Tamás A. Martinek

Application of alicyclic β-amino acids in peptide chemistry

The self-organizing β-peptides have attracted considerable interest in the fields of foldamer chemistry and biochemistry. These compounds exhibit various stable secondary structure motifs that can be exploited to construct biologically active substances and nanostructured tertiary structures. The secondary structures can be controlled via the β-amino acid sequence, and cyclic β-amino acid residues play a crucial role in the design. The most important procedures for the preparation of cyclic β-amino acid monomers and peptides are discussed in this tutorial review. Besides the secondary structure design principles, the methods of folded structure detection are surveyed.

Performance of the general amber force field in modeling aqueous POPC membrane bilayers

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid‐crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPγT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPγT ensemble is applied with a surface tension of 60 mN m−1 per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.

Functionalization of gold nanoparticles with amino acid, β-amyloid peptides and fragment

Gold nanoparticles (Au NPs) were functionalized by cysteine (Cys), beta-amyloid peptides (Cys(0)Abeta(1-28), Cys(0)Abeta(1-40), Abeta(1-42)) and a pentapeptide fragment (Leu-Pro-Phe-Phe-Asp-OH (LPFFD-OH)). Optical absorption spectra of these systems were recorded and the plasmon resonance maximum values (lambda(max)) of the UV-vis spectra together with the transmission electron microscopy (TEM) images were also analysed. Both TEM images and the appearance of a new absorption band between approximately 720 and 750 nm in the visible spectra of the Au-cysteine and Au-LPFFD-OH systems most probably indicate that upon addition of these molecules to Au NPs-containing aqueous dispersions formation of aggregates is occurred. The wavelength shift between the two observed absorption bands in cysteine- and pentapeptide-modified Au NPs systems are Deltalambda=185 and 193 nm, respectively. These results suggest that the monodisperse spherical gold nanoparticles were arranged to chained structure due to the effect of these molecules. For confirmation of the binding of citrate and cysteine onto the plasmonic metal surface (1)H NMR measurements were also performed. (1)H NMR results may suggest that the citrate layer on the metal surface is replaced by cysteine leading to a formation of organic double layer structure. In the presence of beta-amyloid peptides the aggregation was not observed, especially in the Au-Cys(0)Abeta(1-40) and Au-Abeta(1-42) systems, however compared to the cysteine or LPFFD-OH-containing gold dispersion with Cys(0)Abeta(1-28) measurable less aggregation were occurred. The spectral parameters clearly suggest that Abeta(1-42) can attach or bind to the surface of gold nanoparticles via both the apolar and the N-donors containing side-chains of amino acids and no aggregation in the colloidal gold dispersion was observed.

Design of Peptidic Foldamer Helices: A Stereochemical Patterning Approach

Assembly language: The programmed sequences of stereochemical building blocks lead to novel biomimetic helices. The rational design approach offers new possibilities for creating periodic secondary structures.

Peptides containing β-amino acid patterns: challenges and successes in medicinal chemistry.

The construction of bioactive peptides using β-amino acid-containing sequence patterns is a very promising strategy to obtain analogues that exhibit properties of high interest for medicinal chemistry applications. β-Amino acids have been shown to modulate the conformation, dynamics, and proteolytic susceptibility of native peptides. They can be either combined with α-amino acids by following specific patterns, which results in backbone architectures with well-defined orientations of the side chain functional groups, or assembled in de novo-designed bioactive β- or α,β-peptidic sequences. Such peptides display various biological functions, including antimicrobial activity, inhibition of protein-protein interactions, agonism/antagonism of GPCR ligands, and anti-angiogenic activity.

Building β-Peptide H10/12 Foldamer Helices with Six-Membered Cyclic Side-Chains: Fine-Tuning of Folding and Self-Assembly

The ability of the β-peptidic H10/12 helix to tolerate side-chains containing six-membered alicyclic rings was studied. cis-2-Aminocyclohex-3-ene carboxylic acid (cis-ACHEC) residues afforded H10/12 helix formation with alternating backbone configuration. Conformational polymorphism was observed for the alternating cis-ACHC hexamer, where chemical exchange takes place between the major left-handed H10/12 helix and a minor folded conformation. The hydrophobically driven self-assembly was achieved for the cis-ACHC-containing helix which was observed as vesicles ~100 nm in diameter.

