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https://www.readbyqxmd.com/read/29141145/homochiral-versus-heterochiral-trifluoromethylated-pseudoproline-containing-dipeptides-a-powerful-tool-to-switch-the-prolyl-amide-bond-conformation
#1
Grégory Chaume, Julien Simon, Nathalie Lensen, Julien Pytkowicz, Thierry Brigaud, Emeric Miclet
The design of constrained peptides is of prime importance in the development of bioactive compounds and for applications in supramolecular chemistry. Due to its nature, the peptide bond undergoes a spontaneous cis-trans isomerism and the cis isomers are much more difficult to stabilize than the trans forms. By using oxazolidine-based pseudoprolines (ΨPro) substituted by a trifluoromethyl group, we show that the cis peptide bond can be readily switched from 0% to 100% in Xaa-ΨPro dipeptides. Our results prove that changing the configuration of the Cα in Xaa or in ΨPro is sufficient to invert the cis:trans populations while changing the nature of the Xaa side chain finely tuned the conformers ratio...
November 15, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29123677/in-vivo-analysis-of-the-escherichia-coli-ultrastructure-by-small-angle-scattering
#2
Enrico F Semeraro, Juliette M Devos, Lionel Porcar, V Trevor Forsyth, Theyencheri Narayanan
The flagellated Gram-negative bacterium Escherichia coli is one of the most studied microorganisms. Despite extensive studies as a model prokaryotic cell, the ultrastructure of the cell envelope at the nanometre scale has not been fully elucidated. Here, a detailed structural analysis of the bacterium using a combination of small-angle X-ray and neutron scattering (SAXS and SANS, respectively) and ultra-SAXS (USAXS) methods is presented. A multiscale structural model has been derived by incorporating well established concepts in soft-matter science such as a core-shell colloid for the cell body, a multilayer membrane for the cell wall and self-avoiding polymer chains for the flagella...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123501/gonadotropin-releasing-hormone-gnrh-receptor-structure-and-gnrh-binding
#3
REVIEW
Colleen A Flanagan, Ashmeetha Manilall
Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning α-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29117896/discovery-of-a-head-to-tail-cyclic-peptide-as-the-keap1-nrf2-protein-protein-interaction-inhibitor-with-high-cell-potency
#4
Meng-Chen Lu, Qiong Jiao, Tian Liu, Shi-Jie Tan, Hai-Shan Zhou, Qi-Dong You, Zheng-Yu Jiang
Directly disrupting Keap1-Nrf2 protein-protein interaction (PPI) has emerged as a novel way to activate Nrf2. Peptide Keap1-Nrf2 PPI inhibitors have been reported with high Keap1 binding affinity. However, these peptide inhibitors show weak activity in cells. In this study, the head-to-tail cyclic strategy was applied in the development of peptide inhibitors. The privileged residue sequence with minimal acidic residues was used as the template for the cyclic peptide, and the appropriate conjugation method was designed based on the peptide-Keap1 binding mode...
October 19, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29105934/toward-a-novel-drug-to-target-the-egf-egfr-interaction-design-of-metabolically-stable-bicyclic-peptides
#5
Salvador Guardiola, Jesús Seco, Monica Varese, Mireia Díaz-Lobo, Jesus Garcia, Meritxell Teixido, Laura Nevola, Ernest Giralt
In cancer, proliferation of malignant cells is driven by overactivation of growth signaling mechanisms, such as the EGF-EGFR pathway. Despite its therapeutic relevance, this extracellular protein-protein interaction (PPI) has remained elusive to inhibition by synthetic molecules, mostly due to its large size and lack of binding pockets and cavities. Designed peptides, featuring cyclic motifs and other structural constraints, have the potential to modulate such challenging PPIs. Here we present the structure-based design of a series of bicyclic constrained peptides that mimic an interface domain of EGFR and inhibit the EGF-EGFR interaction by targeting the smaller partner (EGF)...
