Portion Of Side Chain Research Articles

Crystal structure and enzyme engineering of the broad substrate spectrum l-amino acid oxidase 4 from the fungus Hebeloma cylindrosporum.

l-Amino acid oxidases (LAAOs) catalyze the oxidative deamination of l-amino acids to α-keto acids. Recombinant production of LAAOs with broad substrate spectrum remains a formidable challenge. We previously achieved this for the highly active and thermostable LAAO4 of Hebeloma cylindrosporum (HcLAAO4). Here, we crystallized a proteolytically truncated surface entropy reduction variant of HcLAAO4 and solved its structure in substrate-free form and in complex with diverse substrates. The ability to support the aliphatic portion of a substrate's side chain by an overall hydrophobic active site is responsible for the broad substrate spectrum of HcLAAO4, including l-amino acids with big aromatic, acidic and basic side chains. Based on the structural findings, we generated an E288H variant with increased activity toward pharmaceutical building blocks of high interest.

Resveratrol is converted to the ring portion of coenzyme Q10 and raises intracellular coenzyme Q10 levels in HepG2 cell.

Coenzyme Q10 is an essential lipid in the mitochondrial electron transport system and an important antioxidant. It declines with age and in various diseases, there is a need for a method to compensate for the decrease in coenzyme Q10. Resveratrol, a well-known anti-aging compound, has been shown to undergo metabolism to coenzyme Q10's benzene ring moiety in cells. However, administration of resveratrol did not alter or only slightly increased total intracellular coenzyme Q10 levels in many cell types. Synthesis of coenzyme Q10 requires not only the benzene ring moiety but also the side chain moiety. Biosynthesis of the side chain portion of coenzyme Q10 is mediated by the mevalonic acid pathway. Here, we explore the impact of resveratrol on coenzyme Q10 levels in HepG2 cells, which possess a robust mevalonic acid pathway. As a results, intracellular coenzyme Q10 levels were increased by resveratrol administration. Analysis using 13C6-resveratrol revealed that the benzene ring portion of resveratrol was converted to coenzyme Q10. Inhibition of the mevalonic acid pathway prevented the increase in coenzyme Q10 levels induced by resveratrol administration. These results indicate that resveratrol may be beneficial as a coenzyme Q10-enhancing reagent in cells with a well-developed mevalonic acid pathway.

Verification of nanoparticle formation, skin permeation, and apoptosis using nobiletin as a methoxyflavonoid derivative

PurposeNobiletin (NOB), a polymethoxyflavonoid, is known for its antioxidant and anti-inflammatory effects and has antitumor activity. However, its poor solubility and low bioavailability pose a significant challenge in its delivery. In this experiment, NOB was added to Soluplus® (Sol)/l-ascorbyl 2,6-dipalmitate (ASC-DP) as a ternary system, and Sol/ASC-DP/NOB nanoparticles were obtained using the hydration method. The purpose of this study was to enhance the solubility of NOB, apply it for skin permeation, and improve antitumor activity.MethodsThe preparation of Sol/ASC-DP/NOB nanoparticles was attempted using the hydration method, and particle size, zeta potential, and stability tests were performed to evaluate the formation of nanoparticles. 1H-1H NOESY/ROESY NMR spectral measurements were also performed to identify molecular interaction between NOB and Sol/ASC-DP. To evaluate its functionality, DPPH radical scavenging, skin permeation, fluorescence microscopy, and cell viability analyses were performed.ResultsThe particles were approximately 100 nm in size in the ternary system (weight ratio (Sol/ASCDP/NOB=8/1/1)) and were relatively stable for approximately 7 days at 25 °C under light-shielded conditions. From the NMR spectrum measurements of Sol/ASCDP/NOB, a cross-peak was observed between the –OCH3 group: C6,8 (3.8 ppm) derived from NOB, the methyl group (2.0 ppm) derived from Sol, and the side chain portion (1.2 ppm) derived from ASC-DP. Cross-peaks were observed between the polyethylene glycol (PEG) backbone of Sol (3.6 ppm) and the side chain of ASC-DP (0.8–1.2 ppm). The formation of Sol/ASC-DP/NOB nanoparticles facilitated its skin permeation, and fluorescence microscopy confirmed improved permeation. The DPPH radical scavenging test revealed that Sol/ASC-DP/NOB had an IC50 of 46.7 μg/mL. Cell viability assays showed a 20–40% decrease in cell viability with the addition of Sol/ASC-DP/NOB at 0.1 mg/mL.ConclusionSol/ASC-DP/NOB nanoparticles were successfully prepared, and these were found to inhibit melanin formation and have antitumor activity.

