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Constrained peptide

Richard J Steel, Maria A O'Connell, Mark Searcey
The Nrf2/Keap1 interaction is a target in the development of new therapeutic agents, where inhibition of the interaction activates Nrf2 and leads to the generation of downstream anti-inflammatory effects. Peptides that mimic the β-turn in the Keap1 active site and are constrained by a disulfide bridge have high affinity for Keap1 but no intracellular activity. The introduction of a perfluoroalkyl-bridging group to constrain the peptides, coupled with a glutamic acid to proline replacement leads to a new peptide with a Ki of 6...
March 3, 2018: Bioorganic & Medicinal Chemistry Letters
Eileen J Kennedy
No abstract text is available yet for this article.
March 15, 2018: Bioorganic & Medicinal Chemistry
Jacob Rodriguez, Sloane O'Neill, Maciej A Walczak
Review primarily covers from 1995-2018Carbohydrate function, recognized in a multitude of biological processes, provides a precedent for developing carbohydrate surrogates that mimic the structure and function of bioactive compounds. In order to constrain highly flexible oligosaccharides, synthetic tethering techniques like those exemplified by stapled peptides are utilized to varying degrees of success. Naturally occurring constrained carbohydrates, however, exist with noteworthy cytotoxic and chemosensitizing properties...
March 7, 2018: Natural Product Reports
Robert M Vaughan, Bradley M Dickson, Evan M Cornett, Joseph S Harrison, Brian Kuhlman, Scott B Rothbart
UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties...
February 28, 2018: Nucleic Acids Research
Rebecca K Campbell, Kerry J Schulze, Saijuddin Shaikh, Rubhana Raqib, Lee S F Wu, Hasmot Ali, Sucheta Mehra, Keith P West, Parul Christian
Environmental enteric dysfunction (EED) and systemic inflammation (SI) are common in developing countries and may cause stunting. In Bangladesh, >40 % of preschool children are stunted, but EED and SI contributions are unknown. We aimed to determine the impact of EED and SI (assessed with multiple indicators) on growth in children (n 539) enrolled in a community-based randomised food supplementation trial in rural Bangladesh. EED was defined with faecal myeloperoxidase, α-1 antitrypsin and neopterin and serum endotoxin core antibody and glucagon-like peptide-2, consolidated into gut inflammation (GI) and permeability (GP) scores, and urinary lactulose:mannitol α-1 acid glycoprotein (AGP) characterised SI...
February 2018: British Journal of Nutrition
Bhanushee Sharma, Srivathsan V Ranganathan, Georges Belfort
Knowing that abeta amyloid peptide (Aβ42) dimers are the smallest and most abundant neurotoxic oligomers for Alzheimer's disease (AD), we used molecular simulations with advanced sampling methods (replica-exchange) to characterize and compare interactions between the N-termini (residues 1-16) of wild type (WT-WT) and five mutant dimers under constrained and unconstrained conditions. The number of contacts and distances between the N-termini, and contact maps of their conformational landscape illustrate substantial differences for only one residue change...
February 21, 2018: ACS Chemical Neuroscience
Aline Dantas de Araujo, Samuel R Perry, David P Fairlie
The use of selenocysteines and various cross-linkers to induce helicity in a bioactive peptide is described. The higher reactivity of selenocysteine, relative to cysteine, facilitates rapid cross-linking within unprotected linear peptides under mild aqueous conditions. Alkylating agents of variable topology and electrophilicity were used to link pairs of selenocysteines within a p53 peptide. Facile selenoether formation enables diverse tailoring of the helical peptide structure.
February 20, 2018: Organic Letters
Chad Townsend, Akihiro Furukawa, Joshua Schwochert, Cameron R Pye, Quinn Edmondson, R Scott Lokey
Cyclic peptides are of great interest as therapeutic compounds due to their potential for specificity and intracellular activity, but specific compounds can be difficult to identify from large libraries without resorting to molecular encoding techniques. Large libraries of cyclic peptides are often DNA-encoded or linearized before sequencing, but both of those deconvolution strategies constrain the chemistry, assays, and quantification methods which can be used. We developed an automated sequencing program, CycLS, to identify cyclic peptides contained within large synthetic libraries...
