The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure

• Francesco Airaghi,
• Andrea Fiorati,
• Giordano Lesma,
• Manuele Musolino,
• Alessandro Sacchetti and
• Alessandra Silvani

Beilstein J. Org. Chem. 2013, 9, 147–154, doi:10.3762/bjoc.9.17

• Discussion In order to investigate the presence of a preferred conformation able to mimic an ordered protein secondary structure, a computer-aided conformational analysis was performed on 1a (6S,12aS-configuration, IUPAC atom numbering as in Figure 2) and diastereoisomeric 1b (6R, 12aS). Compounds 1a and 1b

• were submitted to an unconstrained Monte Carlo (MC) conformational search combined with Molecular Mechanics (MM) minimization (see Table 1 for results). As a main indication of a stable secondary structure, the presence of intramolecular hydrogen bonds was first evaluated. Two H-bonds have been

• -configuration in favoring either an α-turn conformation (1a) or a γ-turn conformation (1b). Finally, having ascertained by means of further calculations the irrelevance of the C3 configuration on the expected secondary structure, we fixed it as 3S. Being interested in unusual reverse turns, we then pursued the

Multivalent display of the antimicrobial peptides BP100 and BP143

• Imma Güell,
• Rafael Ferre,
• Kasper K. Sørensen,
• Esther Badosa,
• Iteng Ng-Choi,
• Emilio Montesinos,
• Eduard Bardají,
• Lidia Feliu,
• Knud J. Jensen and
• Marta Planas

Beilstein J. Org. Chem. 2012, 8, 2106–2117, doi:10.3762/bjoc.8.237

• moderately structured, with the degree of secondary structure formation being higher in the latter solvent. In both cases, two local minima near 205 and 220 nm, and a positive band near 195 nm were observed. In 50% TFE, we estimated an α-helical content of 41% for carbopeptide 1 and of 19% for carbopeptide 3

• preassembly may favor the formation of a more organized amphipathic peptide structure compared to the monomers, which has been correlated with a higher degree of hemolysis [14][36]. BP100 was originally designed based on an ideal α-helical Edmunson wheel and showed a moderate degree of secondary-structure

• formation by CD. As shown by CD spectroscopy, the preassembly of BP100 did not result in a more organized structure, especially for carbopeptide 3, which suggests that the high hemolysis observed for carbopeptides cannot be attributed to a higher degree of secondary-structure formation. A likely explanation

Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120

• Julia Meier,
• Kristin Kassler,
• Heinrich Sticht and
• Jutta Eichler

Beilstein J. Org. Chem. 2012, 8, 1858–1866, doi:10.3762/bjoc.8.214

• for the CD4–gp120 complex (black). (A) Root-mean-square deviation of the peptides and CD4 over simulation time. (B) Root-mean-square fluctuation of individual residues measured for backbone atoms averaged over time. Residues replaced by cysteine in CD4-M2 are indicated in bold face. Secondary

• structure elements are assigned below the plot. Structural presentation of peptide motions in the gp120-bound state during the MD simulation. (A) CD4-M1, (B) CD4-M2, (C) respective sequence stretch of CD4 (the remaining part of CD4 has been omitted for simplicity in this plot). The disulfide bridge that

Dimerization of a cell-penetrating peptide leads to enhanced cellular uptake and drug delivery

• Jan Hoyer,
• Ulrich Schatzschneider,
• Michaela Schulz-Siegmund and
• Ines Neundorf

Beilstein J. Org. Chem. 2012, 8, 1788–1797, doi:10.3762/bjoc.8.204

• not reveal any change of the secondary structure with respect to the parent peptide (Figure 6). They all exhibit a random coil structure in phosphate buffer with transition to an α-helical structure in the helix-inducing environment of trifluoroethanol, which has already been shown for monomeric sC18

Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

• Evan F. Haney,
• Leonard T. Nguyen,
• David J. Schibli and
• Hans J. Vogel

Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130

• , while the band at ~230 nm can be attributed to stacking interactions between nearby aromatic rings [17]. This is in agreement with the fluorescence results and suggests that the gp41w backbone adopts a regular secondary structure when oligomerized in solution. The addition of SDS or DPC micelles to

• to the formation of insoluble peptide–lipid complexes. Unfortunately, due to the loss of CD signal in these samples, it is impossible to determine what type of secondary structure is present in these aggregates. NMR solution structure All the gp41w derivatives were examined by nuclear magnetic

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

• Marta De Zotti,
• Barbara Biondi,
• Cristina Peggion,
• Matteo De Poli,
• Haleh Fathi,
• Simona Oancea,
• Claudio Toniolo and
• Fernando Formaggio

