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Jianhua Ren, Yadwinder S Mann, Yuntao Zhang, Michael D Browne
Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques...
February 21, 2018: Journal of Visualized Experiments: JoVE
Ines Greco, Bernard D Hummel, Jaspreet Vasir, Jeffrey L Watts, Jason Koch, Johannes E Hansen, Hanne Mørck Nielsen, Peter Damborg, Paul R Hansen
Antimicrobial peptides (AMPs) hold promise as the next generation of antimicrobial agents, but often suffer from rapid degradation in vivo. Modifying AMPs with non-proteinogenic residues such as peptoids (oligomers of N -alkylglycines) provides the potential to improve stability. We have identified two novel peptoid-based compounds, B1 and D2 , which are effective against the canine skin pathogen Staphylococcus pseudintermedius , the main cause of antibiotic use in companion animals. We report on their potential to treat infections topically by characterizing their release from formulation and in vitro ADME properties...
March 10, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Satya Prakash Shukla, D Gomika Udugamasooriya
We recently identified a peptide-peptoid hybrid, PPS1, which specifically recognized lipid-phosphatidylserine (PS). PPS1 consists of distinct positively charged and hydrophobic residue-containing regions. PPS1 monomer was inactive, but the dimeric form, PPS1D1, displayed strong cytotoxicity for lung cancer cells compared to normal cells in vitro, and reduced the tumor growth in vivo. The minimum pharmacophore of PPS1D1 showed that the first (methionine) and fourth (N-lysine) residues were not important for PPS1D1 cytotoxic activity...
December 1, 2017: MedChemComm
Alessia Battigelli, Jae Hong Kim, Dilani C Dehigaspitiya, Caroline Proulx, Ellen J Robertson, Daniel J Murray, Behzad Rad, Kent Kirshenbaum, Ronald N Zuckermann
Glycoproteins adhered on the cellular membrane play a pivotal role in a wide range of cellular functions. Their importance is particularly relevant in the recognition process between infectious pathogens (such as viruses, bacteria, toxins) and their host cells. Multivalent interactions at the pathogen-cell interfaces govern binding events and can result in a strong and specific interaction. Here we report an approach to mimic the cell surface presentation of carbohydrate ligands by the multivalent display of sugars on the surface of peptoid nanosheets...
March 7, 2018: ACS Nano
Garrett L Sternhagen, Sudipta Gupta, Yueheng Zhang, Vijay John, Gerald J Schneider, Donghui Zhang
A series of amphiphilic ionic peptoid block copolymers where the total number (1 or 3) and position of ionic monomers along the polymer chain are precisely controlled have been synthesized by the sub-monomer method. Upon dissolution in water at pH = 9, the amphiphilic peptoids self-assemble into small spherical micelles having hydrodynamic radius in ~5 - 10 nm range and critical micellar concentration (CMC) in the 0.034 - 0.094 mg/mL range. Small-angle neutron scattering (SANS) analysis of the micellar solutions revealed unprecedented dependence of the micellar structure on the number and position of ionic monomers along the chain...
March 5, 2018: Journal of the American Chemical Society
Min-Kyung Shin, Yu-Jung Hyun, Ji Hoon Lee, Hyun-Suk Lim
Cyclic peptoids are emerging as an attractive class of peptidomimetics. Compared to their linear counterparts, cyclic peptoids should have increased conformational rigidity and preorganized structures, enabling them to bind more tightly to target proteins without major entropy penalty. Because cyclic peptoids lack the amide protons in their backbones like linear peptoids, it is perceived that cyclic peptoids are seemingly cell permeable as much as linear peptoids. However, no systematic investigation for cell permeability of cyclic peptoids has been reported yet...
February 26, 2018: ACS Combinatorial Science
Yung-Ching Chien, Jinhui Tao, Kuniko Saeki, Alexander F Chin, Jolene L Lau, Chun-Long Chen, Ronald N Zuckermann, Sally J Marshall, Grayson W Marshall, James J De Yoreo
In calcified tissues such as bones and teeth, mineralization is regulated by an extracellular matrix, which includes non-collagenous proteins (NCP). This natural process has been adapted or mimicked to restore tissues following physical damage or demineralization by using polyanionic acids in place of NCPs, but the remineralized tissues fail to fully recover their mechanical properties. Here we show that pre-treatment with certain amphiphilic peptoids, a class of peptide-like polymers consisting of N-substituted glycines that have defined monomer sequences, enhances ordering and mineralization of collagen and induces functional remineralization of dentin lesions in vitro ...
December 11, 2017: ACS Biomaterials Science & Engineering
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
Arushi Prakash, Marcel D Baer, Christopher J Mundy, Jim Pfaendtner
Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling...
February 14, 2018: Biomacromolecules
Chandra Mohan Darapaneni, Prathap Jeya Kaniraj, Galia Maayan
Peptoids - oligomers of N-substituted glycine - are an important class of peptide mimics that are widely used in areas ranging from biology and medicine to metal binding and catalysis. The utility of peptoids, however, especially for applications in aqueous solutions, is often hampered by the hydrophobic nature of their sequences dictated by structural and functional requirements. Herein we describe a simple method to solubilize hydrophobic peptoids in water without modifying their original sequences, via the insertion of biocompatible and low cost piperazine or homopiperazine groups at the N- or C-terminus of the peptoid backbone...
February 7, 2018: Organic & Biomolecular Chemistry
Sherri C Young
Alzheimer's disease (AD) is an incurable form of dementia affecting millions of people worldwide and costing billions of dollars in health care-related payments, making the discovery of a cure a top health, societal, and economic priority. Peptide-based drugs and immunotherapies targeting AD-associated beta-amyloid (Aβ) aggregation have been extensively explored; however, their therapeutic potential is limited by unfavorable pharmacokinetic (PK) properties. Peptoids (N-substituted glycine oligomers) are a promising class of peptidomimetics with highly tunable secondary structures and enhanced stabilities and membrane permeabilities...
