Extra Methyl Research Articles

Corrigendum: Cancer Immunotherapy: Selected Targets and Small-Molecule Modulators.

In Figure 14, the chemical structure of the IDO1 inhibitor epacadostat (INCB024360) has one extra methylene group, which is incorrect. The correct structure can be found below.

Strigolactone Analogues with a D-Ring Modified at C-2.

Strigolactones (SLs) are important new plant hormones that receive much attention in current plant science. SLs are produced by many plants and are exuded by the root system. SLs are, amongst others, germination stimulants for seed of parasitic weeds. Naturally occurring SLs invariably contain three annelated rings, the ABC‐scaffold, connected to a butenolide (the D‐ring) via an enol ether unit. The synthesis of natural SLs requires many steps, therefore there is a continuous search for SL analogues with a simpler structure but with retention of bioactivity. In this study modified D‐ring variants are investigated, especially analogues having a methyl group at C‐2 instead of a hydrogen. For these analogues the ABC‐scaffolds of GR24 and Nijmegen‐1 were used. The coupling reaction proceeds profoundly better with chlorobutenolides than with the corresponding bromides. Bioassays reveal that the introduction an extra methyl at C‐2 does not influence the germination activity, which is relevant for gaining insight in the mode of action of SLs.

Thermal stability of a eutectic mixture of bis(2,2-dinitropropyl) acetal and formal: Part A. Degradation mechanisms in air and under nitrogen atmosphere

We investigated the chemical and thermal stability of a eutectic mixture of bis(2,2-dinitropropyl) acetal (BDNPA) and formal (BDNPF) (referred to as NP) in various environments at temperatures below 70 °C. Changes in the chemical composition of samples aged up to two years were characterized using TGA, FTIR, GPC, ESI-MS, and 1H NMR spectroscopies. The results show that the initial signs of NP degradation can be detected as early as in 12 months at 70 °C in air. The initial step in the degradation is the elimination of HONO molecules, followed by the formation of nitroso-alcohol isomers. While temperature plays a key role in determining the degradation kinetics of the initial stages, the absence or presence of oxygen determines the types and formation rates of various isomers and intermediates during thermal decomposition. In addition, oxygen accelerates the decomposition of the isomers and intermediates, whereas nitrogen has a stabilizing effect. BDNPA shows higher reactivity than BDNPF regardless of the aging conditions, which is attributed to the presence of an extra methyl group in its structure.

Effect of surfactant headgroup on low-fluorine-content CO2-philic hybrid surfactants

The article addresses the role of surfactant headgroup structure on hybrid surfactant performance for water-in-CO2 (w/c) microemulsion stabilization. The synthetic procedure, aqueous properties, and phase behaviour of a new hybrid sulfoglutarate surfactant are described. The sulfoglutarate version has an extra methylene group incorporated into the hydrophilic headgroup. The related hydrocarbon (AOT14 and AOT14GLU) and fluorocarbon (di-CF2 and di-CF2GLU) surfactants were used to form w/c microemulsions. For these two groups, the aqueous properties and w/c phase stability of both sulfoglutarates and sulfosuccinates were found to be similar. The newly synthesized hybrid CF2/AOT14GLU (sodium (4H,4H,5H,5H,5H-pentafluoropentyl-2,2-dimethyl-1-propyl)-2-sulfoglutarate) proved to be more efficient than the normal sulfosuccinate, hybrid CF2/AOT14 in terms of the aqueous behaviour and w/c phase stability. Hybrid CF2/AOT14GLU more effectively decreased the air-water surface tension by ∼2mNm−1 and lowering the cloud pressures on CO2 by ∼150bar.

Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors.

C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.

Molecular modeling study on the drug resistance mechanism of NS5B polymerase to TMC647055.

NS5B polymerase plays an important role in viral replication machinery. TMC647055 (TMC) is a novel and potent non-nucleoside inhibitor of the HCV NS5B polymerase. However, mutations that result in drug resistance to TMC have been reported. In this study, we used molecular dynamics (MD) simulations, binding free energy calculations, and free energy decomposition to investigate the drug resistance mechanism of HCV to TMC resulting from L392I, P495T, P495S, and P495L mutations in NS5B polymerase. From the calculated results we determined that the decrease in the binding affinity between TMC and NS5B(L392I) polymerase is mainly caused by the extra methyl group at the CB atom of Ile. The polarity of the side-chain of residue 495 has no distinct influence on residue 495 binding with TMC, whereas the smaller size of the side-chain of residue 495 causes a substantial decrease in the van der Walls interaction between TMC and residue 495. Moreover, the longer length of the side-chain of residue 495 has a significant effect on the electrostatic interaction between TMC and Arg-503. Finally, we performed the same calculations and detailed analysis on other 3 mutations (L392V, P495V, and P495I). The results further confirmed our conclusions. The computational results not only reveal the drug resistance mechanism between TMC647055 and NS5B polymerase, but also provide valuable information for the rational design of more potent non-nucleoside inhibitors targeting HCV NS5B polymerase.

