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PubMed1978

Empirical calculations on cyclic dipeptides. Conformations of serine, threonine and histidine residues.

Empirical conformational energy calculations were carried out for the dipeptides cyclo-(L-Ser-L-His) and cyclo-(L-Thr-L-His). Various DKP structures have been investigated to study side chain conformations through the DKP ring deformations, and prevalent conformers of monosubstituted and disubstituted dipeptides are discussed. The most stable conformations occur when both side chains are folded over a planar DKP ring, the imidazole ring being in the epsilon-tautomeric form. Theoretical results are consistent with those obtained from n.m.r. and crystallographic studies.

Histidine↗
PubMed1983

Ability of the immunomodulating dipeptide bestatin to activate cytotoxic mononuclear phagocytes.

The aminopeptidase inhibitor Bestatin [2S,3R-(3-amino-2-hydroxy-4-phenylbutanoyl)-L-leucine] was tested for both in vitro and in vivo macrophage activation and antitumor activity in various experimental tumor systems including the metastasizing ESb lymphoma system. Cultures of resting macrophages were rendered nonspecifically tumoricidal for the two lymphoma sublines ESb and 721 (ESb-Cl 18.1), for the mastocytoma P815X, for LS lymphoma cells, and for proliferating lymphoblasts from DBA/2, C57BL/6J, and CBA mice by exposure to Bestatin at 50 micrograms/ml culture medium. Untreated mononuclear phagocytes and Bestatin alone were not directly cytotoxic. Treatment of mice parenterally with Bestatin also induced cytotoxic macrophages for several tumor cells when tested in vitro. Normal peritoneal mouse macrophages from untreated mice or from control mice given injections of phosphate-buffered saline were not cytotoxic. The macrophage activation to lyse tumor cells was sharply dependent on the Bestatin dose and appeared about 24 hr after injection of the dipeptide. Bestatin activates macrophages through a T-cell-independent process to lyse tumor target cells, inasmuch as macrophages from homozygous athymic nude (nu/nu) mice treated i.p. with the dipeptide were also stimulated and cytotoxic for tumor cells. We present evidence that the macrophage is the prominent host cell responsible for tumor cell destruction in animals treated with Bestatin and rule out the possibility that natural killer cells play a major role in the experiments described.

Adjuvants, Immunologic↗
PubMed1982

Vascular clearance of embolic tumor cells and colloidal carbon and the levels of serum lysozyme following muramyl dipeptide administration.

Various doses of coded samples of the parent muramyl dipeptide entity and eight synthetic analogues were injected intravenously into C57BL/6J mice, and the extent of clearance of intravenously injected 5-[125I]iodo-2-deoxyuridine (125I-dUrd) radioactively labeled B16 tumor cells from the lung was measured 3 days later. The results of between one and four experiments with each compound demonstrated that five compounds, including the parent compound, produced dose-dependent increases in the loss of tumor cells from the lung. The same five compounds also caused an increase in the clearance of intravascular carbon clearance. Monitoring of serum lysozyme levels revealed no significant increases compared to controls at doses of up to 1 mg/mouse following muramyl dipeptide (MDP) administration i.v., i.p. or s.c. at any time up to 30 days after administration. Increased pulmonary tumor cell clearance did not occur after s.c. MDP administration and peaked 3 days after i.p. or i.v. MDP, reaching near normal levels by Day 7.

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed1995

Different effect of cyclosporin A on arthritides induced by a muramyl dipeptide analogue or the complete adjuvant in rats.

Muramyl dipeptide-Lys(L18) given by daily subcutaneous injection for 14 days induced arthritis in male Lewis, Fischer and nude rats, to a lesser degree in the last two than in the first strain. On the other hand, a single intradermal administration of Freund's complete adjuvant induced arthritis in Lewis and Fischer but not nude rats. Cyclosporin A (CsA) co-administered for 14 days markedly exacerbated the muramyl dipeptide-Lys(L18) induced arthritis (MIA) in rats of all three strains, but completely blocked the development of the adjuvant induced arthritis (AIA) in Lewis rats. Furthermore, AIA was transferred to recipient Lewis rats through spleen cells obtained from the donors with AIA, whereas MIA was not. Antibodies against type II collagen and DNA were not detected in sera from MIA or AIA rats. These data show a clear difference between MIA and AIA in the pattern of development of arthritis and suggest that delayed hypersensitivity reactions may be involved in the pathogenetic mechanisms of AIA, but not in MIA.

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed1978

Effects of isoprinosine, levamisole, muramyl dipeptide, and SM1213 on lymphocyte and macrophage function in vitro.

