Development of activity-based probes with tunable specificity for protein tyrosine phosphatase subfamilies

Herein we describe the development of activity-based probes toward protein tyrosine phosphatase (PTP) subfamilies. A novel phosphotyrosine analog serving as the latent trapping unit has been designed and explored. It allows addition of various amino acid residues to its C- and N-termini to extend the recognition element. As a proof-of-concept, we have synthesized three tripeptide probes, which carry the phosphotyrosine analog in the middle position and a leucinamide residue at the C-terminus. The three tripeptide probes differed only in their N-terminal amino acid (Glu, Phe, and Lys). The labeling properties of these probes were determined and the results showed the newly synthesized probes could selectively label PTPs in an activity-dependent manner. In addition, the probes’ target specificity was also shown to be influenced by the amino acid residues flanking the phosphotyrosine analog.     

HPLC-SPE-NMR in pharmaceutical development: capabilities and applications

High-performance liquid chromatography-solid phase extraction-NMR spectroscopy (HPLC-SPE-NMR) has recently become commercially available and has been evaluated with regard to its applicability in a pharmaceutical environment. The addition of an automated SPE unit to an HPLC-NMR system for peak trapping results in an improved NMR signal-to-noise ratio (S/N) and also has other practical advantages. The trapping efficiency is shown to depend on compound polarity and is highest for compounds eluting late on reversed-phase HPLC systems. Multiple peak trapping further increases the S/N, again with the best results for less polar compounds. For polar compounds, multiple peak trapping resulted in no S/N gain as the amount of material retained on the SPE cartridge was equivalent to that from a single injection. When compared with conventional HPLC-NMR, a S/N gain of up to five-fold could be achieved for some compounds in a single trapping step. A major advantage of the technique is the independence of the chromatographic step from the NMR step, resulting in greater versatility than conventional HPLC-NMR in the HPLC solvents and NMR solvents that can be used. Practical applications from both drug metabolite and drug impurity identification are presented.     

Reaction of fluorogenic reagents with proteins I. Mass spectrometric characterization of the reaction with 3-(2-furoyl)quinoline-2-carboxaldehyde, Chromeo P465, and Chromeo P503

3-(2-Furoyl)quinoline-2-carboxaldehyde (FQ), Chromeo P465, and Chromeo P503 are weakly fluorescent reagents that react with primary amines to produce fluorescent products. We studied the reaction of these reagents with alpha-lactalbumin by mass spectrometry. The reaction generated a set of products by the addition of one or more labels to the protein. At room temperature, the reaction was an order of magnitude faster with the Chromeo reagents than with FQ; however, the steady-state labeling efficiency was a factor of two higher for FQ compared with the Chromeo reagents. The relative abundance of the products with FQ usually followed a binomial distribution, which suggests that the labeling sites were uniformly accessible to this reagent. In contrast, the distribution of reaction products with the Chromeo reagents did not follow a binomial distribution for reactions performed in the absence of sodium dodecyl sulfate (SDS); it appears that the protein labeled with the Chromeo reagents refolded into a relatively stable secondary structure that hid some reactive sites. The reaction with the Chromeo reagent did follow the binomial distribution if the protein underwent treatment with 1% SDS at 95 degrees C for 5 min, which apparently disrupts the protein's secondary structure and allowed uniform access to all labeling sites. Chromeo 503 labeled seven of the 13 primary amines in denatured alpha-lactalbumin.     

Mapping enzyme active sites in complex proteomes

Genome sequencing projects have uncovered many novel enzymes and enzyme classes for which knowledge of active site structure and mechanism is limited. To facilitate mechanistic investigations of the numerous enzymes encoded by prokaryotic and eukaryotic genomes, new methods are needed to analyze enzyme function in samples of high biocomplexity. Here, we describe a general strategy for profiling enzyme active sites in whole proteomes that utilizes activity-based chemical probes coupled with a gel-free analysis platform. We apply this gel-free strategy to identify the sites of labeling on enzymes targeted by sulfonate ester probes. For each enzyme examined, probe labeling was found to occur on a conserved active site residue, including catalytic nucleophiles (e.g., C32 in glutathione S-transferase omega) and bases/acids (e.g., E269 in aldehyde dehydrogenase-1; D204 in enoyl CoA hydratase-1), as well as residues of unknown function (e.g., D127 in 3 beta-hydroxysteroid dehydrogenase/isomerase-1). These results reveal that sulfonate ester probes are remarkably versatile activity-based profiling reagents capable of labeling a diversity of catalytic residues in a range of mechanistically distinct enzymes. More generally, the gel-free strategy described herein, by consolidating into a single step the identification of both protein targets of activity-based probes and the specific residues labeled by these reagents, provides a novel platform in which the proteomic comparison of enzymes can be accomplished in unison with a mechanistic analysis of their active sites.     

