Discovery of Nanomolar Ligands for 7-Transmembrane G-Protein-Coupled Receptors from a Diverse N-(Substituted)glycine Peptoid Library

Zuckermann, Ronald N.; Martin, Éric; Spellmeyer, David C.; Stauber, Gregory B.; Shoemaker, Kevin R.; Kerr, Janice M.; Figliozzi, Gianine; Goff, Dane A.; Siani, Michael A.; Simon, Reyna J.; Banville, Steven C.; Brown, E. G.; Wang, Liang; Richter, L.; Moos, Walter H.

doi:10.1021/jm00043a007

Cited by 355 publications

(187 citation statements)

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“…2-amino-2Ј-[BOC-amino]ethylene glycol diethyl ether was synthesized from 2,2Ј-(ethylenedioxy)-bis[ethylamine] as described in ref. 18, and its identity confirmed by NMR and mass spectrometry. The NHS ester of the 6-bromo-hexanoic acid was generated in situ by reacting 1.6 g of the acid with equivalent amounts of N-hydroxysuccinimide and EDC dissolved in 20 ml of anhydrous dichloromethane, After stirring for 30 min at room temperature, an equivalent amount of 2-amino-2Ј-[BOC-amino]ethylene glycol diethyl ether was added and stirring was continued overnight at room temperature.…”

Section: Edu Labeling Of Mouse Tissuesmentioning

confidence: 81%

A chemical method for fast and sensitive detection of DNA synthesis in vivo

Salic

Mitchison

2008

Proc. Natl. Acad. Sci. U.S.A.

1,629

1,447

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We have developed a method to detect DNA synthesis in proliferating cells, based on the incorporation of 5-ethynyl-2-deoxyuridine (EdU) and its subsequent detection by a fluorescent azide through a Cu(I)-catalyzed [3 ؉ 2] cycloaddition reaction (''click'' chemistry). Detection of the EdU label is highly sensitive and can be accomplished in minutes. The small size of the fluorescent azides used for detection results in a high degree of specimen penetration, allowing the staining of whole-mount preparations of large tissue and organ explants. In contrast to BrdU, the method does not require sample fixation or DNA denaturation and permits good structural preservation. We demonstrate the use of the method in cultured cells and in the intestine and brain of whole animals.BrdU ͉ click chemistry ͉ DNA replication ͉ EdU ͉ microscopy D etection of DNA synthesis in proliferating cells relies on the incorporation of labeled DNA precursors into cellular DNA during the S phase of the cell cycle (1-3). The labeled DNA precursors, usually pyrimidine deoxynucleosides, are added to cells during replication, and their incorporation into genomic DNA is quantified or visualized after incubation and sample staining. The same labeled deoxynucleosides can be injected into experimental animals to assay cellular proliferation in specific organs and tissues. The most common deoxynucleosides used for assaying DNA replication are [ 3 H]thymidine and 5-bromo-2Ј-deoxyuridine (BrdU). [ 3 H]Thymidine incorporated into DNA is usually detected by autoradiography, whereas detection of BrdU is accomplished immunologically, through specific anti-BrdU antibodies.Although [ 3 H]thymidine and BrdU labeling methods have been very useful for studying cell cycle kinetics, DNA replication, and sister chromatid exchange and for assessing cell proliferation of normal or pathological cells or tissues under different conditions, these methods exhibit several limitations. Working with [ 3 H]thymidine is cumbersome because of its radioactivity. Autoradiography is also labor-intensive and slow (detection often lasts several months), and thus not suitable for rapid high-throughput studies. Finally, microscopic images of [ 3 H]thymidine-labeled DNA suffer from poor resolution and low signal-to-noise ratios. In contrast to [ 3 H]thymidine autoradiography, BrdU immunostaining is both faster (although it still lasts several hours) and allows better microscopic imaging of the labeled DNA. One major disadvantage of BrdU staining is that the complementary base pairing in double-stranded DNA blocks the access of the anti-BrdU antibody to BrdU subunits. To expose the BrdU epitope, cells and tissue samples are subjected to strong denaturing conditions such as concentrated hydrochloric acid or mixtures of methanol and acetic acid. These harsh staining conditions invariably degrade the structure of the specimen while also making the intensity of BrdU staining highly dependent on the conditions used for detection by each investigator (4). Finally, as with any immunohistologic...

