Comparing normal modes across different models and scales: Hessian reduction versus coarse‐graining

Dimension reduction is often necessary when attempting to reach longer length and time scales in molecular simulations. It is realized by constraining degrees of freedom or by coarse‐graining the system. When evaluating the accuracy of a dimensional reduction, there is a practical challenge: the models yield vectors with different lengths, making a comparison by calculating their dot product impossible. This article investigates mapping procedures for normal mode analysis. We first review a horizontal mapping procedure for the reduced Hessian techniques, which projects out degrees of freedom. We then design a vertical mapping procedure for the “implosion” of the all‐atom (AA) Hessian to a coarse‐grained scale that is based upon vibrational subsystem analysis. This latter method derives both effective force constants and an effective kinetic tensor. Next, a series of metrics is presented for comparison across different scales, where special attention is given to proper mass‐weighting. The dimension‐dependent metrics, which require prior mapping for proper evaluation, are frequencies, overlap of normal mode vectors, probability similarity, Hessian similarity, collectivity of modes, and thermal fluctuations. The dimension‐independent metrics are shape derivatives, elastic modulus, vibrational free energy differences, heat capacity, and projection on a predefined basis set. The power of these metrics to distinguish between reasonable and unreasonable models is tested on a toy alpha helix system and a globular protein; both are represented at several scales: the AA scale, a Gō‐like model, a canonical elastic network model, and a network model with intentionally unphysical force constants. Published 2012 Wiley Periodicals, Inc.     

Mode‐tracking based stationary‐point optimization

In this work, we present a transition‐state optimization protocol based on the Mode‐Tracking algorithm [Reiher and Neugebauer, J. Chem. Phys., 2003, 118, 1634]. By calculating only the eigenvector of interest instead of diagonalizing the full Hessian matrix and performing an eigenvector following search based on the selectively calculated vector, we can efficiently optimize transition‐state structures. The initial guess structures and eigenvectors are either chosen from a linear interpolation between the reactant and product structures, from a nudged‐elastic band search, from a constrained‐optimization scan, or from the minimum‐energy structures. Alternatively, initial guess vectors based on chemical intuition may be defined. We then iteratively refine the selected vectors by the Davidson subspace iteration technique. This procedure accelerates finding transition states for large molecules of a few hundred atoms. It is also beneficial in cases where the starting structure is very different from the transition‐state structure or where the desired vector to follow is not the one with lowest eigenvalue. Explorative studies of reaction pathways are feasible by following manually constructed molecular distortions. © 2015 Wiley Periodicals, Inc.     

Monitoring Conformational Changes in the NDM‐1 Metallo‐β‐lactamase by 19F NMR Spectroscopy

The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using ¹⁹F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.     

Ab initio studies of the conformers and conformational distribution of gas‐phase N,N‐dimethylaminopropanol

Systematic and extensive conformational search has been performed to characterize the gas‐phase N,N‐dimethylaminopropanol structures. A total of 91 unique trail structures were generated by allowing for all the single‐bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were optimized at the B3LYP/6‐311G* level of theory and then subjected to further optimization at the B3LYP/6‐311++G**. A total of 36 conformers are found and their zero‐point vibrational enegies, rotational constants, and dipole moments are determined. Vertical ionization energies of 11 low‐lying conformers predicted with the electron propagator theory are in good agreement with the experimental data. The two most stable conformers display intramolecular H bonds (HBs): OH···N. These HBs influence on the molecular electronic structures is exhibited by natural bond orbital analyses. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperature dependence of photoelectron spectra is interpreted. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Collision‐free poisson motion planning in ultra high‐dimensional molecular conformation spaces

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three‐dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra‐high dimensional configuration spaces, and the requirement to avoid (self‐) collisions, which results in low acceptance rates. Here, we present two novel mechanisms to overcome these limitations. First, we introduce temporary constraints between near‐colliding links. The resulting constraint varieties instantaneously redirect the search for collision‐free conformations, and couple motions between distant parts of the linkage. Second, we adapt a randomized Poisson‐disk motion planner, which prevents local oversampling and widens the search, to ultra‐high dimensions. Tests on several model systems show that the sampling acceptance rate can increase from 16% to 70%, and that the conformational coverage in loop modeling measured as average closeness to existing loop conformations doubled. Correlated protein motions identified with our algorithm agree with those from MD simulations. © 2018 Wiley Periodicals, Inc.     

