Search

The reduction of methionine sulfoxide with ammonium iodide in trifluoroacetic acid has been studied in peptides containing cysteine, histidine, tyrosine or tryptophan residues. While histidine and tyrosine have proved to be stable under the experimental conditions, cysteine is oxidized to cystine and tryptophan dimerizes to form 2-indolylindolenine derivatives. The use of methyl sulfide to increase the reduction rate minimizes the problem and protection of indole ring with the formyl group avoids the side reaction for this amino acid.

N,N′-disuccinimidyl carbonate (DSC) has been successfully used to generate carbonates and carbamates on conventional hydroxymethyl and aminomethyl based resins. This methodology extends the applicability of such linkers, which were initially designed for the anchoring of carboxylic acids. Thus, amino and hydroxy groups have been attached onto classical resins to give straightforward access to the solid-phase synthesis of alcohols, carbamates, and cyclic peptides with an evident pharmaceutical interest.

Spontaneous oxidation of a short palindromic peptide with the sequence Ac-C-X-K-L-H-A-E-L-S-S-L-E-A-H-L-K-B-C-G-NH2 (X = Aib) provides up to three different cyclic products: a monomer with an intrachain disulfide bond, an antiparallel dimer, and a trimer with two parallel and an antiparallel chain. Control over the relative amount of the different products can be achieved by adding different amounts of TFE that modulate the population of the α-helix conformation during the reaction. Regioselective disulfide formation affords also the parallel dimer, which was not formed spontaneously, as well as the three possible noncyclic dimers with two protected cysteines and a single disulfide bond. CD spectroscopic studies of these dimers as well as NMR and CD studies of a peptide with the two cysteines replaced by Leu provide the basis for understanding the control of the spontaneous oxidation by TFE and the strong discrimination between parallel and antiparallel dimers. The special topological properties of this ...

The use of Alloc group in SPPS for the Nα protection of amino acids is an alternative to the Boc and Fmoc protecting groups. The smooth removal of Alloc group in neutral conditions with catalytic amounts of Pd(PPh3)4 in the presence of PhSiH3 as a scavenger for the allyl system permits orthogonality with the most common protecting groups. Furthermore, a tandem deprotection-coupling reaction allows the suppression of DKP formation in cases where this side reaction is troublesome.

A peptide fragment corresponding to the third helix of Staphylococcus Aureus protein A, domain B, was chosen to study the effect of the main‒chain direction upon secondary structure formation and stability, applying the retro‒enantio concept. For this purpose, two peptides consisting of the native (Ln) and reversed (Lr) sequences were synthesized and their conformational preferences analysed by CD and NMR spectroscopy. A combination of CD and NMR data, such as molar ellipcitity, NOE connectivities, Hα and NH chemical shifts, 3JαN coupling constants and amide temperature coefficients indicated the presence of nascent helices for both Ln and Lr in water, stabilized upon addition of the fluorinated solvents TFE and HFIP. Helix formation and stabilization appeared to be very similar in both normal and retro peptides, despite the unfavourable charge–macrodipole interactions and bad N-capping in the retro peptide. Thus, these helix stabilization factors are not a secondary structure as determined for this specific peptide. In general, the synthesis and confirmational analysis of peptide pairs with opposite main‒chain directions, normal and retro peptides, could be useful in the determination of secondary structure stabilization factors dependent on the direction. © 1997 European Peptide Society and John Wiley & Sons, Ltd.

A cyclic disulfide peptide corresponding to the G-H loop sequence 134–155 [replacement Tyr136 and Arg153 with Cys]of the capsid protein VP1 of foot-and-mouth disease virus (FMDV) isolate C-S8c1 was examined by proton 2D-NMR spectroscopy in water and in 25% HFIP/water. In water, NMR data supported the presence of a non-canonical turn in the central, conserved cell adhesion RGD motif and suggested the presence of a nascent helix in the C-terminal part, stabilized and slightly extended upon addition of 25% HFIP, a secondary structure stabilizing cosolvent. The formation of the C-terminal helix was evidenced by combined analysis of NOE connectivities, Hα chemical shifts, 3 J NH-Hα coupling constants and amide temperature coefficients. Surprisingly, these global structural features of the cyclic peptide in solution show similarities to previous X-ray structure analysis of (a) a shortened linear peptide complexed with a antivirus antibody and (b) the G-H loop represented on the chemical reduced viral surface of a different serotype. Thus, even in entirely different biological environments the cyclic peptide reflect similar structural features, reinforcing the concept that this viral loop behaves as an independent structural and functional unit.

