Pietro Amodeo

Structural determination of the active site of a sweet protein. A 1H NMR investigation of pMNEI.

pMNEI, a single chain sweet protein related to monellin, has been studied by means of 1H NMR at 500 MHz. A partial sequential assignment performed by means of the MCD method allowed the determination of the secondary structure of a large portion of the β‐sheet of pMNEI that contains a likely ‘sweet finger’: the loop connecting the β‐strands from residue 59 to residue 78, corresponding to segment 16–35 of the A chain of monellin. The detailed three‐dimensional structure of the loop (Tyr66‐Ala67‐Ser68‐Asp69), determined from several interresidue and intraresidue NOEs and subsequent energy minimization, shows that the side chains or Tyr66 and Asp69 fit our model of the sweet receptor in a manner very similar to that of the side chains of Phe and Asp or aspartame.

Solution structure of human calcitonin in membrane‐mimetic environment: The role of the amphipathic helix

The 32 amino acid hormone human calcitonin was studied at pH 3.7 and 7.4 by multidimensional NMR spectroscopy in sodium dodecyl sulfate micelles at 310K. The secondary structure was obtained from nuclear Overhauser enhancement spectroscopy (NOESY), 3JHNα coupling constants, and slowly exchanging amide data. Three‐dimensional structures consistent with NMR data were generated by using distance geometry calculations. A set of 265 interproton distances derived from NOESY experiments, hydrogen‐bond constraints obtained from amide exchange, and coupling constants were used. From the initial random conformations, 30 distance geometry structures with minimal violations were selected for further refinement with restrained energy minimization. In micelles, at both pHs, the hormone assumes an amphipathic α‐helix from Leu9 to Phe16, followed by a type‐I β‐turn between residues Phe16 and Phe19. From His20 onward the molecule is extended and no interaction with the helix was observed. The relevance of the amphipathic helix for the structure–activity relationship, the possible mechanisms of interaction with the receptor, as well as the formation of fibrillar aggregates, is discussed. Proteins 32:314–323, 1998.

New role for leucyl aminopeptidase in glutathione turnover.

A manganese-dependent cysteinyl-glycine hydrolysing activity has been purified to electrophoretic homogeneity from bovine lens. The characterization of the purified enzyme (molecular mass of the native protein, molecular mass of the subunit and extensive primary structure analysis) allowed the unequivocal attribution of the cysteinyl-glycine hydrolysing activity, which is usually associated with alanyl aminopeptidase (EC 3.4.11.2) or membrane-bound dipeptidase (EC 3.4.13.19), to LAP (leucyl aminopeptidase; EC 3.4.11.1). Analysis of the pH dependence of Cys-Gly hydrolysis catalysed by LAP, supported by a molecular modelling approach to the enzyme-substrate conformation, gave insights into the ability of the enzyme to recognize Cys-Gly as a substrate. Due to the effectiveness of LAP in hydrolysing Cys-Gly (K(m)=0.57 mM, kcat=6.0x10(3) min(-1) at pH 7.4 and 25 degrees C) with respect to other dipeptide substrates, a new role for this enzyme in glutathione turnover is proposed.

Preclinical development of a novel class of CXCR4 antagonist impairing solid tumors growth and metastases.

The CXCR4/CXCL12 axis plays a role in cancer metastases, stem cell mobilization and chemosensitization. Proof of concept for efficient CXCR4 inhibition has been demonstrated in stem cell mobilization prior to autologous transplantation in hematological malignancies. Nevertheless CXCR4 inhibitors suitable for prolonged use as required for anticancer therapy are not available. To develop new CXCR4 antagonists a rational, ligand-based approach was taken, distinct from the more commonly used development strategy. A three amino acid motif (Ar-Ar-X) in CXCL12, also found in the reverse orientation (X-Ar-Ar) in the vMIP-II inhibitory chemokine formed the core of nineteen cyclic peptides evaluated for inhibition of CXCR4-dependent migration, binding, P-ERK1/2-induction and calcium efflux. Peptides R, S and I were chosen for evaluation in in vivo models of lung metastases (B16-CXCR4 and KTM2 murine osteosarcoma cells) and growth of a renal cells xenograft. Peptides R, S, and T significantly reduced the association of the 12G5-CXCR4 antibody to the receptor and inhibited CXCL12-induced calcium efflux. The four peptides efficiently inhibited CXCL12-dependent migration at concentrations as low as 10 nM and delayed CXCL12-mediated wound healing in PES43 human melanoma cells. Intraperitoneal treatment with peptides R, I or S drastically reduced the number of B16-CXCR4-derived lung metastases in C57/BL mice. KTM2 osteosarcoma lung metastases were also reduced in Balb/C mice following CXCR4 inhibition. All three peptides significantly inhibited subcutaneous growth of SN12C-EGFP renal cancer cells. A novel class of CXCR4 inhibitory peptides was discovered. Three peptides, R, I and S inhibited lung metastases and primary tumor growth and will be evaluated as anticancer agents.

Rare casbane diterpenoids from the Hainan soft coral Sinularia depressa.

A series of nine casbane diterpenes, compounds 5-13, exhibiting either cis or trans ring junctions were isolated from the Hainan soft coral Sinularia depressa. The structures of this group of compounds, the basic member of which was named depressin (5), were established by detailed spectroscopic analysis. In addition, the absolute configuration of the main metabolite, 10-hydroxydepressin (7), and of its epimer, 1-epi-10-hydroxydepressin (8), was determined by a combination of conformational analysis and the modified Moshers method. A stereochemical relationship between all isolated molecules was investigated by analyzing their circular dichroism profiles. Antiproliferative and antibacterial activities of the depressins were also evaluated.