Rapid preparative isolation of erythrocentaurin from Enicostemma littorale by medium‐pressure liquid chromatography,its estimation by high‐pressure thin‐layer chromatography,and its α‐amylase inhibitory activity

Erythrocentaurin is a relatively simple natural product present among the members of Gentianaceae. A preparative method for the isolation of erythrocentaurin from the ethyl acetate fraction of Enicostemma littorale using medium‐pressure liquid chromatography has been reported. The method consisted of a simple step gradient from 10 to 20% ethyl acetate in n‐hexane. Using a 70 × 460 mm Si60 column, this method is capable of processing 20 g of material in <3 h (purity ≈ 97%). The recovery of erythrocentaurin was 87.77%. Estimation of erythrocentaurin in extracts and fractions based on high‐pressure thin‐layer chromatography was carried out on silica gel 60 F₂₅₄ plates with toluene/ethyl acetate/formic acid (80:18:2 v/v/v) as the mobile phase. The densitometric analysis was performed at 230 nm. A well‐separated compact band of erythrocentaurin appeared at R_f 0.54 ± 0.04. The analytical method showed good linearity in the concentration range of 200–1500 ng/band with a correlation coefficient of 0.99417. The limits of detection and quantification were found to be ≈60 and ≈180 ng/band, respectively. Erythrocentaurin exhibited a concentration‐dependent α‐amylase inhibition (IC₅₀ 1.67 ± 0.28 mg/mL). The outcome of the study should be considered for pharmacokinetic and biotransformation studies involving E. littorale.     

Rapid and sensitive determination of free thiols by capillary zone electrophoresis with near‐infrared laser‐induced fluorescence detection using a new BODIPY‐based probe as labeling reagent

A CZE with near‐infrared (NIR) LIF detection method has been developed for the analysis of six low molecular weight thiols including glutathione, homocysteine, cysteine, γ‐glutamylcysteine, cysteinylglycine, and N‐acetylcysteine. For this purpose, a new NIR fluorescent probe, 1,7‐dimethyl‐3,5‐distyryl‐8‐phenyl‐(4'‐iodoacetamido)difluoroboradiaza‐s‐indacene was utilized as the labeling reagent, whose excitation wavelength matches the commercially available NIR laser line of 635 nm. The optimum procedure included a derivatization step of the free thiols at 45°C for 25 min and CZE analysis conducted within 14 min in the running buffer containing 16 mmol/L pH 7.0 sodium citrate and 60% v/v ACN. The LODs (S/N = 3) ranged from 0.11 nmol/L for N‐acetylcysteine to 0.31 nmol/L for γ‐glutamylcysteine, which are better than or comparable to those reported with other derivatization‐based CE‐LIF methods. As the first trial of NIR CE‐LIF method for thiol determination, the practical application of the proposed method has been validated by detecting thiols in cucumber and tomato samples with recoveries of 96.5–104.3%.     

A Host‐Guest‐Recognition‐Based Electrochemical Sensor for Sequence‐Specific DNA Detection

We herein constructed a sensor that converts target DNA hybridization‐induced conformational transformation of the probe DNA to electrochemical response based on host‐guest recognition and nanoparticle label. In the sensor, the hairpin DNA terminal‐labeled with 4‐((4‐(dimethylamino)phenyl)azo)benzoic acid (dabcyl) and thiol group was immobilized on Au electrode surface as the probe DNA by Au‐S bond, and the CdS nanoparticles surface‐modified with β‐cyclodextrins (CdS‐CDs) were employed as electrochemical signal provider and host‐guest recognition element. Initially, the probe DNA immobilized on electrode kept the stem‐loop configuration, which shielded dabcyl from docking with the CdS‐CDs in solution due to the steric effect. After target hybridization, the probe DNA underwent a significant conformational change, which forced dabcyl away from the electrode. As a result, formerly‐shielded dabcyl became accessible to host‐guest recognition between β‐cyclodextrin (β‐CD) and dabcyl, thus the target hybridization event could be sensitively transduced to electrochemical signal provided by CdS‐CDs. This host‐guest recognition‐based electrochemical sensor has been able to detect as low as picomolar DNA target with excellent differentiation ability for even single mismatch.     

