Rapid detection and characterization of reactive drug metabolites in vitro using several isotope‐labeled trapping agents and ultra‐performance liquid chromatography/time‐of‐flight mass spectrometry

Reactive metabolites are believed to be one of the main reasons for unexpected drug‐induced toxicity issues, by forming covalent adducts with cell proteins or DNA. Due to their high reactivity and short lifespan they are not directly detected by traditional analytical methods, but are most traditionally analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS) after chemical trapping with nucleophilic agents such as glutathione. Here, a simple but very efficient assay was built up for screening reactive drug metabolites, utilizing stable isotope labeled glutathione, potassium cyanide and semicarbazide as trapping agents and highly sensitive ultra‐performance liquid chromatography/time‐of‐flight mass spectrometry (UPLC/TOFMS) as an analytical tool. A group of twelve structurally different compounds was used as a test set, and a large number of trapped metabolites were detected for most of them, including many conjugates not reported previously. Glutathione‐trapped metabolites were detected for nine of the twelve test compounds, whereas cyanide‐trapped metabolites were found for eight and semicarbazide‐trapped for three test compounds. The high mass accuracy of TOFMS provided unambiguous identification of change in molecular formula by formation of a reactive metabolite. In addition, use of a mass defect filter was found to be a usable tool when mining the trapped conjugates from the acquired data. The approach was shown to provide superior detection sensitivity in comparison to traditional methods based on neutral loss or precursor ion scanning with a triple quadrupole mass spectrometer, and clearly more efficient detection and characterization of reactive drug metabolites with a simpler test setup. Copyright © 2009 John Wiley & Sons, Ltd.     

Chemically Induced Sintering of Nanoparticles

We have observed solid‐state growth of pre‐existing silver nanoparticles (AgNPs) upon exposure to trace (ppb) concentrations of reactive gases at room temperature. The consequent change in localized surface plasmon resonances alters the visible absorbance of dried, printed sensor spots made from inks of 10 nm‐AgNPs and provides a novel mechanism for trace detection and dosimetry of reactive gases. Colorimetric sensor arrays based on these AgNP inks offer dosimetric identification of acidic and oxidizing gases and other reactive vapors with limits of detection below ppb levels for 1 h exposures. For an array of AgNP inks with various capping agents, a unique color response pattern is observed for each specific analyte. Excellent discrimination among 11 reactive gases was demonstrated using standard chemometric methods. The chemically induced sintering of NPs paves the way for novel solid‐state sensors for the ultrasensitive detection of reactive gases and their application to the monitoring of trace airborne pollutants.     

“Stainomics”: Identification of mitotracker labeled proteins in mammalian cells

Organelle‐specific cell‐permeable fluorescent dyes are invaluable tools in cell biology as they reveal intracellular dynamics in living cells. Mitrotracker is a family of dyes that strongly label the mitochondrion, a key organelle associated with many crucial cellular functions. Despite the popularity of these dyes, little is known about the molecular mechanism behind their staining specificity. Here, we aimed to identify the protein targets of one member of this dye family, mitotracker red (MTR), by 2DE and MS. MTR bound to cellular proteins covalently, and its fluorescence persisted even after cell lysis, protein solubilization, denaturation, and electrophoresis. This enabled us to display MTR‐labeled proteins by 2DE. The MTR‐specific fluorescent signals on the gel revealed the spots that contained MTR‐conjugated proteins. These spots were analyzed by MS, resulting into the identification of ten proteins. We discovered that one major target is the mitochondrial protein HSP60 and that MTR staining could induce production of HSP60, predisposing cells to heat shock‐like responses. The identification of the molecular targets of biological dyes, or “stainomics,” can help correlate their intracellular staining properties with biochemical affinities. We believe this approach can be applied to a wide range of fluorescent probes.     

Focused grid‐based resampling for protein docking and mapping

The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein‐protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near‐native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc.     