From monomers to polymers: steric and supramolecular effects on dimensionality of coordination architectures of heteroleptic mercury(ii) halogenide–tetradentate Schiff base complexes

We report the synthesis and X-ray characterisation of six mercury(ii) halogenide–tetradentate Schiff base complexes.

Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.

Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.

Effect of C5-methylation of cytosine on the photoreactivity of DNA: a joint experimental and computational study of TCG trinucleotides.

DNA methylation, occurring at the 5 position of cytosine, is a natural process associated with mutational hotspots in skin tumors. By combining experimental techniques (optical spectroscopy, HPLC coupled to mass spectrometry) with theoretical methods (molecular dynamics, DFT/TD-DFT calculations in solution), we study trinucleotides with key sequences (TCG/T5mCG) in the UV-induced DNA damage. We show how the extra methyl, affecting the conformational equilibria and, hence, the electronic excited states, increases the quantum yield for the formation of cyclobutane dimers while reducing that of (6-4) adducts.

Communication between the zinc and tetrahydrobiopterin binding sites in nitric oxide synthase.

The nitric oxide synthase (NOS) dimer is stabilized by a Zn2+ ion coordinated to four symmetry-related Cys residues exactly along the dimer 2-fold axis. Each of the two essential tetrahydrobiopterin (H4B) molecules in the dimer interacts directly with the heme, and each H4B molecule is ∼15 Å from the Zn2+. We have determined the crystal structures of the bovine endothelial NOS dimer oxygenase domain bound to three different pterin analogues, which reveal an intimate structural communication between the H4B and Zn2+ sites. The binding of one of these compounds, 6-acetyl-2-amino-7,7-dimethyl-7,8-dihydro-4(3H)-pteridinone (1), to the pterin site and Zn2+ binding are mutually exclusive. Compound 1 both directly and indirectly disrupts hydrogen bonding between key residues in the Zn2+ binding motif, resulting in destabilization of the dimer and a complete disruption of the Zn2+ site. Addition of excess Zn2+ stabilizes the Zn2+ site at the expense of weakened binding of 1. The unique structural features of 1 that disrupt the dimer interface are extra methyl groups that extend into the dimer interface and force a slight opening of the dimer, thus resulting in disruption of the Zn2+ site. These results illustrate a very delicate balance of forces and structure at the dimer interface that must be maintained to properly form the Zn2+, pterin, and substrate binding sites.

PRIMARY COMBUSTION INTERMEDIATES IN LOW-PRESSURE PREMIXED LAMINAR 2,5-DIMETHYLFURAN/OXYGEN/ARGON FLAMES

Primary combustion intermediates in low-pressure premixed laminar 2,5-dimethylfuran (DMF)/oxygen (O2)/argon (Ar) flames with equivalence ratios of 0.8 and 1.5 were investigated by using tunable synchrotron vacuum ultraviolet photoionization and molecular-beam mass spectrometry. DMF is a promising biofuel, with properties similar to those of gasoline. However, the combustion chemistry of DMF is not well-studied. Possible reaction pathways of DMF and its primary combustion derivatives were proposed based on the combustion intermediates identified in this work. Photoionization efficiency curves (PIEs) of the combustion intermediates in the DMF/O2/Ar flames were recorded. Ionization energies (IEs) were measured from the PIEs. The combustion intermediates were identified by the agreement of the measured IEs with those reported in the literatures or calculated at G3B3 level. H abstraction and the consecutive reaction products were identified, including 5-methylfurfural, (Z)-1-oxo-1,3,4-pentatriene, and 2-ethyl-5-methylfuran, etc. Furan was not observed in the low-pressure DMF flames. H and OH addition products were also identified, including 2-methylfuran, (2Z,3E)-1-oxo-1,3-pentadiene, and 2-oxo-2,3-dihydro-5-methylfuran. The extra methyl side chain may explain the lower laminar burning velocity of DMF relative to that of 2-methylfuran.