The use of N-Fmoc-N-(Hmb)amino acids for the introduction of the Hmb backbone protection into peptides during solid-phase synthesis is described. An efficient two step synthesis of these derivatives is reported and their coupling to the peptide chain is studied.

The use of nucleophiles for the cleavage of an o-nitrobenzylester peptide-resin bond in order to afford peptide alkylesters and alkylamides has been studied. With this purpose, three short peptide sequences anchored to a Nbb-resin were used as models. Peptides were cleaved from the polymeric supports by reaction with primary and secondary amines and by a transesterification process with yields that depended on the nucleophile and the C-terminal amino acid of the sequence. This methodology was applied to the synthesis of leuprolide, an ethylamide peptide of relevant pharmacological interest, which was obtained in a 70% overall yield.

N , N ′-Disuccinimidyl carbonate (DSC) has been successfully used for the efficient conversion of 4-hydroxymethylpolystyrene and 4-hydroxymethyl-3-nitrobenzamido (Nbb) resins into active carbonate resins, which are suitable for the incorporation of molecules via a hydroxyl function. This methodology has been applied to the preparation of the growth hormone inhibitor, Sandostatin.

A new synthesis of 9-hydroxy- and 9-(alkylamino)thiazolo[5,4-b]quinolines by cyclization of 4-(ethoxycarbonyl)-5-(arylamino)thiazoles and 5-(arylamino)-4-carbamoylthiazoles, respectively, is described. In vitro cytotoxicity of a large number of derivatives of these compounds has been tested against several cell lines. The highest activities observed are associated with the presence of a 2-[[(N,N-diethylamino)ethyl]amino] substituent at C-2 and a fluorine atom at the C-7 position of the tricyclic planar heteroaromatic framework. Three structural features seem to be essential for antitumor activities: a positive charge density at carbon C-7, a side chain at position C-2 or C-9 of the thiazoloquinoline skeleton with two basic nitrogens and a pKa value of 7.5−10 in the most basic center, and a conformational flexibility of this basic side chain. These structural requirements must be simultaneously satisfied in order to ensure a significant antitumor activity.

Practical syntheses of protected derivatives of the non-proteinogenic allo-threonines are decribed. The key step is enzymatic resolution of threonine diastereomers, produced on controlled epimerization of the α-carbon atom. The protected allo-threonines are obtained in good overall yield and can be used in standard peptide synthesis protocols.

With a few exceptions, proteins in our biosphereare based exclusively on l-amino acids. The inversionof configuration of all the stereogenic centers in aprotein leads to an all- d compound with ‘mirrorimage’ properties and ‘mirror’ image structure. Wepropose to use the term protein-enantiomerism to describe the relationship betweentwo proteins that have the same sequence but whoseamino acids have opposite configuration. We will usethe term protein-diastereomerism todefine the relationship between two proteins that havethe same sequence in which some amino acids haveopposite configurations. A classification of type I,II, III, and IV protein-diastereomerism isproposed. By extension, a diastereoprotein is aprotein where some amino acids have the sameconfiguration (l or d) while others have the oppositeone (d or l). A particular case of diastereoproteinsare mesoproteins, also analyzed in thisarticle. In addition to the goal of making proteinsresistant to protease degradation, the use of d-amino acids in protein de novo design may give riseto proteins with structures, and perhaps properties,very different to those of native all-L-proteins.

New total syntheses of didemnin A and of dehydrodidemnin B are described. The latter didemnin has the highest antiproliferative activity of all members of this family of macrocyclic depsipeptides. It was produced on coupling the side chain Pyr-Pro-OH to didemnin A, which was itself synthesized by two novel routes. One of these was based on the elaboration of a linear heptadepsipeptide incorporating the first amino acid of the didemnin side chain, (R)-N(Me)-Leu. Deprotection of the amino and carboxyl terminii of this linear precursor followed by macrocyclization gave a protected derivative of didemnin A. The second route involved synthesis of the Boc-protected didemnin macrocycle from a linear hexadepsipeptide lacking (R)-N(Me)-Leu. Removal of the Boc group from the macrocycle followed by its coupling with Boc-(R)-N(Me)-Leu-OH then gave Boc-didemnin A. The overall yield was much higher for the second strategy (27% compared to 4% for the first synthesis), but both allowed synthetic didemnin A, identical with a natural sample, to be prepared. Extensive use was made of phosphonium and uronium salt-based coupling reagents, such as BOP, PyBrOP, PyAOP, HBTU, and HATU for the formation of both the secondary and tertiary amide bonds present in these complex depsipeptides.