Mass Spectrometric Determination of Protein Ubiquitination.

Mass spectrometric methods of determining protein ubiquitination are described. Characteristic mass shifts and fragment ions indicating ubiquitinated lysine residues in tryptic and gluC digests are discussed. When a ubiquitinated protein is enzymatically digested, a portion of the ubiquitin side chain remains attached to the modified lysine. This "tag" can be used to distinguish a ubiquitinated peptide from the unmodified version, and can be incorporated into automated database searching. Several tags are discussed, the GGK and LRGGK tags, resulting from complete and incomplete tryptic digestion of the protein, and the STLHLVLRLRGG tag from a gluC-digested protein.A ubiquitinated peptide has two N-termini-one from the original peptide and the other from the ubiquitin side chain. Thus, it is possible to have two series of b ions and y ions, the additional series is the one that includes fragments containing portions of the ubiquitin side chain, and any diagnostic ions for the modification must include portions of this side chain. Fragment ions involving any part of the "normal" peptide will vary in mass according to the peptide being modified and will therefore not be of general diagnostic use. These diagnostic ions, found through examination of the MS/MS spectra of model ubiquitinated tryptic and gluC peptides, have not previously been reported. These ions can be used to trigger precursor ion scanning in automated MS/MS data acquisition scanning modes.

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties.

The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV-vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical-computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.

Characterization of Cell Wall Composition of Radish (Raphanus sativus L. var. sativus) and Maturation Related Changes.

Cell wall composition affects the texture of plant-based foods. In addition, the main components of plant cell walls are dietary fiber constituents and are responsible for potential physiological effects that are largely affected by the structural composition of the cell walls. Radish (Raphanus sativus L. var. sativus) is known to develop a woody and firm texture during maturation and ripening, most likely due to changes in the cell wall composition. To describe these changes chemically, radish was cultivated and harvested at different time points, followed by detailed chemical analysis of insoluble fiber polysaccharides and lignin. During maturation, changes in polysaccharide profiles were observed, with a decrease in the portion of neutral pectic side chains and an increase in the xylan portion being predominant. Radish lignin was characterized by unexpectedly high incorporation of p-coumaryl alcohol into the polymer. Maturation dependent increases in lignin contents were accompanied by compositional changes of the lignin polymers with sinapyl alcohol being preferentially incorporated.

Design and Synthesis of 1-((1,5-Bis(4-chlorophenyl)-2-methyl-1H-pyrrol-3-yl)methyl)-4-methylpiperazine (BM212) and N-Adamantan-2-yl-N'-((E)-3,7-dimethylocta-2,6-dienyl)ethane-1,2-diamine (SQ109) Pyrrole Hybrid Derivatives: Discovery of Potent Antitubercular Agents Effective against Multidrug-Resistant Mycobacteria.

Novel pyrroles have been designed, synthesized, and evaluated against mycobacterial strains. The pyrroles have originally been designed as hybrids of the antitubercular drugs BM212 (1) and SQ109 (2), which showed common chemical features with very similar topological distribution. A perfect superposition of the structures of 1 and 2 revealed by computational studies suggested the introduction of bulky substituents at the terminal portion of the pyrrole C3 side chain and the removal of the C5 aryl moiety. Five compounds showed high activity toward Mycobacterium tuberculosis, while 9b and 9c were highly active also against multidrug-resistant clinical isolates. Compound 9c showed low eukaryotic cell toxicity, turning out to be an excellent lead candidate for preclinical trials. In addition, four compounds showed potent inhibition (comparable to that of verapamil) toward the whole-cell drug efflux pump activity of mycobacteria, thus turning out to be promising multidrug-resistance-reversing agents.

