Common Moiety Research Articles

High resolution HPLC-MS confirms overestimation of urea in soil by the diacetyl monoxime (DAM) colorimetric method

Urea represents a common form of organic nitrogen (N) which is added to agricultural soils in large quantities in both cropping (e.g. fertiliser) and livestock (e.g. urine) systems. In addition, there is a small, dynamic ambient pool of urea in soil associated with metabolic functioning in the microbial community. The diacetyl monoxime (DAM) colorimetric method is routinely used to quantify urea in soil, however, it lacks specificity due to the potential to react with the ureido group (R1NHCONHR2), a common structural moiety in soil organic matter. The aim of this study was therefore to critically evaluate the accuracy of this method for urea determination in soil. Using the DAM assay, we demonstrated significant cross-reactivity with a range of ureido compounds, many of which are ubiquitous in soil. We conclude therefore that the DAM assay is highly likely to overestimate urea concentrations in environmental materials. Such overestimation was confirmed using high resolution HPLC-Orbitrap MS to quantify urea in grassland soils using standard addition and the concentrations compared with those of the DAM assay. The results obtained show the DAM colorimetric method overestimated urea concentration by between 7.2 and 58 times for the sites studied. This significant overestimation of urea emphasises the need to validate the colorimetric method with reference to the LC-MS assay to ensure the robustness of measured urea concentrations. On this basis we recommend that reporting of the results from the DAM colorimetric method as “urea” concentration be curtailed and reported as “ureido-N” to recognise the contribution of unknown and variable contributions from other compounds. Indeed, given the problems with quantitatively assessing the latter contributions we would recommend the DAM method is now avoided in surveys of urea concentrations in soil and the wider environment.

Catalytic asymmetric acetalization of carboxylic acids for access to chiral phthalidyl ester prodrugs

Carboxylic acids are common moieties in medicines. They can be converted to phthalidyl esters as prodrugs. Unfortunately, phthalidyl esters are now mostly prepared in racemic forms. This is not desirable because the two enantiomers of phthalidyl esters likely have different pharmacological effects. Here we address the synthetic challenges in enantioselective modification of carboxylic acids via asymmetric acetalizations. The key reaction step involves asymmetric addition of a carboxylic acid to the catalyst-bound intermediate. This addition step enantioselectively constructs a chiral acetal unit that lead to optically enriched phthalidyl esters. A broad range of carboxylic acids react effectively under mild and transition metal-free conditions. Preliminary bioactivity studies show that the two enantiomers of chlorambucil phthalidyl esters exhibit different anti-cancer activities to inhibit the growth of Hela cells. Our catalytic strategy of asymmetric acetalizations of carboxylic acids shall benefit future development of chiral phthalidyl ester prodrugs and related molecules.

Photovoltaic donor-acceptor conjugated polymers with minimally substituted acceptor moieties

Abstract A novel family of conjugated donor-acceptor (D-A) copolymers designed with comparatively small methyl substituted acceptor units was synthesized for use as donor phase materials in bulk heterojunction (BHJ) organic photovoltaic (OPV) applications. These polymers make use of common acceptor moieties thieno [3,4-c]pyrrole-4,6-dione (TPD), diketopyrrolopyrrole (DPP), and isoindigo (iI) with methyl side chains to provide sterically unhindered sites for enhanced interactions with a molecular acceptor (MA), either PC71BM or ITIC in this study. The resulting polymers P(T4-TPD-M), P(T4-DPP-M), and P(T4-iI-M) were utilized in BHJ OPV devices where the highest performing D-A polymer, P(T4-TPD-M), obtained a maximum PCE of 7.5% with PC71BM and 4.0% with ITIC. These results indicate that minimally-sized methyl side chain derivatives of TPD, DPP, and iI can be useful acceptor moieties in D-A polymer systems, and the impact of sterics on the acceptor moiety can be elucidated in future studies through modification of the methyl side chain to bulkier aliphatic substituents.