One of the hallmarks of Alzheimer's disease is the self-aggregation of the amyloid beta peptide (Abeta) in extracellular amyloid fibrils. Among the different forms of Abeta, the 42-residue fragment (Abeta1-42) readily self-associates and forms nucleation centers from where fibrils can quickly grow. The strong tendency of Abeta1-42 to aggregate is one of the reasons for the scarcity of data on its fibril formation process. We have used atomic force microscopy (AFM) to visualize in liquid environment the fibrillogenesis of synthetic Abeta1-42 on hydrophilic and hydrophobic surfaces. The results presented provide nanometric resolution of the main structures characteristic of the several steps from monomeric Abeta1-42 to mature fibrils in vitro. Oligomeric globular aggregates of Abeta1-42 precede the appearance of protofibrils, the first fibrillar species, although we have not obtained direct evidence of oligomer-protofibril interconversion. The protofibril dimensions deduced from our AFM images are consistent with a model that postulates the stacking of the peptide in a hairpin conformation perpendicular to the long axis of the protofibril, forming single beta-sheets ribbon-shaped. The most abundant form of Abeta1-42 fibril exhibits a nodular structure with a ~100-nm periodicity. This length is very similar 1) to the length of protofibril bundles that are the dominant feature at earlier stages in the aggregation process, 2) to the period of helical structures that have been observed in the core of fibrils, and 3) to the distance between regularly spaced, structurally weak fibril points. Taken together, these data are consistent with the existence of a ~100-nm long basic protofibril unit that is a key fibril building block.

Reelin is an extracellular matrix protein that is crucial for neural development and adult brain plasticity. While the Reelin signalling cascade has been reported to be associated with Alzheimer's disease (AD), the role of Reelin in this pathology is not understood. Here we use an in vitro approach to show that Reelin interacts with amyloid-β (Aβ42) soluble species, delays Aβ42 fibril formation and is recruited into amyloid fibrils. Furthermore, Reelin protects against both the neuronal death and dendritic spine loss induced by Aβ42 oligomers. In mice carrying the APP(Swe/Ind) mutation (J20 mice), Reelin overexpression delays amyloid plaque formation and rescues the recognition memory deficits. Our results indicate that by interacting with Aβ42 soluble species, delaying Aβ plaque formation, protecting against neuronal death and dendritic spine loss and preventing AD cognitive deficits, the Reelin pathway deserves consideration as a therapeutic target for the treatment of AD pathogenesis.

A screening of the natural product chlorogenic acid, isolated from the Brazilian medicinal plant Hypericum brasiliense, caffeic acid, cinnamic acid, and p-methoxycinnamic acid, and derivatives of caffeoylquinic, caffeoyl, and cinnamoyl against the enzymes prolyl oligopeptidase and dipeptidyl peptidase IV was carried out. Caffeoylquinic, caffeoyl, and cinnamoyl derivatives were prepared using simple derivatization procedures and through coupling reactions with the amino acid proline. The dipeptidyl peptidase IV assay showed inhibitory activity of the tested compounds at a high concentration (500 µM) in the range of 81.5–7.2 %. In contrast, the derivatives methyl ester and 1,7-acetonide obtained from chlorogenic acid, and caffeic acid and its methyl ester derivative showed selectivity and activity as prolyl oligopeptidase inhibitors, with IC50 values of 3 to 14 mM.

Knowledge of the mechanisms of interaction between self-aggregating peptides and nucleic acids or other polyanions is key to the understanding of many aggregation processes underlying several human diseases (e.g. Alzheimer's and Parkinson's diseases). Determining the affinity and kinetic steps of such interactions is challenging due to the competition between hydrophobic self-aggregating forces and electrostatic binding forces. Kahalalide F (KF) is an anticancer hydrophobic peptide which contains a single positive charge that confers strong aggregative properties with polyanions. This makes KF an ideal model to elucidate the mechanisms by which self-aggregation competes with binding to a strongly charged polyelectrolyte such as DNA. We use optical tweezers to apply mechanical forces to single DNA molecules and show that KF and DNA interact in a two-step kinetic process promoted by the electrostatic binding of DNA to the aggregate surface followed by the stabilization of the complex due to hydrophobic interactions. From the measured pulling curves we determine the spectrum of binding affinities, kinetic barriers and lengths of DNA segments sequestered within the KF-DNA complex. We find there is a capture distance beyond which the complex collapses into compact aggregates stabilized by strong hydrophobic forces, and discuss how the bending rigidity of the nucleic acid affects such process. We hypothesize that within an in vivo context, the enhanced electrostatic interaction of KF due to its aggregation might mediate the binding to other polyanions. The proposed methodology should be useful to quantitatively characterize other compounds or proteins in which the formation of aggregates is relevant., Comment: 34 pages, 8 figures, Supplementary Information