Structural determinants of salmon calcitonin bioactivity: the role of the Leu-based amphipathic alpha-helix.

Salmon calcitonin (sCT) forms an amphipathic helix in the region 9–19, with the C-terminal decapeptide interacting with the helix (Amodeo, P., Motta, A., Strazzullo, G., Castiglione Morelli, M. A. (1999) J. Biomol. NMR 13, 161–174). To uncover the structural requirements for the hormone bioactivity, we investigated several sCT analogs. They were designed so as to alter the length of the central helix by removal and/or replacement of flanking residues and by selectively mutating or deleting residues inside the helix. The helix content was assessed by circular dichroism and NMR spectroscopies; the receptor binding affinity in human breast cancer cell line T 47D and the in vivo hypocalcemic activity were also evaluated. In particular, by NMR spectroscopy and molecular dynamics calculations we studied Leu23,Ala24-sCT in which Pro23 and Arg24 were replaced by helix inducing residues. Compared with sCT, it assumes a longer amphipathic α-helix, with decreased binding affinity and one-fifth of the hypocalcemic activity, therefore supporting the idea of a relationship between a definite helix length and bioactivity. From the analysis of other sCT mutants, we inferred that the correct helix length is located in the 9–19 region and requires long range interactions and the presence of specific regions of residues within the sequence for high binding affinity and hypocalcemic activity. Taken together, the structural and biological data identify well defined structural parameters of the helix for sCT bioactivity.

Structural analysis of BldR from Sulfolobus solfataricus provides insights into the molecular basis of transcriptional activation in archaea by MarR family proteins.

The multiple antibiotic resistance regulator (MarR) family constitutes a significant class of transcriptional regulators whose members control a variety of important biological functions such as regulation of response to environmental stress, control of virulence factor production, resistance to antimicrobial agents, and regulation of aromatic catabolic pathways. Although the majority of MarR family members have been characterized as transcriptional repressors, a few examples of transcriptional activators have also been reported. BldR is a newly identified member of this family that has been demonstrated to act as a transcriptional activator in stress response to aromatic compounds in the crenarchaeon Sulfolobus solfataricus. In this work, we report findings on the BldR X-ray crystal structure and present a molecular modeling study on the complex that this protein forms with its cognate DNA sequence, thus providing the first detailed description of the DNA-binding mechanism of an archaeal activator belonging to the MarR family. Two residues responsible for the high binding specificity of this transcriptional regulator were also identified. Our studies demonstrated that, in Archaea, the capability of MarR family members to act as activators or repressors is not related to a particular DNA-binding mechanism but rather could be due to the position of the binding site on the target DNA. Moreover, since genes encoding MarR proteins often control transcription of operons that encode for multisubstrate efflux pumps, our results also provided important insights for the identification of new tools to overcome the microorganisms multidrug resistance.

Design of μ selective opioid dipeptide antagonists

We have recently designed potent δ selective opioid antagonist dipeptides on the basis of a simple conformational analysis. Following a similar procedure we found a μ selective dipeptide antagonist, 2,6‐dimethyl‐Tyr‐d‐Phe‐NH2. Although its selectivity is not as high as those of the quoted δ selective dipeptides it has good in vitro activity and looks very promising for further development since the 2,6‐dimethyl‐Tyr‐D‐Phe message, like the δ selective 2,6‐dimethyl‐Tyr‐1,2,3,4‐tetrahydroisoquinoline‐3‐carboxylic acid counterpart, seems able to impart antagonism to longer peptides.

Conformational sampling of bioactive conformers: a low-temperature NMR study of 15N-Leu–enkephalin

Conformational studies of enkephalins are hampered by their high flexibility which leads to mixtures of quasi‐isoenergetic conformers in solution and makes NOEs very difficult to detect in NMR spectra. In order to improve the quality of the NMR data, Leu–enkephalin was synthesized with 15N‐labelled uniformly on all amide nitrogens and examined in a viscous solvent medium at low temperature. HMQC NOESY spectra of the labelled Leu–enkephalin in a DMSOd6/H2O mixture at 275 K do show numerous NOEs, but these are not consistent with a single conformer and are only sufficient to describe the conformational state as a mixture of several conformers. Here a different approach to the structure–activity relationships of enkephalins is presented: it is possible to analyse the NMR data in terms of limiting canonical structures (i.e. β‐ and γ‐turns) and finally to select only those consistent with the requirements of δ selective agonists and antagonists. This strategy results in the prediction of a family of conformers that may be useful in the design of new δ selective opioid peptides.

Physical and water sorption properties of chemically modified pectin with an environmentally friendly process.

A synthetic process was developed to modify pectin samples under solvent free conditions, obtaining pectin at increasing concentration of palmitic, oleic, and linoleic acids. The weight loss of the modified powders showed a degradation path very similar to the pure pectin, indicating that the pristine structure was preserved after the chemical modification. A decreasing mass of evaporating water on increasing the fatty acid concentration, in particular for the palmitic acid modification, indicated a reduced water sorption by the modified powders. Differential scanning calorimetry confirmed the thermogravimetric results and in addition indicated the crystallization of the lateral chains in the case of palmitic-acid-modified pectins. This result was confirmed by X-ray diffractograms of the palmitic acid samples, indicating the main crystallization of the form C, although possible orientation phenomena can be inferred. The sorption curves of either the pristine pectin or the modified samples showed a dual sorption behavior. The sorption curves were interpreted by the BET and GAB equations, both giving very similar results. Palmitic acid modification was very effective in reducing all sorption parameters, whereas in the case of oleic and linoleic acids, only at high concentrations was the hydrophobic influence detected.