Charged-particle interactions with this species unfortunately remain mostly unknown. In this study, we report on measured total cross sections for positron scattering from 2,2,4-trimethylpentane in the energy range from 0.12 to 50 eV. We also present calculations of the total cross sections, elastic integral and differential cross sections, positronium formation cross sections, and inelastic integral cross sections at energies from 1 to 1000 eV using the independent atom model with screening corrected additivity rule. A knowledge of those scattering cross sections might, through simulation models, help to improve the accuracy of current radiation detection devices and hence provide better estimates of the extent of any charged-particle-induced damage in biomolecular systems.

A methyltransferase essential for the methoxypyrazine-derived flavour of wine.

Methoxypyrazines are a family of potent volatile compounds of diverse biological significance. They are used by insects and plants in chemical defence, are present in many vegetables and fruit and, in particular, impart herbaceous/green/vegetal sensory attributes to wines of certain varieties, including Cabernet Sauvignon. While pathways for methoxypyrazine biosynthesis have been postulated, none of the steps have been confirmed genetically. We have used the F2 progeny of a cross between a rapid flowering grapevine dwarf mutant, which does not produce 3-isobutyl-2-methoxypyrazine (IBMP), and Cabernet Sauvignon to identify the major locus responsible for accumulation of IBMP in unripe grape berries. Two candidate methyltransferase genes within the locus were identified and one was significantly associated with berry IBMP levels using association mapping. The enzyme encoded by this gene (VvOMT3) has high affinity for hydroxypyrazine precursors of methoxypyrazines. The gene is not expressed in the fruit of Pinot varieties, which lack IBMP, but is expressed in Cabernet Sauvignon at the time of accumulation of IBMP in the fruit. The results suggest that VvOMT3 is responsible for the final step in methoxypyrazine synthesis in grape berries and is the major determinant of IBMP production.

Total synthesis and structural elucidation of ent-micropyrone and (+)-ascosalipyrone.

The total synthesis of 6-[(1S,3S)-1,3-dimethyl-2-oxopentyl]-4-hydroxy-3,5-dimethyl-2H-pyran-2-one (22), the enantiomer of the natural product micropyrone (1), was achieved in 9 linear steps (10% overall yield), from Evans auxiliary (R)-12 with key coupling of the dianion of dione 17 and aldehyde 11. Formation of the pyrone ring and subsequent oxidation at C7 was achieved without epimerization of the sensitive position α to both the pyrone ring and the carbonyl. The same sequence using the alternate dione 24 achieved the total synthesis of 6-[(1S,3S)-1,3-dimethyl-2-oxopentyl]-4-hydroxy-3-methyl-2H-pyran-2-one (28), the (+)-enantiomer of the natural product, ascosalipyrone (2). In both cases diastereomeric aldehydes 11 and 16 were taken through the synthetic sequence to give two possible diastereomers of the natural products. Comparison of the (1)H and (13)C NMR data for the synthetic isomers with that reported for the natural products determined their relative stereochemistry. Comparison of the optical rotation obtained for 22 established it to be the enantiomer of micropyrone.

Two O-methyltransferases involved in the biosynthesis of methoxypyrazines: grape-derived aroma compounds important to wine flavour.

Methoxypyrazines (MPs) are volatile, grape-derived aroma compounds that contribute to the distinct herbaceous characters of some wines. Although the full pathway leading to MP production has not been elucidated, there is strong evidence that the final step involves the methylation of non-volatile hydroxypyrazine (HP) precursors. Two cDNA encoding O-methyltransferases (OMTs) that have homology to an enzyme previously purified and shown to catalyse the methylation of HPs were isolated from Cabernet Sauvignon. Recombinant protein from the cDNAs (VvOMT1 and VvOMT2) was produced in E. coli and activity assays demonstrated that both encode OMTs able to methylate HPs to produce MPs, however both showed greatest activity against the flavonol quercetin. VvOMT1 has higher catalytic activity against isobutyl hydroxypyrazine compared to isopropyl hydroxypyrazine, whereas the converse is true for VvOMT2. The timing of the expression of VvOMT1 in the skin and the flesh of developing Cabernet Sauvignon grape berries was associated with the period of MP accumulation in these tissues, while VvOMT2 expression was greatest in roots, which were found to contain high levels of MPs. The MP composition of these tissues also reflects the relative levels of expression of these genes and their substrate preference. The identification of genes responsible for MP production in grapevine will help in understanding the effect of different viticultural and environmental factors on MP accumulation.