Simultaneous determination of 9‐dehydro‐17‐hydro‐andrographolide and sodium 9‐dehydro‐17‐hydro‐andrographolide‐19‐yl sulfate in rat plasma by UHPLC‐ESI‐MS/MS after administration of xiyanping injection: application to a pharmacokinetic study

9‐Dehydro‐17‐hydro‐andrographolide (DHA) and sodium 9‐dehydro‐17‐hydro‐andrographolide‐19‐yl sulfate (DHAS) are active ingredients of xiyanping injection in clinical use. A simple, rapid and sensitive UHPLC‐ESI‐MS/MS method was developed for the determination of DHA and DHAS in rat plasma, and the pharmacokinetics of DHA and DHAS after intravenous administration of xiyanping injection was investigated. The plasma samples were treated with methanol to precipitate out protein, and the separation of DHA and DHAS was achieved on a Waters BEH C₁₈ column with a mobile phase consisting of acetonitrile and 10 mmol/L ammonium acetate solution at a flow rate of 0.4 mL/min. DHA, DHAS and the internal standard (internal standard, IS) diethylstilbestrol were detected at negative ion mode. The precursor‐product ion pairs used in multiple reaction monitoring mode were: m/z 349.1 → 286.9 (DHA), m/z 428.9 → 96.0 (DHAS) and m/z 267.1 → 236.9 (IS). Calibration curves offered satisfactory linearity within the test range, and all correlation coefficients were >0.995. The lower limit of detection of DHA and DHAS in plasma samples were determined to be 0.1 ng/mL. The lower limit of quantitation was 0.5 ng/mL for DHA and DHAS. All the recoveries of the quality control samples were in the range of 86.0–102.4%. The ratios of matrix effect were between 89.2 and 105.1%. The method was fully validated and successfully applied to the pharmacokinetic study of DHA and DHAS in rats. The study showed that both DHA and DHAS were distributed and eliminated rapidly in rats. Copyright © 2013 John Wiley & Sons, Ltd.     

Identification of the metabolites of gigantol in rat urine by ultra‐performance liquid chromatography combined with electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry

Gigantol is a typical bibenzyl compound isolated from Dendrobii Caulis that has been widely used as a medicinal herb in China for the treatment of diabetic cataract, cancer and arteriosclerosis obliterans and as a tonic for stomach nourishment, saliva secretion promotion and fever reduction. However, few studies have been carried out on its in vivo metabolism. In the present study, a rapid and sensitive method based on ultra‐performance liquid chromatography/electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry (UPLC‐Q/TOF‐MS) in positive ion mode was developed and applied to identify the metabolites of gigantol in rat urine after a single oral dose (100 mg/kg). Chromatographic separation was performed on an Acquity UPLC HSS T3 column (100 × 2.1 mm i. d., 1.8 µm) using acetonitrile and 0.1% aqueous formic acid as mobile phases. A total of 11 metabolites were detected and identified as all phase II metabolites. The structures of the metabolites were identified based on the characteristics of their MS, MS² data and chromatographic retention times. The results showed that glucuronidation is the principal metabolic pathway of gigantol in rats. The newly identified metabolites are useful to understand the mechanism of elimination of gigantol and, in turn, its effectiveness and toxicity. As far as we know, this is the first attempt to investigate the metabolic fate of gigantol in vivo. Copyright © 2014 John Wiley & Sons, Ltd.     

BF2‐Chelate Complexes of 6‐(4‐Iodophenyl)‐2,3,4,8,9,10‐hexamethyldipyrrin and 2‐(4‐Iodobenzoyl)‐3,4,5‐trimethylpyrrole: Fluorescent Dyes with a Chemical Anchor Group

The one‐pot condensation/coordination reaction of 4‐iodobenzoylchloride, 2,3,4‐trimethylpyrrole and BF₃ × Et₂O yields the BF₂ chelate complexes of the 1:1 condensation product 2‐(4‐iodobenzoyl)‐3,4,5‐trimethylpyrrole and of the 1:2 product 6‐(4‐iodophenyl)‐2,3,4,8,9,10‐hexamethyldipyrrin, as separable compounds in 6 and 38 % yield, respectively. Both new boron derivatives are fluorescent already upon exitation with ambient light. While the fluorescence quantum yield of the benzoyl derivative is very low, this value is significantly higher for the related boron dipyrrin (BODIPY) derivative. Single crystal X‐ray diffraction studies of both compounds reveal that the reason for these deviating physical properties are structural in nature. For the BODIPY an essentially flat structure of the fluorophor has been established, in addition to restricted rotation of the 4‐iodophenyl substituent, so that no conformational dynamic facilitates radiationless deactivations. The 1:1 condensation product on the other hand allows a fast equilibration of the photophysical exitation by dynamic processes and therefore exhibits a low fluorescence quantum yield. Both luminophores contain an iodoaryl moiety with potential uses for further functionalization and bioconjugation.     

