- The microenvironment and pKaperturbation of aminoacyl-tRNA guided the selection of cationic amino acids
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The proteinogenic lysine (Lys) and arginine (Arg) have multiple methylene groups between α-carbon and the terminal charged centre. Why nature did not select ornithine (Orn), 2,4-diamino butyric acid (Dab) and 2,3-diamino propionic acid (Dpr) with fewer methylene groups in the side chain remains an important question! The propensity of aminoacyl-tRNA (aa-tRNA) model substrates towards self-degradationviaintramolecular lactamization was studied using UV spectroscopy and1H-NMR titration, which showed that Lys and Arg remain stable, and Orn and Dab cyclize to lactam. Hydrophobicity-assisted surface mediated model peptide formation highlighted that the microenvironment and pKaperturbation led to poor regioselectivity (α-aminevs.terminal amine) in Dpr and other non-proteinogenic analogues. The α-selectivity became even poorer in the presence of phosphate, making them ill-suited for peptide synthesis. Superior regioselectivity of the Lys aa-tRNA model substrate suggests that the extra methylene bridge helped nature to separate the microenvironments of the α-amine and ε-amine to synthesize the peptide backbone.
- Hazra, Bibhas,Prasad, Mahesh,Roy, Rajat,Tarafdar, Pradip K.
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supporting information
p. 8049 - 8056
(2021/10/04)
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- METHODS AND COMPOUNDS FOR THE TREATMENT OF GENETIC DISEASE
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The present disclosure relates to compounds and methods for modulating the expression of dmpk, and treating diseases and conditions in which dmpk plays an active role. The compound can be a transcription modulator molecule having a first terminus, a second terminus, and oligomeric backbone, wherein: a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to a nucleotide repeat sequence CAG or CTG; b) the second terminus comprises a protein-binding moiety binding to a regulatory molecule that modulates an expression of a gene comprising the nucleotide repeat sequence CAG or CTG; and c) the oligomeric backbone comprising a linker between the first terminus and the second terminus.
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Paragraph 00844; 001290; 001291; 001292
(2021/08/13)
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- Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance
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Hydroxylation of aliphatic carbons by nonheme Fe(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H?) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe(III)-coordinated oxygen (termed rebound). Enzymes that use H?-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C-C desaturations, it has been proposed that a second HAT to the Fe(III)-OH complex from the carbon α to the radical preempts rebound. Deuterium (2H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related l-arginine-modifying iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the l-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H? first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors 1H or 2H. By contrast, an unexpected 3,4-desaturation of l-homoarginine (l-hArg) by VioC, the l-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors 2H. Anchimeric assistance by N6 permits removal of the C4-H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (≤3.5 ?) of both l-hArg carbons to the oxygen ligand in an X-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may make competing hydroxylation unavoidable, thus explaining the presence of α-heteroatoms in nearly all native substrates for Fe/2OG desaturases.
- Dunham, Noah P.,Chang, Wei-Chen,Mitchell, Andrew J.,Martinie, Ryan J.,Zhang, Bo,Bergman, Jonathan A.,Rajakovich, Lauren J.,Wang, Bo,Silakov, Alexey,Krebs, Carsten,Boal, Amie K.,Bollinger, J. Martin
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p. 7116 - 7126
(2018/05/15)
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- An Allyl Protection and Improved Purification Strategy Enables the Synthesis of Functionalized Phosphonamidate Peptides
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For modern biophysical methods such as isothermal titration calorimetry, high purity of the inhibitor of interest is indispensable. Herein, we describe a procedure for the synthesis and purification of functionalized phosphonamidate peptides that is able to generate inhibitors for the metalloprotease thermolysin for use in biophysical experiments. The method utilizes an allyl ester/alloc protection strategy and takes advantage of a fast and effective solid-phase extraction (SPE) purification step. Applying this strategy, we were able to synthesize a series of highly polar inhibitors featuring amino- and hydroxy-functionalized side chains in excellent purity.
- Cramer, Jonathan,Klebe, Gerhard
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supporting information
p. 1857 - 1866
(2017/04/06)
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- Peptides
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A peptide which can adopt a 310-helical conformation in which the side chains of two amino acid residues in the peptide backbone are linked by a group comprising an aromatic 5-membered ring.
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Page/Page column 25; 26; 40
(2016/02/03)
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- A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds
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Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.
- Isidro-Llobet, Albert,Hadje Georgiou, Kathy,Galloway, Warren R. J. D.,Giacomini, Elisa,Hansen, Mette R.,Méndez-Abt, Gabriela,Tan, Yaw Sing,Carro, Laura,Sore, Hannah F.,Spring, David R.
