Improvement on binding of chondroitin sulfate derivatives to midkine by increasing hydrophobicity

The relative binding affinities of sulfated, fully protected chondroitin sulfate oligosaccharides for midkine are much higher than those displayed by the natural deprotected sequences.

Detection and quantitative analysis of two independent binding modes of a small ligand responsible for DC-SIGN clustering

Multiple binding modes at the same binding site can explain the higher binding affinity of a pseudotrimannotrioside compared to a pseudomannobioside.

NMR structural studies of oligosaccharides related to cancer processes

A summary of spectroscopic methods for structural and conformational elucidation of bioactive carbohydrates based on nuclear magnetic resonance (NMR) is described. The formation of carbohydrate-protein complexes is often the initial step of biological responses. Therefore, knowledge about the structural factors that stabilize the complex may be relevant and contribute to predict the structural/conformational requirements of new drugs acting as agonists. Two examples of medical significance in the cancer research field are discussed (1) conformational studies of glycoconjugates related to antitumour vaccines (2) conformational analysis of glycosaminoglycans and the interaction heparin-fibroblast growth factor (FGF).

Tachykinins and tachykinin receptors: structure and activity relationships

In addition to the classical neurotransmitters, acetylcholine and noradrenaline, a wide number of peptides with neurotransmitter activity have been identified in the past few years. Among them, the tachykinins substance P (SP), neurokinin A (NKA) and neurokinin B (NKB) appear to act as mediators of nonadrenergic, noncholinergic (NANC) excitatory neurotransmission. Tachykinins interact with specific membrane proteins, belonging to the family of G protein-coupling cell membrane receptors. Until now, three tachykinin receptors termed NK1 (NK1R), NK2 (NK2R) and NK3 (NK3R) have been cloned in different species. A large amount of reports suggests that these peptides are involved in nociception and neuroimmunomodulation, and in the development of different diseases such as bronchial asthma, inflammatory bowel syndrome and psychiatric disorders. Tachykinin receptor antagonists are therefore promising, therapeutically relevant agents. However, and in spite of extensive research, the obtention of selective antagonists of tachykinin receptors have revealed very difficult. An understanding of how ligands interact with their receptors is essential to permit a rational design of compounds acting selectively at the tachykinin receptor level. The major aim of the present article is to review the structure-activity data that exist for tachykinins and their receptors, with the purpose of getting insight into basic structural requirements that determine ligand/receptor interaction.

The activation of fibroblast growth factors by heparin: synthesis, structure, and biological activity of heparin-like oligosaccharides

An effective strategy has been designed for the synthesis of oligosaccharides of different sizes structurally related to the regular region of heparin; this is illustrated by the preparation of hexasaccharide 1 and octasaccharide 2. This synthetic strategy provides the oligosaccharide sequence containing a D-glucosamine unit at the nonreducing end that is not available either by enzymatic or chemical degradation of heparin. It may permit, after slight modifications, the preparation of oligosaccharide fragments with different charge distribution as well. NMR spectroscopy and molecular dynamics simulations have shown that the overall structure of 1 in solution is a stable right-hand helix with four residues per turn. Hexasaccharide 1 and, most likely, octasaccharide 2 are, therefore, chemically well-defined structural models of naturally occurring heparin-like oligosaccharides for use in binding and biological activity studies. Both compounds 1 and 2 induce the mitogenic activity of acid fibroblast growth factor (FGF1), with the half-maximum activating concentration of 2 being equivalent to that of heparin. Sedimentation equilibrium analysis with compound 2 suggests that heparin-induced FGF1 dimerization is not an absolute requirement for biological activity.