Screening strategy for the rapid detection of in vitro generated glutathione conjugates using high‐performance liquid chromatography and low‐resolution mass spectrometry in combination with LightSight® software for data processing

The knowledge of drug metabolism in the early phases of the drug discovery process is vital for minimising compound failure at later stages. As chemically reactive metabolites may cause adverse drug reactions, it is generally accepted that avoiding formation of reactive metabolites increases the chances of success of a molecule. In order to generate this important information, a screening strategy for the rapid detection of in vitro generated reactive metabolites trapped by glutathione has been developed. The bioassay incorporated the use of native glutathione and its close analogue the glutathione ethyl ester. The generic conditions for detecting glutathione conjugates that undergo constant neutral loss of 129 Da were optimised using a glutathione‐based test mix of four compounds. The final liquid chromatography/tandem mass spectrometry constant neutral loss method used low‐resolution settings and a scanning window of 200 amu. Data mining was rapidly and efficiently performed using LightSight® software. Unambiguous identification of the glutathione conjugates was significantly facilitated by the analytical characteristics of the conjugate pairs formed with glutathione and glutathione ethyl ester, i.e. by chromatographic retention time and mass differences. The reliability and robustness of the screening strategy was tested using a number of compounds known to form reactive metabolites. Overall, the developed screening strategy provided comprehensive and reliable identification of glutathione conjugates and is well suited for rapid routine detection of trapped reactive metabolites. This new approach allowed the identification of a previously unreported diclofenac glutathione conjugate. Copyright © 2009 John Wiley & Sons, Ltd.     

Array‐based “Chemical Nose” Sensing in Diagnostics and Drug Discovery

Array‐based sensor “chemical nose/tongue” platforms are inspired by the mammalian olfactory system. Multiple sensor elements in these devices selectively interact with target analytes, producing a distinct pattern of response and enabling analyte identification. This approach offers unique opportunities relative to “traditional” highly specific sensor elements such as antibodies. Array‐based sensors excel at distinguishing small changes in complex mixtures, and this capability is being leveraged for chemical biology studies and clinical pathology, enabled by a diverse toolkit of new molecular, bioconjugate and nanomaterial technologies. Innovation in the design and analysis of arrays provides a robust set of tools for advancing biomedical goals, including precision medicine.     

Dendronized polymers via Diels–Alder “click” reaction

A modular approach toward the synthesis of polymers containing dendron groups as side chains is developed using the Diels–Alder “click” reaction. For this purpose, a styrene‐based polymer appended with anthracene groups as reactive side chains was synthesized. First through third‐generation polyester dendrons containing furan‐protected maleimide groups at their focal point were synthesized. Facile, reagent‐free, thermal Diels–Alder cycloaddition between the anthracene‐containing polymer and latent‐reactive dendrons leads to quantitative functionalization of the polymer chains to afford dendronized polymers. The efficiency of this functionalization step was monitored using ¹H and ¹³C NMR spectroscopy and FTIR and UV–vis spectrometry. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 410–416, 2010     

High‐Throughput Kinetic Analysis for Target‐Directed Covalent Ligand Discovery

Cysteine‐reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high‐quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan‐reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine‐reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2‐selective allosteric (type IV) kinase inhibitor whose novel mode‐of‐action could be exploited therapeutically.     

Synthesis of “Clickable” Nano Metal‐organic Framework by Generic Postsynthetic Modification Route

Organic azides have been somewhat popularized due to their pivotal role in the emerging field of “click chemistry”. A simple approach has been used for the synthesis of uniform nano Fe‐MIL‐88B‐NH₂, and a generic postsynthetic modification route has been developed for the synthesis of azide‐modified nano Fe‐MIL‐88B‐N₃. The approach also has been used to synthesize the azide‐modified IRMOF‐3(‐N₃). These new azide‐modified Fe‐MIL‐88B‐N₃ nanocrystals hold promising potential for the applications in the fields of “click chemistry”, nanotechnology devices and nano composite membranes.     

Mass defect filter technique and its applications to drug metabolite identification by high‐resolution mass spectrometry

Identification of drug metabolites by liquid chromatography/mass spectrometry (LC/MS) involves metabolite detection in biological matrixes and structural characterization based on product ion spectra. Traditionally, metabolite detection is accomplished primarily on the basis of predicted molecular masses or fragmentation patterns of metabolites using triple‐quadrupole and ion trap mass spectrometers. Recently, a novel mass defect filter (MDF) technique has been developed, which enables high‐resolution mass spectrometers to be utilized for detecting both predicted and unexpected drug metabolites based on narrow, well‐defined mass defect ranges for these metabolites. This is a new approach that is completely different from, but complementary to, traditional molecular mass‐ or MS/MS fragmentation‐based LC/MS approaches. This article reviews the mass defect patterns of various classes of drug metabolites and the basic principles of the MDF approach. Examples are given on the applications of the MDF technique to the detection of stable and chemically reactive metabolites in vitro and in vivo. Advantages, limitations, and future applications are also discussed on MDF and its combinations with other data mining techniques for the detection and identification of drug metabolites. Copyright © 2009 John Wiley & Sons, Ltd.     