Less than 2% of all potential neurotherapeutics cross the blood-brain barrier (BBB). Here, we sought to build a construct with the capacity to cross this barrier, to behave as a chemical delivery system, and, once inside the central nervous system, to be transformed and then act as an enzyme inhibitor. With all this in mind, here, we describe the entire process to obtain such a compound, from the initial candidate selection to preparation of the compound library and posterior evaluation and final selection of the most promising candidates in terms of selectivity, serum stability, and BBB-transport.

The {Trp-phenylglycinol} pseudodipeptide (αR,3R∗,4R∗)-N-(2-acetoxy-1-phenylethyl)-3-amino-4-indolyl-2-piperidone 33 has been synthezised by condensation of the 3-amino-substituted anhydride 30 with (R)-(-)-phenylglycinol followed by reduction of the resulting imide.

The conformational preferences of several 4,5-bis(alkylcarbamoyl)-1,3-dioxolanes in R,R configuration were examined by FT-IR, 1H-NMR, 13C-NMR and computational methodologies. On the other hand, both the coupling of the 13C satellite signals of dioxolane methine protons observed in 1H-NMR spectra and the 3JCH coupling constants in the C-O-C-H segments observed in 13C-NMR were consistent with the two low energy conformations derived from quantum mechanical calculations. These preferred conformations were envelope forms predicted to be ≈ 3.5 – 4 kcal/mol more stable than the twist forms.

Solid-phase synthesis of cyclic head-to-tail peptides using Boc-based protection schemes and side chain anchoring via the β-carboxyl of Asp can lead to substantial levels of epimerization at the α-carbon of Asp. These problems arise largely from the chemistry used for the incorporation of Boc-Asp(OH)-OFm to the polymer. Several conditions for the attachment of this β-carboxyl to hydroxymethyl or bromomethyl resins have been evaluated, in an attempt to achieve effective, epimerization-free anchorings. The most successful routes involve the use of cesium or zinc salts of Boc-Asp(OH)-OFm.

Short peptides spanning the helicoidal sequences of the uteroglobin monomer (crystal forms P21 and C2221) were synthesized and studied by circular dichroism spectroscopy. None of them showed any secondary structure in the absence of HFIP. However, most peptides achieved a helical conformation when this structuring agent was used, with the exception of the analogue corresponding to the helicoidal fragment 19–24 (helix II, crystal P21). These results indicate that other factors, such as interchain interactions, have to contribute to helix stabilization in the molecule. On the other hand, while peptides corresponding to N- and C-terminal fragments that contain the first and fourth helices of the monomer, respectively (1–14 and 48–70) achieved a β-like structure when 10–15% of HFIP was used, this behaviour was not observed when TFE was used. Moreover, substitution of cysteine by α-aminobutyric acid at position 3 increased both the helicity of fragment 1–14 and its ability to adopt a β-like structure, but the opposite effect was observed for fragment 48–70 when α-aminobutyric acid was introduced at position 69. These results indicate that this part of the protein might be sensitive to the chemical environment it is exposed to and that the two cysteine residues at positions 3 and 69 of the monomer could play a different role in the folding process.

The syntheses of the two protected derivatives 7 and 16 of (2S,4S)-4-hydroxy-2,5-dimethyl-3-oxohexanoic acid, a constituent of the didemnin family of antineoplastic macrocyclic depsipeptides are described. The preparation of 7 was carried out by modification of a previously reported synthetic route whereas the use of derivative 16 represents a novel approach to the management of this sub-unit. Removal of the carboxy protecting groups from 7 or 16, followed by amide bond formation with derivatives of (S)-leucine, and oxidation in the cases of compounds deriving from 16, generates the diastereoisomeric intermediates 11, 22 and 23. In each of these either of the protecting groups can be removed in the presence of the other, allowing them to be elaborated further at either terminus. Previous work indicates that diastereoisomeric mixtures of such intermediates can, in principle, be used to obtain optically pure didemnins.