January 31, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Alexandra M Webster, Steven Lorimer Cobb
Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo...
January 22, 2018: Chemistry: a European Journal
Haibao Jin, Yan-Huai Ding, Mingming Wang, Yang Song, Zhihao Liao, Christina J Newcomb, Xuepeng Wu, Xian-Qiong Tang, Zheng Li, Yuehe Lin, Feng Yan, Tengyue Jian, Peng Mu, Chun-Long Chen
Despite recent advances in the assembly of organic nanotubes, conferral of sequence-defined engineering and dynamic response characteristics to the tubules remains a challenge. Here we report a new family of highly designable and dynamic nanotubes assembled from sequence-defined peptoids through a unique "rolling-up and closure of nanosheet" mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers crystallize to form well-defined nanosheets before folding to form single-walled nanotubes...
January 18, 2018: Nature Communications
Assunta D'Amato, Giovanni Pierri, Chiara Costabile, Giorgio Della Sala, Consiglia Tedesco, Irene Izzo, Francesco De Riccardis
Chiral induction was utilized for the synthesis of diastereopure cyclic peptoids containing an N-benzyl alanine residue. Molecular modeling, NMR spectroscopy, single-crystal X-ray diffraction studies, and HPLC with chiral stationary phase demonstrated easy formation of free and sodium/benzylammonium complexed cyclic oligomers through strategic incorporation of a single stereogenic center in the oligomeric backbone. The synthesis of cyclic peptoids with defined conformational chirality and appropriate side chain topology is now possible...
January 17, 2018: Organic Letters
Nam Tran Hoang, Thomas Kodadek
One-bead-one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are comprised of oligoamides, particularly peptides, peptoids and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Towards this end, we report here the efficient proline-catalyzed asymmetric Mannich reaction between immobilized aldehydes and soluble ketones and anilines. The reaction conditions do not compromise the amplification of DNA by the PCR...
January 9, 2018: ACS Combinatorial Science
Jiyoun Lee, Dahyun Kang, Jieun Choi, Wei Huang, Mayken Wadman, Annelise E Barron, Jiwon Seo
Peptoids are peptidomimetic polymers that are resistant to proteolysis and less prone to immune responses; thus, they can provide a practical alternative to peptides. Among the various therapeutic applications that have been explored, cationic amphipathic peptoids have demonstrated broad-spectrum antibacterial activity, including activity towards drug-resistant bacterial strains. While their potency and activity spectrum can be manipulated by sequence variations, bacterial selectivity and systemic toxicity need to be improved for further clinical development...
January 15, 2018: Bioorganic & Medicinal Chemistry Letters
Nathaniel P Chongsiriwatana, Jennifer S Lin, Rinki Kapoor, Modi Wetzler, Jennifer A C Rea, Maruti K Didwania, Christopher H Contag, Annelise E Barron
Many organisms rely on antimicrobial peptides (AMPs) as a first line of defense against pathogens. In general, most AMPs are thought to kill bacteria by binding to and disrupting cell membranes. However, certain AMPs instead appear to inhibit biomacromolecule synthesis, while causing less membrane damage. Despite an unclear understanding of mechanism(s), there is considerable interest in mimicking AMPs with stable, synthetic molecules. Antimicrobial N-substituted glycine (peptoid) oligomers ("ampetoids") are structural, functional and mechanistic analogs of helical, cationic AMPs, which offer broad-spectrum antibacterial activity and better therapeutic potential than peptides...
December 1, 2017: Scientific Reports
A D'Amato, R Schettini, G Della Sala, C Costabile, C Tedesco, I Izzo, F De Riccardis
Most of the structural studies made on the secondary structure of peptoids describe their geometric attributes in terms of the classic Ramachandran plot (based on the local analysis of ω, ψ, χ, φ dihedral angles). However, little intuitive understanding is available from internal coordinates when stereochemistry is involved. In this contribution we list all the conformationally stable cyclic peptoids reported up to the year 2017 and propose a simple method to define their geometric arrangement in terms of planar chirality...
November 29, 2017: Organic & Biomolecular Chemistry
Justin D Northrup, Giulia Mancini, Claire R Purcell, Christian E Schafmeister
Creating functional macromolecules that possess the diversity and functionality of proteins poses an enormous challenge, as this requires large, preorganized macromolecules to facilitate interactions. Peptoids have been shown to interact with proteins, and combinatorial libraries of peptoids have been useful in discovering new ligands for protein binding. We have created spiroligomer-peptoid hybrids that have a spirocyclic core that preorganizes functional groups in three-dimensional space. By utilizing spiroligomers, we can reduce the number of rotatable bonds between functional groups while increasing the stereochemical diversity of the molecules...
December 15, 2017: Journal of Organic Chemistry
Woojin Yang, Boyeong Kang, Vincent A Voelz, Jiwon Seo
Nature utilizes optimally organized pigments in light-harvesting complexes. To mimic the natural photosynthetic proteins, effective control over inter-pigment interactions is necessary to attain the desired photophysical properties. Previously, we developed porphyrin-peptoid conjugates (PPCamide) and displayed two porphyrins at defined positions on an α-helical peptoid using a flexible n-butyl linker. Herein, we synthesized new porphyrin-peptoid conjugates (PPCC-C), where porphyrins are conjugated through a rigid C-C linkage to the helical peptoid via the Suzuki-Miyaura cross-coupling reaction...
November 22, 2017: Organic & Biomolecular Chemistry
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