Development and use of an atomistic CHARMM‐based forcefield for peptoid simulation

Peptoids are positional isomers of peptides: peptoid sidechains are attached to backbone nitrogens rather than α‐carbons. Peptoids constitute a class of sequence‐specific polymers resistant to biological degradation and potentially as diverse, structurally and functionally, as proteins. While molecular simulation of proteins is commonplace, relatively few tools are available for peptoid simulation. Here, we present a first‐generation atomistic forcefield for peptoids. Our forcefield is based on the peptide forcefield CHARMM22, with key parameters tuned to match both experimental data and quantum mechanical calculations for two model peptoids (dimethylacetamide and a sarcosine dipeptoid). We used this forcefield to demonstrate that solvation of a dipeptoid substantially modifies the conformations it can access. We also simulated a crystal structure of a peptoid homotrimer, H‐(N‐2‐phenylethyl glycine)₃‐OH, and we show that experimentally observed structural and dynamical features of the crystal are accurately described by our forcefield. The forcefield presented here provides a starting point for future development of peptoid‐specific simulation methods within CHARMM. © 2013 Wiley Periodicals, Inc.     

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

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peptoids’ based on aromatic building blocks, in which the N-alkylaminoacetyl group of the peptoid backbone has been replaced by an N-alkylaminomethylbenzoyl spacer.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 poly-amide oligomers with potential application in a variety of biological contexts.     

Stable helical peptoids via covalent side chain to side chain cyclization

Peptoids are oligomeric N-substituted glycines with potential as biologically relevant compounds. Helical peptoids provide an attractive fold for the generation of protein-protein interaction inhibitors. The generation of helical peptoid folds in organic and aqueous media has been limited to strict design rules, as peptoid-folding is mainly directed via the steric direction of alpha-chiral side-chains. Here a new methodology is presented to induce helical folds in peptoids with the aid of side chain to side chain cyclization. Cyclic peptoids were generated via solid-phase synthesis and their folding was studied. The cyclization induces significant helicity in peptoids in organic media, aids the folding in aqueous media, and requires the incorporation of only relatively few chiral aromatic side chains.     

Tuning peptoid secondary structure with pentafluoroaromatic functionality: a new design paradigm for the construction of discretely folded peptoid structures

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.     

A CGenFF-based force field for simulations of peptoids with both cis and trans peptide bonds

Peptoids, or poly-n-substituted glycines, are peptide-like polymers composed of a flexible backbone decorated with diverse chemical side chains. Peptoids can form a variety of self-assembling structures based on the type and sequence of the side chains attached to their backbones. All-atom molecular dynamics simulations have been useful in predicting the conformational structures of proteins and will be valuable tools for identifying combinations of peptoid side chains that may form interesting folded structures. However, peptoid models must address a major degree of freedom not common in proteins – the cis/trans isomerization of the peptide bond. This work presents CHARMM general force field (CGenFF) parameters developed to accurately represent peptoid conformational behavior, with an emphasis on a correct representation of both the cis and trans isomers of the peptoid backbone. These parameters are validated against experimental and quantum mechanics data and used to simulate three peptoid side chains in explicitly solvated systems. © 2019 Wiley Periodicals, Inc.     

Facile method for the synthesis of triazole- and tetrazole-containing peptoids on a solid support

The late-stage functionalization of a biomimetic foldamer such as a peptoid is a useful tool to achieve structural diversity. Herein, a facile method for the synthesis of triazole- or tetrazole-containing peptoids using post-synthetic modifications has been reported. On a resin-bound peptoid with a chloroalkyl side chain(s), substitution with nucleophiles (azide or cyanide) and the subsequent [3?+?2]-cycloaddition reaction were optimized. Peptoids with azide, triazole, and tetrazole functional groups could be readily synthesized and could potentially be utilized further for orthogonal bioconjugation or metal recognition.     

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C–H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

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Optical and antibacterial activity of biogenic core-shell ZnO@TiO2 nanoparticles

Inorganic nanocomposites, due to increased stability and safety, are gaining importance in wide range of engineering and medical applications. In view of this, the present study demonstrates the optical and antibacterial activity of core-shell ZnO@TiO₂ nanoparticles synthesized via biogenic method using Azadirachta indica flower extract. The synthesized nanocomposite is characterized by XRD, TEM and EDS. The optical activity of the ZnO@TiO₂ nanoparticle, assessed by photoluminescence spectra, indicated concentration dependent increase in the number of defects. The antibacterial activity of synthesized core-shell ZnO@TiO₂ nanoparticles was determined by agar disc diffusion method against 9 clinical isolates (Gram positive - S. aureus, S. pneumonia, B. subtilis and Gram negative - E. coli, S. dysenteriae, K. pneumonia, V. cholera, P. aeruginosa, and P. vulgaris). The synthesized nanoparticle exhibited significant antibacterial activity against all the strains tested. The synthesized core-shell ZnO@TiO₂ nanoparticle can be a potential antimicrobial candidate for various biomedical applications.     