Most potential drugs for the treatment of central nervous system disorders do not cross the blood-brain barrier (BBB). Much research effort has been devoted to the discovery of new BBB-shuttle peptides-most of which have been identified by phage display. Here we report for the first time on the use of phage display against a human BBB cellular model which mimics the characteristics of the BBB. From the panning experiment of a 12-mer library, the SGVYKVAYDWQH (SGV) peptide sequence was selected and its permeability validated in the aforementioned model. Furthermore, internalization studies suggested that SGV internalizes through a clathrin-mediated mechanism and that it increases the uptake of a cargo in endothelial cells. These results highlight the usefulness of in vitro BBB models for the discovery of BBB-shuttle peptides through phage display libraries.

Fluorescent labelling of peptides is necessary in a wide range of cell biological applications. In the last decade, the application of cell-penetrating molecules has been advanced by the use of peptides, which have proven efficient in aiding nonpermeant molecules to cross the cell membrane. Currently, the development of new cell-penetrating peptides based on the design and synthesis of labelled peptide libraries is becoming critically important. Here we report an improved method for the solid-phase labelling of peptides, mediated by the activation of 5(6)-carboxyfluorescein with PyAOP/ HOAt.

Background HIV-1 entry is a dynamic process with two main actors: HIV-1 envelope glycoproteins: gp120 and gp41. The entry is a key step of the infection: blockade of this step leads to an inhibition of the viral replication. Our main focus in this study is the key actor of the viral entry and fusion: gp41. Our goal is to develop HIV-1 entry inhibitors using two strategies: i) the development of immunogens capable to induce neutralizing antibodies, ii) the modeling and synthesize as monomeric or trimeric peptide inhibitors derived from the HR1 and HR2 regions of gp41.

The electronic spin filtering capability of a single chiral helical peptide is measured. A ferromagnetic electrode source is employed to inject spin-polarized electrons in an asymmetric single-molecule junction bridging an α-helical peptide sequence of known chirality. The conductance comparison between both isomers allows the direct determination of the polarization power of an individual chiral molecule.

A 22-residue peptide with a sidechain lactam bridge involving 18 residues (60-atom cycle) has been synthesized. Three different protection schemes using Fmoc/tBu/cyclohexyl, Fmoc/tBu/allyl or Boc/Bzl/ fluorenylmethyl protecting group combinations have been explored for the solid phase of the linear precursors, which have been subsequently cyclized in solution or in the solid phase. Cyclization yields in solution have been consistently better than on solid phase; however, the solid-phase strategy requires fewer purification steps and therefore global yields are comparable.

A derivative of 2-amino-6-mercaptohexanoic acid (Amh) suitable for Boc solid phase synthesis has been prepared by conversion of the e-NH 3 group of lysine into a 4-methylbenzyl thioether. The derivative has been used in the synthesis of a 22-residue peptide with a 62-atom cyclic disulfide. Amh(Meb) is stable to acidolysis but can be conveniently deprotected, with simultaneous disulfide formation, by treatment with diphenyl sulfoxide and trichloromethylsilane.

Methionine sulfoxide reduction by NH4I has been studied in some disulfide containing peptides. In general, this reagent has proved to be effective in neat TFA at 0°C, with the obtention of the unprotected peptides in more than 99% yields and without reduction of the disulfide bridge bond. The use of Me2S as an additive resulted in faster reactions and disulfide scrambling was not observed. Whereas the Acm group proved to be stable to the reaction conditions, unprotected cysteine containing peptides afforded the corresponding parallel dimers.

A 22-residue cyclic peptide with a 56-atom (18-residue) intramolecular disulfide has been synthesized on solid phase. Two synthetic schemes, based on Boc/benzyl chemistry and either acetamidomethyl (Acm) or 9-fluorenylmethyl (Fm) groups for cysteine protection, have been compared. The deprotection-oxidation of both S-protecting groups has been explored under several experimental conditions. The most successful route involved on-the-resin disulfide formation via Cys(Fm) deprotection-oxidation.

The handle N-[(9-hydroxymethyl)-2-fluorenyl]succinamic acid (HMFS) is reported for the preparation of protected peptide segments in combination with a Boc/Bzl protection scheme. Treatment of peptide-resins with morpholine in DMF renders protected peptides in high yields and purities.