Changes in the expression of tachykinin receptors in the rat uterus during the course of pregnancy

In the mammalian female reproductive tract, tachykinin neuropeptides, such as substance P (SP), are localized to a population of sensory fibers and their precise physiological role is still unknown. The aim of the present study was to characterize the population of tachykinin receptors in the pregnant rat uterus and to assess their regulation during the course of pregnancy and after delivery. The expression of the tachykinin NK(1) receptor (NK(1)R), the tachykinin NK(2) receptor (NK(2)R), and the tachykinin NK(3) receptor (NK(3)R) in uteri from rats at different stages of pregnancy and on Day 1 postpartum was investigated by using a semiquantitative reverse transcription-polymerase chain reaction. The contractile effect of tachykinin receptor agonists acting selectively on the NK(1)R, the NK(2)R, or the NK(3)R was investigated by conventional organ bath techniques. Serum levels of estrogen and progesterone were measured by RIA. Our data show that the expression and function of NK(1)R and NK(3)R varied along the course of pregnancy and at postpartum. Uterine NK(2)R mRNA levels remain stable during the course of pregnancy and at Day 1 postpartum; and the contractions elicited by activating selectively the NK(2) receptor in the presence of the neutral endopeptidase inhibitor phosphoramidon (1 microM) were similar in early, mid, or late pregnancy. These results show that the expression and function of tachykinin receptors within the uterus vary with reproductive state and length of gestation, supporting a role for tachykinins in pregnancy and/or parturition in the rat.

Inositolphosphoglycan mediators structurally related to glycosyl phosphatidylinositol anchors: synthesis, structure and biological activity

The preparation of the pseudopentasaccharide 1a, an inositol-phosphoglycan (IPG) that contains the conserved linear structure of glycosyl phosphatidylinositol anchors (GPI anchors), was carried out by using a highly convergent 2+3-block synthesis approach which involves imidate and sulfoxide glycosylation reactions. The preferred solution conformation of this structure was determined by using NMR spectroscopy and molecular dynamics simulations prior to carrying out quantitative structure--activity relationship studies in connection with the insulin signalling process. The ability of 1a to stimulate lipogenesis in rat adipocytes as well as to inhibit cAMP dependent protein kinase and to activate pyruvate dehydrogenase phosphatase was investigated. Compound 1a did not show any significant activity, which may be taken as a strong indication that the GPI anchors are not the precursors of the IPG mediators.

Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains

BACKGROUND

Many plants respond to pathogenic attack by producing defense proteins that are capable of reversible binding to chitin, a polysaccharide present in the cell wall of fungi and the exoskeleton of insects. Most of these chitin-binding proteins include a common structural motif of 30 to 43 residues organized around a conserved four-disulfide core, known as the 'hevein domain' or 'chitin-binding' motif. Although a number of structural and thermodynamic studies on hevein-type domains have been reported, these studies do not clarify how chitin recognition is achieved.

RESULTS

The specific interaction of hevein with several (GlcNAc)(n) oligomers has been studied using nuclear magnetic resonance (NMR), analytical ultracentrifugation and isothermal titration microcalorimetry (ITC). The data demonstrate that hevein binds (GlcNAc)(2-4) in 1:1 stoichiometry with millimolar affinity. In contrast, for (GlcNAc)(5), a significant increase in binding affinity is observed. Analytical ultracentrifugation studies on the hevein-(GlcNAc)(5,8) interaction allowed detection of protein-carbohydrate complexes with a ratio of 2:1 in solution. NMR structural studies on the hevein-(GlcNAc)(5) complex showed the existence of an extended binding site with at least five GlcNAc units directly involved in protein-sugar contacts.

CONCLUSIONS

The first detailed structural model for the hevein-chitin complex is presented on the basis of the analysis of NMR data. The resulting model, in combination with ITC and analytical ultracentrifugation data, conclusively shows that recognition of chitin by hevein domains is a dynamic process, which is not exclusively restricted to the binding of the nonreducing end of the polymer as previously thought. This allows chitin to bind with high affinity to a variable number of protein molecules, depending on the polysaccharide chain length. The biological process is multivalent.

alpha-Alkyl-alpha-Amino-beta-Lactam Peptides: Design, Synthesis, and Conformational Features

Remarkable asymmetric induction is achieved in the alkylation of the lithium enolate of the beta-lactam 1. This allows the first time access to a new family of peptidomimetics 2 with predictable conformational constraints.