Cyclization of peptoids by formation of boronate esters

Introduction of conformational constraints into peptoids (N-substituted oligoglycines) will enable new applications in molecular recognition and self-assembly. Peptoids that contain both a phenylboronic acid side chain and a vicinal diol cyclize by intramolecular condensation to form boronate esters. A fluorescent indicator of free boronic acid was used to assay esterification. A galactose moiety 2 to 5 monomer units away from a boronic acid side chain in a peptoid reacts with the boronic acid in competition with the indicator. The intramolecular reaction predominates in each case, with 80-90% of the peptoid cyclized. When the diol is a simple 2,3-dihydroxypropyl group, esterification is less favored but still appreciable.     

Synthesis of biaryl-linked cyclic peptoids

Peptoids, a class of peptidomimetic, have gained considerable attention as potential therapeutic agents due to properties such as biocompatibility and resistance to enzymatic degradation. In linear peptoids, conformational heterogeneity can arise due to cis/trans isomerization around the backbone tertiary amide bond which has led to an increasing interest in cyclic peptoids. Biaryl linkages appear as a common structural motif in many synthetic and naturally occurring cyclic peptides but they are yet to be utilized in the formation of cyclic peptoids. Herein, we describe the application of a solid-phase Suzuki cross-coupling strategy as a means to prepare of a series of biaryl-linked cyclic peptoids. The methodology presented allows access to a range of novel biaryl containing cyclic peptoids with varying ring sizes.     

Microwave solid phase synthesis, characterization, and antimicrobial activities of one mononuclear manganese(II) complex with 4-chlorobenzoic acid 4-[3-(4-chlorophenyl)-3-hydroxyacryloyl]-3-hydroxyphenyl ester

One mononuclear complex has been designed and synthesized by a β-dikertone ligand 4-chlorobenzoic acid 4-[3-(4-chlorophenyl)-3-hydroxyacryloyl]-3-hydroxyphenyl ester (L) with MnCl₂ · 4H₂O in microwave radiation assistance. The complex was characterized by X-ray crystallography, confirming that the central manganese(II) atom was coordinated by four oxygens from two L and two oxygens from two water. The complex was assayed for in vitro antibacterial (B. subtilis, S. aureus, S. faecalis, P. aeruginosa, E. coli, and E. cloacae) activities and showed better antimicrobial activity against Gram positive strains than Gram negative strains.     

Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of α-chiral aromatic N-1-naphthylethyl side chains

Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 ?. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.     

Phenolic glucosides and chromane analogs from the insect fungus Conoideocrella krungchingensis BCC53666

Six new compounds, named conoideoglucosides A − C and conoideochromanes A − C, together with eight known compounds, including eutypinic acid, 2,2-dimethyl-2H-1-chromene-6-carboxylic acid, (−)-luteoskyrin, (−)-4a-oxyluteoskyrin, chrysophanol, islandicin, catenarin, and (22E)-5α,8α-epidioxyergosta-6,22-dien-3β-ol were isolated from the insect fungus Conoideocrella krungchingensis BCC53666. (−)-Luteoskyrin exhibited a broad range of antimicrobial activity such as antimalarial (IC₅₀ 0.51 μg/mL), antitubercular (MIC 6.25 μg/mL), antibacterial (both Gram positive; MIC 0.39–1.56 μg/mL and Gram negative; MIC 3.13–12.50 μg/mL), and antifungal (against various plant pathogens; MIC 3.13–50.00 μg/mL) activities, while (−)-4a-oxyluteoskyrin and catenarin showed weaker antibacterial activity. Moreover, eutypinic acid, (−)-luteoskyrin, (−)-4a-oxyluteoskyrin, and catenarin showed cytotoxicity against NCI-H187 cells with IC₅₀ in a range of 0.16–17.99 μg/mL, while eutypinic acid and catenarin had no cytotoxicity against non-cancerous (Vero) cells at maximum tested concentration (50 μg/mL). The complete NMR spectral data and biological activity of the known (−)-4a-oxyluteoskyrin was also reported for the first time.     

Unique β-Turn Peptoid Structures and Their Application as Asymmetric Catalysts

Peptoids, N-substituted glycine oligomers, represent an important class of peptidomimetics that can fold into three-dimensional structures in solution. Most of the folded peptoid structures, however, resemble helices, and this can limit their applications, specifically in asymmetric catalysis. In this work, for the first time, unique examples of pyrrolidine-based β-turn-like peptoids are described and characterized, both in the solid state, by single-crystal X-ray analysis, and in solution, by circular dichroism spectroscopy. Furthermore, their highly efficient and enantioselective catalytic activity for the production of γ-nitro aldehydes by asymmetric Michael reaction in water was demonstrated. The structural properties and DFT-D3 calculations of the new β-turn-like peptoids, as well as catalytic and spectroscopic studies on designed pyrrolidine-based helical peptoids, suggest that the β-turn structure plays a key role in the stereoselectivity of the catalytic reaction.     