GalaxyDock2: Protein–ligand docking using beta‐complex and global optimization

In this article, an enhanced version of GalaxyDock protein–ligand docking program is introduced. GalaxyDock performs conformational space annealing (CSA) global optimization to find the optimal binding pose of a ligand both in the rigid‐receptor mode and the flexible‐receptor mode. Binding pose prediction has been improved compared to the earlier version by the efficient generation of high‐quality initial conformations for CSA using a predocking method based on a beta‐complex derived from the Voronoi diagram of receptor atoms. Binding affinity prediction has also been enhanced by using the optimal combination of energy components, while taking into consideration the energy of the unbound ligand state. The new version has been tested in terms of binding mode prediction, binding affinity prediction, and virtual screening on several benchmark sets, showing improved performance over the previous version and AutoDock, on which the GalaxyDock energy function is based. GalaxyDock2 also performs better than or comparable to other state‐of‐the‐art docking programs. GalaxyDock2 is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html . © 2013 Wiley Periodicals, Inc.     

Restricted dead‐end elimination: Protein redesign with a bounded number of residue mutations

Dead‐end elimination (DEE) has emerged as a powerful structure‐based, conformational search technique enabling computational protein redesign. Given a protein with n mutable residues, the DEE criteria guide the search toward identifying the sequence of amino acids with the global minimum energy conformation (GMEC). This approach does not restrict the number of permitted mutations and allows the identified GMEC to differ from the original sequence in up to n residues. In practice, redesigns containing a large number of mutations are often problematic when taken into the wet‐lab for creation via site‐directed mutagenesis. The large number of point mutations required for the redesigns makes the process difficult, and increases the risk of major unpredicted and undesirable conformational changes. Preselecting a limited subset of mutable residues is not a satisfactory solution because it is unclear how to select this set before the search has been performed. Therefore, the ideal approach is what we define as the κ‐restricted redesign problem in which any κ of the n residues are allowed to mutate. We introduce restricted dead‐end elimination (rDEE) as a solution of choice to efficiently identify the GMEC of the restricted redesign (the κGMEC). Whereas existing approaches require n‐choose‐κ individual runs to identify the κGMEC, the rDEE criteria can perform the redesign in a single search. We derive a number of extensions to rDEE and present a restricted form of the A* conformation search. We also demonstrate a 10‐fold speed‐up of rDEE over traditional DEE approaches on three different experimental systems. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Rotamer optimization for protein design through MAP estimation and problem‐size reduction

The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP‐hard optimization problem. Dead‐end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this work, we present an exact solution method, named BroMAP (branch‐and‐bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch‐and‐bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by lower bounds from approximate maximum‐a‐posteriori (MAP) estimation. The lower bounds are also exploited in branching and subproblem selection for fast discovery of strong upper bounds. Our computational results show that BroMAP tends to be faster than DEE/A* for large protein design cases. BroMAP also solved cases that were not solved by DEE/A* within the maximum allowed time, and did not incur significant disadvantage for cases where DEE/A* performed well. Therefore, BroMAP is particularly applicable to large protein design problems where DEE/A* struggles and can also substitute for DEE/A* in general GMEC search. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Single‐ended transition state finding with the growing string method

Reaction path finding and transition state (TS) searching are important tasks in computational chemistry. Methods that seek to optimize an evenly distributed set of structures to represent a chemical reaction path are known as double‐ended string methods. Such methods can be highly reliable because the endpoints of the string are fixed, which effectively lowers the dimensionality of the reaction path search. String methods, however, require that the reactant and product structures are known beforehand, which limits their ability for systematic exploration of reactive steps. In this article, a single‐ended growing string method (GSM) is introduced which allows for reaction path searches starting from a single structure. The method works by sequentially adding nodes along coordinates that drive bonds, angles, and/or torsions to a desired reactive outcome. After the string is grown and an approximate reaction path through the TS is found, string optimization commences and the exact TS is located along with the reaction path. Fast convergence of the string is achieved through use of internal coordinates and eigenvector optimization schemes combined with Hessian estimates. Comparison to the double‐ended GSM shows that single‐ended method can be even more computationally efficient than the already rapid double‐ended method. Examples, including transition metal reactivity and a systematic, automated search for unknown reactivity, demonstrate the efficacy of the new method. This automated reaction search is able to find 165 reaction paths from 333 searches for the reaction of NH₃BH₃ and (LiH)₄, all without guidance from user intuition. © 2015 Wiley Periodicals, Inc.     

SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity

Structure‐based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this “ab initio” approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT‐Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD‐E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding‐homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org . © 2016 Wiley Periodicals, Inc.     