A Visible‐Light‐Driven Molecular Motor Based on Pyrene

AbstractThe aromatic core of an overcrowded alkene‐based molecular motor is extended with the goal of inducing isomerization with visible light instead of harmful UV light. In our design, the common naphthalene moiety in the upper half of the motor is changed to pyrene. The photochemical and thermal isomerization processes are studied in detail using DFT calculations as well as NMR and UV/VIS spectroscopy. Our studies confirm that extension of the π‐system of the upper half successfully leads to a shift of the excitation wavelength into the visible region, while retaining proper rotary function.

Investigating How Chirality of a Threading Binuclear Ruthenium Complex Affects the DNA Threading Intercalation using Optical Tweezers

Using optical tweezers, we have been able to study the interactions of small molecules and prospective cancer drugs with DNA. One type of these molecules, known as threading intercalators, has a flat planar moiety in between the molecule's bulky side chains. In order to bind with DNA they have to thread their bulky side chains in between the base pairs. Due to this requirement for binding, these molecules tend to have high binding affinities and slow kinetics. We have been investigating the binding properties of the ruthenium-based threading intercalator ∧∧-[μ-bidppz(phen)4Ru2]4+, or ∧∧-P for short. This complex has the exact chemical components but an opposite chirality to the previously studied ΔΔ-P complex. Preliminary data show that the change in chirality affects the DNA binding kinetics, the association and dissociation rates, to at least a threefold in favor of the left-handed ∧∧-P complex. The data also confirm that both the left-handed and right-handed molecule have a similar binding affinity as a result of their common intercalating moiety. This comparison will give us a better understanding of how chirality affects the binding to DNA and will contribute towards improved designs of potential cancer treatment drugs.

Application of quantitative structure‐activity relationship analysis on an antibody and alternariol‐like compounds interaction study

The antigen-antibody interaction determines the sensitivity and specificity of competitive immunoassay for hapten detection. In this paper, the specificity of a monoclonal antibody against alternariol-like compounds was evaluated through indirect competitive ELISA. The results showed that the antibody had cross-reactivity with 33 compounds with the binding affinity (expressed by IC50 ) ranging from 9.4ng/mL to 12.0μg/mL. All the 33 compounds contained a common moiety and similar substituents. To understand how this common moiety and substituents affected the recognition ability of the antibody, a three-dimensional quantitative structure-activity relationship (3D-QSAR) between the antibody and the 33 alternariol-like compounds was constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The q2 values of the CoMFA and CoMSIA models were 0.785 and 0.782, respectively, and the r2 values were 0.911 and 0.988, respectively, indicating that the models had good predictive ability. The results of 3D-QSAR showed that the most important factor affecting antibody recognition was the hydrogen bond mainly formed by the hydroxyl group of alternariol, followed by the hydrophobic force mainly formed by the methyl group. This study provides a reference for the design of new hapten and the mechanisms for antibody recognition.

Alkyne Versus Ynamide Reactivity: Regioselective Radical Cyclization of Yne-Ynamides.

Ynamides are typically more reactive than simple alkynes and olefins. However, a serendipitous observation revealed a rare case where the reactivity of simple alkynes exceeds that of ynamides. This led to the development of a unique sulfur-radical-triggered cyclization of yne-tethered ynamides, which involves attack of the alkyne by a thiyl radical followed by cyclization with the ynamide. A wide range of novel 4-thioaryl pyrroles that could tolerate common functional moieties and N-protecting groups were expediently constructed by this strategy. The current method contrasts with the typical cyclization of yne-ynamides, which involves the attack of the alkyne moiety by the ynamide core. Control experiments and DFT calculations supported the participation of the sulfur radical in the reaction and the regioselective cyclization. The synthetic potential of the substituted pyrroles is also discussed.