Surface Design for Immobilization of an Antimicrobial Peptide Mimic for Efficient Anti-Biofouling

Microbial surface attachment negatively impacts a wide range of devices from water purification membranes to biomedical implants. Mimics of antimicrobial peptides (AMPs) constituted from poly(N-substituted glycine) „peptoids“ are of great interest as they resist proteolysis and can inhibit a wide spectrum of microbes. We investigate how terminal modification of a peptoid AMP-mimic and its surface immobilization affect antimicrobial activity. We also demonstrate a convenient surface modification strategy for enabling alkyne–azide „click“ coupling on amino-functionalized surfaces. Our results verified that the N- and C-terminal peptoid structures are not required for antimicrobial activity. Moreover, our peptoid immobilization density and choice of PEG tether resulted in a „volumetric“ spatial separation between AMPs that, compared to past studies, enabled the highest AMP surface activity relative to bacterial attachment. Our analysis suggests the importance of spatial flexibility for membrane activity and that AMP separation may be a controlling parameter for optimizing surface anti-biofouling.     

Stabilising Peptoid Helices Using Non‐Chiral Fluoroalkyl Monomers

Stability towards protease degradation combined with modular synthesis has made peptoids of considerable interest in the fields of chemical biology, medicine, and biomaterials. Given their tertiary amide backbone, peptoids lack the capacity to hydrogen‐bond, and as such, controlling secondary structure can be challenging. The incorporation of bulky, charged, or chiral aromatic monomers can be used to control conformation but such building blocks limit applications in many areas. Through NMR and X‐ray analysis we demonstrate that non‐chiral neutral fluoroalkyl monomers can be used to influence the K_cis/trans equilibria of peptoid amide bonds in model systems. The cis‐isomer preference displayed is highly unprecedented given that neither chirality nor charge is used to control the peptoid amide conformation. The application of our fluoroalkyl monomers in the design of a series of linear peptoid oligomers that exhibit stable helical structures is also reported.     

Synthesis,characterization and antimicrobial screening of quinoline based quinazolinone-4-thiazolidinone heterocycles

In an attempt to find new pharmacologically active molecules, we report here the synthesis and in vitro antimicrobial activity of various 2-(2-chloro-6-methyl(3-quinolyl))-3-[2-(4-chlorophenyl)-4-oxo(3-hydroquinazolin-3-yl)]-5-[(aryl)methylene]-1,3-thiazolidin-4-ones. In vitro antimicrobial activity of the title compounds are screened against two Gram positive bacteria (Staphylococcus aureus, Streptococcus pyogenes), two Gram negative bacteria (Escherichia coli, Pseudomonas aeruginosa) and three strains of fungi (Candida albicans, Aspergillus niger, Aspergillus clavatus) using broth micro dilution method. Some derivatives bearing chloro or hydroxy group exhibited very good antimicrobial activity.     

Multifunctional PES fabrics modified with colloidal Ag and TiO2 nanoparticles

This study is aimed to highlight the possibility of engineering the multifunctional textile nanocomposite material based on the polyester (PES) fabric modified with colloidal Ag and TiO₂ nanoparticles (NPs). The effects of concentration of NPs as well as the order of Ag and TiO₂ NPs loading on antimicrobial, UV protective, and photocatalytic properties of PES fabrics were examined. The antimicrobial activity of differently modified PES fabrics was tested against Gram‐negative bacterium Escherichia coli, Gram‐positive bacterium Staphylococcus aureus, and fungus Candida albicans. The concentration of Ag colloid and the order of Ag and TiO₂ NPs loading considerably affected the antimicrobial efficiency of PES fabrics. The fabrics provided maximum UV protection upon surface modification with Ag and TiO₂ NPs. Ag NPs enhanced Ag NPs enhanced the photodegradation activity of TiO₂ NPs and total photodegradation of methylene blue was achieved after 24 hr of UV illumination. Copyright © 2010 John Wiley & Sons, Ltd.     

Atroposelective synthesis of N-aryl peptoid atropisomers via a palladium(ii)-catalyzed asymmetric C–H alkynylation strategy

The introduction of chirality into peptoids is an important strategy to determine a discrete and robust secondary structure. However, the lack of an efficient strategy for the synthesis of structurally diverse chiral peptoids has hampered the studies. Herein, we report the efficient synthesis of a wide variety of N-aryl peptoid atropisomers in good yields with excellent enantioselectivities (up to 99% yield and 99% ee) by palladium-catalyzed asymmetric C–H alkynylation. The inexpensive and commercially available l-pyroglutamic acid was used as an efficient chiral ligand. The exceptional compatibility of the C–H alkynylation with various peptoid oligomers renders this procedure valuable for peptoid modifications. Computational studies suggested that the amino acid ligand distortion controls the enantioselectivity in the Pd/l-pGlu-catalyzed C–H bond activation step.

The introduction of chirality into peptoids is an important strategy to determine a discrete and robust secondary structure.     

Electron Capture Dissociation Studies of the Fragmentation Patterns of Doubly Protonated and Mixed Protonated-Sodiated Peptoids

The fragmentation patterns of a group of doubly protonated ([P + 2H]²⁺) and mixed protonated-sodiated ([P + H + Na]²⁺) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-C_α bonds. The N-terminal fragment ions, the C-ions (protonated) and the C′-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z^?-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z^?′-series of ions in addition to the C′-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H]^?+) and the sodiated peptoids ([P + H + Na]^?+). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.