Franciszek Kasprzykowski

Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods

Conformational analysis of the neurohypophyseal hormones oxytocin (OT) and arginine-vasopressin (AVP) has been carried out using two different computational approaches and three force fields, namely by the Electrostatically Driven Monte Carlo (EDMC) method, with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field or with the ECEPP/3 force field plus a hydration-shell model, and by simulated-annealing molecular dynamics with the Consistent Valence Force Field (CVFF). The low-energy conformations obtained for both hormones were classified using the minimal-tree clustering algorithm and characterized according to the locations of beta-turns in the cyclic moieties. Calculations with the CVFF force field located conformations with a beta-turn at residues 3 and 4 as the lowest energy ones both for OT and for AVP. In the ECEPP/3 force field the lowest energy conformation of OT contained a beta-turn at residues 2 and 3, conformations with this location of the turn being higher in energy for AVP. The latter difference can be attributed to the difference in the size of the side chain in position 3 of the sequences: the bulkier phenylalanine residue of AVP in combination with the bulky Tyr2 residue hinders the formation of a turn at residues 2 and 3. Conformations of OT and AVP with a turn at residues 3,4 were in the best agreement with the x-ray structures of deaminooxytocin and pressinoic acid (the cyclic moiety of vasopressin), respectively, and with the nmr-derived distance constraints. Generally, the low-energy conformations obtained with the hydration-shell model were in a better agreement with the experimental data than the conformations calculated in vacuo. It was found, however, that the obtained low-energy conformations do not satisfy all of the nmr-derived distance constraints and the nuclear Overhauser effect pattern observed in nmr studies can be fully explained only by assuming a dynamic equilibrium between conformations with beta-turns at residues 2,3, 3,4, and 4,5. The low-energy structures of OT with a beta-turn at residues 2,3 have the disulfide ring conformations close to the model proposed recently for a potent bicyclic antagonist of OT [M. D. Shenderovich et al. (1994) Polish Journal of Chemistry, Vol. 25, pp. 921-927], although the native hormone differs from the bicyclic analogue by the conformation of the C-terminal tripeptide. This finding confirms the hypothesis of different receptor-bound conformations of agonists and antagonists of OT.

How non-bonding amino acid side-chains may enormously increase the stability of a Cu(II)—peptide complex

Abstract A combined pH-metric and spectroscopic (UV—Vis, circular dichroism and electron paramagnetic resonance) study of Cu(II) binding to analogues of Asn-Ser-Phe-Arg-Tyr-NH 2 systematically substituted with Ala residues revealed the presence of indirect, additive conformational effects resulting in a very high stability enhancement for 4N complexes. The major contribution to the stability is exerted by non-binding side-chains of 4th and 5th amino acids. This effect is explained on the basis of spectroscopic data by the formation of a secondary fence shielding the Cu(II) binding site from the bulk of the solution. Such a structure, not reported previously, is of possible importance for the understanding of interactions of metal ions with proteins.

Cystatin C Based Peptidyl Diazomethanes as Cysteine Proteinase Inhibitors: Influence of the Peptidyl Chain Length

The peptidyl diazomethanes Cbz-Gly-CHN2, Boc-Val-Gly-CHN2, H-Leu-Val-Gly-CHN2, Cbz-Leu-Val-Gly-CHN2 and Cbz-Arg-Leu-Val-Gly-CHN2, with peptidyl portions modelled after the proposed cysteine proteinase interacting N-terminal segment of human cystatin C, were synthesized. Their efficiency as cysteine proteinase inhibitors was tested against papain, human cathepsin B and bovine cathepsin B. All, except Cbz-Gly-CHN2, were found to be irreversible inhibitors of the tested enzymes. Each addition of an amino acid residue to their peptidyl portions resulted in an increased inhibition rate of all three enzymes. These data suggest that the arginyl residue of the tetrapeptidyl diazomethane, and also the corresponding arginyl residue in native cystatin C, interact with a S4 substrate pocket subsite of both papain and cathepsin B. The most efficient inhibitor, Cbz-Arg-Leu-Val-Gly-CHN2, inhibited papain and cathepsin B with rate constants of the same order of magnitude as those for L-3-carboxy-trans-2,3-epoxypropionyl-leucylamido-(4-guanidin o)butane (E-64). The high water-solubility of Cbz-Arg-Leu-Val-Gly-CHN2 allowing it to be dissolved to molar concentrations without use of non-physiological additives, makes it suitable for in vitro and in vivo cysteine proteinase inhibition studies.