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supporting information
p. 4570 - 4580
(2015/04/14)
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- TUMOUR RADIOLABELLING IMAGING AGENTS COMPRISING ORNITHINE AND DERIVATIVES THEREOF
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The present invention relates to a radiolabelling imaging agent comprising ornithine and derivatives thereof modified to incorporate a Technetium (99n,Tc) radiolabel. The radioiabelled imaging agents are substrates for Ornithine Decarboxylase (ODC) and can be used for imaging of cancers in which ODC expression is upregulated.
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Page/Page column 21-22
(2011/11/06)
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- Stapling of a 310-helix with click chemistry
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Short peptides are important as lead compounds and molecular probes in drug discovery and chemical biology, but their well-known drawbacks, such as high conformational flexibility, protease lability, poor bioavailability and short half-lives in vivo, have prevented their potential from being fully realized. Side chain-to-side chain cyclization, e.g., by ring-closing olefin metathesis, known as stapling, is one approach to increase the biological activity of short peptides that has shown promise when applied to 310-and α-helical peptides. However, atomic resolution structural information on the effect of side chain-to-side chain cyclization in 310-helical peptides is scarce, and reported data suggest that there is significant potential for improvement of existing methodologies. Here, we report a novel stapling methodology for 310-helical peptides using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction in a model aminoisobutyric acid (Aib) rich peptide and examine the structural effect of side chain-to-side chain cyclization by NMR, X-ray diffraction, linear IR and femtosecond 2D IR spectroscopy. Our data show that the resulting cyclic peptide represents a more ideal 310-helix than its acyclic precursor and other stapled 310-helical peptides reported to date. Side chain-to-side chain stapling by CuAAC should prove useful when applied to 3 10-helical peptides and protein segments of interest in biomedicine.(Figure Presented)
- Jacobsen, yvind,Maekawa, Hiroaki,Ge, Nien-Hui,Goerbitz, Carl Henrik,Rongved, Pal,Ottersen, Ole Petter,Amiry-Moghaddam, Mahmood,Klaveness, Jo
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supporting information; experimental part
p. 1228 - 1238
(2011/04/24)
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- AMINOGLYCOSIDE DERIVATIVES
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The present invention relates to antimicrobial and antibiotic aminoglycoside derivatives. The compounds of the present application have the following chemical structures. The invention also relates to compositions, methods of preparation and methods of treatment of bacterial infections using the above aminoglycoside derivative.
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Page/Page column 48
(2011/12/02)
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- Inhibitors of N α-acetyl-l-ornithine deacetylase: Synthesis, characterization and analysis of their inhibitory potency
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A series of N α-acyl (alkyl)- and N α- alkoxycarbonyl-derivatives of l- and d-ornithine were prepared, characterized, and analyzed for their potency toward the bacterial enzyme N α-acetyl-l-ornithine deacetylase (ArgE). Ar
- Hlavacek,Picha,Vanek,Jiracek,Slaninova,Fucik,Budesinsky,Gilner,Holz
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experimental part
p. 1155 - 1164
(2010/08/06)
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- Nα-Fmoc-protected ω-azido- and ω-alkynyl-L- amino acids as building blocks for the synthesis of "clickable" peptides
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The growing interest in the 1,4-disubstituted-1,2,3-triazolyl moiety as an amide bond surrogate and its formation through very mild, chemoselective, and bioorthogonal CuI-catalyzed Huisgen 1,3-dipolar [3+2] cycloaddition of an alkynyl to an azi
- Isaad, Alexandra Le Chevalier,Barbetti, Francesca,Rovero, Paolo,D'Ursi, Anna Maria,Chelli, Mario,Chorev, Michael,Papini, Anna Maria
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experimental part
p. 5308 - 5314
(2009/06/18)
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- PROCESS FOR THE PREPARATION OF ε-ALKOXYCARBONYLLYSINES AND THEIR ANALOGUES
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A process for the preparation of ω-alkoxycarbonylamino-α-aminoacids and α,ω orthogonally diprotected diaminoacids from α,ω-diaminoacids using 1- alkoxycarbonylbenzotriazoles as protecting agents is disclosed. In an alternative embodiment, carbamoylating agents in the presence of benzotriazoles are used instead of 1-alkoxycarbonylbenzotriazoles. This reaction is preferably applied to the preparation of ε- alkoxycarbonyllysines from lysine. A process for the preparation of t-butoxycarbonylbenzotriazoles and novel complexes of ω-alkoxycarbonylamino-α-aminoacids with benzotriazoles are also disclosed.
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Page/Page column 14-15
(2008/06/13)
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- Highly functionalised sulfur-based silica scavengers for the efficient removal of palladium species from active pharmaceutical ingredients
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The use of multidentate sulfur-based silica scavengers 1,2, and 3 as highly effective adsorbents for the removal of precious metals, specifically palladium residues in this paper, from highly functionalised synthetic intermediates and APIs is described. The synthesis and purification of the polar and electron-rich reaction products, containing multiple functional groups, from palladium-catalysed removals of commonly used protecting groups such as benzyl, benzyloxycarbonyl, and allyloxycarbonyl and Sonogashira, Suzuki, Heck, and Buchwald-Hartwig coupling reactions is reported. The significant levels of residual palladium species, typically associated with these reaction products, are successfully and rapidly removed to below acceptable regulatory levels, of less than 5 ppm, by simple, unoptimised treatment with the designed silica scavengers at room temperature. Performance aspects, including broad solvent compatibility, excellent stability, and high metal affinity, combined with large-scale availability, ease of handling, and minimal loss of API make these silica scavengers particularly useful to process development groups.
