Maciej Makowski

Peptide p-nitrophenylanilides containing (E)-dehydrophenylalanine—synthesis, structural studies and evaluation of their activity towards cathepsin C

Tetrapeptide p-nitroanilides containing (E)-dehydrophenylalanine were synthesized and evaluated as inhibitors and substrates of cathepsin C. Peptides containing a free, unblocked amino group appeared to be quite good substrates of the enzyme, whereas fully protected peptides acted as very weak inhibitors. Structural studies by means of NMR and CD, alongside with molecular modelling, have proved that these peptides are hydrolysed in one step by direct removal of p-nitroaniline from the tetrapeptide.

Pentapeptides containing two dehydrophenylalanine residues - synthesis, structural studies and evaluation of their activity towards cathepsin C

Synthesis, structural and biological studies of pentapeptides containing two ΔPhe residues (Z and E isomers) in position 2 and 4 in peptide chain were performed. All the investigated peptides adopted bent conformation and majority of them could exist as two different conformers in solution. Only pentapeptides, containing free N‐termini appeared to act as weak inhibitors of cathepsin C with the slow‐binding, competitive mechanism of inhibition, free acids being bound slightly better than their methyl esters. Results of molecular modeling suggested significant difference between peptides, depending of the type of amino acid residue in position 5 in peptide chain. Dehydropeptides containing Gly residue in this position may act as competitive slow‐reacting substrates and therefore exhibit inhibitory‐like properties. Copyright

Impact of α,β-dehydroamino acid residues on the binding abilities of di-, tri- and tetra-peptides

Insertion of a dehydroamino acid residue into a sequence of di-, tri- or tetra-peptide changed considerably the binding abilities of peptide ligands towards copper(II) ions. Potentiometric and spectroscopic (EPR, UV-VIS and CD) data have shown that the amide nitrogen of the dehydroamino acid residue is more effective in co-ordination than its parent analogue. In the case of the bulky ΔPhe residue also the (Z–E) isomerisation has a critical impact on the co-ordination equilibria in the system studied.

N-[tert-Butoxy­carbonyl­glycyl-(Z)-α,β-de­hydro­phenyl­alanyl­glycyl-(E)-α,β-de­hydro­phenyl­alanyl]­glycine methyl ester dihydrate

The title pentapeptide, Boc0—Gly1–ΔZPhe2—Gly3–ΔEPhe4—Gly5—OMe, C30H35N5O8·2H2O, adopts the type I β-turn conformation for the ΔZPhe2—Gly3 residues. It is stabilized by a 4\rightarrow1 intramolecular hydrogen bond between the ΔEPhe4 NH and Gly1 CO groups. All the amino acid residues in the pentapeptide sequence are linked trans to each other. The crystal structure is stabilized by intra- and intermolecular hydrogen bonds.

Conformation of dehydropentapeptides containing four achiral amino acid residues – controlling the role of L-valine

Summary Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.

Binding abilities of dehydropeptides towards Cu(II) and Ni(II) ions. Impact of Z–E isomerization on metal ion binding

The study on the binding ability of dehydro-tri- and tetrapeptides has shown that the alpha,beta-double bond has a critical effect on the peptide coordination to metal ions. It may affect the binding of the vicinal amide nitrogens by the electronic effect and stabilize the complex due to steric effects. The (Z) isomer is the most effective in stabilizing of the complexes formed. The presence of large side chain in the dehydroamino acid residue may also be critical for the coordination mode in the metallopeptide systems.

Synthesis of dehydrodipeptide esters and their evaluation as inhibitors of cathepsin C

The procedures for the synthesis of esters of dehydropeptides containing C-terminal (Z)-dehydrophenylalanine and dehydroalanine have been elaborated. These esters appeared to be moderate or weak inhibitors of cathepsin C, with some of them exhibiting slow-binding behavior. As shown by molecular modeling, they are rather bound at the surface of the enzyme and are not submersed in its binding cavities.

N-p-Amino- and N-p-nitro-phenylsulfonyl derivatives of dipeptides, a new family of ligands for copper(II). Potentiometric and spectroscopic studies

The co-ordination ability of four dipeptide analogues substituted on the N-terminal amino group with p-nitrophenylsulfonyl (nps-Ala-Ala and nps-Ala-His) and p-aminophenylsulfonyl (aps-Ala-Ala and aps-Ala-His) groups was studied by potentiometric and spectroscopic (UV/VIS absorption, CD and EPR) techniques. The N-terminal sulfonyl substituent drastically changes the acidity of the sulfonamide proton making nitrogen very efficient in binding to CuII. The sulfonamide nitrogen having pK between 9 and 11 does not need any anchoring binding group to form complexes with CuII. The para substituent on the phenyl ring (amino or nitro) influences very strongly the acidity of the sulfonamide proton. The nps or aps moieties change the co-ordination equilibria considerably when compared to the parent dipeptide Ala-His. Both groups enforce the formation of dimeric complexes, whereas in the case of the parent dipeptide the major species are only monomeric.

Crystal structure of N-(tert-but­oxy­carbon­yl)glycyl-(Z)-β-bromo­dehydro­alanine methyl ester [Boc–Gly–(β-Br)(Z)ΔAla–OMe]

The title compound, C11H17BrN2O5, is a de-hydro-amino acid with a C=C bond between the α- and β-C atoms. The amino acid residues are linked trans to each other and there are no strong intra-molecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the mol-ecule. The dipeptide folding is influenced by an inter-molecular N-H⋯O hydrogen bond and also minimizes steric repulsion. In the crystal, mol-ecules are linked by strong N-H⋯O hydrogen bonds, generating (001) sheets. The sheets are linked by weak C-H⋯O and C-H⋯Br bonds and short Br⋯Br [3.4149 (3) Å] inter-actions.

Crystal structure of N-(tert-but­oxy­carbon­yl)phenyl­alanylde­hydro­alanine isopropyl ester (Boc–Phe–ΔAla–OiPr)

In the crystal structure of the dehydrodipeptide (Boc-Phe-ΔAla-OiPr), the molecule has a trans configuration of the N-methylamide group. Its geometry is different from saturated peptides but is in excellent agreement with other dehydroalanine compounds. In the crystal, an N—H⋯O hydrogen bond links the molecules in a herringbone packing arrangement.