An Investigation of the Interaction of Co‐Solvent with Substrates in the Pig Liver Esterase‐Catalyzed Hydrolysis of Malonate Esters

AbstractPreviously, we have reported the effect of several co‐solvents, including ethanol, on the enantioselective outcome of pig liver esterase (PLE) hydrolysis reactions. The greatest improvements were observed in those substrates that contained an atom capable of forming a hydrogen bond in the sidechain portion of the molecule. To further explore the interaction between substrate and ethanol, a second series of substrates were synthesized, in which the hydrogen bonding atoms of the side chain were modified, and subjected to PLE hydrolysis. Substrates containing atoms capable of forming hydrogen bonds showed the largest equilibrium constants. However, a large equilibrium constant did not always produce significant changes in enantioselectivity as hypothesized. Finally, molecular modeling experiments were performed to obtain a better understanding of the interactions. These experiments revealed that there are substrate–enzyme interactions that can be influenced by the addition of ethanol.

Depolymerization Model for Coal Devolatilization: Bridges and Side Chains as the Reaction Centers

A phenomenological extension is developed for coal devolatilization, based on FLASHCHAIN’s mechanism for tar and lumped noncondensables. It segregates the reaction center population further into bridges and side chains with dissimilar reactivities that vary with rank. At low and medium temperatures, most bridges dissociate to produce tar precursors and noncondensables, whereas only a minor portion of side chains decomposes into gases; a fraction of both types of reaction centers may also be shuttled away as an element in tar molecules. When devolatilization continues to sufficiently high temperatures, bridges are depleted and side chain decomposition takes over to dominate gas formation. In the evaluations against atmospheric reaction dynamics of 16 coals from lignite to anthracite, the extension predicts with accuracy the disparate time scales for the evolution of tar and noncondensables, as well as the rank-dependent devolatilization rates. Also, except for the earlier evolution history at low heating rates, the extension demonstrates extrapolations within experimental uncertainty over a broad domain of operating conditions (heating rates from 1 to 104 K/s and pressures from vacuum to 9 MPa) for coals across the entire rank spectrum.

Synthesis and Determination of Absolute Configuration of Lentztrehalose A.

The synthesis of lentztrehalose A, a naturally occurring trehalose derivative exhibiting various biological activities including autophagy-inducing activity, was achieved. The synthesis commenced with the selective protection of hydroxyl groups of commercially available trehalose, followed by the introduction of the side chain moiety by two methods: 1) prenylation and successive diastereoselective dihydroxylation; or 2) etherification by opening of the chiral epoxide. The present synthetic study clarified the unreported absolute configuration of the secondary alcohol part in the side chain portion.

Synthesis and structure-activity relationships for cytotoxicity and apoptosis-inducing activity of (+)-halichonine B.

Halichonine B is a sesquiterpene alkaloid isolated from the marine sponge Halichondria okadai Kadota. Halichonine B has exhibited cytotoxicity against mammalian cancer cells and induced apoptosis in the human leukemia cell line HL60. Here we established a practical route for the synthesis of halichonine B and its analogues, and we evaluated their biological activities. It was revealed that the secondary amino groups in the side chain portion are important for the strong cytotoxicity of halichonine B and that the N(11)-prenyl group is unimportant. Halichonine B and its analogues were also observed to induce apoptosis in HL60 cells.

Determinants of Substrate Specificity for Saccharopine Dehydrogenase from Saccharomyces cerevisiae

A survey of NADH, alpha-Kg, and lysine analogues has been undertaken in an attempt to define the substrate specificity of saccharopine dehydrogenase and to identify functional groups on all substrates and dinucleotides important for substrate binding. A number of NAD analogues, including NADP, 3-acetylpyridine adenine dinucleotide (3-APAD), 3-pyridinealdehyde adenine dinucleotide (3-PAAD), and thionicotinamide adenine dinucleotide (thio-NAD), can serve as a substrate in the oxidative deamination reaction, as can a number of alpha-keto analogues, including glyoxylate, pyruvate, alpha-ketobutyrate, alpha-ketovalerate, alpha-ketomalonate, and alpha-ketoadipate. Inhibition studies using nucleotide analogues suggest that the majority of the binding energy of the dinucleotides comes from the AMP portion and that distinctly different conformations are generated upon binding of the oxidized and reduced dinucleotides. Addition of the 2'-phosphate as in NADPH causes poor binding of subsequent substrates but has little effect on coenzyme binding and catalysis. In addition, the 10-fold decrease in affinity of 3-APAD in comparison to NAD suggests that the nicotinamide ring binding pocket is hydrophilic. Extensive inhibition studies using aliphatic and aromatic keto acid analogues have been carried out to gain insight into the keto acid binding pocket. Data suggest that a side chain with three carbons (from the alpha-keto group up to and including the side chain carboxylate) is optimal. In addition, the distance between the C1-C2 unit and the C5 carboxylate of the alpha-keto acid is also important for binding; the alpha-oxo group contributes a factor of 10 to affinity. The keto acid binding pocket is relatively large and flexible and can accommodate the bulky aromatic ring of a pyridine dicarboxylic acid and a negative charge at the C3 but not the C4 position. However, the amino acid binding site is hydrophobic, and the optimal length of the hydrophobic portion of the amino acid carbon side chain is three or four carbons. In addition, the amino acid binding pocket can accommodate a branch at the gamma-carbon, but not at the beta-carbon.

