Targeting G†Protein-Coupled Receptors by Capture Compound Mass Spectrometry: A Case Study with Sertindole.

Unbiased chemoproteomic profiling of small-molecule interactions with endogenous proteins is important for drug discovery. For meaningful results, all protein classes have to be tractable, including G protein-coupled receptors (GPCRs). These receptors are hardly tractable by affinity pulldown from lysates. We report a capture compound (CC)-based strategy to target and identify GPCRs directly from living cells. We synthesized CCs with sertindole attached to the CC scaffold in different orientations to target the dopamine D2 receptor (DRD2) heterologously expressed in HEK 293 cells. The structure-activity relationship of sertindole for DRD2 binding was reflected in the activities of the sertindole CCs in radioligand displacement, cell-based assays, and capture compound mass spectrometry (CCMS). The activity pattern was rationalized by molecular modelling. The most-active CC showed activities very similar to that of unmodified sertindole. A concentration of DRD2 in living cells well below 100 fmol used as an experimental input was sufficient for unambiguous identification of captured DRD2 by mass spectrometry. Our new CCMS workflow broadens the arsenal of chemoproteomic technologies to close a critical gap for the comprehensive characterization of drug-protein interactions.

A novel approach to detect resistance mechanisms reveals FGR as a factor mediating HDAC inhibitor SAHA resistance in B-cell lymphoma.

Histone deacetylase (HDAC) inhibitors such as suberoylanilide hydroxamic acid (SAHA) are not commonly used in clinical practice for treatment of B-cell lymphomas, although a subset of patients with refractory or relapsed B-cell lymphoma achieved partial or complete remissions. Therefore, the purpose of this study was to identify molecular features that predict the response of B-cell lymphomas to SAHA treatment. We designed an integrative approach combining drug efficacy testing with exome and captured target analysis (DETECT). In this study, we tested SAHA sensitivity in 26 B-cell lymphoma cell lines and determined SAHA-interacting proteins in SAHA resistant and sensitive cell lines employing a SAHA capture compound (CC) and mass spectrometry (CCMS). In addition, we performed exome mutation analysis. Candidate validation was done by expression analysis and knock-out experiments. An integrated network analysis revealed that the Src tyrosine kinase Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR) is associated with SAHA resistance. FGR was specifically captured by the SAHA-CC in resistant cells. In line with this observation, we found that FGR expression was significantly higher in SAHA resistant cell lines. As functional proof, CRISPR/Cas9 mediated FGR knock-out in resistant cells increased SAHA sensitivity. In silico analysis of B-cell lymphoma samples (n = 1200) showed a wide range of FGR expression indicating that FGR expression might help to stratify patients, which clinically benefit from SAHA therapy. In conclusion, our comprehensive analysis of SAHA-interacting proteins highlights FGR as a factor involved in SAHA resistance in B-cell lymphoma.

Identification of Potential Off-target Toxicity Liabilities of Catechol-O-methyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry.

Structurally related inhibitors of a shared therapeutic target may differ regarding potential toxicity issues that are caused by different off-target bindings. We devised a differential competition capture compound mass spectrometry (dCCMS) strategy to effectively differentiate off-target profiles. Tolcapone and entacapone are potent inhibitors of catechol-O-methyl transferase (COMT) for the treatment of Parkinson's disease. Tolcapone is also known for its hepatotoxic side effects even though it is therapeutically more potent than entacapone. Here, we identified 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) as a possible toxicity-causing off-target of tolcapone, and this protein is not bound by the less toxic COMT inhibitor entacapone. Moreover, two novel compounds from a focused library synthesized in-house, N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide and 5-(3,4-dihydroxy-5-nitrobenzylidene)-3-ethylthiazolidine-2,4-dione, were utilized to gain insight into the structure-activity relationships in binding to COMT and the novel off-target HIBCH. These compounds, especially N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide, could serve as starting point for the development of improved and more specific COMT inhibitors.

Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability.

Double cyclization of short linear peptides obtained by solid phase peptide synthesis was used to prepare bridged bicyclic peptides (BBPs) corresponding to the topology of bridged bicyclic alkanes such as norbornane. Diastereomeric norbornapeptides were investigated by 1H-NMR, X-ray crystallography and CD spectroscopy and found to represent rigid globular scaffolds stabilized by intramolecular backbone hydrogen bonds with scaffold geometries determined by the chirality of amino acid residues and sharing structural features of ß-turns and α-helices. Proteome profiling by capture compound mass spectrometry (CCMS) led to the discovery of the norbornapeptide 27c binding selectively to calmodulin as an example of a BBP protein binder. This and other BBPs showed high stability towards proteolytic degradation in serum.

Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins.

S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 µM, 6.0 ± 2.9 µM, and 10.06 ± 2.87 µM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.