Isolation and characterization of a new bacteriochlorophyll-c bearing a neopentyl substituent at the 8-position from the bciD-deletion mutant of the brown-colored green sulfur bacterium Chlorobaculum limnaeum

We recently constructed the mutant of the brown-colored green sulfur bacterium Chlorobaculum limnaeum lacking BciD which was responsible for formation of a formyl group at the 7-position in bacteriochlorophyll(BChl)-e biosynthesis. This mutant exclusively gave BChl-c, but not BChl-e, as the chlorosome pigments (Harada et al. in PLoS One 8(4):e60026, 2013). By the mutation, the homolog and epimer composition of the pigment was drastically altered. The methylation at the 8(2)-position in the mutant cells proceeded to create BChl-c carrying large alkyl substituents at this position. Correspondingly, the content of BChls-c having the (S)-configuration at the chiral 3(1)-position remarkably increased and accounted for 80.6% of the total BChl-c. Based on the alteration of the pigment composition in the mutant cells, a new BChl-c bearing the bulkiest, triple 8(2)-methylated neopentyl substituent at the 8-position ([N,E]BChl-c) was identified. The molecular structure of [N,E]BChl-c was fully determined by its NMR, mass, and circular dichroism spectra. The newly identified [N,E]BChl-c was epimerically pure at the chiral 3(1)-position and its stereochemistry was determined to be an (S)-configuration by modified Mosher's method. Further, the effects of the C8(2)-methylation on the optical absorption properties of monomeric BChls-c were investigated. The Soret but not Qy absorption bands shifted to longer wavelengths by the extra methylation (at most 1.4nm). The C8(2)-methylation induced a slight but apparent effect on absorption properties of BChls-c in their monomeric states.

Effect of Phytosterols Supplemented Health Food (Papaya Fruit Bar) On Serum Cholesterol and Ldl Cholesterol Levels In Normocholesterolemic And Mildly Hypercholesterolemic Subjects – A Pilot Study

Phytosterols exist as naturally occurring plant sterols that are present in the nonsaponifiable fraction of plant oils. Phytosterols are plant components that have a chemical structure similar to cholesterol except for the addition of an extra methyl or ethyl group; however, phytosterol absorption in humans is considerably less than that of cholesterol. Phytosterols (plant sterols and stanols) are well known for their total cholesterol and LDLcholesterol lowering effect. The technologies adopted for processing of fruit and vegetables range from traditional sun-drying to sophisticated and state-of-the-art techniques of juice concentration and freeze drying. The traditional way of dehydrating pulp into leather now turned into sophisticated fruit bars. Papaya fruit bars were formulated by incorporating phytosterol powder at 1.5% level. Physico-chemical and proximate composition studies were conducted for the fruit bar. A randomized doubleblind parallel study was conducted to evaluate the effect of phytosterol incorporated papaya fruit bar on the cholesterol levels in human subjects. 12 subjects were supplemented with papaya fruit bar either enriched with 1.5 g phytosterols (experimental) or without phytosterols (control) for 30 days. Significant (P < 0.05) decrease in serum total cholesterol (6.12%), triglycerides (6.21%) and LDL cholesterol (9.05%) was seen in experimental group compared to control group. These results indicate that phytosterol enriched food products could be a good vehicle for reducing plasma cholesterol in hypercholesterolemic subjects.

Modulating the Copper-Sulfur Interaction in Type 1 Blue Copper Azurin by Replacing Cys112 with Nonproteinogenic Homocysteine.

The Cu-SCys interaction is known to play a dominant role in defining the type 1 (T1) blue copper center with respect to both its electronic structure and electron transfer function. Despite this importance, its role has yet to be probed by mutagenesis studies without dramatic change of its T1 copper character. We herein report replacement of the conserved Cys112 in azurin with the nonproteinogenic amino acid homocysteine. Based on electronic absorption, electron paramagnetic resonance, and extended x-ray absorption fine structural spectroscopic studies, this variant displays typical type 1 copper site features. Surprisingly, instead of increasing the strength of the Cu-sulfur interaction by the introduction of the extra methylene group, the Cys112Hcy azurin showed a decrease in the covalent interaction between SHcy and Cu(II) when compared with the WT SCys-Cu(II) interaction. This is likely due to geometric adjustment of the center that resulted in the copper ion moving out of the trigonal plane defined by two histidines and one Hcy and closer to Met121. These structural changes resulted in an increase of reduction potential by 35 mV, consistent with lower Cu-S covalency. These results suggest that the Cu-SCys interaction is close to being optimal in native blue copper protein. It also demonstrates the power of using nonproteinogenic amino acids in addressing important issues in bioinorganic chemistry.