1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase

1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogues of the antibacterial drug brodimoprim (2,4-diamino-5-(3', 5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogues had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making additional interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4, 6-dicarboxylate brodimoprim analogues. The spectra from both complexes showed four resolved signals for the four NHeta protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analogue. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally observed for such nuclei. This pattern of deshielding is that expected for a symmetrical end-on interaction of the carboxylate oxygens with the NHeta12 and NHeta22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogues and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analogue does not feature any deshielded Arg NHeta protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to determine whether the 6-carboxylate in this analogue is interacting directly with any residue in the protein. 1H/15N HSQC spectra have been fully assigned for the complexes with the three brodimoprim analogues and chemical shift mapping used to explore interactions in the binding site. The 1H signals of the bound ligands for all three brodimoprim analogues have been assigned. Their 1H chemical shifts were found to be fairly similar in the different complexes indicating that the 2, 4-diaminopyrimidine and the benzyl ring are binding in essentially the same binding sites and with the same overall conformation in the different complexes. The rotation rate about the NepsilonCzeta bond in the brodimoprim-4,6-dicarboxylate complex with DHFR has been determined from a zz-HSQC exchange experiment, and its value is quite similar to that observed in the DHFR.methotrexate complex (24 +/- 10 s-1 at 8 degrees C and 50 +/- 10 s-1 at 15 degrees C, respectively). The 1H and 15N chemical shift differences of selected amide and guanidino NH groups, measured between the DHFR complexes, provided further evidence about the interactions involving Arg57 with the 4-carboxylate and 4,6-dicarboxylate brodimoprim analogues.

Correlated bond rotations in interactions of arginine residues with ligand carboxylate groups in protein ligand complexes

The 1H/15N HSQC NMR spectra of complexes of Lactobacillus casei dihydrofolate reductase containing methotrexate recorded at 1 degree C show four resolved signals for the four NH(eta) protons of the Arg57 residue. This is consistent with hindered rotation in the guanidino group resulting from interactions with the alpha-carboxylate of methotrexate. Increasing the temperature causes exchange line-broadening and coalescence of signals. Rotation rates for the N(epsilon)C(zeta) and C(zeta)N(eta) bonds have been calculated from lineshape analysis and from zz-HSQC exchange experiments. The interactions between the methotrexate alpha-carboxylate group and the Arg57 guanidino group decrease the rotation rates for the N(epsilon)C(zeta) bond by about a factor of 10 and those for the C(zeta)N(eta) bonds by more than a factor of 100 with respect to their values in free arginine. Furthermore, the relative rates of rotation about these two bonds are reversed in the protein complexes compared with their values in free arginine indicating that there are concerted rotations about the N(epsilon)C(zeta) bond of the Arg57 guanidino group and the C'C(alpha) bond of the glutamate alpha-carboxylate group of methotrexate.

NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase

1H-NMR and 15N-NMR signal assignments have been made for the eight arginine residues in Lactobacillus casei dihydrofolate reductase in its binary complex with methotrexate and in its ternary complex with methotrexate and NADPH. 1H-NMR chemical shifts for the guanidino groups of two of the arginines (Arg57 and Arg43) were sensitive to different modes of binding of the guanidino groups with charged oxygen atoms of the ligands. In the complexes formed with methotrexate, Arg57 showed four non-equivalent NH eta proton signals indicating hindered rotation about the N epsilon-C zeta and C zeta-N eta bonds. The NH eta 12 and NH eta 22 protons showed large downfield shifts, which would be expected for a symmetric end-on interaction of these protons with the charged oxygen atoms of a carboxylate group in methotrexate. These effects were not observed for the complex formed with trimethoprim, which does not contain any carboxylate groups. In the complex formed with NADPH present, Arg43 showed a large downfield chemical shift for its NH epsilon proton and a retardation of its rate of exchange with water. This pattern of deshielding contrasts with that detected for Arg57 and is that expected for a side-on interaction of the guanidino group protons with charged oxygen atoms of the ribose 2'-phosphate group of NADPH.