Four immunopotentiators, levamisole, isoprinosine, muramyl dipeptide, and SM1213, were analyzed in vitro for their effect on phytohemagglutinin-induced lymphocyte proliferation and lymphokine-induced macrophage proliferation and activation to kill Listeria monocytogenes. Isoprinosine augmented all three functions. Levamisole augmented lymphocyte proliferation and lymphokine-induced macrophage activation. Muramyl dipeptide and SM1213 induced macrophage activation directly. The effects of these agents on these cells at concentrations relevant to in vivo therapy support their immunopharmacologic application to modify cellular immunity.

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed2000

Thermodynamic origin of cis/trans isomers of a proline-containing beta-turn model dipeptide in aqueous solution: a combined variable temperature 1H-NMR, two-dimensional 1H,1H gradient enhanced nuclear Overhauser effect spectroscopy (NOESY), one-dimensional steady-state intermolecular 13C,1H NOE, and molecular dynamics study.

The cis/trans conformational equilibrium of the two Ac-Pro isomers of the beta-turn model dipeptide [13C]-Ac-L-Pro-D-Ala-NHMe, 98% 13C enriched at the acetyl carbonyl atom, was investigated by the use of variable temperature gradient enhanced 1H-nmr, two-dimensional (2D) 1H,1H nuclear Overhauser effect spectroscopy (NOESY), 13C,1H one-dimensional steady-state intermolecular NOE, and molecular dynamics calculations. The temperature dependence of the cis/trans Ala(NH) protons are in the region expected for random-coil peptides in H2O (delta delta/delta T = -9.0 and -8.9 ppb for the cis and trans isomers, respectively). The trans NH(CH3) proton indicates smaller temperature dependence (delta delta/delta T approximately -4.8 ppb) than that of the cis isomer (-7.5 ppb). 2D 1H,1H NOESY experiments at 273 K demonstrate significant NOEs between ProH alpha-AlaNH and AlaNH-NH(R) for the trans isomer. The experimental NOE data, coupled with computational analysis, can be interpreted by assuming that the trans isomer most likely adopts an ensemble of folded conformations. The C-CONH(CH3) fragment exhibits significant conformational flexibility; however, a low-energy conformer resembles closely the beta II-turn folded conformations of the x-ray structure of the related model peptide trans-BuCO-L-Pro-Me-D-Ala-NHMe. On the contrary, the cis isomer adopts open conformations. Steady-state intermolecular solute-solvent (H2O) 13C,1H NOE indicates that the water accessibility of the acetyl carbonyl carbons is nearly the same for both isomers. This is consistent with rapid fluctuations of the conformational ensemble and the absence of a highly shielded acetyl oxygen from the bulk solvent. Variable temperature 1H-nmr studies of the cis/trans conformational equilibrium indicate that the trans form is enthalpically favored (delta H degree = -5.14 kJ mole-1) and entropically (delta S degree = -5.47 J.K-1.mole-1) disfavored relative to the cis form. This demonstrates that, in the absence of strongly stabilizing sequence-specific interresidue interactions involving side chains and/or charged terminal groups, the thermodynamic difference of the cis/trans isomers is due to the combined effect of intramolecular and intermolecular (hydration) induced conformational changes.

Alanine↗
PubMedDate not supplied

Interference of rheumatoid factor activity by aspartame, a dipeptide methyl ester.

Circulating autoimmune complexes of IgM rheumatoid factors (RF) bound to the Fc portions of normal, polyclonal IgG antibodies are frequently present in humans with rheumatoid arthritis (RA). The sweet tasting methyl ester of L-Asp-L-Phe (aspartame or APM) was found to relieve pain and improve joint mobility in subjects with osteo- and mixed osteo/rheumatoid arthritis [Edmundson, A. B. and Manion, C. V. (1998). Clin. Pharmac. Ther. 63, 580-593]. These clinical observations prompted the testing of the inhibition by APM of the binding interactions of human IgM RFs with IgG Fc regions. The propensity of APM to inhibit IgM RF binding was assessed by competitive enzyme immunoassays with solid-phase human IgG. Ten RA serum samples and three purified monoclonal cryoglobulins, all of which had RF activity, were tested in this system. We found that the presence of APM significantly reduced the binding of IgM RFs. The inhibitory propensity of APM with monoclonal RF cryoglobulins was increased by the addition of CaCl(2) to the binding buffer. Similar inhibition of the binding of RA derived RFs to IgG was observed for Asp-Phe and its amidated derivative, indicating that the methyl ester is not required for APM's interaction with IgM antibodies. A human (Mez) IgM known to bind octameric peptides derived from the Fc portion of a human IgG(1) antibody was tested for binding of dipeptides by the Pepscan method of combinatorial chemistry. The relative binding constants of Asp-Phe and Phe-Asp were ranked among the highest values for 400 possible combinations of the 20 most common amino acids. Possible blocking interactions of APM were explored by computer-assisted docking studies with the model of a complex of an RF Fab with the Fc of a human IgG(4) antibody. Modeling of ternary immune complexes revealed a few key residues, which could act as molecular recognition sites for APM. A structural hypothesis is presented to explain the observed interference with RF reactivity by APM. Extrapolations of the current results suggest that APM may inhibit the binding of IgG in a substantial proportion of IgM RFs. Interference of RF reactivity, especially in RA patients, may alleviate the pain and immobility resulting from chronic inflammation of the joints.