New strigolactone mimics: Structure–activity relationship and mode of action as germinating stimulants for parasitic weeds

Strigolactones (SLs) are new plant hormones with varies important bio-functions. This Letter deals with germination of seeds of parasitic weeds. Natural SLs have a too complex structure for synthesis. Therefore, there is an active search for SL analogues and mimics with a simpler structure with retention of activity. SL analogues all contain the D-ring connected with an enone moiety through an enol ether unit. A new mechanism for the hydrolysis SL analogues involving bidentate bound water and an α,β-hydrolase with a Ser-His-Asp catalytic triad has been proposed. Newly discovered SL mimics only have the D-ring with an appropriate leaving group at C-5. A mode of action for SL mimics was proposed for which now supporting evidence is provided. As predicted an extra methyl group at C-4 of the D-ring blocks the germination of seeds of parasitic weeds.

The Interaction of Isopenicillin N Synthase with Homologated Substrate Analogues δ‐(L‐α‐Aminoadipoyl)‐L‐homocysteinyl‐D‐Xaa Characterised by Protein Crystallography

Isopenicillin N synthase (IPNS) converts the linear tripeptide δ-(L-α-aminoadipoyl)-L-cysteinyl-D-valine (ACV) into bicyclic isopenicillin N (IPN) in the central step in the biosynthesis of penicillin and cephalosporin antibiotics. Solution-phase incubation experiments have shown that IPNS turns over analogues with a diverse range of side chains in the third (valinyl) position of the substrate, but copes less well with changes in the second (cysteinyl) residue. IPNS thus converts the homologated tripeptides δ-(L-α-aminoadipoyl)-L-homocysteinyl-D-valine (AhCV) and δ-(L-α-aminoadipoyl)-L-homocysteinyl-D-allylglycine (AhCaG) into monocyclic hydroxy-lactam products; this suggests that the additional methylene unit in these substrates induces conformational changes that preclude second ring closure after initial lactam formation. To investigate this and solution-phase results with other tripeptides δ-(L-α-aminoadipoyl)-L-homocysteinyl-D-Xaa, we have crystallised AhCV and δ-(L-α-aminoadipoyl)-L-homocysteinyl-D-S-methylcysteine (AhCmC) with IPNS and solved crystal structures for the resulting complexes. The IPNS:Fe(II):AhCV complex shows diffuse electron density for several regions of the substrate, revealing considerable conformational freedom within the active site. The substrate is more clearly resolved in the IPNS:Fe(II):AhCmC complex, by virtue of thioether coordination to iron. AhCmC occupies two distinct conformations, both distorted relative to the natural substrate ACV, in order to accommodate the extra methylene group in the second residue. Attempts to turn these substrates over within crystalline IPNS using hyperbaric oxygenation give rise to product mixtures.

Continuous β-turn fold of an alternating alanyl/homoalanyl peptide nucleic acid

The crystal structure of the PNA (peptide nucleic acid) oligomer H-Lys-HalG-AlaG-HalC-AlaG-HalC-AlaC-Lys-NH(2) (PNA1, amino acids with D-configuration are underlined, Ala = alanyl, Hal = homoalanyl) has been determined by ab initio direct methods and refined against 1.0 Å data. The asymmetric unit consists of a tetrameric cage with almost ideal Watson-Crick C-G base pairing of all the guanine and cytosine side-chain substituents. Each PNA strand has a 90° β-turn every second residue, stabilized by three hydrogen bonds between the backbone amides. The first, second, fifth and sixth bases stack on one side of the monomer and pair with the corresponding complementary bases of a second monomer to form a dimer. The two remaining bases on each side of the resulting dimer form Watson-Crick pairs with the complementary bases of a second dimer, leading to a unique cage structure. The extra methylene groups in the homoalanyl residues enable stacking of the bases with an optimal distance between base-planes but also with an appreciable lateral displacement (slide).