Synthesis of cysteine proteinase inhibitors structurally based on the proteinase interacting N-terminal region of human cystatin C.

Fibronectin contains two latent gelatinolytic enzymes, FN-gelatinase and FN-laminase that can be activated in the presence of Ca2+ from the purified cathepsin D-produced 190-kDa fibronectin fragment. The results of this work show that Achromobacter collagenase cleaves fibronectin and generates an active FN-gelatinase. In contrast to the cathepsin D digest, the collagenase digest directly exhibits gelatinolytic activity without additional activation. The gelatinolytic activity of the total collagenase digest can be inhibited by phenylmethanesulfonyl fluoride, a serine proteinase inhibitor and by pepstatin A, an aspartic-acid proteinase inhibitor. FN-laminase activity, when assayed with its synthetic substrate GPAGPR and also with laminin was revealed after separation of the collagenase digest of fibronectin on heparin Ultrogel. FN-gelatinase and FN-laminase activities were found in heparin unretained and heparin strongly retained fractions. These results have demonstrated that in contrast to cathepsin D, Achromobacter collagenase activates two matrix-degrading proteinases from fibronectin, FN-Gelatinase und FN-Laminase.

A peptidyl derivative structurally based on the inhibitory center of cystatin C inhibits bone resorption in vitro

Human cystatin C is a cysteine proteinase inhibitor belonging to the cystatin superfamily, which previously has been shown to inhibit bone resorption in bone organ culture. The aminoterminal segment, Arg(8)-Leu(9)-Val(10)-Gly(11) (RLVG), of the single polypeptide chain of cystatin C constitutes an essential part of its inhibitory center. In the present study, the effect of benzyloxycarbonyl-Arg(8)-Leu(9)-Val(10)-Gly(11)-diazomethane (Z-RLVG-CHN(2)) on bone resorption in vitro was compared with the effects of cystatin C and calcitonin. Bone resorption was assessed by the release of (45)Ca and (3)H from mouse calvarial bones prelabeled with [(45)Ca]CaCl(2) and [(3)H]-proline, respectively. Z-RLVG-CHN(2) concentration-dependently inhibited the release of (45)Ca and (3)H in bones stimulated by parathyroid hormone (PTH), with half-maximal inhibition obtained at 1 micromol/L. The inhibitory actions of Z-RLVG-CHN(2) and cystatin C were persistent, whereas action induced initially by calcitonin was lost with time. The inhibition caused by Z-RLVG-CHN(2) and cystatin C on PTH-stimulated (45)Ca release was observed after 6 h, whereas inhibition by calcitonin was seen already after 2 h. In contrast, the inhibitory effects of Z-RLVG-CHN(2) and cystatin C, as well as that of calcitonin, on (3)H release was seen already after 2 h. Z-RLVG-CHN(2), in which the reactive carboxyterminal diazomethane was substituted by nonreactive groups [-OH, -NH(2), or -N(CH(3))(2)], resulted in peptidyl derivatives, which, in contrast to Z-RLVG-CHN(2) and cystatin C, inhibited neither cysteine proteinases nor bone resorption. In contrast to wild-type cystatin C, recombinant human cystatin C with Gly substitutions for residues Arg(8), Leu(9), Val(10), and Trp(106), and with low or nonexistent affinity for cysteine proteinases, did not display any inhibitory effect on bone resorption. These data strongly indicate that Z-RLVG-CHN(2) inhibits bone resorption in vitro by a mechanism that seems primarily to be due to an inhibition of bone matrix degradation via cysteine proteinases. The data also corroborate the hypothesis that cystatin C inhibits bone resorption by virtue of its cysteine proteinase inhibitory capacity.

New antimicrobial cystatin C-based peptide active against gram-positive bacterial pathogens, including methicillin-resistant Staphylococcus aureus and multiresistant coagulase-negative staphylococci.