Recent structural determinations have shown that thiolate-protected gold nanoparticles are not as regular and symmetric as initially thought, but characteristic substructures (staple motifs) are formed on their surface. However, their mechanism of formation, especially the fate of the sulfur protons upon thiol binding, remains one of the most intriguing unanswered questions in gold cluster chemistry. By means of ab initio molecular dynamics (AIMD), we monitor the trajectory of thiol protons reacting with a gold cluster, demonstrating that the staple motif forms in a multiple-pathway chemical reaction, releasing molecular hydrogen. The results obtained also reconcile the conclusions of structural determinations with the interpretations of spectroscopic experiments on solution, suggesting the presence of intact thiols or chemisorbed hydrogen.

In the context of our studies on the applications of 3-aminolactams as conformationally restricted pseudodipeptides, we report here the synthesis of a library of potential dimerisation inhibitors of HIV1-protease. Two of the pseudopeptides were active on the wild type virus (HIV1) at micromolar levels (EC(50)). Although the peptides showed lower anti-viral activity than previously reported dimerisation inhibitors, our results demonstrate that the piperidone moiety does not prevent cell penetration, and hence that such derivatization is compatible with potential anti-HIV treatment.

The phenylpropanoid glycoside verbascoside [2-(3,4-dihydroxyphenylethyl)-1-O-α-L-rhamnopyranosyl-(1→3)-β-D-(4-O-caffeyl)-glucopyranoside] (1) has been isolated as the main constituent of the crude extract of Buddleja brasiliensis Jacq. ex Spreng from Southern Brazil. The crude extract, main fractions and the compound 1 were evaluated for inhibition of the enzymes acetylcholinesterase (AChE), dipeptidyl peptidase-IV (DPP-IV) and prolyl oligopeptidase (POP). Compound 1 showed weak activity against DPP-IV with an IC(50)150 µM and was inactive against AChE, with a pMIQ determined by bioautography of 9.6. In contrast, 1 displayed significant inhibition of POP in a dose-dependent manner with an IC(50) value of 1.3 ± 0.2 µM, similar to the positive control, baicalin, with a POP IC(50) of 12 ± 3 µM.

The treatment of Alzheimer's disease and many other brain-related disorders is limited because of the presence of the blood-brain barrier, which highly regulate the crossing of drugs. Metal nanoparticles have unique features that could contribute to the development of new therapies for these diseases. Nanoparticles have the capacity to carry several molecules of a drug; furthermore, their unique physico-chemical properties allow, for example, photothermal therapy to produce molecular surgery to destroy tumor cells and toxic structures. Recently, we demonstrated that gold nanoparticles conjugated to the peptide CLPFFD are useful to destroy the toxic aggregates of β-amyloid, similar to the ones found in the brains of patients with Alzheimer's disease. However, nanoparticles, like many other compounds, have null or very low capacity to cross the blood-brain barrier. In order to devise a strategy to improve drug delivery to the brain, here we introduced the peptide sequence THRPPMWSPVWP into the gold nanoparticle-CLPFFD conjugate. This peptide sequence interacts with the transferrin receptor present in the microvascular endothelial cells of the blood-brain barrier, thus causing an increase in the permeability of the conjugate in brain, as shown by experiments in vitro and in vivo. Our results are highly relevant for the therapeutic applications of gold nanoparticles for molecular surgery in the treatment of neurodegenerative diseases such as Alzheimer's disease.

The immune system is the responsible for body integrity and prevention of external invasion. On one side, nanoparticles are no triggers that the immune system is prepared to detect, on the other side it is known that foreign bodies, not only bacteria, viruses and parasites, but also inorganic matter, can cause various pathologies such as silicosis, asbestosis or inflammatory reactions. Therefore, nanoparticles entering the body, after interaction with proteins, will be either recognized as self-agents or detected by the immune system, encompassing immunostimulation or immunosuppression responses. The nature of these interactions seems to be dictated not specially by the composition of the material but by modifications of NP coating (composition, surface charge and structure). Herein, we explore the use of gold nanoparticles as substrates to carry multifunctional ligands to manipulate the immune system in a controlled manner, from undetection to immunostimulation. Murine bone marrow macrophages can be activated with artificial nanometric objects consisting of a gold nanoparticle functionalized with peptides. In the presence of some conjugates, macrophage proliferation was stopped and pro-inflammatory cytokines were induced. The biochemical type of response depended on the type of conjugated peptide and was correlated with the degree of ordering in the peptide coating. These findings help to illustrate the basic requirements involved in medical NP conjugate design to either activate the immune system or hide from it, in order to reach their targets before being removed by phagocytes. Additionally, it opens up the possibility to modulate the immune response in order to suppress unwanted responses resulting from autoimmunity, or allergy or to stimulate protective responses against pathogens.