- Galaffu, Nicola,Man, Siud Pui,Wilkes, Robin D.,Wilson, John R. H.
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p. 406 - 413
(2012/12/31)
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- Synthesis and biological evaluation of two chemically modified peptide epitopes for the class i MHC protein HLA-B*2705
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The T-cell receptor of a CD8+ T-cell recognises peptide epitopes bound by class I major histocompatibility complex (MHC) glycoproteins presented in a groove on their upper surface. Within the groove of the MHC molecule are 6 pockets, two of whi
- Jones, Matthew A.,Hislop, Andrew D.,Snaith, John S.
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p. 3769 - 3777
(2008/09/18)
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- Design, synthesis, and biological testing of potential heme-coordinating nitric oxide synthase inhibitors
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Based on computer modeling of the active site of nitric oxide synthases (NOS), a series of 10 amidine compounds (9-18) was designed including potential inhibitors that involve the coordination of side-chain functional groups with the iron of the heme cofactor. The most potent and selective compound was the methylthio amidine analogue 9, which was more potent than l-nitroarginine with 185-fold selectivity for inhibition of neuronal NOS over endothelial NOS. It also exhibited time-dependent inhibition, but did not involve the mechanism previously proposed for other amidine inhibitors of NOS. None of the compounds, however, exhibited heme-binding characteristics according to absorption spectroscopy.
- Litzinger, Elizabeth A.,Martasek, Pavel,Roman, Linda J.,Silverman, Richard B.
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p. 3185 - 3198
(2007/10/03)
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- Presentation and detection of azide functionality in bacterial cell surface proteins
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An improved protocol for copper-catalyzed triazole formation on the bacterial cell surface is described. Addition of highly pure CuBr to cells treated with azidohomoalanine (2) leads to ca. 10-fold more extensive cell surface labeling than previously observed. This highly active catalyst allows detection of the methionine analogues azidoalanine (1), azidonorvaline (3), and azidonorleucine (4) in cell surface proteins. Azidoalanine was previously believed to be silent with regard to the cellular protein synthesis machinery.
- Link, A. James,Vink, Mandy K. S.,Tirrell, David A.
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p. 10598 - 10602
(2007/10/03)
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- An efficient, scalable synthesis of the molecular transporter octaarginine via a segment doubling strategy.
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[reaction: see text]. Short oligomers of arginine function as remarkably efficient molecular transporters of drugs and probe molecules into cells and tissue. Currently, these compounds are prepared on resin through a unidirectional solid-phase synthesis.
- Wender,Jessop,Pattabiraman,Pelkey,VanDeusen
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p. 3229 - 3232
(2007/10/03)
-
- Selective factor Xa inhibitors
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Novel compounds, their salts and compositions related thereto having activity against mammalian factor Xa are disclosed. The compounds are useful in vitro or in vivo for preventing or treating coagulation disorders.
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- Examination of N-hydroxylation as a prerequisite mechanism of nitric oxide synthase inactivation
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L-N5-(1-Hydroxyiminoethyl)-ornithine (L-NHIO) and L-N6-(1-hydroxyiminoethyl)-lysine (L-NHIL) were synthesized and tested as potential intermediates in the mechanism-based inactivation of nitric oxide synthase (NOS) by L-N5-iminoethyl-ornithine (L-NIO) and L-N6-iminoethyllysine (L-NIL). Although these compounds were determined to be competitive inhibitors, mechanism-based inactivation was not observed. (C) 2000 Elsevier Science Ltd. All rights reserved.
- Maurer, Tristan S.,Pan, Jianping,Booth, Brian P.,Kalman, Thomas I.,Fung, Ho-Leung
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p. 1077 - 1080
(2007/10/03)
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- Cyclic peptides and use thereof
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Cyclic peptides and their salts have antagonistic activity on endothelin receptors and antagonistic activity on NK2 receptors. The peptides have the formula STR1 wherein X and Y each represent α-amino acid residues, A represents a D-acidic-α-amino acid residue, B represents a neutral α-amino acid residue, C represents an L-α-amino acid residue and D represents a D-α-amino acid residue having an aromatic ring group; wherein hydroxy, thiol, amino, imino and carboxyl groups can be substituted or unsubstituted. Pharmaceutical compositions containing such peptides are also described.
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- Inhibitors of nitric oxide biosynthesis
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The present invention is a method of treating hypotension and shock using select ornithine or NG -arginine derivatives.
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