Adult↗
PubMed2000

Design and synthesis of acidic dipeptide hydroxamate inhibitors of procollagen C-proteinase.

Procollagen C-proteinase (PCP) is essential for the cleavage of procollagen to collagen in the extracellular matrix of animals and is, therefore, of major relevance to studies of ectopic deposition of collagen during fibrosis. In this study, we describe the design and synthesis of acidic side chain hydroxamate dipeptide inhibitors of PCP having IC50 values in the range 0.1-10 microM that mimic the location of aspartic acid residues in the P1' and P2' positions (i.e. immediately C-terminal) of the PCP cleavage site in procollagen. Assays of PCP using purified human type I procollagen (a natural substrate of PCP) showed that the structure activity relationship of the inhibitors was improved with a glutamic acid mimic at the P1' position. The results also showed that the presence of an acidic side chain at the P2' position was not necessary for PCP inhibition. Marimastat and BB3103, which are highly effective inhibitors of matrix metalloproteinases and ADAMS proteinases, respectively, did not inhibit PCP.

Amino Acid Sequence↗
PubMed2001

Nanotube formation by hydrophobic dipeptides.

A wide range of applications has been suggested for peptide-based nanotubes, which first attracted considerable interest as model systems for membrane channels and pores. The intriguing and unprecedented observation of nanotube formation by supramolecular self-assembly of the four dipeptides L-Leu-L-Leu, L-Leu-L-Phe, L-Phe-L-Leu and L-Phe-L-Phe is described here. These simple compounds crystallize with hydrogen-bonded head-to-tail chains in the shape of helices with four to six peptide molecules per turn. The resulting structures have chiral hydrophilic channels with a van der Waals' diameter up to 10 A.

Crystallography, X-Ray↗
PubMed2002

A novel one-step approach for the preparation of alpha-amino acids, alpha-amino amides, and dipeptides from azetidine-2,3-diones.

A remarkable reaction of azetidine-2,3-diones with primary as well as secondary amines, and water is presented. Simply by varying the nucleophile, an unprecedented one-step synthesis of alpha-amino acids, alpha-amino amides, and dipeptides, was developed in both the racemic and optically pure forms. The current mechanistic hypothesis invokes a concerted process involving CO extrusion. However, a stepwise pathway can also account for these novel transformations.

Amines↗
PubMed2002

A theoretical study of potassium cation binding to glycylglycine (GG) and alanylalanine (AA) dipeptides.

By combining Monte Carlo conformational search technique with high-level density functional calculations, the geometry and energetics of K(+) interaction with glycylglycine (GG) and alanylalanine (AA) were obtained for the first time. The most stable K(+)-GG and K(+)-AA complexes are in the charge-solvated (CS) form with K(+) bound to the carbonyl oxygens of the peptide backbone, and the estimated 0 K binding affinities (DeltaH(0)) are 152 and 157 kJ mol(-1), respectively. The K(+) ion is in close alignment with the molecular dipole moment vector of the bound ligand, that is, electrostatic ion-dipole interaction is the key stabilizing factor in these complexes. Furthermore, the strong ion-dipole interaction between K(+) and the amide carbonyl oxygen atom of the peptide bond is important in determining the relative stabilities of different CS binding modes. The most stable zwitterionic (ZW) complex involves protonation at the amide carbonyl oxygen atom and is approximately 48 kJ mol(-1) less stable than the most stable CS form. The usefulness of proton affinity (PA) as a criterion for estimating the relative stability of ZW versus CS binding modes is examined. The effect of chain length and the nature of metal cations on cation-dipeptide interactions are discussed. Based on results of this study, the interaction of K(+) with longer peptides consisting of aliphatic amino acids are rationalized.