Linker histone H1 is a major chromatin component that binds internucleosomal DNA and mediates the folding of nucleosomes into a higher-order structure, namely the 30-nm chromatin fiber. Multiple post-translational modifications (PTMs) of core histones H2A, H2B, H3 and H4 have been identified and their important contribution to the regulation of chromatin structure and function is firmly established. In contrast, little is known about histone H1 modifications and their function. Here we address this question in Drosophila melanogaster, which, in contrast to most eukaryotic species, contains a single histone H1 variant, dH1. For this purpose, we combined bottom-up and top-down mass-spectrometry strategies. Our results indicated that dH1 is extensively modified by phosphorylation, methylation, acetylation and ubiquitination, with most PTMs falling in the N-terminal domain. Interestingly, several dH1 N-terminal modifications have also been reported in specific human and/or mouse H1 variants, suggesting that they have conserved functions. In this regard, we also provide evidence for the contribution of one of such conserved PTMs, dimethylation of K27, to heterochromatin organization during mitosis. Furthermore, our results also identified multiple dH1 isoforms carrying several phosphorylations and/or methylations, illustrating the high structural heterogeneity of dH1. In particular, we identified several non-CDK sites at the N-terminal domain that appear to be hierarchically phosphorylated. This study provides the most comprehensive PTM characterization of any histone H1 variant to date. © 2012 Elsevier B.V., This work was supported by grants from MICINN (CSD2006-49, BIO2008-00799 and BFU2009-07111), the CSIC (200420E391) and the “Generalitat de Catalunya” (SGR2009-1023 and SGR2009-1005). This work was carried out within the framework of the “Xarxa de Referència en Biotecnologia” of the “Generalitat de Catalunya”.

In the forthcoming era of cancer gene therapy, efforts will be devoted to the development of new efficient and non-toxic gene delivery vectors. In this regard, the use of Fmoc/Boc-protected oligo(ethane amino)acids as building blocks for solid-phase-supported assembly represents a novel promising approach towards fully controlled syntheses of effective gene vectors. Here we report on the synthesis of defined polymers containing the following: (i) a plasmid DNA (pDNA) binding domain of eight succinoyl-tetraethylenpentamine (Stp) units and two terminal cysteine residues; (ii) a central polyethylene glycol (PEG) chain (with twenty-four oxyethylene units) for shielding; and (iii) specific peptides for targeting towards cancer cells. Peptides B6 and c(RGDfK), which bind transferrin receptor and avß3 integrin, respectively, were chosen because of the high expression of these receptors in many tumoral cells. This study shows the feasibility of designing these kinds of fully controlled vectors and their success for targeted pDNA-based gene transfer.

The N,N′ -disuccinimidyl carbonate (DSC) has been successfully used for the efficient conversion of conventional hydroxymethyl resins into active carbonate resins, which are suitable for the incorporation of protected amino acids via an amino function, allowing the preparation of “head-to-tail” cyclic lysine containing peptides.

Introduction Proteins play a crucial role in many molecular recognition processes. Over the past few years, thanks to the effort of several research laboratories, we have learned something of the mechanisms that regulate these interactions [ 11. Peptide molecules have served, and are serving, as model compounds in these kinds of studies. Nevertheless, slowly, as we learn more about the basis of molecular recognition, we are starting to have a certain predictive ability. A reliable predictive capability would open the door to the design and synthesis of peptide molecules which have as an inherent characteristic a certain molecular-recognition feature. As illustrated in Figure 1, from a purely 'host-guest chemistry' point of view, peptide molecules provide a series of advantageous features that can be exploited for the design of new compounds. Hydrogen bonding has been recognized as one of the most efficient non-covalent interactions and we can use the tendency of the peptide backbone to form intraand inter-chain hydrogen bonds to mould the global shape of the molecule. Chirality at the a-carbon provides the opportunity of exploring several 'configurational versions' of the molecule; because we are using chemical synthesis, we are not constrained to use only the homochiral 1.-amino acid series. We can exploit the wealth of functional groups available at the amino acid side chains to improve, or modulate, the recognition properties of our compounds. We can use our present knowledge of peptide and protein conformational analysis to control, to some extent, the three-dimensional structure of our compounds. Finally, but also very importantly, we have at our disposal efficient synthetic methods for the preparation of peptides. In addition to the already enumerated possible control elements, we have another possibility for the design of new peptides for molecular-recognition studies: formation of disulphide bridges between cysteine residues. In this paper we will focus on this aspect.