Alkyne Versus Ynamide Reactivity: Regioselective Radical Cyclization of Yne‐Ynamides

AbstractYnamides are typically more reactive than simple alkynes and olefins. However, a serendipitous observation revealed a rare case where the reactivity of simple alkynes exceeds that of ynamides. This led to the development of a unique sulfur‐radical‐triggered cyclization of yne‐tethered ynamides, which involves attack of the alkyne by a thiyl radical followed by cyclization with the ynamide. A wide range of novel 4‐thioaryl pyrroles that could tolerate common functional moieties and N‐protecting groups were expediently constructed by this strategy. The current method contrasts with the typical cyclization of yne‐ynamides, which involves the attack of the alkyne moiety by the ynamide core. Control experiments and DFT calculations supported the participation of the sulfur radical in the reaction and the regioselective cyclization. The synthetic potential of the substituted pyrroles is also discussed.

Outer-Sphere Control for Divergent Multicatalysis with Common Catalytic Moieties.

We herein report two examples of one-pot, simultaneous reactions, mediated by multiple, orthogonal catalysts with the same catalytic motif. First, BINOL-derived chiral phosphoric acids (CPA) and phosphothreonine (pThr)-embedded peptides were found to be matched for two different steps in double reductions of bisquinolines. Next, two π-methylhistidine (Pmh)-containing peptides catalyzed enantio- and chemoselective acylations and phosphorylations of multiple substrates in one pot. The selectivity exhibited by common reactive moieties is adjusted solely by the appended chiral scaffold through outer-sphere interactions.

Generic Hapten Synthesis, Broad-Specificity Monoclonal Antibodies Preparation, and Ultrasensitive ELISA for Five Antibacterial Synergists in Chicken and Milk.

An antibody with broad specificity and principally depending on hapten structure and size is a key reagent for developing a class-selective immunoassay. In the present study, three new generic haptens of antibacterial synergists (ASGs) were proposed using trimethoprim as the starting molecule. These haptens contained carboxyl groups on the meta position of trimethoxybenzene for conjugating to protein, while, the common moiety of ASGs, i.e., diaminopyrimidine, was intentionally and maximally exposed to the immune system in animals in order to induce antibodies with broad specificity against ASGs. Five monoclonal antibodies (mAbs) were finally obtained, and 5C4 from the hapten with a short spacer arm, named Hapten A, showed not only uniform broad specificity but also high affinity to all five ASGs. We further determined the possible recognition mechanism of mAbs in terms of conformational and electronic aspects. An indirect competitive ELISA (icELISA)-based 5C4 was established and exhibited IC50 values of 0.067-0.139 μg L-1 with cross-reactivity of 48.2%-418.7% for the five ASGs in buffer under optimal conditions. The calculated limits of detection of the icELISA for chicken and milk were 0.06-0.8 μg kg-1 and 0.05-0.6 μg L-1, respectively. The recoveries in spiked chicken and milk samples were 75.2%-101.4% with a coefficient of variation less than 14.3%. In summary, we have developed, for the first time, a rapid and reliable icELISA for ASGs with significantly improved sensitivity and class selectivity.

Linking Aromatic Hydroxy Metabolic Functionalization of Drug Molecules to Structure and Pharmacologic Activity.

Drug functionalization through the formation of hydrophilic groups is the norm in the phase I metabolism of drugs for the modification of drug action. The reactions involved are mainly oxidative, catalyzed mostly by cytochrome P450 (CYP) isoenzymes. The benzene ring, whether phenyl or fused with other rings, is the most common hydrophobic pharmacophoric moiety in drug molecules. On the other hand, the alkoxy group (mainly methoxy) bonded to the benzene ring assumes an important and sometimes essential pharmacophoric status in some drug classes. Upon metabolic oxidation, both moieties, i.e., the benzene ring and the alkoxy group, produce hydroxy groups; the products are arenolic in nature. Through a pharmacokinetic effect, the hydroxy group enhances the water solubility and elimination of the metabolite with the consequent termination of drug action. However, through hydrogen bonding, the hydroxy group may modify the pharmacodynamics of the interaction of the metabolite with the site of parent drug action (i.e., the receptor). Accordingly, the expected pharmacologic outcome will be enhancement, retention, attenuation, or loss of activity of the metabolite relative to the parent drug. All the above issues are presented and discussed in this review using selected members of different classes of drugs with inferences regarding mechanisms, drug design, and drug development.