Conformationally Restricted (+)-Cacospongionolide B Analogues. Influence on Secretory Phospholipase A2 Inhibition

A new approach to (+)-cacospongionolide was developed to access conformationally restricted variants of the natural product. The flexible aliphatic region between the decalin and side chain portion of the natural product was replaced with alkenyl and alkynyl linkers to probe the influence of structural rigidity in the inhibition of secretary phospholipase A2 (sPLA2). It was found that when the aliphatic section is replaced with a Z-olefin or an alkyne, sPLA2 inhibitory activity suffered relative to the natural product; however, an E-olefin-containing analogue led to an enhanced activity. These results suggest that preferred sPLA2 binding conformation of the natural product is similar to the geometry of the E-olefin-containing analogue.

Physicochemical properties and amylopectin chain profiles of cowpea, chickpea and yellow pea starches

Starches from cowpea and chickpea seeds were isolated and their properties were compared with those of commercial yellow pea starch. Amylose contents were 25.8%, 27.2%, and 31.2%, and the volume mean diameter of granules, determined in the dry state, were 15.5, 17.9, and 33.8 μm for cowpea, chickpea and yellow pea starches, respectively. All three legume starches showed a C-type X-ray diffraction pattern and two-stage swelling pattern. Amylopectin populations were isolated and the unit chain profiles were analyzed by HPLC after debranching with pullulanase. The degree of polymerization (DP) of short chain populations was about 6–50 and the populations of long chain had a DP of 50–80. Cowpea showed a lower weight ratio of short:long chains than chickpea and yellow pea starches. The larger portion of long side chains in cowpea amylopectin can be correlated with a higher gelatinization temperature, greater pasting peak and a slight difference in crystalline structure found for cowpea starch. Chickpea and yellow pea starches exhibited similarity in unit chain profile of amylopectin as well as in gelatinization temperature and pasting profile, while they differed in amylose content, particle size and syneresis. It is assumed that the chain length distribution of amylopectin has a large influence on starch properties.

Study of the Interaction between Actin and Antitumor Substance Aplyronine A with a Novel Fluorescent Photoaffinity Probe

The interaction between actin and aplyronine A, a potent antitumor and actin-depolymerizing substance of marine origin, was investigated by photoaffinity labeling experiments. Photoaffinity probes consisting of a side-chain portion of aplyronine A as a ligand, a diazirine moiety as a photoaffinity group, and a fluorophore as a detecting group were synthesized. Photolabeling experiments between actin and the probe were carried out. Actin was successfully photolabeled by the fluorescent probe and visualized clearly. The present results provide the first chemical evidence for the direct interaction between actin and the side-chain portion of aplyronine A.

Parallel synthesis and antimalarial screening of a 4-aminoquinoline library.

Due to growing problems with drug resistance, there is an outstanding need for new, cost-effective drugs for the treatment of malaria. The 4-aminoquinolines have provided a number of useful antimalarials, and Plasmodium falciparum, the causative organism for the most deadly form of human malaria, is generally slow to develop resistance to these drugs. Therefore, diverse screening libraries of quinolines continue to be useful for antimalarial drug discovery. We report herein the development of an efficient method for producing libraries of 4-aminoquinolines variant in the side chain portion of the molecule. The effects of these substitutions were evaluated by screening this library for activity against P. falciparum, revealing four potent compounds active against drug-resistant strains.