The trapping of indoor air contaminants

The removal of indoor air contaminants by reactivity with air filters coated with reagents has been found to be effective for aldehydes, acidic and basic vapours as well as isocyanates Coatings of polymeric amines were used for formaldehyde trapping as well as for the removal of acidic vapours and for the removal of isocyanates. The addition of glycerol as a plasticizer for the coating can also be an effective reagent.     

Rhodamine B Piperazinoacetohydrazine: A Water‐Soluble Spectroscopic Reagent for Pyruvic Acid Labeling

A new water‐soluble reagent, rhodamine B piperazinoacetohydrazine (RBPH), with improved spectroscopic and reaction properties, has been developed and characterized for pyruvic acid labeling. The reagent RBPH is designed and synthesized by using rhodamine B as a spectroscopic unit, and hydrazine as a carbonyl‐specific labeling unit; the two units are connected by a well‐chosen linker of piperazine, which prohibits the formation of the nonfluorescent spirocyclic structure of rhodamine B, thereby keeping the spectroscopic response of the reagent in a stable state. Such a design enables RBPH not only to maintain its excellent spectroscopic properties over a wide pH range, but also to exist as a stable cation with high water solubility. Moreover, the hydrazino group of RBPH is expected to react selectively with carbonyl compounds under mild conditions through the rapid formation of hydrazones. These important features make RBPH of great potential use in the labeling of aldehydes or ketones in various biosystems, and such an application of RBPH as a precolumn derivatizing reagent has been successfully demonstrated on the analysis of pyruvic acid in human serum by high‐performance liquid chromatography with common UV/Vis detection.     

A Self‐Immobilizing and Fluorogenic Probe for β‐Lactamase Detection

The spread of antibiotic resistance in pathogenic bacteria has become one of the major concerns to public health. Improved monitoring of drug resistance is of high importance for infectious disease control. One of the major mechanisms for bacteria to overcome treatment of antibiotics is the production of β‐lactamases, which are enzymes that hydrolyze the β‐lactam ring of the antibiotic. In this study, we have developed a self‐immobilizing and fluorogenic probe for the detection of β‐lactamase activity. This fluorogenic reagent, upon activation by β‐lactamases, turns on a fluorescence signal and, more importantly, generates a covalent linkage to the target enzymes or the nearby proteins. The covalent labeling of enzymes was confirmed by SDS‐PAGE analysis and MALDI‐TOF mass spectrometry. The utility of this structurally simple probe was further confirmed by the fluorescent labeling of a range of β‐lactamase‐expressing bacteria.     

Proton-exchanged montmorillonite-mediated reactions of methoxybenzyl esters and ethers

Proton-exchanged montmorillonite (H-mont) was found to be an eco-friendly and cost-effective catalyst for the generation of O-methylated quinone methides (QM) from the corresponding p or o-methoxybenzyl esters and ethers. Nucleophilic trapping of the O-methylated QM with arenes, alcohols, 1,3-dicarbonyl compounds, silyl enol ethers, and allylsilanes has been carried out, respectively, leading to eco-friendly benzylation reactions. Using this protocol, H-mont-mediated deprotection of PMB-protected esters and ethers have been realized for the first time. This work would pave the way for further exploration in O-alkylated QM that are of chemical and biological significance.     