Beilstein J. Org. Chem. 2012, 8, 1161–1171, doi:10.3762/bjoc.8.129

• ], backbone amide surrogates have attracted remarkable attention from organic and medicinal chemists. Not only may these modifications impart to a peptide an increased resistance to enzymatic hydrolysis as well as higher receptor affinity and specificity, but they may also influence its preferred secondary

• structure. A ψ[CS-NH] thioamide group is one of the closest mimics of an amide (peptide) linkage. However, it exhibits significantly different chemical and physical properties, some of which are of great potential interest to peptide chemists [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• peptides are more stable to proteolysis due to the lack of free N- and C-termini, as well as reduced conformational freedom. Stability can also be achieved by modifying peptides into “peptidomimetics” that mimic and/or stabilize the secondary structure that modifies associated biological processes, thus

Parallel solid-phase synthesis of diaryltriazoles

• Matthias Wrobel,
• Jeffrey Aubé and
• Burkhard König

Beilstein J. Org. Chem. 2012, 8, 1027–1036, doi:10.3762/bjoc.8.115

• protein–protein interactions. Keywords: chemical diversity; Huisgen cycloaddition; library synthesis; peptidomimetics; solid phase synthesis; triazole; Introduction The α-helix was the first-described secondary structure of peptides discovered by Linus Pauling in 1951 [1]. With about 30% of the amino

• acids in proteins being part of α-helices [2], it is the most common secondary structure found in proteins [3]. Protein–protein as well as protein–DNA and protein–RNA interactions often involve α-helices as recognition motifs on protein surfaces [4]. These helices are important targets for new drugs

Asymmetric synthesis of quaternary aryl amino acid derivatives via a three-component aryne coupling reaction

• Elizabeth P. Jones,
• Peter Jones,
• Andrew J. P. White and
• Anthony G. M. Barrett

Beilstein J. Org. Chem. 2011, 7, 1570–1576, doi:10.3762/bjoc.7.185

• . Incorporation of such units into peptidomimetics, not only affects lipophilicity, but also the secondary structure and hence the conformational rigidity, which can increase the resistance to enzymatic degradation [15][16][17][18][19]. Such units are also found in biologically interesting natural products, such

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• interaction with a receptor [20]. As a consequence, a wide variety of methods to restrict the conformational freedom has been developed. One approach to get round this problem is the isosteric replacement of the amide bond in the peptide with a suitable mimetic to induce a specific secondary structure. Recent

• (THF) amino acids were optimised in order to study the influence of ring configuration and protecting groups on the secondary structure in these carbopeptoids. Short oligomeric chains of C-glycosyl β-D-arabino THF amino acids 14 and 15 (where the C-2 and C-5 substituents of the THF ring are cis to each

• other) exhibit a well defined repeating turn secondary structure stabilised by inter-residual hydrogen bonds, whereas the epimeric α-D-arabinofuranose oligomer 12 (with the C-2 and C-5 substituents in trans relative disposition) do not show any secondary structure in solution [34]. NMR and IR studies on

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

• Ana Maria Castilla,
• M. Morgan Conn and
• Pablo Ballester

Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5

• commonly found in the secondary structure of many biologically relevant proteins. We start from a schematic termolecular complex mimicking a three-stranded β-sheet in which the central strand corresponds to the target guest peptide and the two outer strands constitute the structure of the host (Figure 1

• of dipeptides on the basis of the interactions that occur in the β-sheets commonly found in the secondary structure of many biologically relevant proteins. The geometry of the putative complex used in the design of the receptors implies the threading of the dipeptide guest through the macrocyclic

Synthesis of new C^α-tetrasubstituted α-amino acids

• Andreas A. Grauer and
• Burkhard König

Beilstein J. Org. Chem. 2009, 5, No. 5, doi:10.3762/bjoc.5.5

• ; Introduction The secondary structure of an amino acid sequence is of key importance for the biological activity of proteins [1][2]. In most cases short natural peptide sequences containing L α-amino acids are very flexible and do not show a distinct secondary structure in aqueous solution. Therefore small

• Andreas A. Grauer Burkhard Konig Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93040 Regensburg, Germany 10.3762/bjoc.5.5 Abstract Cα-Tetrasubstituted α-amino acids are important building blocks for the synthesis of peptidemimetics with stabilized secondary

• structure, because of their ability to rigidify the peptide backbone. Recently our group reported a new class of cyclic Cα-tetrasubstituted tetrahydrofuran α-amino acids prepared from methionine and aromatic aldehydes. We now report the extension of this methodology to aliphatic aldehydes. Although such