Rapid tentative identification of synthetic cathinones in seized products taking advantage of the full capabilities of triple quadrupole analyzer

In this work, a new approach for synthetic cathinone identification in seized products, consisting of a rapid pseudo-target screening using liquid chromatography coupled to low-resolution tandem mass spectrometry (MS/MS), is proposed based on typical common product ions and neutral losses observed for this drug class. The term “pseudo-target” screening indicates that although a pre-defined target compound list is not used, the search is limited to synthetic cathinones with expected common moieties. A total of 22 neutral losses and 36 common product ions were monitored and used for cathinone identification. In order to test the approach, 14 blind samples were analyzed and the results compared with high-resolution mass spectrometry data. From the data obtained, the different moieties of the cathinones (and therefore their structures) could be derived, allowing their tentative identification. This methodology will be useful for the first and rapid synthetic cathinone detection in laboratories that have low-resolution MS/MS instrumentation.

Structure-based design of free fatty acid receptor 1 agonists bearing non-biphenyl scaffold

The free fatty acid receptor 1 (FFA1) enhances the glucose-stimulated insulin secretion without the risk of hypoglycemia. However, most of FFA1 agonists have a common biphenyl moiety, leading to a relative deprivation in structure types. Herein, we describe the exploration of non-biphenyl scaffold based on the co-crystal structure of FFA1 to increase additional interactions with the lateral residues, which led to the identification of lead compounds 3 and 9. In induced-fit docking study, compound 3 forms an edge-on interaction with Trp150 by slightly rotating the indole ring of Trp150, and compound 9 has additional hydrogen bond and δ-π interactions with Leu135, which demonstrated the feasibility of our design strategy. Moreover, lead compounds 3 and 9 revealed improved polar surface area compared to GW9508, and have considerable hypoglycemic effects in mice. This structure-based study might inspire us to design more promising FFA1 agonists by increasing additional interactions with the residues outside of binding pocket.

Visual and Colorimetric High-Throughput Analysis of Chiral Carboxylic Acids Based on Enantioselective Charge Shielding of Gold Nanoparticles.

Because chiral carboxylic acids (CCAs) are a class of important biological molecules and common functional moieties found in pharmaceutical molecules, the chiral analysis of CCAs has received much attention. Herein, we developed a simple, rapid, and cost-effective method for visual and colorimetric high-throughput analysis of CCAs using chiral di-imine structure-modified gold nanoparticles (C-AuNPs) as the probe. The C-AuNPs are positively charged in the presence of zinc ion, and they can be enantioselectively shielded by the negatively charged CCA enantiomers. Therefore, upon the addition of different concentrations and enantiomeric excess (ee) of CCAs, the C-AuNP-based sensor shows the different levels of aggregation along with the visual changes in solution color, which can achieve simultaneous analysis of the concentration and ee of CCAs. The chiral recognition mechanism based on C-AuNPs was investigated by the determination of binding constants ( K) and molecular simulation methods. Our approach is expected to have the wide-ranging applications in the developing region for enantio-sensing of various chiral drugs and biomolecules.

Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry.

Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS1). Significant water/alcohol loss (>30% abundance in MS1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. Graphical Abstract ᅟ.

Substructure-activity relationship studies on antibody recognition for phenylurea compounds using competitive immunoassay and computational chemistry

Based on the structural features of fluometuron, an immunizing hapten was synthesized and conjugated to bovine serum albumin as an immunogen to prepare a polyclonal antibody. However, the resultant antibody indicated cross-reactivity with 6 structurally similar phenylurea herbicides, with binding activities (expressed by IC50 values) ranging from 1.67 µg/L to 42.71 µg/L. All 6 phenylurea herbicides contain a common moiety and three different substitutes. To understand how these three different chemical groups affect the antibody-phenylurea recognition activity, quantum chemistry, using density function theory (DFT) at the B3LYP/6-311++ G(d,p) level of theory, was employed to optimize all phenylurea structures, followed by determination of the 3D conformations of these molecules, pharmacophore analysis, and molecular electrostatic potential (ESP) analysis. The molecular modeling results confirmed that the geometry configuration, pharmacophore features and electron distribution in the substituents were related to the antibody binding activity. Spearman correlation analysis further elucidated that the geometrical and electrostatic properties on the van der Waals (vdW) surface of the substituents played a critical role in the antibody-phenylurea recognition process.