Alanine↗
PubMed2001

pH-dependence of complexion constants and complex mobility in capillary electrophoresis separations of dipeptide enantiomers.

The chiral separation of the LL- and DD-enantiomers of the dipeptides Ala-Tyr, Phe-Phe, and Asp-PheOMe has been investigated at pH 2.5 and pH 3.5 using beta-cyclodextrin (beta-CD), heptakis-(2,6-di-O-methyl)-beta-cyclodextrin, and heptakis-(2,3,6-tri-O-methyl)-beta-cyclodextrin as chiral selectors. According to electrospray mass spectrometry, heptakis-(2,6-di-O-methyl)-beta-cyclodextrin was a mixture of six isomers. Reversal of the enantiomer migration order upon increasing the buffer pH from 2.5 to 3.5 was observed for all peptides with beta-cyclodextrin, for Ala-Tyr and Phe-Phe in the presence of heptakis-(2,3,6-tri-O-methyl)-beta-cyclodextrin, and for Ala-Tyr using heptakis-(2,6-di-O-methyl)-beta-cyclodextrin. The migration behavior could be explained on the basis of the complexation constants and the mobilities of the peptide-cyclodextrin complexes. Both, the binding constants and complex mobilities decreased with increasing pH as the overall-charge of the peptides decreased. While the complexation constants primarily determined the migration order at pH 2.5, complex mobility dominated in most cases at pH 3.5.

Buffers↗
PubMed1992

Ketomethylene analogues of phosphoryl dipeptides related to phosphoramidon: synthesis and inhibition of proteases.

Non-rhamnose-containing phosphoramidon analogues, in which the amide bond was replaced by the isosteric ketomethylene group, have been synthesized in order to stabilize these compounds to peptidase degradation. The key step in this synthesis was suitable alkylation of a 4-ketodiester, prepared from Z-Leu chloromethyl ketone and dimethyl malonate. The ketomethylene dipeptide derivatives P-Leu psi (COCH2)(RS)Xaa-OMe (Xaa = Trp, Phe) are good inhibitors of thermolysin, ACE and specially enkephalinase.

Dipeptides↗
PubMed2005

Homoserine-derived cyclic sulfamidate as chiral educt for the diversity-oriented synthesis of lactam-bridged dipeptides.

Introduction of structural constraint into peptides is an effective way for studying their conformation-activity relationships. Conformationally restrained dipeptidyl lactams, important building blocks for the synthesis of peptidomimetics, have now been synthesized from N-[9-(9-phenylfluorenyl)]-L-aspartic acid alpha-cumyl beta-methyl diester as an inexpensive chiral educt. After selective reduction of the beta-methyl ester with diisobutylaluminum hydride (DIBAL-H), homoserine was treated with thionyl chloride, imidazole, and triethylamine to give sulfamidites. Diastereoisomers were separated by chromatography and oxidation of the major sulfamidite (2R,4S)- with catalytic ruthenium trichloride afforded sulfamidate. A series of gamma-lactam-bridged dipeptides was then obtained by ring opening of sulfamidate cumyl ester with a series of amino esters, selective cumyl ester removal, and lactam formation. The resulting dipeptidyl lactams possessed aliphatic, aromatic, amino, thioether, and carboxylate side chains. A gamma-lactam analog of Pro-Leu-Gly-NH2 (PLG), was synthesized to illustrate the potential for using this approach in the synthesis of biologically active peptide mimics.

Biomimetics↗
PubMed1990

Thermodynamic cycle-perturbation study of the binding of trifluoroacetyl dipeptide anilide inhibitors with porcine pancreatic elastase.

The variety of results of crystallographic studies of the serine proteases complexed with isocoumarin inhibitors presents a challenging problem to modeling methods and molecular energetics. Therefore, the thermodynamic cycle-perturbation technique has been used to study a model system of elastase and two peptidic inhibitors. Using the program AMBER, the technique correctly predicts changes of the binding constants for the trifluoroacetyl dipeptide inhibitors in comparison with available experimental (kinetic and crystallographic) data. However, the absolute values obtained are shown to be sensitive to the specific electrostatic interaction potential parameters used in the simulations. The reader and user are cautioned that thermodynamic cycle-perturbation results may be too optimistic by underestimating the accuracy of free energy values. This is especially a matter of concern for those cases where a direct comparison with experimental values is not possible, viz., (1) the stimulation of binding of novel compounds, (2) structurally uncertain binding sites, or (3) structurally different binding modes. With our best 4-31G* ESP (electrostatic potential) charges we were able to reproduce experimentally determined free energy differences (delta delta A) with an accuracy of about 1.5 kcal/mol. Dynamically induced structural changes in the binding site of elastase, and particularly changes in hydrogen-bond patterns of the binding site, are also reported.