Cinerin C: a macrophyllin-type bicyclo[3.2.1]octane neolignan from Pleurothyrium cinereum (Lauraceae).

The structure of naturally-occurring cinerin C [systematic name: (7S,8R,3'R,4'S,5'R)-Δ(8')-4'-hydroxy-5,5',3'-trimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan], isolated from the ethanol extract of leaves of Pleurothyrium cinereum (Lauraceae), has previously been established by NMR and HRMS spectroscopy, and its absolute configuration established by circular dichroism measurements. For the first time, its crystal structure has now been established by single-crystal X-ray analysis, as the monohydrate, C(22)H(26)O(7)·H(2)O. The bicyclooctane moiety comprises fused cyclopentane and cyclohexenone rings which are almost coplanar. An intermolecular O-H···O hydrogen bond links the 4'-OH and 5'-OCH(3) groups along the c axis.

Dabigatran and dabigatran ethyl ester: potent inhibitors of ribosyldihydronicotinamide dehydrogenase (NQO2).

Recent studies have revealed that compounds believed to be highly selective frequently address multiple target proteins. We investigated the protein interaction profile of the widely prescribed thrombin inhibitor dabigatran (1), resulting in the identification and subsequent characterization of an additional target enzyme. Our findings are based on an unbiased functional proteomics approach called capture compound mass spectrometry (CCMS) and were confirmed by independent biological assays. 1 was shown to specifically bind ribosyldihydronicotinamide dehydrogenase (NQO2), a detoxification oxidoreductase. Molecular dockings predicted and biological experiments confirmed that dabigatran ethyl ester (2) inhibits NQO2 even more effectively than the parent 1 itself. Our data show that 1 and 2 are inhibitors of NQO2, thereby revealing a possible new aspect in the mode of action of 1. We present a workflow employing chemical proteomics, molecular modeling, and functional assays by which a compound's protein-interaction profile can be determined and used to tune the binding affinity.

Dasatinib, imatinib and staurosporine capture compounds - Complementary tools for the profiling of kinases by Capture Compound Mass Spectrometry (CCMS).

Capture Compound Mass Spectrometry (CCMS) is a platform technology for the functional isolation of subproteomes. Here we report the synthesis of two new kinase Capture Compounds (CCs) based on the tyrosine-kinase specific inhibitors dasatinib and imatinib and compare their interaction profiles to that of our previously reported staurosporine-CCs. CCs are tri-functional molecules: they comprise a sorting function (e.g. the small molecule or drug of interest) which interacts with target proteins, a photo-activatable reactivity function to covalently trap the interacting proteins, and a sorting function to isolate the CC-protein conjugates from complex biological samples for protein identification by liquid chromatography/mass spectrometry (LC-MS/MS). We present data of CCMS experiments from human HepG2 cells and compare the profiles of the kinases isolated with dasatinib, imatinib and staurosporine CC, respectively. Dasatinib and imatinib have a more selective kinase binding profile than staurosporine. Moreover, the new CCs allow isolation and identification of additional kinases, complementing the staurosporine CC. The family of kinase CCs will be a valuable tool for the proteomic profiling of this important protein class. Besides sets of expected kinases we identified additional specific interactors; these off-targets may be of relevance in the view of the pharmacological profile of dasatinib and imatinib.

The first diastereoselective synthesis of cinerins A-C, PAF-antagonistic macrophyllin-type bicyclo[3.2.1]octane neolignans, using a novel Pd-catalysed oxyarylation.

The first diastereoselective synthesis of PAF-antagonistic cinerins A-C, macrophyllin-type bicyclo[3.2.1]octane neolignans from Pleurothyrium cinereum, has been accomplished using a novel Pd-catalysed oxyarylation to afford a 2,3-dihydrobenzofuran as the key intermediate.

One-pot, Pd-catalyzed synthesis of trans-dihydrobenzofurans from o-aminophenols.

An efficient and facile synthesis of trans-dihydrobenzofurans has been accomplished from o-aminophenols and phenylpropenes via a novel (one-pot) diastereoselective Pd-catalyzed oxyarylation reaction. The development and optimization of this method is described.

Comprehensive identification of staurosporine-binding kinases in the hepatocyte cell line HepG2 using Capture Compound Mass Spectrometry (CCMS).