November 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29094944/design-of-mc1r-selective-%C3%AE-msh-analogues-with-canonical-amino-acids-leads-to-potency-and-pigmentation
#6
Yang Zhou, Saghar Mowlazadeh Haghighi, Ioanna Zoi, Jonathon R Sawyer, Victor J Hruby, Minying Cai
Melanoma is a lethal form of skin cancer. Skin pigmentation, which is regulated by the melanocortin 1 receptor (MC1R), is an effective protection against melanoma. However, the endogenous MC1R agonists lack selectivity for the MC1R and thus can have side effects. The use of noncanonical amino acids in previous MC1R ligand development raises safety concerns. Here we report the development of the first potent and selective hMC1R agonist with only canonical amino acids. Using γ-MSH as a template, we developed a peptide, [Leu(3), Leu(7), Phe(8)]-γ-MSH-NH2 (compound 5), which is 16-fold selective for the hMC1R (EC50 = 4...
November 13, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29083864/a-major-step-in-opening-the-black-box-of-high-molecular-weight-dissolved-organic-nitrogen-by-isotopic-labeling-of-synechococcus-and-multibond-two-dimensional-nmr
#7
Xiaoyan Cao, Margaret R Mulholland, John R Helms, Peter W Bernhardt, Pu Duan, Jingdong Mao, Klaus Schmidt-Rohr
Dissolved organic nitrogen (DON) comprises the largest pool of fixed N in the surface ocean, yet its composition has remained poorly constrained. Knowledge of the chemical composition of this nitrogen pool is crucial for understanding its biogeochemical function and reactivity in the environment. Previous work has suggested that high-molecular-weight (high-MW) DON exists only in two closely related forms, the secondary amides of peptides and of N-acetylated hexose sugars. Here, we demonstrate that the chemical structures of high-MW DON may be much more diverse than previously thought...
October 30, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29081052/peptides-as-bio-inspired-molecular-electronic-materials
#8
John Horsley, Jingxian Yu, Yuan Qi Yeoh, Andrew Abell
Understanding the electronic properties of single peptides is not only of fundamental importance to biology, but it is also pivotal to the realization of bio-inspired molecular electronic materials. Natural proteins have evolved to promote electron transfer in many crucial biological processes. However, their complex conformational nature inhibits a thorough investigation, so in order to study electron transfer in proteins, simple peptide models containing redox active moieties present as ideal candidates. Here we highlight the importance of secondary structure characteristic to proteins/peptides, and its relevance to electron transfer...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29036827/validation-by-magnetic-resonance-imaging-of-the-diagnostic-potential-of-a-heptapeptide-functionalized-imaging-probe-targeted-to-amyloid-%C3%AE-and-able-to-cross-the-blood-brain-barrier
#9
Séverine André, Emilie Ansciaux, Elamine Saidi, Lionel Larbanoix, Dimitri Stanicki, Denis Nonclercq, Luce Vander Elst, Sophie Laurent, Robert N Muller, Carmen Burtea
The diagnosis of Alzheimer's disease (AD) is a critical step in the management of patients. We have developed a non-invasive diagnosis tool based on magnetic resonance molecular imaging (MRMI) of amyloid-β peptide using ultra-small particles of iron oxide (USPIO) functionalized with a disulfide constrained cyclic heptapeptide (PHO) identified by phage display (USPIO-PHO). After previously demonstrating the optimal pharmacologic properties of USPIO-PHO and its capacity to cross the blood-brain barrier (BBB), the ability of USPIO-PHO to target amyloid plaques (AP) by MRMI has been validated in the present work on AD transgenic mice...