Positive mode electrospray ionization mass spectrometry of bisphosphonates using dicationic and tricationic ion-pairing agents

A general method for detecting bisphosphonate drugs by ESI-MS and LC-ESI-MS as positive ions has been developed. Bisphosphonates can have multiple negative charges in solution. Tricationic ion-pairing reagents were paired with bisphosphonates to form a positively charged complex. It was clear that this facile pairing method worked. However, an appreciable presence of −1 bisphosphonate species were observed in positive mode ESI-MS (i.e. as the +2 complex with tricationic reagents). This led to an extended investigation on the use of dicationic pairing agents. The use of dicationic reagents improved the detection sensitivity for all of the bisphosphonates. Tandem mass spectrometry also improved the limits of detection for most of the bisphosphonates using both the tricationic and dicationic pairing reagents. A tricationic reagent also was used as an ion-pairing reagent in chromatography experiments. Thus the addition of a single reagent produced benefits in that it increased chromatographic retention and enhanced the ESI-MS detection of bisphosphonates.     

Development of interdigitated arrays coated with functional polyaniline/MWCNT for electrochemical biodetection: application for human papilloma virus

In this study, polyaniline-multiwalled carbon nanotube film (PANi-MWCNT) has been polymerized on interdigitated platinum electrode arrays (IDA), fabricated by MEMS technology for the detection of human papillomavirus (HPV) infection, using immobilized peptide aptamers as affinity capture reagent. Label-free, electrochemical detection of the specific immune reaction between antigen peptide aptamer HPV-16-L1 (with a molecular weight of 1825 Da), the most common genotype in cytological normal women worldwide, and its specific antibody of HPV-16 (which is much bigger with molecular weight of ca. 150 kDa) on multifunctional PANi-MWCNT based arrays was reported. The most significant advantage of this technique consists of reagentless and multiple detection of antigen-antibody complex formation on well conducting IDA interface of PANi-MWCNT, without intermediate steps or any labeling reagents, as normally required in the previous works.     

Compartmentalization and separation of aqueous reagents in the water droplets of water-in-oil high internal phase emulsions

We have compartmentalized aqueous reagents and indicator species within the micrometer-sized water droplets of mixed high internal phase emulsions (HIPEs). Mass transport of the reagents across the micrometer-thickness oil films separating the water droplets followed by reaction with the indicator species produces a visible color change which provides a simple method to measure the trapping times of the reagents. Trapping times have been measured for an uncharged reagent (hydrogen peroxide) and charged reagents (HCl and NaClO) in different HIPEs. The trapping times are discussed in terms of a model in which the transferring species partitions from the water to the oil film followed by a rate-determining step of diffusion across the oil film. Rather surprisingly, it is found that trapping times are of similar orders of magnitude for both uncharged and charged aqueous species transferring across liquid oil films.     

Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography–mass spectrometry

Metabolomic profiling involves relative quantification of metabolites in comparative samples and identification of the significant metabolites that differentiate different groups (e.g., diseased vs. controls). Chemical isotope labeling (CIL) liquid chromatography–mass spectrometry (LC–MS) is an enabling technique that can provide improved metabolome coverage and metabolite quantification. However, chemical identification of labeled metabolites can still be a challenge. In this work, a new set of isotopic labeling reagents offering versatile properties to enhance both detection and identification are described. They were prepared by a glycine molecule (or its isotopic counterpart) and an aromatic acid with varying structures through a simple three-step synthesis route. In addition to relatively low costs of synthesizing the reagents, this reaction route allows adjusting reagent property in accordance with the desired application objective. To date, two isotopic reagents, 4-dimethylaminobenzoylamido acetic acid N-hydroxylsuccinimide ester (DBAA-NHS) and 4-methoxybenzoylamido acetic acid N-hydroxylsuccinimide ester (MBAA-NHS), for labeling the amine-containing metabolites (i.e., amine submetabolome) have been synthesized. The labeling conditions and the related LC–MS method have been optimized. We demonstrate that DBAA labeling can increase the metabolite detectability because of the presence of an electrospray ionization (ESI)-active dimethylaminobenzoyl group. On the other hand, MBAA labeled metabolites can be fragmented in MS/MS and pseudo MS³ experiments to provide structural information on metabolites of interest. Thus, these reagents can be tailored to quantitative profiling of the amine submetabolome as well as metabolite identification in metabolomics applications.     