Synthesis and transformations of enantiomeric 1,2-disubstituted monoterpene derivatives

Abstract Regio- and stereospecific addition of chlorosulfonyl isocyanate to (+)- and (−)-α-pinene 1 resulted in enantiomerically pure β-lactams 2 , which were converted to enantiomeric β-amino esters 3 and 1,3-amino alcohols 4 and 6 with ee >99%. The resulting 1,3-difunctional compounds 3 , 4 and 6 were transformed to fused saturated 1,3-heterocycles such as tetrahydro-1,3-oxazines 7 and 9 , 2,4-pyrimidinedione 11 and 2-thioxopyrimidin-4-one 13 enantiomers.

A Simple Synthesis of β-Alkyl-Substituted β-Amino Acids

Abstract By the condensation of branched-chain aliphatic or alicyclic aldehydes with malonic acid in the presence of ammonium acetate, β-alkyl-substituted β-amino acids were prepared.

Foldameric α/β-peptide analogs of the β-sheet-forming antiangiogenic anginex: structure and bioactivity.

The principles of β-sheet folding and design for α-peptidic sequences are well established, while those for sheet mimetics containing homologated amino acid building blocks are still under investigation. To reveal the structure-function relations of β-amino-acid-containing foldamers, we followed a top-down approach to study a series of α/β-peptidic analogs of anginex, a β-sheet-forming antiangiogenic peptide. Eight anginex analogs were developed by systematic α → β(3) substitutions and analyzed by using NMR and CD spectroscopy. The foldamers retained the β-sheet tendency, though with a decreased folding propensity. β-Sheet formation could be induced by a micellar environment, similarly to that of the parent peptide. The destructuring effect was higher when the α → β(3) exchange was located in the β-sheet core. Analysis of the β-sheet stability versus substitution pattern and the local conformational bias of the bulky β(3)V and β(3)I residues revealed that a mismatch between the H-bonding preferences of the α- and β-residues played a minor role in the structure-breaking effect. Temperature-dependent CD and NMR measurements showed that the hydrophobic stabilization was scaled-down for the α/β-peptides. Analysis of the biological activity of the foldamer peptides showed that four anginex derivatives dose-dependently inhibited the proliferation of a mouse endothelial cell line. The α → β(3) substitution strategy applied in this work can be a useful approach to the construction of bioactive β-sheet mimetics with a reduced aggregation tendency and improved pharmacokinetic properties.

A Foldamer-Dendrimer Conjugate Neutralizes Synaptotoxic β-Amyloid Oligomers

Background and Aims Unnatural self-organizing biomimetic polymers (foldamers) emerged as promising materials for biomolecule recognition and inhibition. Our goal was to construct multivalent foldamer-dendrimer conjugates which wrap the synaptotoxic β-amyloid (Aβ) oligomers with high affinity through their helical foldamer tentacles. Oligomeric Aβ species play pivotal role in Alzheimers disease, therefore recognition and direct inhibition of this undruggable target is a great current challenge. Methods and Results Short helical β-peptide foldamers with designed secondary structures and side chain chemistry patterns were applied as potential recognition segments and their binding to the target was tested with NMR methods (saturation transfer difference and transferred-nuclear Overhauser effect). Helices exhibiting binding in the µM region were coupled to a tetravalent G0-PAMAM dendrimer. In vitro biophysical (isothermal titration calorimetry, dynamic light scattering, transmission electron microscopy and size-exclusion chromatography) and biochemical tests (ELISA and dot blot) indicated the tight binding between the foldamer conjugates and the Aβ oligomers. Moreover, a selective low nM interaction with the low molecular weight fraction of the Aβ oligomers was found. Ex vivo electrophysiological experiments revealed that the new material rescues the long-term potentiation from the toxic Aβ oligomers in mouse hippocampal slices at submicromolar concentration. Conclusions The combination of the foldamer methodology, the fragment-based approach and the multivalent design offers a pathway to unnatural protein mimetics that are capable of specific molecular recognition, and has already resulted in an inhibitor for an extremely difficult target.