October 12, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28993277/structure-folding-and-stability-of-a-minimal-homologue-from-anemonia-sulcata-of-the-sea-anemone-potassium-channel-blocker-shk
#10
Bankala Krishnarjuna, Christopher A MacRaild, Punnepalli Sunanda, Rodrigo A V Morales, Steve Peigneur, Jason Macrander, Heidi H Yu, Marymegan Daly, Srinivasarao Raghothama, Vikas Dhawan, Satendra Chauhan, Jan Tytgat, Michael W Pennington, Raymond S Norton
Peptide toxins elaborated by sea anemones target various ion-channel sub-types. Recent transcriptomic studies of sea anemones have identified several novel candidate peptides, some of which have cysteine frameworks identical to those of previously reported sequences. One such peptide is AsK132958, which was identified in a transcriptomic study of Anemonia sulcata and has a cysteine framework similar to that of ShK from Stichodactyla helianthus, but is six amino acid residues shorter. We have determined the solution structure of this novel peptide using NMR spectroscopy...
October 6, 2017: Peptides
https://www.readbyqxmd.com/read/28979940/concentration-driven-assembly-and-sol-gel-transition-of-%C3%AF-conjugated-oligopeptides
#11
Yuecheng Zhou, Bo Li, Songsong Li, Herdeline Ann M Ardoña, William L Wilson, John D Tovar, Charles M Schroeder
Advances in supramolecular assembly have enabled the design and synthesis of functional materials with well-defined structures across multiple length scales. Biopolymer-synthetic hybrid materials can assemble into supramolecular structures with a broad range of structural and functional diversity through precisely controlled noncovalent interactions between subunits. Despite recent progress, there is a need to understand the mechanisms underlying the assembly of biohybrid/synthetic molecular building blocks, which ultimately control the emergent properties of hierarchical assemblies...
September 27, 2017: ACS Central Science
https://www.readbyqxmd.com/read/28973862/de-novo-design-of-covalently-constrained-mesosize-protein-scaffolds-with-unique-tertiary-structures
#12
Bobo Dang, Haifan Wu, Vikram Khipple Mulligan, Marco Mravic, Yibing Wu, Thomas Lemmin, Alexander Ford, Daniel-Adriano Silva, David Baker, William F DeGrado
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature...
October 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28972753/click-chemistry-mediated-synthesis-of-selective-melanocortin-receptor-4-agonists
#13
Daniel Palmer, Juliana P L Gonçalves, Louise V Hansen, Boqian Wu, Helle Hald, Sanne Schoffelen, Frederik Diness, Sebastian T Le Quement, Thomas E Nielsen, Morten Meldal
The melanocortin receptor 4 (MC4R) subtype of the melanocortin receptor family is a target for therapeutics to ameliorate metabolic dysfunction. Endogenous MC4R agonists possess a critical pharmacophore (HFRW), and cyclization of peptide agonists often enhances potency. Thus, 17 cyclized peptides were synthesized by solid phase click chemistry to develop novel, potent, selective MC4R agonists. Using cAMP measurements and a transcriptional reporter assay, we observed that several constrained agonists generated by a cycloaddition reaction displayed high selectivity (223- to 467-fold) toward MC4R over MC3R and MC5R receptor subtypes without compromising agonist potency...
October 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28970902/double-quick-double-click-reversible-peptide-stapling
#14
Claire M Grison, George M Burslem, Jennifer A Miles, Ludwig K A Pilsl, David J Yeo, Zeynab Imani, Stuart L Warriner, Michael E Webb, Andrew J Wilson
The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28969573/efficient-one-pot-access-to-trisubstituted-2-benzazepin-3-ones-as-constrained-pseudopeptide-analogues-and-privileged-scaffolds
#15
Olivier Van der Poorten, Mouhamad Jida, Dirk Tourwé, Steven Ballet
BACKGROUND: Benzazepines received great attention in the field of medicinal chemistry since this scaffold has been recognized to belong to the important family of privileged templates. More specifically, the 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) is used as a core structure in a variety of constrained therapeutic peptide (turn) mimetics. Most of the synthetic approaches towards this template have focused on cyclizations which form the central 7-membered azepine ring. OBJECTIVE: Previous investigations in our group allowed an expansion of the substitution patterns in the 4-amino-benzazepin-3-one scaffold by introduction of methyl substituents at positions 4 and 5 of the azepinone ring system, but also to 1-aryl substituted compounds...