Azide-Functionalized Derivatives of the Virulence-Associated Sugar Pseudaminic Acid: Chiral Pool Synthesis and Labeling of Bacteria

Pseudaminic acid (Pse) is a significant prokaryotic monosaccharide found in important Gram-negative and Gram-positive bacteria. This unique sugar serves as a component of cell-surface-associated glycans or glycoproteins and is associated with their virulence. We report the synthesis of azidoacetamido-functionalized Pse derivatives as part of a search for Pse-derived metabolic labeling reagents. The synthesis was initiated with d -glucose (Glc), which served as a cost-effective chiral pool starting material. Key synthetic steps involve the conversion of C1 of Glc into the terminal methyl group of Pse, and inverting deoxyaminations at C3 and C5 of Glc followed by backbone elongation with a three-carbon unit using the Barbier reaction. Metabolic labeling experiments revealed that, of the four Pse derivatives, ester-protected C5 azidoacetamido-Pse successfully labeled cells of Pse-expressing Gram-positive and Gram-negative strains. No labeling was observed in cells of non-Pse-expressing strains. The ester-protected and C5 azidoacetamido-functionalized Pse is thus a useful reagent for the identification of bacteria expressing this unique virulence-associated nonulosonic acid.     

New uses for the Burgess reagent in chemical synthesis: methods for the facile and stereoselective formation of sulfamidates, glycosylamines, and sulfamides

Although the Burgess reagent (methoxycarbonylsulfamoyltriethylammonium hydroxide, inner salt) has found significant use in chemical synthesis as a dehydrating agent, almost no work has been directed towards its potential in other synthetic applications. As this article will detail, we have found that the Burgess reagent is remarkably effective at accomplishing a number of non-dehydrative synthetic tasks when applied to appropriate substrates, such as the formation of sulfamidates from 1,2-diols or epoxyalcohols, alpha- and beta-glycosylamines from carbohydrates, and cyclic sulfamides from 1,2-aminoalcohols. Beyond delineating the power of these new reaction manifolds, we also describe the construction of a group of alternative Burgess-type reagents that extends the scope of these new reactions even further.     

Native FKBP12 engineering by ligand-directed tosyl chemistry: labeling properties and application to photo-cross-linking of protein complexes in vitro and in living cells

The ability to modify target "native" (endogenous) proteins selectively in living cells with synthetic molecules should provide powerful tools for chemical biology. To this end, we recently developed a novel protein labeling technique termed ligand-directed tosyl (LDT) chemistry. This method uses labeling reagents in which a protein ligand and a synthetic probe are connected by a tosylate ester group. We previously demonstrated its applicability to the selective chemical labeling of several native proteins in living cells and mice. However, many fundamental features of this chemistry remain to be studied. In this work, we investigated the relationship between the LDT reagent structure and labeling properties by using native FK506-binding protein 12 (FKBP12) as a target protein. In vitro experiments revealed that the length and rigidity of the spacer structure linking the protein ligand and the tosylate group have significant effects on the overall labeling yield and labeling site. In addition to histidine, which we reported previously, tyrosine and glutamate residues were identified as amino acids that are modified by LDT-mediated labeling. Through the screening of various spacer structures, piperazine was found to be optimal for FKBP12 labeling in terms of labeling efficiency and site specificity. Using a piperazine-based LDT reagent containing a photoreactive probe, we successfully demonstrated the labeling and UV-induced covalent cross-linking of FKBP12 and its interacting proteins in vitro and in living cells. This study not only furthers our understanding of the basic reaction properties of LDT chemistry but also extends the applicability of this method to the investigation of biological processes in mammalian cells.     

A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems

A multicentered integrated QM/QM technique has been developed. By separating high-level calculations in distinct regions of molecules, the multicentered approach supplants a single large high-level calculation with several smaller calculations. Due to the steep polynomial scaling of traditional ab initio quantum chemical methods, this separation significantly enhances the computational efficiency of QM/QM methods. The straightforward implementation of this multicentered approach is illustrated with several large poly-alcohols that form hydrogen bonds with water. The largest alcohol-water complex contains 81 atoms. For properly selected model systems, this multicentered approach introduces essentially no error in the dissociation energies of these complexes relative to conventional QM/QM schemes. This multicentered technique should be easily extended to other, more general integrated methods (QM/MM, ONIOM, etc).     