We describe the synthesis and antibacterial properties of a novel antimicrobial peptidyl derivative, (2S)‐2‐(Nα‐benzyloxycarbonyl‐arginyl‐leucylamido‐1‐[(E)‐cinnamoylamido]‐3‐methylbutane, structurally based upon the inhibitory centre of the human cysteine protease inhibitor, cystatin C. The derivative, here called Cystapep 1, displayed antibacterial activity against several clinically important gram‐positive bacteria. It displayed minimal inhibitory and bactericidal concentrations of about 16 μg/ml for both Staphylococcus aureus and Streptococcus pyogenes. In radial agar diffusion assays, groups A, B, C and G streptococci as well as staphylococci were generally susceptible to the action of Cystapep 1, whereas pneumococci and enterococci were less susceptible. No activity against gram‐negative bacteria was observed. Cystapep 1 also showed high activity against methicillin‐resistant S. aureus (MRSA) and multiantibiotic‐resistant coagulase‐negative staphylococci (CNS), suggesting that its mechanism of action differs from those of most currently used antibiotics.

Synthesis and antibacterial properties of peptidyl derivatives and cyclopeptides structurally based upon the inhibitory centre of human cystatin C: Dissociation of antiproteolytic and antibacterial effects

Cysteine protease‐inhibiting proteins of the cystatin superfamily can inhibit the replication of certain viruses and bacteria. The inhibitory centre of human cystatin C, the most widely distributed human cystatin, comprises three peptide segments. The present work describes the synthesis and antibacterial activity of 27 new peptidyl derivatives or cyclopeptides based upon the aminoterminal segment Arg8‐Leu9‐Val10‐Gly11. Fourteen of the new compounds displayed antibacterial activity against from 1 up to 9 of 17 clinically important bacterial species tested. Antiproteolytic activity of a compound was usually not required for its antibacterial capacity. Peptidyl diazomethanes generally had a very narrow antibacterial spectrum, inhibiting only Streptococcus pyogenes, whereas cyclopeptides and peptidyl derivatives of the general structure X‐Arg‐Leu‐NH‐CH(iPr)‐CH2‐NH‐Y had a much wider spectrum. The most potent of these substances displayed approximately equal minimal inhibitory and bactericidal concentrations of about 20 μg/ml for both Staphylococcus aureus and S. pyogenes and were devoid of antiproteolytic activity. Several of the new substances could protect mice against lethal intraperitoneal challenge with S. pyogenes. Though their target remains to be disclosed, the group of substances here reported might be promising for the development of antibacterial drugs and the discovery of novel principles of action.

Coordination abilities of neurokinin A and its derivative and products of metal-catalyzed oxidation

The classical tachykinins, substance P, neurokinin A and neurokinin B are predominantly found in the nervous system where they act as neurotransmitters and neuromodulators. Significantly reduced levels of these peptides were observed in neurodegenerative diseases and it may be suggested that this reduction may also result from the copper(II)-catalyzed oxidation. The studies of the interaction of copper(II) with neurokinin A and the copper(II)-catalyzed oxidation were performed. Copper(II) complexes of the neurokinin A (His-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met-NH(2)) and acetyl-neurokinin A (Ac-His-Lys-Thr-Asp-Ser-Phe-Val-Gly-Leu-Met-NH(2)) were studied by potentiometric, UV-Vis (UV-visible), CD (circular dichroism) and EPR spectroscopic methods to determine the stoichiometry, stability constants and coordination modes in the complexes formed. The histidine residue in first position of the peptide chain of neurokinin A coordinates strongly to Cu(II) ion with histamine-like {NH(2), N(Im)} coordination mode. With increasing of pH, the formation of a dimeric complex Cu(2)H(2)L(2) was found but this dimeric species does not prevent the deprotonation and coordination of the amide nitrogens. In the Ac-neurokinin A case copper(II) coordination starts from the imidazole nitrogen of the His; afterwards three deprotonated amide nitrogens are progressively involved in copper coordination. To elucidate the products of the copper(II)-catalyzed oxidation of the neurokinin A and Ac-neurokinin A, liquid chromatography-mass spectrometry (LC-MS) method and Cu(II)/hydrogen peroxide as a model oxidizing system were employed. Oxidation target for both studied peptides is the histidine residue coordinated to the metal ions. Both peptides contain Met and His residues and are very susceptible on the copper(II)-catalyzed oxidation.