Synthesis,complex formation,and dilute‐solution associative behavior of linear poly(methacrylic acid)‐graft‐poly(2‐ethyl‐2‐oxazoline)*

Poly(methacrylic acid) (PMA) and poly(2‐ethyl‐2‐oxazoline) (PEOZO) are a polyacid/polybase pair capable of forming reversible, pH‐responsive, hydrogen‐bonding complexes stabilized by hydrophobic effects in aqueous media. Linear PMA was modified with long‐chain (number‐average molecular weight: 10,000) PEOZO via statistical coupling reactions in organic media to prepare a series of PMA‐graft‐PEOZO copolymers. Potentiometric titrations revealed that the presence of tethered PEOZO markedly increases the pK_a values for PMA‐g‐PEOZO copolymers as compared with simple PMA/PEOZO mixtures at degrees of ionization, α, between 0.0 and 0.1. The dilute‐solution PMA–PEOZO intramolecular association has been probed by monitoring the PEOZO NMR spin–spin (T₂) relaxation as a function of pH. Covalently attached PEOZO side chains participate in complexation at higher values of α than untethered PEOZO. Surprisingly, most PEOZO side chains did not take part in hydrogen bonding at low α, and the highest level of PEOZO incorporation induced a decrease in the number of PMA/PEOZO hydrogen bonds. The polymer self‐diffusion as a function of α was measured with dynamic light scattering. At low pH, the copolymers had no charge and they were in a collapsed form. At high pH, the expected conformational expansion of the PMA units was enhanced at moderate levels of PEOZO incorporation. However, the highest PEOZO incorporation induced the onset of intramolecular associations between PEOZO units along the copolymer chains. Low shear rheometry and light scattering measurements were used in conjunction with the T₂ NMR measurements to propose a model consistent with the aforementioned behavior. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2520–2533, 2004     

Development of a mass spectrometric hydroxyl‐position determination method for the hydroxyindole metabolites of JWH‐018 by GC‐MS/MS

One of the many issues of designer drugs of abuse like synthetic cannabinoids (SCs) such as JWH‐018 is that details on their metabolism has yet to be fully elucidated and that multiple metabolites exist. The presence of isomeric compounds poses further challenges in their identification. Our group has previously shown the effectiveness of gas chromatography‐electron ionization‐tandem mass spectrometry (GC‐EI‐MS/MS) in the mass spectrometric differentiation of the positional isomers of the naphthoylindole‐type SC JWH‐081, and speculated that the same approach could be used for the metabolite isomers. Using JWH‐018 as a model SC, the aim of this study was to differentiate the positional isomers of its hydroxyindole metabolites by GC‐MS/MS. Standard compounds of JWH‐018 and its hydroxyindole metabolite positional isomers were first analyzed by GC‐EI‐MS in full scan mode, which was only able to differentiate the 4‐hydroxyindole isomer. Further GC‐MS/MS analysis was performed by selecting m/z 302 as the precursor ion. All four isomers produced characteristic product ions that enabled the differentiation between them. Using these ions, MRM analysis was performed on the urine of JWH‐018 administered mice and determined the hydroxyl positions to be at the 6‐position on the indole ring. GC‐EI‐MS/MS allowed for the regioisomeric differentiation of the hydroxyindole metabolite isomers of JWH‐018. Furthermore, analysis of the fragmentation patterns suggests that the present method has high potential to be extended to hydroxyindole metabolites of other naphthoylindole type SCs in identifying the position of the hydroxyl group on the indole ring. Copyright © 2016 John Wiley & Sons, Ltd.     

Analysis of low‐density lipoprotein‐associated proteins using the method of digitized native protein mapping

The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel‐cutting, and quantitative LC‐MS/MS (in data‐independent acquisition mode, or MS^E), was improved by using a new MS/MS mode, ion mobility separation enhanced‐MS^E (HDMS^E), and applied to analyze the area of human plasma low‐density lipoprotein (LDL). An 18 mm × 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid‐cut into 72 square gel pieces and subjected to quantitative LC‐MS/MS. Compared with MS^E, HDMS^E showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. A total of 253 proteins were assigned with LC‐HDMS^E and the quantity distribution of each was reconstructed as a native protein map. The maps showed that Apo B‐100 was the most abundant protein in the grid‐cut area, concentrated at pI ca. 5.4–6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39–42. An Excel macro was prepared to search protein maps which showed protein quantity peaks localized within this concentrated region of Apo B‐100. Twenty‐two proteins out of the 252 matched this criterion, in which 19 proteins have been reported to be associated with LDL. This method only requires several microliters of a plasma sample and the principle of the protein separation is totally different from the commonly used ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL.