Raffaele Riccio

Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts.

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.

Determination of the relative stereochemistry of flexible organic compounds by Ab initio methods: conformational analysis and Boltzmann-averaged GIAO 13C NMR chemical shifts.

Ab initio calculations at the Hartree-Fock level with full-geometry optimization using the 6-31G(d) basis set, and GIAO (gauge including atomic orbitals) (13)C NMR chemical shifts, are presented here as a support in the study of the stereochemistry of low-polar organic compounds having an open-chain structure. Four linear stereoisomers, fragments of a natural product previously characterized by experimental (13)C NMR spectra, which possesses three stereogenic centers, 11 carbon atoms, and 38 atoms in total, were considered. Conformational searches, by empirical force-field molecular dynamics, pointed out the existence of 8-13 relevant conformers per stereoisomer. Thermochemical calculations at the ab initio level in the harmonic approximation of the vibrational modes, allowed the evaluation, at 298.15 K, of the standard Gibbs free energy of the conformers. The (13)C NMR chemical shift of a given carbon atom in each stereoisomer was considered as the average chemical shift value of the same atom in the different conformers. The averages were obtained by the Boltzmann distribution, using the relative standard free energies as weighting factors. Computed parameters related to linear correlation plots of experimental (13)C chemical shifts versus the corresponding computed average data allowed us to distinguish among the four stereoisomers.

Structure-Based Discovery of Inhibitors of Microsomal Prostaglandin E2 Synthase−1, 5-Lipoxygenase and 5-Lipoxygenase-Activating Protein: Promising Hits for the Development of New Anti-inflammatory Agents

Microsomal prostaglandin E(2) synthase (mPGES)-1 catalyzes the transformation of PGH(2) to PGE(2) that is involved in several pathologies like fever, pain, and inflammatory disorders. To identify novel mPGES-1 inhibitors, we used in silico screening to rapidly direct the synthesis, based on the copper-catalyzed 3 + 2 Huisgens reaction (click chemistry), of potential inhibitors. We designed 26 new triazole-based compounds in accordance with the pocket binding requirements of human mPGES-1. Docking results, in agreement with ligand efficiency values, suggested the synthesis of 15 compounds that at least in theory were shown to be more efficient in inhibiting mPGES-1. Biological evaluation of these selected compounds has disclosed three new potential anti-inflammatory drugs: (I) compound 4 displaying selectivity for mPGES-1 with an IC(50) value of 3.2 μM, (II) compound 20 that dually inhibits 5-lipoxygenase and mPGES-1, and (III) compound 7 apparently acting as 5-lipoxygenase-activating protein inhibitor (IC(50) = 0.4 μM).

Biological activity of saponins and saponin-like compounds from starfish and brittle-stars

Twenty-four saponins and saponin-like compounds, isolated from starfish and brittle-stars, have been tested in four in vitro tests, based upon bacterial and cell tissue cultures. Saponin-like compounds from brittle-stars have previously not been tested for biological activity. In an antibacterial test based on an agar diffusion test, the Gram positive bacterium S. aureus was affected by the polyhydroxylated steroidal glycosides, polyhydroxylated sterols and disulfated sterols. However, none of the 21 compounds tested were active against the Gram negative bacterium E. coli. In a cytotoxicity test all 21 compounds tested influenced the cells at a concentration of 100 micrograms/ml, while the cells were unaffected at 1 microgram/ml. In an antitumor test, 16 compounds were tested on two lymphoma cell lines. Inhibition of cell growth, at a concentration of 5 ng/ml, was seen for three polyhydroxylated sterols, in one cell line. Weak activity was seen in an antiviral test at a concentration of 10 micrograms/ml.

Two new guanidine alkaloids from the Mediterranean sponge Crambe crambe

Crambine A (1) and B (2) were isolated from the Mediterranean sponge Crambe crambe. Their structures were determined mainly by extensive NMR 2D experiments at 600 MHz.

Dactylolide, a New Cytotoxic Macrolide from the Vanuatu SpongeDactylospongia sp.

Dactylolide (1), a new cytotoxic 20-membered macrolide, was isolated from a marine sponge of the genus Dactylospongia collected off the coast of the Vanuatu islands. It co-occurred with other known bioactive macrolides: latrunculin A (2), laulimalide (3), isolaulimalide (4) and with the anthelminthic mycothiazole (5). The structure of 1, which is a minor metabolite, was elucidated by spectroscopy (mainly by 1D/2D NMR and MS techniques). It showed cytotoxic activity against the L1210 and SK-OV-3 tumor cell lines (63% and 40% inhibition at 3.2 μg/mL).

Ptilomycalin A, crambescidin 800 and related new highly cytotoxic guanidine alkaloids from the starfishes Fromia monilis and Celerina heffernani

Abstract Two novel pentacyclic guanidine alkaloids, celeromycalin 3 and fromiamycalin 4 , have been isolated from the New Caledonian starfishes Celerina heffernani and Fromia monilis , respectively. Also found in Celerina heffernani are the known ptilomycalin A ( 1 ) and crambescidin 800 ( 2 ), which latter has been also isolated from Fromia monilis . The new compounds exhibited an high cytotoxic activity like the previous crambescidins. These complex pentacyclic guanidines are typical sponges metabolites and their occurence in starfishes is noteworthy. Fromia monilis also contained the less active component 5 , made up from an hydroxyspermidine residue linked to a long chain ω-hydroxyacid.

Crambines C1 and C2 : two further ichthyotoxic guanidine alkaloids from the sponge Crambe crambe

Recently we reported the isolation and structure determination of two ichthyotoxic guanidine compounds, crambines A 111 and B 121, from a specimen of the encrusting Mediterranean sponge Crambe crambe Schmidt (Poecilosclerida; Crambidae) collected near Banyuls, France (1). The toxic n-BuOH extract from which these two compounds were isolated is a complex mixture. After repetitive chromatographies on Sephadex LH 20, Si gel, and polyvinylpolypyrrolidone, a further toxic Sakaguchi-positive fraction homogeneous by tlc could be isolated. This fraction contained a new guanidine alkaloid, crambine C1 131, accompanied by a series of homologues of 3 where n = 8, 10, and 11. The same compound was also isolated as a minor component from specimens of C. cram& collected off Favignana, Italy together with crambine A (major), crambine B, and a further minor compound, crambine C2 [4]. Crambine C1 was also isolated from a specimen of C. crambe collected near Nice, France, but in this last sample, crambine C1 was, together with crambine A, one of the major compounds of the toxic extract. Crambine C1 131 displayed an [M + HI+ ion at d z 48 1.390 in positive hrfabms, which corresponds to the molecular formula CZSH48N@3 for the corresponding free base. This molecular formula was further confirmed by negative fabms which exhibits peaks at d z 479 [M wand 5 15 [M H +Ha]-. These fab mass spectra also showed peaks

Isolation and structure elucidation of four new triterpenoid estersaponins from fruits of Pittosporum tobira AIT.

Abstract Four new triterpenoid estersaponins, tentatively designated as IIIA2 ( 1 ), IIIA3 ( 2 ), IIIB2 ( 3 ), and IIIC4 ( 4 ) have been isolated from fruits of Pittosporum tobira ait . and their structures elucidated by spectroscopic and chemical analyses. All the four compounds consist of an acylated pentacyclic triterpenoid aglycone which bears the same oligosaccharide portion. The crude saponin mixture (CIDI) was found to show significant in vitro and in vivo cytotoxicity in different human cancer cell lines.

9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain

The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.