Second-generation difluorinated cyclooctynes for copper-free click chemistry

The 1,3-dipolar cycloaddition of azides and activated alkynes has been used for site-selective labeling of biomolecules in vitro and in vivo. While copper catalysis has been widely employed to activate terminal alkynes for [3 + 2] cycloaddition, this method, often termed "click chemistry", is currently incompatible with living systems because of the toxicity of the metal. We recently reported a difluorinated cyclooctyne (DIFO) reagent that rapidly reacts with azides in living cells without the need for copper catalysis. Here we report a novel class of DIFO reagents for copper-free click chemistry that are considerably more synthetically tractable. The new analogues maintained the same elevated rates of [3 + 2] cycloaddition as the parent compound and were used for imaging glycans on live cells. These second-generation DIFO reagents should expand the use of copper-free click chemistry in the hands of biologists.     

MeCAT—new iodoacetamide reagents for metal labeling of proteins and peptides

Besides protein identification via mass spectrometric methods, protein and peptide quantification has become more and more important in order to tackle biological questions. Methods like differential gel electrophoresis or enzyme-linked immunosorbent assays have been used to assess protein concentrations, while stable isotope labeling methods are also well established in quantitative proteomics. Recently, we developed metal-coded affinity tagging (MeCAT) as an alternative for accurate and sensitive quantification of peptides and proteins. In addition to absolute quantification via inductively coupled plasma mass spectrometry, MeCAT also enables sequence analysis via electrospray ionization tandem mass spectrometry. In the current study, we developed a new labeling approach utilizing an iodoacetamide MeCAT reagent (MeCAT-IA). The MeCAT-IA approach shows distinct advantages over the previously used MeCAT with maleinimide reactivity such as higher labeling efficiency and the lack of diastereomer formation during labeling. Here, we present a careful characterization of this new method focusing on the labeling process, which yields complete tagging with an excess of reagent of 1.6 to 1, less complex chromatographic behavior, and fragmentation characteristics of the tagged peptides using the iodoacetamide MeCAT reagent.     

Current trends in isotope-coded derivatization liquid chromatographic-mass spectrometric analyses with special emphasis on their biomedical application

Currently, LC–MS has various applications in different areas such as metabolomics, pharmacokinetics, and pathological studies. Yet, matrix effects resulting from co-existing constituents remain a major problem for LC–MS [or LC–tandem mass spectrometry (LC–MS/MS)]. Moreover, technical problems and instrumental drifts may lead to ion abundance variance. Thus, an internal standard (IS) is required to guarantee the accuracy and precision of the method. Because of their limited number, isotope-coded derivatization (ICD) has been recently introduced to overcome this problem. For ICD, a stable heavy isotope-coded moiety is used for labeling the standard or the control sample and the formed products can act as ISs. A light form of the reagent is used for labeling the sample. Then, both are mixed and analyzed by LC–MS(/MS). This strategy permits the identification of different unknown analytes including potential metabolites and disease biomarkers. All these attributes lead to persistent growth in the applications of ICD LC–MS(/MS) in various biomedical branches. In this article we review the ICD methods published in the last eight years for biomedical applications as well as briefly summarize other applications for environmental and food analyses as some of their used ICD reagents were further applied for analyzing biological specimens or have the potential for that.     

Fluorine transfer to alkyl radicals

The development of new synthetic technologies for the selective fluorination of organic compounds has increased with the escalating importance of fluorine-containing pharmaceuticals. Traditional methods potentially applicable to drug synthesis rely on the use of ionic forms of fluorine (F(-) or F(+)). Radical methods, while potentially attractive as a complementary approach, are hindered by a paucity of safe sources of atomic fluorine (F(?)). A new approach to alkyl fluorination has been developed that utilizes the reagent N-fluorobenzenesulfonimide as a fluorine transfer agent to alkyl radicals. This approach is successful for a broad range of alkyl radicals, including primary, secondary, tertiary, benzylic, and heteroatom-stabilized radicals. Furthermore, calculations reveal that fluorine-containing ionic reagents are likely candidates for further expansion of this approach to polar reaction media. The use of these reagents in alkyl radical fluorination has the potential to enable powerful new transformations that otherwise would take multiple synthetic steps.