Carbon Side Chain Research Articles

From Chemistry to Behavior. Molecular Structure and Bioactivity of Repellents against Ixodes ricinus Ticks

Tick-borne zoonoses are considered as emerging diseases. Tick repellents represent an effective tool for reducing the risk of tick bite and pathogens transmission. Previous work demonstrated the repellent activity of the phenylpropanoid eugenol against Ixodes ricinus; here we investigate the relationship between molecular structure and repellency in a group of substances related to that compound. We report the biological activity of 18 compounds varying for the presence/number of several moieties, including hydroxyl and methoxy groups and carbon side-chain. Each compound was tested at different doses with a bioassay designed to measure repellency against individual tick nymphs. Both vapor pressure and chemical features of the tested compounds appeared to be related to repellency. In particular, the hydroxyl and methoxy groups as well as the side-chain on the benzene ring seem to play a role. These results are discussed in light of available data on chemical perception in ticks. In the course of the study new repellent compounds were identified; the biological activity of some of them (at least as effective as the “gold standard” repellent DEET) appears to be very promising from a practical point of view.

Four new cyclic peroxides from the Marine Sponge Plakortis simplex

Four new cyclic peroxide compounds (1~4) were isolated from the marine sponge Plakortis simplex. Their structures including relative stereochemistry were determined by MS and NMR analysis. All compounds, a side carbon chain with 10 carbons, were very unstable. After transformation into methyl ester analogues, the structure determination was conducted. Compounds 1a and 2a are stereoisomers, assigned as <TEX>$3S^*$</TEX>, <TEX>$4S^*$</TEX>, <TEX>$6R^*$</TEX> and <TEX>$3R^*$</TEX>, <TEX>$4S^*$</TEX>, <TEX>$6R^*$</TEX>, respectively. Similarly, compounds 3a and 4a, replaced the methoxy group with an aliphatic methyl, are also stereoisomers. Compounds 1a and 2a exhibited the strong antifungal effect against the fungus Candida albicans.

A Computational Study of the Effects of 13C–13C Scalar Couplings on 13C CEST NMR Spectra: Towards Studies on a Uniformly 13C‐Labeled Protein

Read the label: The NMR CEST experiment can be used to reconstruct spectra of sparsely populated, transiently formed protein conformers so long as they exchange with a highly populated ground state with rates of 20-300 s(-1) . Here we establish that accurate (13) C chemical shifts of side-chain carbon nuclei can be obtained from uniformly (13) C-labeled samples, without interference from the coupled (13) C spin network.

Backbone and side-chain resonance assignments of the membrane localization domain from Pasteurella multocida toxin.

(1)H, (13)C, and (15)N chemical shift assignments are presented for the isolated four-helical bundle membrane localization domain (MLD) from Pasteurella multocida toxin (PMT) in its solution state. We have assigned 99% of all backbone and side-chain carbon atoms, including 99% of all backbone residues excluding proline amide nitrogens. Secondary chemical shift analysis using TALOS+ demonstrates four helices, which align with those observed within the MLD in the crystal structure of the C-terminus of PMT (PDB 2EBF) and confirm the use of the available crystal structures as templates for the isolated MLDs.

Backbone and side-chain assignments of an effector membrane localization domain from Vibrio vulnificus MARTX toxin.

(1)H, (13)C, and (15)N chemical shift assignments are presented for the isolated four-helical bundle membrane localization domain from the domain of unknown function 5 (DUF5) effector (MLD(VvDUF5)) of the MARTX toxin from Vibrio vulnificus in its solution state. We have assigned 97% of all backbone and side-chain carbon atoms, including 96% of all backbone residues. Secondary chemical shift analysis using TALOS+ demonstrates four helices that align with those predicted by structure homology modeling using the MLDs of Pasteurella multocida toxin (PMT) and the clostridial TcdB and TcsL toxins as templates. Future studies will be towards solving the structure and determining the dynamics in the solution state.