A Novel Fatty Acid, 12,17‐Dimethyloctadecanoic Acid, from the Extremophile Thermogemmatispora sp. (Strain T81)

The major fatty acids of a novel species of Thermogemmatispora sp. (strain T81) from the phylum Chloroflexi were identified as i18:0 (42.8 % of total fatty acids), i19:0 (9.7 %), and i17:0 (5.9 %). Also observed was a number of unidentified fatty acids, including a major acid (16.3 %) with ECL of 19.04 (BP1), and 18.76 (TG-WAXMS A). GCMS revealed that this compound is a saturated 20-carbon atom fatty acid. (1)H- and (13)C-NMR, with (1)H-(1)H-COSY and (1)H-(13)C-HSQC experiments suggested the structure of dimethyl octadecanoic acid with iso-branching, and an extra middle-chain methyl group. A pyrrolidide derivative demonstrated the characteristic gaps in GCMS indicating methyl branching at C12 and C17, which was eventually confirmed by a (1)H-(13)C-HSQC-TOCSY experiment. This 12,17-dimethyloctadecanoic acid has not been previously detected or described in these organisms. However, a recent description of a phylogenetically related species of Thermogemmatispora (Yabe et al., Int J Syst Evol Microbiol 61:903-910, 2010), noted an unidentified 20:0 fatty acid with matching GC behavior and GCMS data to that of strain T81. These data suggest that Thermogemmatispora share an ability to synthesize the same fatty acid. A number of other dimethyl-branched fatty acids, namely 8,14-diMe 15:0; 12,15-diMe 16:0; 10,15-diMe 16:0; 12,16-diMe 17:0; 10,16-diMe 17:0; 12,17-diMe 18:0; 12,18-diMe 19:0; 14,19-diMe 20:0, were also identified in strain T81.

Synthesis of Reported and Revised Structures of Amathamide D and Synthesis of Convolutamine F, H and Lutamide A, C

Total synthesis of the published structure of amathamide D is described. Methyl 2,3,4-tribromo-5-hydroxybenzoate was selected as starting compound because it is readily accessible via acid-mediated Grob fragmentation-aromatization reaction of 1,4,5,6-tetrabromo-7,7-dimethoxybicyclo[2.2.1]hept-5-en-2-one. The aforementioned ester was transformed into the reported structure of amathamide D through methylation of a hydroxyl group and conversion of the ester moiety to a β-aminoethyl side chain. The NMR data of the synthetic compound did not conform to the reported natural product structure possessing contiguously positioned β-aminoethyl side chain, a set of three adjacent bromines, and a methyl ether linkage on the phenyl ring. This prompted us to redefine the natural product structure by synthesizing a product whose spectral data exactly matched with the reported data of amathamide D. The convolutamine H, with completely substituted phenyl ring adorned with an extra methyl ether functional group, has also been synthesized by application of Grob fragmentation-aromatization strategy to 3-(benzyloxy)-1,4,5,6-tetrabromo-7,7-dimethoxybicyclo[2.2.1]hept-5-en-2-one. This approach furnished directly methyl 2,3,4-tribromo-5,6-dimethoxybenzoate, which was converted straightforwardly into convolutamine H. Further, synthesis of convolutamine F and lutamide A and C is also described.

Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: A molecular dynamics study

Herein, we report a comparative modelling study of 1,2-dimethoxyethane (DME) and 1,2-dimethoxypropane (DMP) at 298 K and 318 K in the liquid state, water mixtures, and at infinite dilution condition in water, methanol, carbon tetrachloride, and n-heptane. Both DME and DMP are united-atom models compatible with GROMOS∕OPLS force fields. Calculated thermodynamic and structural properties of the pure DME and DMP liquids resulted in excellent agreement with the experimental data. In aqueous solutions, densities, diffusion coefficients, and concentration dependent conformers of DME, were in agreement with experimental data. The calculated free energy of solvation (ΔG(hyd)) at 298 K is equal to -22.1 ± 0.8 kJ mol(-1) in good agreement with the experimental value of 20.2 kJ mol(-1). In addition, the free energy of solvation of DME in non-aqueous solvents follows the trend methanol ≈ water < carbon tetrachloride < n-heptane, consistently with the dielectric constant of the solvents. On contrary, the presence of an extra methyl group on chiral carbon makes DMP less soluble than DME in water (ΔG(hyd) = -16.0 ± 1.1 kJ mol(-1)) but more soluble in non-polar solvents as n-heptane. Finally, for the DMP the chiral discrimination of the two enantiomers was calculated as solvation free energy difference of one DMP isomer in the solution of the other. The obtained value of ΔΔG(RS) = -3.7 ± 1.4 kJ mol(-1) indicates a net chiral discrimination of the two enantiomers.