Anilides↗
PubMed1991

Cyclic retro-inverso dipeptides with two aromatic side chains. I. Synthesis.

A series of cyclic retro-inverso dipeptides--2-[(4-hydroxy)benzyl]-5-benzyl-4,6(1H,2H,3H,5H)-pyrimidinedi one (c[mPhe-gTyr]), 2-benzyl-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[mTyr-gPhe]), and 2-benzyl-5-amino-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[(alpha-amino)mTyr-gPhe])--were synthesized in order to define the minimum structural requirements for binding affinity with opiate receptors and biological activity. Although the first two compounds lack a free amine proposed to be necessary for receptor recognition, the c[mPhe-gTyr] and c[mTyr-gPhe] analogues serve as model molecules in conformational studies of the target analogue, c[(alpha-amino)mTyr-gPhe]. The cis- and trans-c[(alpha-amino)mTyr-gPhe] contain all the functional groups such as the amine and phenolic groups in the tyrosine, and the aromatic group in the phenylalanine, necessary for opiate activity. In addition, the c[(alpha-amino)mTyr-gPhe] analogues possess similar geometries to the Tyr-Pro part of morphiceptin (Tyr-Pro-Phe-Pro-NH2) whose high mu-receptor activity is attributed to conformations with the Tyr-Pro amide bond in a cis conformation because the peptide bonds assume a cis conformation. However, both analogues are inactive in the guinea pig ileum and the mouse vas deferens assays. This may result from wrong orientation of the benzyl group of the gPhe residue with respect to the (alpha-amino)mTyr residue. Conformational studies of these molecules using 1H-nmr spectroscopy and molecular mechanics calculations will be reported in the following paper. Results of conformational analysis should provide information about backbone-side-chain interactions in the retro-inverso peptide chains since all the fundamental structural elements of the retro-inverso peptides are included in these model systems even though the peptide bonds must assume a cis conformation.

Amino Acid Sequence↗
PubMed1995

Conformational studies of heterochiral peptides with diastereoisomeric residues: crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo-isoleucine.

The x-ray diffraction analyses of three N- and C-terminally blocked L,D dipeptides, namely t-Boc-D-Leu-L-Leu-OMe (1), t-Boc-L-Ile-D-aIle-OMe (2), and t-Boc-D-aIle-L-Ile-OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final Rf actors of 0.077, 0.058, and 0.072 for (1), (2), and (3), respectively. Peptides 1-3 all assume a similar U-shaped structure with phi and psi torsion angles corresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*, D* and H* for D residues). The peptide backbones of 1-3 are almost superimposable [provided that the appropriate inversion of the chiral centers of (2) is made]. Side-chain conformations of Leu residues in peptide (1) are g- (tg-) for the L-Leu residue and the mirrored g+ (tg+) for the D-Leu residue; however, in peptides (2) and (3) the conformations of the isoconfigurational side chains of the Ile or allo-Ile residues are (g-t) t and (tg+) t for the L-Ile and the D-allo-Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of beta-branched residues statistically found in crystal structures of small peptides. The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main-chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent.

Crystallography, X-Ray↗
PubMed2001

Novel kinetic analysis of enzymatic dipeptide synthesis: effect of pH and substrates on thermolysin catalysis.

The point of maximum activity is specific to a particular substrate-enzyme system but may vary with different substrates and the same enzyme. The specificity of enzymes has, however, been generally reported only at their "optimal" pH. In this article, we introduce the Michaelis-Menten equation taking pH into account, and apply it to the pH-activity profile of the thermolysin-catalyzed dipeptide synthesis. It has been reported to date that the pH-activity profile of thermolysin follows a bell-shaped curve with a maximal activity at or near pH 7.0. The profiles obtained in this study, however, indicated that the optimal pH varied from 5.8 (for F-AspPheOMe) to 7.3 (for Z-ArgPheOMe), and the order of thermolysin activity was greatly dependent on the pH of reaction media. We have succeeded in evaluating the substrates-induced change of the dissociation states of the active site of thermolysin using the hydrophobicity of substrates. We have obtained apparent kinetic parameters which are independent of the pH of reaction media. The apparent specificity of thermolysin which were independent of pH of the reaction media was in order L-Leu > L-Asp > L-Arg > L-Ala > L-Gly > L-Val and Z > Boc = F at P1 and P2 positions, respectively.

Amino Acids↗