The central role of kinases in cell signaling has set them in the focus of biomedical research. In functional proteomics analyses, large- scale profiling of kinases has become feasible through the use of affinity pulldown beads that carry immobilized kinase inhibitors. As an alternative approach to solid phase beads, Capture Compound Mass Spectrometry (CCMS) enables the functional isolation of protein-classes on the basis of small molecule-protein interactions in solution. Capture Compounds are trifunctional probes: a selectivity function interacts with the native target proteins in equilibrium, upon irradiation a photoactivatable reactivity function forms an irreversible covalent bond to the target proteins, and a sorting function allows the captured proteins to be isolated from a complex protein mixture. We report the design and application of a novel, fully water-soluble Capture Compound that carries the broadband kinase inhibitor staurosporine as selectivity function. We used this Capture Compound to profile the kinome of the human liver-derived cell line HepG2 and identified one hundred kinases. HepG2 cells are a widely used model system for hepatocarcinoma, hepatitis, and for investigation of drug toxicity effects. CCMS experiments in membrane fractions of human placenta are given as example for the applicability to human tissue.

GDP-capture compound--a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS).

The functional isolation of proteome subsets based on small molecule-protein interactions is an increasingly popular and promising field in functional proteomics. Entire protein families may be profiled on the basis of their common interaction with a metabolite or small molecule inhibitor. This is enabled by novel multifunctional small molecule probes. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate Capture Compound-protein conjugates from complex biological samples for direct trypsinisation and protein identification by liquid chromatography/mass spectrometry (CCMS). We here present the synthesis and application of a novel GDP-Capture Compound for the functional enrichment of GTPases, a pivotal protein family that exerts key functions in signal transduction. We present data from CCMS experiments on two biological lysates from Escherichia coli and from human-derived Hek293 cells. The GDP-Capture Compound robustly captures a wide range of different GTPases from both systems and will be a valuable tool for the proteomic profiling of this important protein family.

COX, LOX and platelet aggregation inhibitory properties of Lauraceae neolignans.

The anti-inflammatory potential of 26 neolignans (14 of the bicyclooctane-type and 12 of the benzofuran-type), isolated from three Lauraceae species (Pleurothyrium cinereum, Ocotea macrophylla and Nectandra amazonum), was evaluated in vitro through inhibition of COX-1, COX-2, 5-LOX and agonist-induced aggregation of rabbit platelets. Benzofuran neolignans were found to be selective COX-2 inhibitors, whereas bicyclooctane neolignans inhibit selectively the PAF-action as well as COX-1 and 5-LOX. The neolignan 9-nor-7,8-dehydro-isolicarin B 15 and cinerin C 7 were found to be the most potent COX-2 inhibitor and PAF-antagonist, respectively. Nectamazin C 10 exhibited dual 5-LOX/COX-2 inhibition.

The cAMP capture compound mass spectrometry as a novel tool for targeting cAMP-binding proteins: from protein kinase A to potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels.

The profiling of subproteomes from complex mixtures on the basis of small molecule interactions shared by members of protein families or small molecule interaction domains present in a subset of proteins is an increasingly important approach in functional proteomics. Capture Compound Mass Spectrometry (CCMS) is a novel technology to address this issue. CCs are trifunctional molecules that accomplish the reversible binding of target protein families to a selectivity group (small molecule), covalent capturing of the bound proteins by photoactivated cross-linking through a reactivity group, and pullout of the small molecule-protein complexes through a sorting function, e.g. biotin. Here we present the design, synthesis, and application of a new Capture Compound to target and identify cAMP-binding proteins in complex protein mixtures. Starting with modest amounts of total protein mixture (65-500 microg), we demonstrate that the cAMP-CCs can be used to isolate bona fide cAMP-binding proteins from lysates of Escherichia coli, mammalian HepG2 cells, and subcellular fractions of mammalian brain, respectively. The identified proteins captured by the cAMP-CCs range from soluble cAMP-binding proteins, such as the catabolite gene activator protein from E. coli and regulatory subunits of protein kinase A from mammalian systems, to cAMP-activated potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channels from neuronal membranes and specifically synaptosomal fractions from rat brain. The latter group of proteins has never been identified before in any small molecule protein interaction and mass spectrometry-based proteomics study. Given the modest amount of protein input required, we expect that CCMS using the cAMP-CCs provides a unique tool for profiling cAMP-binding proteins from proteome samples of limited abundance, such as tissue biopsies.

PAF-antagonistic bicyclo[3.2.1]octanoid neolignans from leaves of Ocotea macrophylla Kunth. (Lauraceae).