A Facile Synthesis of Novel (Z)‐ethyl‐3‐(5‐substituted‐1‐alkyl/aryl‐1H‐indol‐3‐yl)‐2‐(1H‐tetrazol‐5‐yl)acrylate

A novel route was developed for synthesis of high potential 1H‐tetrazoles by using conventional method. Tetrazole scaffold is a promising pharmacophore fragment, frequently used in the development of various novel drugs. Here, the novel (Z)‐3‐(N‐alkyl‐indol‐3‐yl)‐2‐(1H‐tetrazole‐5‐yl)acrylates 5 ( a – i ) have been synthesized from (Z)‐ethyl‐3‐(1H‐indol‐3‐yl)2‐(1H‐tetrazol‐5‐yl)acrylates 4 ( a – c ) by using various alkylating agents such as Dimethyl Sulphate (DMS), Diethyl Sulphate (DES), and benzyl chloride; 4 ( a – c ) were synthesized from sodium azide in the presence of copper sulfate in dimethylformamide; 3 ( a – c ) have been prepared by Knoevenagel condensation of indole‐3‐carbaldehyde 1 ( a – c ) and ethylcyanoacetate 2 in the presence of L‐Proline as a catalyst at room temperature in ethanol for an hour. This is an efficient and clean click chemistry method that has various advantages such as easy workup, higher yields, shorter reaction times, and more economical.     

Catalytic Reductive N‐Alkylations Using CO2 and Carboxylic Acid Derivatives: Recent Progress and Developments

N‐Alkylamines are key intermediates in the synthesis of fine chemicals, dyes, and natural products, and hence are highly valuable building blocks in organic chemistry. Consequently, the development of greener and more efficient procedures for their production continues to attract the interest of both academic and industrial chemists. Reductive procedures such as reductive amination or N‐alkylation through hydrogen autotransfer by employing carbonyl compounds or alcohols as alkylating agents have prevailed for the synthesis of amines. In the last few years, carboxylic/carbonic acid derivatives and CO₂ have been introduced as alternative and convenient alkylating sources. The safety, easy accessibility, and high stability of these reagents makes the development of new reductive transformations with them as N‐alkylating agents a useful alternative to existing procedures. In this Review, we summarize reported examples of one‐pot reductive N‐alkylation methods that use carboxylic/carbonic acid derivatives or CO₂ as alkylating agents.     

Synthesis of Multivalent Organotellurium Chain‐Transfer Agents by Post‐modification and Their Applications in Living Radical Polymerization

Functionalized or multivalent organotellurium chain‐transfer agents (CTAs) for living radical polymerization were synthesized by post‐modification, which involved the condensation between a carboxylic‐acid‐functionalized CTA and various amines in excellent yields without affecting the reactive tellurium moiety. The CTAs exhibited high synthetic versatility for radical polymerization and gave structurally well‐controlled polymers, such as multiarmed polymers, from various monomers. Because all new CTAs are easily available on a large scale by simple purification, the current method significantly facilitates macromolecular engineering based on organotellurium‐mediated radical polymerization (TERP).     

Preparation of a long‐alkyl‐chain‐based hybrid monolithic column with mixed‐mode interactions using a “one‐pot” process for pressurized capillary electrochromatography

A simple “one‐pot” approach for the preparation of a new vinyl‐functionalized organic–inorganic hybrid monolithic column is described. In this improved method, the hydrolyzed alkoxysilanes of tetramethoxysilane and triethoxyvinylsilane were used as precursors for the synthesis of a silica‐based monolith, while 1‐hexadecene and sodium ethylenesulfonate were used as vinyl functional monomers along with azobisisobutyronitrile as an initiator. The effects of reaction temperature, urea content, and composition of organic monomers on the column properties (e.g. morphology, mechanical stability, and chromatographic performance) were investigated. The monolithic column was used for the separation of neutral solutes by reversed‐phase pressurized capillary. Furthermore, the monolith can separate various aromatic amines, which indicated its excellent cation‐exchange capability and hydrophobic interactions. The baseline separation of the aromatic amines was obtained with a column efficiency of up to 78 000 plates/m.     