Coordination Abilities of a Fragment Containing D1 and H12 Residues of Neuropeptide γ and Products of Metal-Catalyzed Oxidation

Stoichiometry, stability constants, and solution structures of copper(II) complexes of the (1-2,10-21)NPgamma (D(1)-A(2)-K(10)-R-H(12)-K-T-D-S-F-V-G-L-M(21)-NH(2)) and Ac-(1-2,10-21)NPgamma (Ac-D(1)-A(2)-K(10)-R-H(12)-K-T-D-S-F-V-G-L-M(21)-NH(2)) fragments of neuropeptide gamma were determined in aqueous solution in the pH range 2.5-10.5. The potentiometric and spectroscopic data (UV-vis, CD, EPR) show that an N-terminal Asp residue stabilizes significantly the copper(II) complexes with 1N {NH(2), beta-COO(-)} and 2N {NH(2), beta-COO(-), N(Im)} coordination modes of the (1-2,10-21)NPgamma as the result of coordination through the beta-carboxylate group. In a wide pH range of 4-9, the imidazole nitrogen of His(12) is coordinated to form a macrochelate. The (1-2,10-21)NPgamma peptide consists of 14 amino acid residues and contains an N-terminal amine group and the histidine residue, and as it is suggested, this fragment is able to bind two equivalents of copper(II) ions. The postmortem studies support the involvement of oxidative stress and the production of reactive oxygen species in neurodegenerative diseases. The susceptibility of proteins to oxidative damage is highly dependent on the specific properties of individual proteins, such as unique sequence motifs, surface accessibility, protein folding, and subcelluar localization. Metal-catalyzed oxidation of proteins is mainly a site-specific process in which one or a few amino acids at metal-binding sites on the protein are preferentially oxidized. To elucidate the products of the copper(II)-catalyzed oxidation of the (1-2,10-21)NPgamma and Ac-(1-2,10-21)NPgamma fragments of neuropeptide gamma, the liquid chromatography-mass spectrometry method and the use of Cu(II)/hydrogen peroxide as a model oxidizing system were employed. For both peptides, the oxidation of the methionine residue to methionine sulfoxide for the solutions containing peptide-hydrogen peroxide was observed. The oxidations of the histidine to 2-oxo-histidine and the methionine sulfoxide to sulfone were detected for the Cu(II)-Ac-(1-2,10-21)NPgamma-hydrogen peroxide 1:1:4 molar ratio system. Fragmentations of both peptides near the His residue were observed, supporting the participation of this (His) residue in the coordination of the copper(II) ions.

Potential allosteric modulators of the proteasome activity

Proteasome, consisting of a tube-shaped proteolytic core particle and attached to it regulatory modules, is a multifunctional enzymatic complex essential for the ubiquitin-proteasome metabolic pathway. Due to its immense involvement in regulation of cellular physiology, the proteasome is an acknowledged anticancer drug target and potential target to treat inflammatory or degenerative diseases. So far, competitive inhibitors of the core particle gain most consideration as drugs. We postulate that noncompetitively-acting small-molecule compounds would provide excellent means to precisely regulate actions of the proteasome. In this study, we evaluated five short peptides based on sequences of two proteins known to interact with the core proteasome: HIV-1 Tat and PA28/REG activator. We performed Circular Dichroism (CD), Fourier Transformed Infrared Spectroscopy (FTIR), and Nuclear Magnetic Resonance (NMR) analysis, supplemented by MD simulations, and tested influence of the peptides on performance of the core particle active sites and functioning of regulatory modules. We found that PP2-containing Tat peptides are noncompetitive inhibitors of the core, interfering with the actions of PA28alphabeta activator. In addition, at low concentrations the turn-prone Tat2 is able to activate the latent core. The random coil-structured PA28-derived peptides display only weak or nondetectable direct effects on the core activities, exhibiting, however, a positive cooperation with activity-enhancing actions of PA28alphabeta.