Di-nor-benzofuran neolignan aldehydes, Delta(7)-3,4-methylenedioxy-3'-methoxy-8',9'-dinor-4',7-epoxy-8,3'-neolignan-7'-aldehyde (ocophyllal A) 1, Delta(7)-3,4,5,3'-tetramethoxy-8',9'-dinor-4',7-epoxy-8,3'-neolignan-7'-aldehyde (ocophyllal B) 2, and macrophyllin-type bicyclo[3.2.1]octanoid neolignans (7R, 8R, 3'S, 4'S, 5'R)-Delta(8)'-4'-hydroxy-5'-methoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan (ocophyllol A) 3, (7R, 8R, 3'S, 4'S, 5'R)-Delta(8)'-4'-hydroxy-3,4,5'-trimethoxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan (ocophyllol B) 4, (7R, 8R, 3'S, 4'S, 5'R)-Delta(8)'-4'-hydroxy-3,4,5,5'-tetramethoxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan (ocophyllol C) 5, as well as 2'-epi-guianin 6 and (+)-licarin B 7, were isolated and characterized from leaves of Ocotea macrophylla (Lauraceae). The structures and configuration of these compounds were determined by extensive spectroscopic analyses. Inhibition of platelet activating factor (PAF)-induced aggregation of rabbit platelets were tested with neolignans 1-7. Although compound 6 was the most potent PAF-antagonist, compounds 3-5 showed some activity.

Macrophyllin-type bicyclo[3.2.1]octanoid neolignans from the leaves of Pleurothyrium cinereum.

Four new macrophyllin-type bicyclo[3.2.1]octanoid neolignans, (7S,8R,3'S,5'R)-Delta(8')-5,5',3'-trimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2',4'-dioxo-7.3',8.5'-neolignan (cinerin A), 1, (7R,8R,3'S,4'R,5'R)-Delta(8')-4'-hydroxy-5,5'-dimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan (cinerin B), 2, (7S,8R,3'R,4'S,5'R)-Delta(8')-4'-hydroxy-5,5',3'-trimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-2'-oxo-7.3',8.5'-neolignan (cinerin C), 3, and (7S,8R,2'R,3'S,5'R)-Delta(8')-2'-hydroxy-5,5'-dimethoxy-3,4-methylenedioxy-2',3',4',5'-tetrahydro-4'-oxo-7.3',8.5'-neolignan (cinerin D), 4, along with the known diterpene kaurenoic acid 5, were isolated from the leaves of Pleurothyrium cinereum. The structures and configuration of these compounds were determined by extensive spectroscopic analysis. Cinerins A-D (1-4) were tested for their inhibition efficacy of platelet activating factor (PAF)-induced aggregation of rabbit platelets. Compound 3 was the most potent PAF antagonist. Compounds 1-5 were tested against Mycobacterium tuberculosis (H(37)Rv strain) using the MABA method. Compound 5 induced 91.3% growth inhibition at 50 microg mL(-1). Compounds 1-5 showed no significant inhibitory activity against some Gram-positive and Gram-negative bacteria by the agar-well diffusion method.

Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles.

The non-supervised construction of a mass spectral and retention time index data base (MS/RI library) from a set of plant metabolic profiles covering major organs of potato (Solanum tuberosum), tobacco (Nicotiana tabaccum), and Arabidopsis thaliana, was demonstrated. Typically 300-500 mass spectral components with a signal to noise ratio > or =75 were obtained from GC/EI-time-of-flight (TOF)-MS metabolite profiles of methoxyaminated and trimethylsilylated extracts. Profiles from non-sample controls contained approximately 100 mass spectral components. A MS/RI library of 6205 mass spectral components was accumulated and applied to automated identification of the model compounds galactonic acid, a primary metabolite, and 3-caffeoylquinic acid, a secondary metabolite. Neither MS nor RI alone were sufficient for unequivocal identification of unknown mass spectral components. However library searches with single bait mass spectra of the respective reference substance allowed clear identification by mass spectral match and RI window. Moreover, the hit lists of mass spectral searches were demonstrated to comprise candidate components of highly similar chemical nature. The search for the model compound galactonic acid allowed identification of gluconic and gulonic acid among the top scoring mass spectral components. Equally successful was the exemplary search for 3-caffeoylquinic acid, which led to the identification of quinic acid and of the positional isomers, 4-caffeoylquinic acid, 5-caffeoylquinic acid among other still non-identified conjugates of caffeic and quinic acid. All identifications were verified by co-analysis of reference substances. Finally we applied hierarchical clustering to a complete set of pair-wise mass spectral comparisons of unknown components and reference substances with known chemical structure. We demonstrated that the resulting clustering tree depicted the chemical nature of the reference substances and that most of the nearest neighbours represented either identical components, as judged by co-elution, or conformational isomers exhibiting differential retention behaviour. Unknown components could be classified automatically by grouping with the respective branches and sub-branches of the clustering tree.

Uncatalyzed Friedel-Crafts alkylation of aromatic compounds through reactive benzyl cations generated from N-sulfamoylcarbamates.

[reaction: see text] A new method for the generation of highly reactive benzyl cations by thermal decomposition of aryl-benzyl-sulfamoylcarbamates, obtained in a one-pot reaction from chlorosulfonyl isocyanate, is described. The generated cations alkylate aromatic compounds efficiently in the absence of catalysts.