The conformation of a peptide that represents antigenic site A of foot-and-mouth disease virus strain C-S8c1 (residues 136–156 of VP1; YTASARGDLAHLTTTHARHLP) has been studied by circular dichroism and compared with three analogs that reproduce amino acid substitutions at position 146 (His→Arg, Gln or Asp) which affect antibody recognition. Four other peptides, incorporating replacements at position 147 predicted to maintain (Leu→Ile, Nle and Ala) or disrupt (Leu→Gly) helical structure at this site, have also been studied. In aqueous solution or in 4 M urea, the spectra of all eight peptides were typical of aperiodic conformation and independent of concentration or pH. However, upon addition of solvents such as methanol or hexafluoroisopropanol, spectral patterns evidenced significant levels (ca. 50%) of helical structure. The single residue substitutions at positions 146 and 147 caused minor to significant variations in the calculated amount of α-helix of the peptides. An attempt to relate these changes in helical content to the antigenic behaviour of the peptides towards five monoclonal antibodies elicited with virus and mapping at site A could not find any straightforward correspondence between the two sets of results. The parent peptide and its His146→Arg analog were also analyzed by circular dichroism in the presence of the Fab fragment of SD6, a monoclonal antibody mapping at site A and much less reactive with viruses carrying the referred mutation. Although a peptide-antibody interaction was evident from spectral changes, careful inspection of the difference spectra (peptide-Fab minus Fab) of both peptides failed to detect any significant distinction between them that could be attributed to their different immunoreactivity. While these findings do not necessarily conflict with previous reports that the interaction of antigenic site A with antibodies is mediated to some extent by the adoption of a helix structure, they suggest that, at least for C-serotype viruses, other structural features in addition to a helical conformation are critically involved in antigenic recognition.

High yields for the cleavage reaction of Fmoc-protected peptide segments from an allylic handle may be obtained using tributyltin hydride in the presence of (Ph3P)PdCl2 in a 1:1 mixture of DMF/DCM. Alternatively the cleavage reaction may be carried out using NMA as nucleophile in a 2:2:1 mixture of DMSO/THF/0.5M HCl in the presence of (Ph3P)4Pd. The Fmoc group is completely stable to both these cleavage methods.

Acidolytic cleavage of C-terminal Met-containing peptides from the solid support can lead to the formation of the homoserine lactone peptide as the major product. Formation of such undesired peptides may be avoided by removal of all tert-butyl groups from Met-containing peptides before cleavage from the resin.

Nuclear magnetic resonance (NMR) has evolved into a powerful tool for characterizing protein-ligand interactions in solution under near physiological conditions. It is now frequently harnessed to assess the affinity and specificity of interactions; to identify binding epitopes on proteins and ligands; and to characterize the structural rearrangements induced by binding.The first section of this chapter provides a general overview of the NMR study of protein-ligand interactions. The section is divided according to two main categories of experiments: those based on observing protein signals and those based on observing ligand signals. The next section explains two case studies performed in the authors' laboratory. The first of these deals with the interaction between vascular endothelial growth factor and a peptidic ligand, and includes a detailed protocol of chemical shift perturbation experiments. The second one reports on the interaction between prolyl oligopeptidase and a small molecule as monitored by ligand saturation transfer difference (STD), and illustrates how NMR can be used to confirm binding and to identify the binding epitope of a ligand.

Amyloid-β protein (Aβ) aggregation into amyloid fibrils is central to the origin and development of Alzheimer’s disease (AD), yet this highly complex process is poorly understood at the molecular level. Extensive studies have shown that Aβ fibril growth occurs through fibril elongation, whereby soluble molecules add to the fibril ends. Nevertheless, fibril morphology strongly depends on aggregation conditions. For example, at high ionic strength, Aβ fibrils laterally associate into bundles. To further study the mechanisms leading to fibril growth, we developed a single-fibril growth assay based on differential labeling of two Aβ42 variants with gold nanoparticles. We used this assay to study Aβ42 fibril growth under different conditions and observed that bundle formation is preceded by lateral interaction of soluble Aβ42 molecules with pre-existing fibrils. Based on this data, we propose template-assisted lateral fibril growth as an additional mechanism to elongation for Aβ42 fibril growth.