DFT calculations of the IR and Raman spectra of anthraquinone dyes and lakes

AbstractThe IR and Raman spectra of alizarin, purpurin, kermesic acid, and carminic acid have been computed performing density functional theory calculations at the B3LYP/6‐31G(d) level of theory. The computational approach adopted has been validated on the basis of a series of calculations with different level of theory on the anthraquinone molecule, the common moiety of these dyes. The computed vibrational frequencies have been adopted as a guideline to propose the vibrational assignment of the dyes and to obtain useful information on the Raman spectra of their aluminum complexes.

Advanced NMR-Based Structural Investigation of Glucosinolates and Desulfoglucosinolates

Glucosinolates (GLs) constitute a class of plant secondary metabolites that are characteristic of the order Brassicales. They each contain a common hydrophilic moiety connected to a mostly hydrophobic side chain whose constitution is the most frequent structural variant. Their transformations by myrosinases lead to intensively studied and highly reactive compounds of biological relevancy. In other respects, the enzymatic desulfation of GLs produces derivatives (DS-GLs) that are useful for GL analysis. A collection of 31 compounds, GLs and DS-GLs, representing 17 different side chains was established in order to report accurate descriptions of the molecules' 1H-, 13C-, and 15N-NMR parameters. The descriptions of the 1H-NMR spectra were achieved using the PERCH software, which accurately analyzed the complex coupling patterns that arose from strongly coupled nuclei. The chemical shift assignments were supported by 2D COSY, HSQC, and HMBC spectra. The impact of desulfation and the influence of the nature of the side chains on the chemical shift values are discussed. The results of the spectroscopic analysis and the 3D chemical-structure models of the studied molecules were grouped in structure-and-data-format (SDF) files. The NMR parameters were also collected in a simple text file, a spreadsheet file, and a relational database.

Receptor for advanced glycation end products (RAGE)-mediated cytotoxicity of 3-hydroxypyridinium derivatives.

Advanced glycation end products (AGEs) formed from glyceraldehyde (Gcer) and glycolaldehyde (Gcol) are involved in the pathogenesis of diabetic complications, via interactions with a receptor for AGEs (RAGE). In this study, we aimed to elucidate the RAGE-binding structure in Gcer and Gcol-derived AGEs and identify the minimal moiety recognized by RAGE. Among Gcer and Gcol-derived AGEs, GLAP (glyceraldehyde-derived pyridinium) and GA-pyridine elicited toxicity in PC12 neuronal cells. The toxic effects of GLAP and GA-pyridine were suppressed in the presence of anti-RAGE antibody or the soluble form of RAGE protein. Furthermore, the cytotoxicity test using GLAP analog compounds indicated that the 3-hydroxypyridinium (3-HP) structure is sufficient for RAGE-dependent toxicity. Surface plasmon resonance analysis showed that 3-HP derivatives directly interact with RAGE. These results indicate that GLAP and GA-pyridine are RAGE-binding epitopes, and that 3-HP, a common moiety of GLAP and GA-pyridine, is essential for the interaction with RAGE.

HTS by NMR for the Identification of Potent and Selective Inhibitors of Metalloenzymes.

We have recently proposed a novel drug discovery approach based on biophysical screening of focused positional scanning libraries in which each element of the library contained a common binding moiety for the given target or class of targets. In this Letter, we report on the implementation of this approach to target metal containing proteins. In our implementation, we first derived a focused positional scanning combinatorial library of peptide mimetics (of approximately 100,000 compounds) in which each element of the library contained the metal-chelating moiety hydroxamic acid at the C-terminal. Screening of this library by nuclear magnetic resonance spectroscopy in solution allowed the identification of a novel and selective compound series targeting MMP-12. The data supported that our general approach, perhaps applied using other metal chelating agents or other initial binding fragments, may result very effective in deriving novel and selective agents against metalloenzyme.