A Supramolecular‐Based Dual‐Wavelength Phototherapeutic Agent with Broad‐Spectrum Antimicrobial Activity Against Drug‐Resistant Bacteria

With the ever‐increasing threat posed by the multi‐drug resistance of bacteria, the development of non‐antibiotic agents for the broad‐spectrum eradication of clinically prevalent superbugs remains a global challenge. Here, we demonstrate the simple supramolecular self‐assembly of structurally defined graphene nanoribbons (GNRs) with a cationic porphyrin (Pp4N) to afford unique one‐dimensional wire‐like GNR superstructures coated with Pp4N nanoparticles. This Pp4N/GNR nanocomposite displays excellent dual‐modal properties with significant reactive‐oxygen‐species (ROS) production (in photodynamic therapy) and temperature elevation (in photothermal therapy) upon light irradiation at 660 and 808 nm, respectively. This combined approach proved synergistic, providing an impressive antimicrobial effect that led to the complete annihilation of a wide spectrum of Gram‐positive, Gram‐negative, and drug‐resistant bacteria both in vitro and in vivo. The study also unveils the promise of GNRs as a new platform to develop dual‐modal antimicrobial agents that are able to overcome antibiotic resistance.     

Micro-HPLC 1: Linear “breakthrough-gradients” using the discontinuous interface between eluents in a packed gradient-generator column

A new approach is described for micro-HPLC for generating nearly linear gradients in the 40 to 550 μl volume range. These “linear” gradients have a straight line middle portion with a gentle curved onset of the gradient andd rapid attainment of the final 100% composition. Such “breakthrough-gradients” are produced by the interface between weak and strong eluent when a small (3 × 0.46 cm) packed “gradient-generator” column is switched abruptly from weak to strong eluent. The model system described here, without an analytical column, shows gradients from weak eluent (water) to strong eluent (modele with water plus acetone) using a 12-port high pressure valve to 1) vent the “flush” eluent, and simultaneously 2) begin the gradient and 3) make the sample injection. The volume of the gradient can be changed in two ways. If the breakthrough-generator is packed with very large (300 to 1600 μm nonporous particles, the gradient volume is nearly independent of the flush flow rate. The flush flow is used to quickly move the breakthrough-interface to the head of the micro-HPLC column. However, the gradient volume can be increased by using larger solid particles in the gradient-generator column because of increased eddy diffusion. If the gradient-generator is packed with porous particles (75–150 μm), the gradient volume can be changed over a broad range by simply changing the flush flow rate. This simple control over the gradient volume is due to the increased mass transfer of weak eluent out of the porous particles into the strong eluent at higher flush flows. The breakthrough-interface gradient-generator column approach provides the following advantages for micro-HPLC:

• – Gradient volumes can be readily varied over the micro-HPLC range 40–550 μl.
• – Gradient are linear with smooth and rapid onset of intial and final concentrations.
• – Gradient are produced inexpensively with a single high-pressure precision pump.
• – Gradient can be automated with a timer and single 12-port valve that provides both column regeneration and sample injection.

     

Pintoxolanes A–C,Highly Functionalized 3,14‐Oxa‐bridged Cembranoids from the Caribbean Gorgonian Coral Eunicea pinta

Three new cembrane‐based diterpenes possessing the rare 3,14‐oxa‐bridged moiety were isolated from the hexane extract of a southwestern Caribbean gorgonian octocoral, Eunicea pinta, together with seven known cembranoid diterpenes. The structures of pintoxolanes A–C ( 1 – 3 , resp.), including their relative configurations, were deduced from spectroscopic data and chemical‐correlation experiments. Experimental evidence hinting to a plausible biogenesis of the 3,14‐oxalane moiety is provided. Preliminary cytotoxicity data for compounds 1 – 3 toward human cancer cell lines are also provided.     