Proton-Detected Solid-State NMR Spectroscopy at Aliphatic Sites: Application to Crystalline Systems

When applied to biomolecules, solid-state NMR suffers from low sensitivity and resolution. The major obstacle to applying proton detection in the solid state is the proton dipolar network, and deuteration can help avoid this problem. In the past, researchers had primarily focused on the investigation of exchangeable protons in these systems. In this Account, we review NMR spectroscopic strategies that allow researchers to observe aliphatic non-exchangeable proton resonances in proteins with high sensitivity and resolution. Our labeling scheme is based on u-[(2)H,(13)C]-glucose and 5-25% H2O (95-75% D2O) in the M9 bacterial growth medium, known as RAP (reduced adjoining protonation). We highlight spectroscopic approaches for obtaining resonance assignments, a prerequisite for any study of structure and dynamics of a protein by NMR spectroscopy. Because of the dilution of the proton spin system in the solid state, solution-state NMR (1)HCC(1)H type strategies cannot easily be transferred to these experiments. Instead, we needed to pursue ((1)H)CC(1)H, CC(1)H, (1)HCC or ((2)H)CC(1)H type experiments. In protonated samples, we obtained distance restraints for structure calculations from samples grown in bacteria in media containing [1,3]-(13)C-glycerol, [2]-(13)C-glycerol, or selectively enriched glucose to dilute the (13)C spin system. In RAP-labeled samples, we obtained a similar dilution effect by randomly introducing protons into an otherwise deuterated matrix. This isotopic labeling scheme allows us to measure the long-range contacts among aliphatic protons, which can then serve as restraints for the three-dimensional structure calculation of a protein. Due to the high gyromagnetic ratio of protons, longer range contacts are more easily accessible for these nuclei than for carbon nuclei in homologous experiments. Finally, the RAP labeling scheme allows access to dynamic parameters, such as longitudinal relaxation times T1, and order parameters S(2) for backbone and side chain carbon resonances. We expect that these measurements will open up new opportunities to obtain a more detailed description of protein backbone and side chain dynamics.

Structure–activity-relationship studies on dihydrofuran-fused perhydrophenanthrenes as an anti-Alzheimer’s disease agent

As an extended study on development of anti-Alzheimer’s disease agent, we newly synthesized various dihydrofuran-fused perhydrophenanthrenes via o-quinodimethane chemistry. This study revealed that the introduction of carbon side-chain on 8-position or removal of the acetal moiety on 3-position arose a cytotoxicity on rat cortical neurons. On the other hand, the ethereal or thio-ethereal substituent on 8-position enhanced the elongation effect on Aβ-damaged neurons. The necessity of the cyano group on 10b position was also proved in this structure–activity-relationship study.

13C longitudinal relaxation time measurements and DFT-GIAO NMR computations for two ammonium ions of a tetraazamacrocyclic scorpiand system

Spin–lattice relaxation times, T 1s, for 13C nuclei in two cations Hn 1 n+ (n = 1, 5) of N-(2-aminoethyl)-cyclam (1, scorpiand) were determined by means of 13C{1H} NMR experiments in aqueous solution at pH 11.5 and 0.2. The theoretical study [modeling with OPLS-AA, B3LYP/6-31G(d) geometry optimizations, dispersion-corrected energies (DFT-D3), and DFT-GIAO predictions of the NMR chemical shifts (including an IEF-PCM simulation of hydration)] was also done for several conformers of the tautomer iso-H4 1 4+ not investigated before. The binding directions in protonated polyamino receptors necessary for efficient complexation of the nitrate anion(s) were briefly outlined, as well. All these results were discussed in terms of ‘abnormal’ 13C chemical shift changes found previously for the side-chain carbons of amine 1 in strongly acidic solution (HNO3). In conclusion, an earlier proposal of its association with NO3 − at pH <1 was rejected. Instead, the participation of small amounts of a micro-species iso-H4 1 4+ D hydr under such conditions can be proposed.Graphical A small contribution of iso-H4 1 4+ D hydr (see figure) to an ionic mixture of pentamine 1 was proposed to explain the ‘abnormal’ 13C NMR shifts observed for atoms C11 and C12 in its side-chain arm, at pH <1. Electronic supplementary materialThe online version of this article (doi:10.1007/s10847-013-0298-x) contains supplementary material, which is available to authorized users.