Improvement in 193 nm Photoresists Performance by 172 nm VUV Curing

In order to make the enhancement of dry etching durability of methacrylate-based ArF resists induced by VUV curing consistent with low film shrinkage, i.e., less CD deviation, characteristics of several methacrylate-based polymers were studied. It was found that the film shrinkage mainly depended on the side chain structures and polymers containing acrylate group in main chain and norbornane lactone group in side chain portion showed dry etching resistance equal to commercially available KrF resists with lower film shrinkage than methacrylate-based ArF resists by VUV curing and suitable for the process. Curing reaction mechanism of methacrylate-based polymers were also studied using an infrared micro spectrometry with gradient shaving preparation. It was confirmed that the linkage radiolysis around carbonyl sites, mainly lactone portion of methacrylate-based ArF resist polymers induced by 15sec VUV light irradiation proceeded from the film surface to the interface with the substrate. VUV curing less than 1 minute was noticed to be effective for improvement in methacrylate-based ArF resists performance and might be met with the process tact time required for mass production phase.

산화환원 효소의 최적 pH 예측

본 논문에서는 산화 환원 효소의 최적 pH를 예측해 보았다. Boltzman 분배를 이용하여 어떤 아미노산의 side chain이 물에서 발견될수 있는 상대적 확률이나 물에 대한 상대적 친화력을 구하였으며 p<TEX>$K_R$</TEX>을 이용해 protonated 아미노산의 양과 deprotonated 아미소산의 양을 계산하였다. 효소의 최적 pH는 아미노산의 side chain이 물에서 발견될수 있는 상대적 확률과 protonated 또는 deprotonated된 아미노산 양의 곱인 유효 protonated된 양과 유효 depotonated된 양이 같아지는 pH로 예측하였다. 문헌 값과 비교해 보았을 때 예측치는 상당히 일치하는 경향을 보였으며 이 결과 로 효소 자체의 전도도가 생물학적 기능에 있어 매우 중요한 역할을 하는 것을 알 수있다. For various oxidoreductases, the optimum pHs of the enzymes can be calculated using the rule based on proton transfer. Relative probability of a certain amino acid side chain to be in the water, or the relative affinity to the water was calculated using Boltzman distribution. Also, the protonated and deprotonated portions of a certain amino acid side chain were calculated using p<TEX>$K_R$</TEX> of that and the effective protonated and deprotonated protions were the product of relative probability and the protonated and deproteonated protions. Where the total effective protonated portion was equal to the effective deprotonated portion of amino acid side chains, it was expected that oxidoreductases have max-imum activities. The optimum pHs calculated by our rule were compared with the experimental results.

ChemInform Abstract: A Total Synthesis of the Unique Tris-Oxazole Macrolide Ulapualide A Produced by the Marine Nudibranch Hexabranchus sanguineus.

A total synthesis of ulapualide A (1), whose relative stereochemistry was assigned on the basis of an earlier molecular mechanics study of its hypothetical metal chelated complex 9, is described. The synthesis is based on: i, elaboration of the double functionalised tris-oxazole 11; ii, synthesis and installation of the top side chain 16 (C-26–C-41) via a stereoselective Wittig reaction, leading to 17; iii, conversion of 17 into 73a and attachment of the C-1–C-9 portion 18; iv, macrocyclisation of 19 by an intramolecular Wadsworth–Emmons olefination leading to the macrolide 20; v, incorporation of the C-9 methyl group (to 80) and, finally vi, manipulation of the side chain functionality in 80 and introduction of the terminal formyl enamine residue. The synthetic ulapualide A showed NMR spectroscopic data which were almost identical to those described for the natural product, and did not separate from the natural material in HPLC analysis. Small differences in the 13C NMR spectroscopic data however lead us to conclude that the stereochemistry of the synthetic ulapualide differs from that in the natural product at one or more of the stereogenic centres along the C-28–C-33 portion of the side chain.

Alkenylzinc-Mediated Approach to the Vitamin D Skeleton. Application to the Synthesis of 6-Methyl Analogs of Vitamin and Previtamin D

Palladium-catalyzed cross-coupling of alkenylzinc reagents, bearing the C,D-ring/side chain portion, and (Z)-1-iodo-1,3-bis-exocyclic dienes (as A-ring precursors), provides a mild, convergent entry to the vitamin D skeleton, that is suitable for the synthesis of thermally labile derivatives such as those bearing substituents on the triene system.