A Rapid and Efficient Way to Dynamic Creation of Cross‐Reactive Sensor Arrays Based on Ionic Liquids

Based on the simple counterion exchange of ionic liquids, a rapid, facile, and efficient strategy to create a cross‐reactive sensor array with a dynamic tunable feature was developed, and exemplified by the construction of a sensor array for the identification and classification of nitroaromatics and explosives mimics. To achieve a good sensing system with fast response, good sensitivity, and low detection limit, the synthesized ionic liquid receptors were tethered onto a silica matrix with a macro‐mesoporous hierarchical structure. Through the facile anion exchange approach, abundant ionic‐liquid‐based individual receptors with diversiform properties, such as different micro‐environments, diverse molecular interactions, and distinctive physico‐chemical properties, were easily and quickly synthesized to generate a distinct fingerprint of explosives for pattern recognition. The reversible anion exchange ability further endowed the sensor array with a dynamic tunable feature as well as good controllability and practicality for real‐world application. With the assistance of statistical analysis, such as principal component analysis (PCA) and linear discrimination analysis (LDA), an optimized‐size array with a good resolution was rationally established from a large number of IL‐based receptors. The performed experiments suggested that the ionic‐liquid‐based sensing protocol is a general and powerful strategy for creating a cross‐reactive sensor array that could find a wide range of applications for sensing various analytes or complex mixtures.     

FET‐Based Biosensors for The Direct Detection of Organophosphate Neurotoxins

Recent world‐wide terrorist events associated with the threat of hazardous chemical agent proliferation, and outbreaks of chemical contamination in the food supply has demonstrated an urgent need for sensors that can directly detect the presence of dangerous chemical toxins. Such sensors must enable real‐time detection and accurate identification of different classes of pesticides (e.g., carbamates and organophosphates) but must especially discriminate between widely used organophosphate (OP) pesticides and G‐ and V‐type organophosphate chemical warfare nerve agents. Present field analytic sensors are bulky with limited specificity, require specially‐trained personnel, and, in some cases, depend upon lengthy analysis time and specialized facilities. Most bioanalytical based systems are biomimetic. These sensors utilize sensitive enzyme recognition elements that are the in‐vivo target of the neurotoxic agents which the sensor is attempting to detect. The strategy is well founded; if you want to detect cholinesterase toxins use cholinesterase receptors. However, this approach has multiple limitations. Cholinesterase receptors are sensitive to a wide range of non‐related compounds and require lengthy incubation time. Cholinesterase sensors are inherently inhibition mode and therefore require baseline testing followed by sample exposure, retest and comparison to baseline. Finally, due to the irreversible nature of enzyme‐ligand interactions, inhibition‐mode sensors cannot be reused without regeneration of enzyme activity, which in many cases is inefficient and time‐consuming. In 1996, we pioneered a new “kinetic” approach for the direct detection of OP neurotoxins based on agent hydrolysis by the enzyme organophosphate hydrolase (OPH; EC 3.1.8.2; phosphotriesterase) and further identified a novel multi‐enzyme strategy for discrimination between different classes of neurotoxins. The major advantage of this sensor strategy is it allows direct and continuous measurement of OP agents using a reversible biorecognition element. We also investigated incorporation of enzymes with variations in substrate specificity (e.g., native OPH, site‐directed mutants of OPH, and OPAA (EC 3.1.8.1), based upon preferential hydrolysis of P? O, P? F and P? S bonds to enable discrimination among chemically diverse OP compounds. Organophosphate hydrolase enzymes were integrated with several different transduction platforms including conventional pH electrodes, fluoride ion‐sensitive electrodes, and pH‐responsive fluorescent dyes. Detection limit for most systems was in the low ppm concentration range. This article reviews our integration of organophosphate hydrolase enzymes with pH sensitive field effect transistors (FETs) for OP detection.     

Azide/alkyne‐“click”‐reactions on amino resin materials: An LC‐ESI‐TOF analysis

This article describes the reaction of amino resins with functional molecules using the azide/alkyne‐“click”‐reaction, opening a simple chemical modification of amino resins under aqueous conditions. Alkyne‐modified melamine‐formaldehyde resins are prepared via a direct cocondensation approach using propargylic alcohol (21.6–86.3 mmol) as additive. Subsequently, alkyne‐modified mono‐, bi‐, and trinuclear melamine‐species are identified via LC‐ESI‐TOF methods proving the covalent incorporation of alkyne‐moieties in amounts of up to 3.9 mol %. Subsequent modification of the alkyne‐modified resins was accomplished by reaction of functional azides (octyl azide (1), (azidomethyl)benzene (2), 1‐(6‐azidohexyl) thymine (3), and 4‐azido‐N‐(2,2,6,6‐tetramethylpiperidin‐4‐yl)benzamide (4)) with Cu(I)Br and DIPEA as a base. The formation of triazolyl‐modified MF‐resins was proven by LC‐ESI‐TOF methods, indicating the successful covalent modification of the amino resin with the azides 1 – 4 . © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010