Mechanical and other characteristics of cellulose ester bonded with modified cardanol from cashew nut shells and additional aliphatic and aromatic components

Novel cellulose-based bioplastics, mainly using inedible plant resources, were produced by bonding cellulose diacetate (CDA), a modified cardanol, and additional aliphatic and aromatic components. Cardanol is a phenol derivative with a linear unsaturated hydrocarbon side chain (carbon number: 15), derived from cashew nut shells. Esterification of the modified cardanol (3-pentadecylphenoxy acetic acid: PAA) and CDA resulted in a thermoplastic PAA-bonded CDA with high tenacity (long elongation while keeping maximum bending strength), heat resistance, and water resistance. These properties were better than those of a conventional CDA composite consisting of CDA and a conventional plasticizer. By comparing the PAA-bonded CDA with a CDA bonded with stearic acid (SA), which has a linear structure similar to that of PAA’s side chain but has no phenyl part, it was suggested that the linear side chain in PAA has a main role in these prominent properties of the PAA-bonded CDA, while the phenyl part in PAA has pronounced effects on its maximum bending strength and water resistance. Additional bonding of linear alkanoic acids, especially SA as aliphatic components improved the PAA-bonded CDA’s impact strength, and additional bonding of benzoic acid (BA) as an aromatic component further increased its maximum bending strength and elastic modulus. These components improved the thermoplasticity and water resistance of the PAA-bonded CDA while maintaining its high heat resistance relatively well.

Development of Unprotected Syntheses in Aqueous Media

Introduction of carbon side chain at C(3)-position of indole ring was accomplished by using Pd-catalyzed allylation and vinylation. The selective vinylation at C(3)-position of 4-bromoindole was applied to the synthesis of optically active 4-bromotryptophan derivatives, which was used as a starting material for the synthesis of several optically active ergot alkaloids, which were clavicipitic acids, chanoclavine-I, costacalvine, and 1,1-dimethylallyltryptophan (DMAT). The three-step synthesis of optically active clavicipitic acids were accomplished without using a protecting group starting from 4-bromoindole and dl-serine. Some new synthetic reactions using unprotected amino acids were developed. Those were the biomimetic synthesis of tryptophan, the bromination of free aromatic amino acids, and the Pd-catalyzed N-allylation of free amino acids with allylic alcohol in aqueous media. Unique reactivity of π-allyl palladium complex or η3-(benzyl)palladium complex in aqueous media was found through Pd-catalyzed reaction of anthranilic acid, 2-aminobenzamide, and indole with allylic alcohols or benzyl alcohols, respectively.

Pteridine-, thymidine-, choline- and imidazole-derived alkaloids from the Australian ascidian, Leptoclinides durus

Four new acylated pteridine alkaloids, duramidines A-D, two new acylated thymidine alkaloids, leptoclinidines A and B, two new 1-acylglyceryl-3-(O-carboxyhydroxymethylcholine) alkaloids, durabetaines A and B, three new 1,3-dimethyl-5-methylsulfanylimidazole alkaloids, leptoclinidamines D-F, and the known alkaloids leptoclinidamines B and C and 6-bromo-1H-indolo-3-yl-oxoacetic acid methyl ester were isolated from the Australian ascidian Leptoclinides durus. The duramidines are the first pteridine alkaloids, possessing a three carbon side chain esterified at C-1' with a 4-hydroxy-2'-methoxycinnamic acid, and are either hydroxylated or sulfated at C-2'. The leptoclinidines are the first 3'-indole-3-carboxylic acid ester derivatives of thymidine to be reported in the literature. The durabetaines are the first glyceryl-3-(O-carboxyhydroxymethylcholine) alkaloids to be reported from an animal source and are also the only known derivatives from this class to be acylated with aromatic carboxylic acids. MS and NMR data analysis established the structures of the new compounds. All compounds were shown to be inactive when tested for cytotoxic activity against prostate (LNCaP) and breast (MDA-MB-231) cancer cell lines and antimicrobial activity against Pseudomonas aeruginosa and Staphylococcus aureus.

Synthesis of new coumarin derivatives with suspected anticoagulant activity

Objectives: To synthesize three series of new coumarin derivatives and to screen their anticoagulant activity in rabbits in order to define in more exact terms the structural features that responsible for the anticoagulant activity of coumarins. Methods: the first series was synthesized by esterification the 7-hydroxycoumarin with benzoic acid, salicylic acid and 5-amino salicylic acid to give derivatives I-III; the second series was synthesized by the formation of amide linkage between 6-aminocoumarin and benzoic acid, salicylic acid and 5-amino salicylic acid to give derivatives IV-VI while the third series was synthesized by esterification the coumarin-6-carboxylic acid with phenol, resorcinol and m-chlorophenol to give derivatives VII-IX. The anticoagulant activity of these derivatives (I-IX) was investigated in rabbits via Quick's one-stage method; the initial effect of each derivative on the prothrombine time for five rabbits before and after oral administration was measured. Results: The chemical structure of these derivatives was characterized by physical and spectroscopic techniques as FTIR, UV and 13C-NMR spectra. Depending on prothrombin time measurements, derivatives II and VIII showed a significant anticoagulant activity through increasing the prothrombine time while the other derivatives showed an insignificant anticoagulant activity. Conclusion: This study proposed that the coumarin derivatives contained an ester linkage at position 6 or 7 separated from a hydroxyl group by short carbon side chain may show anticoagulant activity.

On the mechanism of formation of arterenone in insect cuticular hydrolyzates

Arterenone (2-amino-3′,4′-dihydroxy acetophenone) is an important hydrolytic product generated from lightly colored sclerotized cuticle that use N-acyldopamine derivatives for crosslinking reactions. It seems to arise from 1,2-dehydro-N-acetyldopamine (dehydro NADA) that has been crosslinked to the cuticular components. However, the mechanism of generation of arterenone, which has two protons on the α-carbon and no proton on the β-carbon atom from dehydro NADA crosslinks that have one proton each on these two side chain carbons, remained elusive and undetermined. To investigate the mechanism of this transformation, we synthesized specifically labeled β-deuterated dehydro NADA and incubated with Sarcophaga bullata cuticle undergoing larval puparial transformation. We also isolated the dimeric products formed during the tyrosinase-mediated oxidation of dehydro NADA. Hydrolysis of both β-deuterated dehydro NADA treated cuticle and β-deuterated dehydro NADA dimer generated arterenone as the major hydrolytic product. Liquid chromatography-mass spectrometric analysis of this arterenone revealed the retention of deuterium from the β-position of dehydro NADA at the α-carbon atom of arterenone. Hydrolysis of β-deuterated dehydro NADA also generated the labeled arterenone under oxidative conditions, but not under anaerobic conditions. These results indicate the unique hydride shift from β-carbon to α-carbon during acid hydrolysis and reveal the mechanism of liberation of arterenone and related compounds from dehydro NADA linked cuticle.

Mapping Inhibitor Binding Modes on an Active Cysteine Protease via Nuclear Magnetic Resonance Spectroscopy

Cruzain is a member of the papain/cathepsin L family of cysteine proteases, and the major cysteine protease of the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We report an autoinduction methodology that provides soluble cruzain in high yields (>30 mg/L in minimal medium). These increased yields provide sufficient quantities of active enzyme for use in nuclear magnetic resonance (NMR)-based ligand mapping. Using circular dichroism and NMR spectroscopy, we also examined the solution-state structural dynamics of the enzyme in complex with a covalently bound vinyl sulfone inhibitor (K777). We report the backbone amide and side chain carbon chemical shift assignments of cruzain in complex with K777. These resonance assignments were used to identify and map residues located in the substrate binding pocket, including the catalytic Cys25 and His162. Selective [(15)N]Cys, [(15)N]His, and [(13)C]Met labeling was performed to quickly assess cruzain-ligand interactions for a set of eight low-molecular weight compounds exhibiting micromolar binding or inhibition. Chemical shift perturbation mapping verified that six of the eight compounds bind to cruzain at the active site. Three different binding modes were delineated for the compounds, namely, covalent, noncovalent, and noninteracting. These results provide examples of how NMR spectroscopy can be used to screen compounds for fast evaluation of enzyme-inhibitor interactions to facilitate lead compound identification and subsequent structural studies.

The cellular uptake and localization of non-emissive iridium(III) complexes as cellular reaction-based luminescence probes

Improvement of cellular uptake and subcellular resolution remains a major obstacle in the successful and broad application of cellular optical probes. In this context, we design and synthesize seven non-emissive cyclometalated iridium(III) solvent complexes [Ir(CˆN)2(solv)2]+L− (LIr2–LIr8, in which CˆN = 2-phenylpyridine (ppy) or its derivative; solv = DMSO, H2O or CH3CN; L− = PF6− or OTf−) applicable in live cell imaging to facilitate selective visualization of cellular structures. Based on the above variations (including different counter ions, solvent ligands, and CˆN ligands), structure–activity relationship analyses reveal a number of clear correlations: (1) variations in counter anions and solvent ligands of iridium(III) complexes do not affect cellular imaging behavior, and (2) length of the side carbon chain in CˆN ligands has significant effects on cellular uptake and localization/accumulation of iridium complexes in living cells. Moreover, investigation of the uptake mechanism via low-temperature and metabolism inhibitor assays reveal that [Ir(4-Meppy)2(CH3CN)2]+OTf− (LIr5) with 2-phenylpyridine derivative with side-chain of methyl group at the 4-position as CˆN ligand permeates the outer and nuclear membranes of living cells through an energy-dependent, non-endocytic entry pathway, and translocation of the complex from the cell periphery towards the perinuclear region possibly occurs through a microtubule-dependent transport pathway. Nuclear pore complexes (NPCs) appear to selectively control the transport of iridium(III) complexes between the cytoplasm and nucleus. A generalization of trends in behavior and structure–activity relationships is presented, which should provide further insights into the design and optimization of future probes.

Molecular characterization of ltp3 and ltp4, essential for C24-branched chain sterol-side-chain degradation in Rhodococcus rhodochrous DSM 43269

A previously identified sterol catabolic gene cluster is widely dispersed among actinobacteria, enabling them to degrade and grow on naturally occurring sterols. We investigated the physiological roles of various genes by targeted inactivation in mutant RG32 of Rhodococcus rhodochrous, which selectively degrades sterol side-chains. The ltp3 and ltp4 deletion mutants were each completely blocked in side-chain degradation of β-sitosterol and campesterol, but not of cholesterol. These results indicated a role for ltp3 and ltp4 in the removal of C24 branches specifically. Bioinformatic analysis of the encoded Ltp3 and Ltp4 proteins revealed relatively high similarity to thiolase enzymes, typically involved in β-oxidation, but the catalytic residues characteristic for thiolase enzymes are not conserved in their amino acid sequences. Removal of the C24-branched side-chain carbons of β-sitosterol was previously shown to proceed via aldolytic cleavage rather than by β-oxidation. Our results therefore suggest that ltp3 and ltp4 probably encode aldol-lyases rather than thiolases. This is the first report, to our knowledge, on the molecular characterization of genes with specific and essential roles in carbon-carbon bond cleavage of C24-branched chain sterols in Rhodococcus strains, most likely acting as aldol-lyases. The results are a clear contribution to our understanding of sterol degradation in actinobacteria.

Chemoassay Screening of DNA-Reactive Mutagenicity with 4-(4-Nitrobenzyl)pyridine – Application to Epoxides, Oxetanes, and Sulfur Heterocycles

Organic electrophiles have the potential to covalently attack DNA bases, and thus initiate mutagenic and carcinogenic processes. In this context, aromatic nitrogen sites of the DNA bases are often particularly nucleophilic, with guanine N7 being one of the most favored sites of adduct formation with electrophilic xenobiotics. Employing 4-(4-nitrobenzyl)pyridine (NBP) as model nucleophile with a respective aromatic ═N- unit, a new kinetic variant of a photometric chemoassay for sensing the DNA reactivity of organic compounds is introduced and applied to 21 three- and four-membered oxygen and sulfur heterocycles (15 epoxides, two thiiranes, three oxetanes, and one thietane). Besides six unreactive compounds (oxetanes, thietane, and aliphatic epoxides with six or more side-chain carbons), second-order rate constants of the electrophile-NBP reaction, k(NBP), were obtained for 15 compounds, ranging from (1.16 ± 0.05)·10⁻³ to (36.5 ± 0.6)·10⁻³ L mol⁻¹ min⁻¹ in a methanol/tris-HCl buffer (16/84 v/v) reaction medium. Solvolysis as confounding factor was addressed by determining respective first-order rate constants k(solv). Analysis of the k(NBP) values resulted in structure-reactivity relationships, and comparison with literature data from the Ames test bacterial strains TA100, TA1535, and TA97 (Salmonella typhimurium) as well as from WP2 uvrA (Escherichia coli) revealed significant log-log relationships between the mutagenic potency of the heterocycles and their reactivity toward NBP. The latter demonstrates the potential of the NBP chemoassay as a nonanimal component of integrated testing strategies for REACH, enabling an efficient screening of organic electrophiles with respect to their DNA reactivity and associated mutagenicity and carcinogenicity.

NMR a critical tool to study the production of carbon fiber from lignin

The structural changes occurring to hardwood Alcell™ lignin as a result of fiber devolatilization/extrusion, oxidative thermo-stabilization and carbonization are investigated in this study by solid-state and solution nuclear magnetic resonance (NMR) spectroscopy techniques. Solution based 1H–13C correlation NMR of the un-spun Alcell™ lignin powder and extruded lignin fiber detected modest changes occurring due to fiber devolatilization/extrusion in the type and proportion of aliphatic side-chain carbons or monolignol inter-unit linkages. Molecular weight analysis by gel permeation chromatography (GPC), along with an additional 31P NMR method used to indicate changes in terminal hydroxyl functionality, suggest fiber devolatilization/extrusion causes both chain scission and condensation reactions. 1H CRAMPS (combined rotation and multiple-pulse spectroscopy) and 13C cross-polarization/magic angle spinning (CP/MAS) spectra of extruded and stabilized lignin fibers indicate stabilization severely reduces the proportion of methoxy groups present, while also increasing the relative proportion of carbonyl and carboxyl-related structures, typically associated with cross-linking chemistries. 13C direct-polarization/magic angle spinning (DP/MAS) analysis of stabilized and carbonized fibers shows an increased relative amount of carbon–carbon bonds on aryl structures and a relative decrease of aryl ethers. DP/MAS dipolar dephasing experiments suggest that a majority of non-protonated carbons convert from carbonyl to aryl and condensed aryl structures during carbonization.

Design, Synthesis and Antihistamine Evaluations of Several N-hydroxyalkyl Desloratadine Analogues

Several N-hydroxyalkyl desloratadines and N-methoxyl ethyl desloratadine were prepared and evaluated for H1 antihistamine activity. The effects on isolated ileum smooth muscle tension in guinea pigs in vitro and asthma-relieving effects on the histamine-induced asthmatic reaction in guinea-pigs in vivo were examined. Most of them exhibited satisfactory H1 antihistamine activity and were obviously more potent than loratadine. Among these, Compound 3, N-(3-hydroxy)propyl desloratadine was the most active one. And it was chosen as a candidate for evaluation of acute toxicity (LD(50)= 0.876(0.784-0.980) g/kg), significantly superior to that of desloratadine (LD(50)=0.353 g/kg). Meanwhile, the experimental results demonstrated that the oxygen atom in the side carbon chain is crucial for enhancing the antihistamine activities.

Cation Symmetry effect on the Volatility of Ionic Liquids

This work reports the first data for the vapor pressures at several temperatures of the ionic liquids, [C(N/2)C(N/2)im][NTf(2)] (N = 4, 6, 8, 10, 12) measured using a Knudsen effusion apparatus combined with a quartz crystal microbalance. The morphology and the thermodynamic parameters of vaporization derived from the vapor pressures, are compared with those for the 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide series, [C(N-1)C(1)im][NTf(2)] (N = 3 - 9, 11, and 13). It was found that the volatility of [C(N/2)C(N/2)im][NTf(2)] series is significantly higher than the asymmetric cation ILs with the same total number of carbons in the alkyl side chains, [C(N-1)C(1)im][NTf(2)]. The observed higher volatility is related with the lower enthalpy of vaporization. The symmetric cation, [C(N/2)C(N/2)im][NTf(2)], presents lower entropies of vaporization compared with the asymmetric [C(N-1)C(1)im][NTf(2)], indicating an increase of the absolute liquid entropy in the symmetric cation ILs, being a reflection of a change of the ion dynamics in the IL liquid phase. Moreover both the enthalpy and entropy of vaporization of the [C(N/2)C(N/2)im][NTf(2)] ILs, present a clear odd-even effect with higher enthalpies/entropies of vaporization for the odd number of carbons in each alkyl chain ([C(3)C(3)im][NTf(2)] and [C(5)C(5)im][NTf(2)]).