February 3, 2018: Bioorganic & Medicinal Chemistry
Maruthi Konda, Rohit G Jadhav, Sayan Maiti, Shaikh M Mobin, Brice Kauffmann, Apurba K Das
Constrained γ-amino acid gababutin (Gbn) based peptides that form different conformations have been synthesized. Striving to rationalize the impact of side chain orientations framing tetrapeptide-based supramolecular organic frameworks and morphological entities, Gbn incorporated hybrid peptides Boc-Gbn-Aib-Aaa-Aib-OMe (where Aaa = Phe(F) for peptide 1, Leu(L) for peptide 2 and Tyr(Y) for peptide 3) were synthesized by changing the amino acid at the third position. The solution state dual folded conformation (C12 /C10 H-bonded) is probed by 2D NMR spectroscopy in support of a DMSO-d6 titration and VT NMR experiments...
February 19, 2018: Organic & Biomolecular Chemistry
Sarah Chérasse, Boris Baer, Morten Schiøtt, Jacobus J Boomsma
Leaf-cutting ant queens mate with multiple males during a single nuptial flight and store sperm for up to two decades. During mating, males transfer sperm from their accessory testes to the queen bursa copulatrix from where it enters the spermatheca, an insect sperm storage organ that has become highly specialised in long-lived ant queens who never re-mate later in life. Long-term storage without the possibility to obtain new sperm creates an immune defence dilemma, because recognition of non-self cells eliminates infections but may also target irreplaceable sperm and reduce lifetime reproductive success...
February 14, 2018: Journal of Experimental Biology
Andrew Collins, Andrew R Jones
The recent establishment of cloud computing, high throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimised desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualised in a high quality cross-platform interface via a web browser. There are number of emerging platforms for cloud based mass spectrometry data analysis, however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider...
February 5, 2018: Journal of Proteome Research
Conan K Wang, Joakim Erik Swedberg, Peta J Harvey, Quentin Kaas, David J Craik
Several cyclic peptides have been reported to have unexpectedly high membrane permeability. Of these, cyclosporin A is perhaps the most well-known example, particularly in light of its relatively high molecular weight. Observations that cyclosporin A changes conformation depending on its solvent environment led to the hypothesis that conformational dynamics is a prerequisite for its permeability; however, this hypothesis has been difficult to validate experimentally. Here, we use extended timeframe molecular dynamics simulations to explicitly determine the conformational behavior of cyclosporin A and other related cyclic peptides as they spontaneously transition between different environments, including through a lipid bilayer...
February 5, 2018: Journal of Physical Chemistry. B
Joel Haywood, Jason W Schmidberger, Amy M James, Samuel G Nonis, Kirill V Sukhoverkov, Mikael Elias, Charles S Bond, Joshua S Mylne
Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus...
January 31, 2018: ELife
B Franke, J S Mylne, K J Rosengren
Covering: 1999 up to the end of 2017The small cyclic peptide SunFlower Trypsin Inhibitor-1 (SFTI-1) from sunflower seeds is the prototypic member of a novel family of natural products. The biosynthesis of these peptides is intriguing as their gene-encoded peptide backbone emerges from a precursor protein that also contains a seed storage albumin. The peptide sequence is cleaved out from the precursor and cyclised by the albumin-maturing enzymatic machinery. Three-dimensional solution NMR structures of a number of these peptides, and of the intact precursor protein preproalbumin with SFTI-1, have now been elucidated...
January 30, 2018: Natural Product Reports
Dorian Migoń, Damian Neubauer, Wojciech Kamysz
Antimicrobial peptides are promising candidates for anti-infective pharmaceuticals. Unfortunately, because of their low proteolytic and chemical stability, their usage is generally narrowed down to topical formulations. Until now, numerous approaches to increase peptide stability have been proposed. One of them, peptide hydrocarbon stapling, a modification based on stabilizing peptide secondary structure with a side-chain covalent hydrocarbon bridge, have been successfully applied to many peptides. Moreover, constraining secondary structure of peptides have also been proven to increase their biological activity...