October 2, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28948715/-r-x-r-4-motif-peptides-containing-conformationally-constrained-cyclohexane-derived-spacers-effect-on-cellular-uptake
#16
Govind S Bhosle, Moneesha Fernandes
Arginine-rich peptides having the (R-X-R)n motif are among the most effective cell-penetrating peptides (CPPs). Herein we report a several-fold increase in the efficacy of such CPPs if the linear flexible spacer (-X-) in the (R-X-R) motif is replaced by constrained cyclic 1,4-substituted-cyclohexane-derived spacers. Internalization of these oligomers in mammalian cell lines was found to be an energy-dependent process. Incorporation of these constrained, non-proteinogenic amino acid spacers in the CPPs is shown to enhance their proteolytic stability...
September 26, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28917447/cell-penetrating-peptides-to-dissect-host-pathogen-protein-protein-interactions-in-theileria-transformed-leukocytes
#17
REVIEW
Malak Haidar, Perle Latré de Laté, Eileen J Kennedy, Gordon Langsley
One powerful application of cell penetrating peptides is the delivery into cells of molecules that function as specific competitors or inhibitors of protein-protein interactions. Ablating defined protein-protein interactions is a refined way to explore their contribution to a particular cellular phenotype in a given disease context. Cell-penetrating peptides can be synthetically constrained through various chemical modifications that stabilize a given structural fold with the potential to improve competitive binding to specific targets...
September 7, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28911855/conformationally-constrained-peptides-target-the-allosteric-kinase-dimer-interface-and-inhibit-egfr-activation
#18
Melody D Fulton, Laura E Hanold, Zheng Ruan, Sneha Patel, Aaron M Beedle, Natarajan Kannan, Eileen J Kennedy
Although EGFR is a highly sought-after drug target, inhibitor resistance remains a challenge. As an alternative strategy for kinase inhibition, we sought to explore whether allosteric activation mechanisms could effectively be disrupted. The kinase domain of EGFR forms an atypical asymmetric dimer via head-to-tail interactions and serves as a requisite for kinase activation. The kinase dimer interface is primarily formed by the H-helix derived from one kinase monomer and the small lobe of the second monomer...
September 5, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28885004/gold-catalyzed-solid-phase-synthesis-of-3-4-dihydropyrazin-2-1h-ones-relevant-pharmacophores-and-peptide-backbone-constraints
#19
Adam Přibylka, Viktor Krchňák
Here, we report the efficient solid-phase synthesis of N-propargyl peptides using Fmoc-amino acids and propargyl alcohol as key building blocks. Gold-catalyzed nucleophilic addition to the triple bond induced C-N bond formation, which triggered intramolecular cyclization, yielding 1,3,4-trisubstituted-5-methyl-3,4-dihydropyrazin-2(1H)-ones. Conformations of acyclic and constrained peptides were compared using a two-step conformer distribution analysis at the molecular mechanics level and density functional theory...
September 12, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28882503/synthesis-and-%C3%AE-sheet-propensity-of-constrained-n-amino-peptides
#20
Matthew P Sarnowski, Kyle P Pedretty, Nicole Giddings, H Lee Woodcock, Juan R Del Valle
The stabilization of β-sheet secondary structure through peptide backbone modification represents an attractive approach to protein mimicry. Here, we present strategies toward stable β-hairpin folds based on peptide strand N-amination. Novel pyrazolidinone and tetrahydropyridazinone dipeptide constraints were introduced via on-resin Mitsunobu cyclization between α-hydrazino acid residues and a serine or homoserine side chain. Acyclic and cyclic N-amino peptide building blocks were then evaluated for their effect on β-hairpin stability in water using a GB1-derived model system...
August 31, 2017: Bioorganic & Medicinal Chemistry
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