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Section: Edu Labeling Of Mouse Tissuesmentioning

confidence: 81%

A chemical method for fast and sensitive detection of DNA synthesis in vivo

Salic

Mitchison

2008

Proc. Natl. Acad. Sci. U.S.A.

1,629

1,447

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“…When NMR spectra were obtained at 100°C in DMSO-d 6 , the spectra for pentamers based on amine 9 were greatly simplified and amenable to straightforward interpretation; however, pentamers based on amine 7 degraded (in both DMSO-d 6 and D 2 O) at the high temperatures required to coalesce the amide rotamers 3 . Pentamers incorporating amine 7 were found to be highly water-soluble (80 mg/ml), suggesting that the backbone's intrinsic hydrophobicity can be overcome with appropriate hydrophilic side chains to generate water-soluble extended peptoids.…”

mentioning

confidence: 99%

Extended peptoids: a new class of oligomers based on aromatic building blocks

Combs

Lokey

2007

Tetrahedron Letters

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Peptoids (N-substituted polyglycines) represent a class of bioinspired oligomers that have unique physical and structural properties. Here we report the construction of "extended peptoids" based on aromatic building blocks, in which the N-alkylaminoacetyl group of the peptoid backbone has been replaced by an N-alkylaminomethylbenzoyl spacer. Both meta-and para-bromomethylbenzoic acids were synthesized, providing access to a new class of peptoids. Further, inclusion of hydrophilic side chains confers water solubility to these compounds, showing that, like simple peptoids, extended peptoids add an extra dimension to synthetic polyamide oligomers with potential application in a variety of biological contexts. Keywordspeptoids; N-alkyl glycines; oligomers; bioinspired polymers Peptoids 1 (N-substituted glycines) represent an interesting class of biomimetic oligomers that are structurally related to peptides but have different biological 2,3 and conformational 4-6 properties. The submonomer method of peptoid synthesis introduced by Zuckermann, et al., 7 allows for considerable diversity to be incorporated into the construction of peptoid libraries due to the large number of commercially available primary amines. The submonomer method has been applied extensively in the creation of peptoid libraries 8-12 , and it has shown great versatility in incorporating a diverse set of amines 13, 14 and hydrazines 15 . The peptoid scaffold has been further modified to create ureapeptoids 16, 17 and incorporate a variety of chemoselective functionalities 18 . The bulk of these studies, however, have preserved the haloacetic acid component while focusing on variations in the nucleophilic displacement step. Here we report the solid-phase synthesis of a new class of peptoid-inspired biomimetics in which the haloacetic acid groups are replaced by either meta-or para-halomethylbenzoic acids ( Figure 1b). These extended peptoids add further geometric diversity to oligomers based on the peptoid concept.The synthesis of meta-extended peptoids is shown in Scheme 1. m-and p-bromomethylbenzoic acids were readily synthesized by bromination of the corresponding toluic acids 19 . All of the extended peptoids described here were synthesized on Wang resin (100-200 mesh, 1.1 mmole/ g) 2 . The first bromomethylbenzoic acid submonomer was coupled to the resin with Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript diisopropylcarbodiimide (DIC) and 4-dimethylaminopyridine (DMAP) in dry DCM over one hour at room te...

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“…N-substituted glycine "peptoids" are an attractive class of synthetic molecules that can be constructed by linking component N-substituted glycines at sequential nitrogen-carbon bonds; they are directly analogous to the linking of amino acids into peptides [53]. Glyphosate is of course an N-substituted glycine, where the nitrogen side chain is a methyl phosphonyl group.…”

Section: Shikimate Pathway Inhibition Revisitedmentioning

confidence: 99%