January 12, 2018: Protein Journal
Edit Mesterházy, Colette Lebrun, Attila Jancsó, Pascale Delangle
Peptide design is an efficient strategy to create relevant models of natural metal binding sites found in proteins. The two short tetrapeptides Ac-Cys-dPro-Pro-Cys-NH2 (CdPPC) and Ac-Cys-Pro-Gly-Cys-NH2 (CPGC) were synthesized and studied as mimics of Cu(I) binding sites involved in Cu homeostasis. Both sequences contain β turn inducing motifs to rigidify the peptide backbone structure and thereby preorganize the metal-binding side chains. The more constrained structure of the peptide CdPPC with respect to CPGC was evidenced by the measurements of the temperature coefficients of the amide protons by 1H NMR, which suggest a solvent-shielded intramolecular hydrogen bond in CdPPC, and no H-bond in CPGC...
January 12, 2018: Inorganic Chemistry
Xiyuan Wu, Zixuan Liu, Xiaohui Ding, Danwei Yu, Huamian Wei, Bo Qin, Yuanmei Zhu, Huihui Chong, Sheng Cui, Yuxian He
SC29EK is an electronically constrained α-helical peptide HIV-1 fusion inhibitor highly effective against both wild-type and enfuvirtide (T20)-resistant viruses. In this study, we focused on investigating the mechanism of HIV-1 resistance to SC29EK by two approaches. First, SC29EK-escaping HIV-1 variants were selected and characterized. Three mutant viruses, which possessed two (E43K/E49A) or three (Q39R/N43K/N126K, N43K/E49A/N126K) amino acid substitutions in the N- and C-terminal repeat regions of gp41 were identified as conferring high resistance to SC29EK and cross-resistance to the first-generation (T20, C34) and newly-designed (sifuvirtide, MT-SC29EK, 2P23) fusion inhibitors...
January 10, 2018: Journal of Virology
Govind S Bhosle, Shalmali Kharche, Santosh Kumar, Durba Sengupta, Souvik Maiti, Moneesha Fernandes
We report a hundred-fold increase in binding affinity of the Tat(48-57) peptide to HIV-1 TAR RNA by replacing R52, an essential and critical residue for Tat's specific binding, by (2S,4S)-4-guanidinoproline. The resulting αTat1M peptide is a far superior binder than γTat1M, a peptide containing another conformationally constrained arginine mimic, (2S,4S)-4-amino-N-(3-guanidinopropyl)-proline, or even the control Tat (CtrlTat) itself. Our observations are supported by CD, ITC, gel electrophoresis and UV spectroscopy studies...
January 4, 2018: ChemMedChem
Anjali Jha, Mothukuri Ganesh Kumar, Hosahudya N Gopi, Kishore M Paknikar
Designing peptide based drugs to target the β-sheet rich toxic intermediates during the aggregation of amyloid-β 1-42 (Aβ1-42) has been a major challenge. In general, β-sheet breaker peptides (BSBPs) are designed to complement the enthalpic interactions with the aggregating protein and entropic effects are usually ignored. Here, we have developed a conformationally constrained cyclic BSBP by the use of an unnatural amino acid and a disulfide bond. We show that our peptide strongly inhibits the aggregation of Aβ1-42 in a concentration-dependent manner...
December 28, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Aldo Franco, Sanaz Dovell, Carolina Moller, Meghan Grandal, Evan Clark, Frank Marí
The mini-M conotoxins are peptidic scaffolds found in the venom of cones snails. These scaffolds are tightly folded structures held together by three disulfide bonds with a CC-C-C-CC arrangement (conotoxin framework III) and belong to the M Superfamily of conotoxins. Here we describe twenty-five mini-M conotoxins from the venom of Conus regius, a Western Atlantic worm-hunting cone snail species using transcriptomic and peptidomic analyses. These C. regius conotoxins belong to three different subtypes: M1, M2, and M3...
December 28, 2017: FEBS Journal
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