Dimitri Komiotis

Rapid and selective detritylation of primary alcohols using formic acid

Abstract A facile and chemoselective method of detritylation is described. Several polyfunctionalized examples were tested to emphasize the selectivity of the system over different protecting groups.

Antioxidant and chemopreventive properties of polyphenolic compounds derived from Greek legume plant extracts.

Recently, phytochemical compounds present in legumes have gained a lot of interest because they are considered to be possible chemopreventive agents. In the present study, 14 polyphenolic compounds were extracted and identified from two unique varieties of Leguminosae family plants cultivated in Greece and screened for their antioxidant and chemopreventive properties. Ten polyphenolic fractions, which are mainly mixtures of two compounds and five pure flavonoids, were isolated from the methanolic extracts of aerial plant parts of Vicia faba and Lotus edulis (Leguminosae), respectively. All of these fractions exhibited significant DPPH(*) radical scavenging capacity. Furthermore, they exerted significant protective activity against free radical-induced DNA damage. This activity was more potent against ROO(*) radical-induced DNA damage than against that induced by OH(*) radicals. Finally, they exhibited significant ability to inhibit the activity of the topoisomerase I enzyme. These results imply that the polyphenolic compounds identified in the fractions were responsible of the observed properties of the fractions and the initial extracts and indicate different mechanisms by which these phenolic compounds may act as chemopreventive agents.

Antiviral Unsaturated Nucleosides

In the search for effective, selective and nontoxic antiviral agents, a variety of nucleoside analogues have been synthesized, with different functionalities in the carbohydrate moiety. Unsaturated nucleoside analogues are recognized as an important class of biologically active compounds and appear to be prominent drugs in the management of several viral infections, including HSV, HIV, HBV, HCV and HCMV infections. Currently, unsaturated nucleoside mimetics, such as stavudine, abacavir and entecavir have been approved for the treatment of viral infections, while elvucitabine and � -L-2� - F-d4C are in clinical trials. The purpose of this review is to give an update of the recent developments on unsaturated nu- cleoside and nucleoside analogues, in both cyclic and acyclic forms, which possess promising therapeutic potential, mainly antiviral. It covers analogues with ring sizes from three to six and provides useful data, in the aim to enhance chemical reactivity or to study the fixation of the sugar conformation.

Dissipation, metabolism and sorption of pesticides used in fruit-packaging plants: Towards an optimized depuration of their pesticide-contaminated agro-industrial effluents.

Wastewaters from the fruit-packaging industry constitute a serious point source contamination with pesticides. In the absence of effective depuration methods, they are discharged in municipal wastewater treatment plants or spread to land. Modified biobeds could be an applicable solution for their treatment. We studied the dissipation of thiabendazole (TBZ), imazalil (IMZ), ortho-phenylphenol (OPP), diphenylamine (DPA) and ethoxyquin (EQ), used by the fruit-packaging industry, in anaerobically digested sewage sludge, liquid aerobic sewage sludge and in various organic substrates (biobeds packing materials) composed of soil, straw and spend mushroom substrate (SMS) in various volumetric ratios. Pesticide sorption was also determined. TBZ and IMZ showed higher persistence especially in the anaerobically digested sewage sludge (DT50=32.3-257.6d), in contrast to OPP and DPA which were rapidly dissipated especially in liquid aerobic sewage sludge (DT50=1.3-9.3d). EQ was rapidly oxidized mainly to quinone imine (QI) which did not persist and dimethyl ethoxyquinoline (EQNL, minor metabolite) which persisted for longer. Sterilization of liquid aerobic sewage sludge inhibited pesticide decay verifying the microbial nature of pesticide dissipation. Organic substrates rich in SMS showed the highest dissipation capacity with TBZ and IMZ DT50s of ca. 28 d compared to DT50s of >50 d in the other substrates. TBZ and IMZ showed the highest sorption affinity, whereas OPP and DPA were weakly sorbed. Our findings suggest that current disposal practices could not guarantee an efficient depuration of effluents from the fruit-packaging industry, whereas SMS-rich biobed organic substrates show efficient depuration of effluents from the fruit-packaging industry via accelerated dissipation even of recalcitrant fungicides.

3′‐Axial CH2OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM‐PBSA Calculations Suggest Why

Glycogen phosphorylase is a molecular target for the design of potential hypoglycemic agents. Structure‐based design pinpointed that the 3′‐position of glucopyranose equipped with a suitable group has the potential to form interactions with enzyme’s cofactor, pyridoxal 5′‐phosphate (PLP), thus enhancing the inhibitory potency. Hence, we have investigated the binding of two ligands, 1‐(β‐d‐glucopyranosyl)5‐fluorouracil (GlcFU) and its 3′‐CH2OH glucopyranose derivative. Both ligands were found to be low micromolar inhibitors with Ki values of 7.9 and 27.1 μm, respectively. X‐ray crystallography revealed that the 3′‐CH2OH glucopyranose substituent is indeed involved in additional molecular interactions with the PLP γ‐phosphate compared with GlcFU. However, it is 3.4 times less potent. To elucidate this discovery, docking followed by postdocking Quantum Mechanics/Molecular Mechanics – Poisson–Boltzmann Surface Area (QM/MM‐PBSA) binding affinity calculations were performed. While the docking predictions failed to reflect the kinetic results, the QM/MM‐PBSA revealed that the desolvation energy cost for binding of the 3′‐CH2OH‐substituted glucopyranose derivative out‐weigh the enthalpy gains from the extra contacts formed. The benefits of performing postdocking calculations employing a more accurate solvation model and the QM/MM‐PBSA methodology in lead optimization are therefore highlighted, specifically when the role of a highly polar/charged binding interface is significant.

Dideoxy fluoro-ketopyranosyl nucleosides as potent antiviral agents: Synthesis and biological evaluation of 2,3- and 3,4-dideoxy-3-fluoro-4-and -2-keto-β-D-glucopyranosyl derivatives of N4-benzoyl cytosine

Abstract The synthesis of the dideoxy fluoro ketopyranonucleoside analogues, 1-(2,3-dideoxy-3-fluoro-6-O-trityl-β-d-glycero-hexopyranosyl-4-ulose)-N 4-benzoyl cytosine (7a), 1-(3,4-dideoxy-3-fluoro-6-O-trityl-β-d-glycero-hexopyranosyl-2-ulose)-N 4-benzoyl cytosine (13a) and their detritylated analogues 8a and 14a, respectively, is described. Condensation of peracetylated 3-deoxy-3-fluoro-d-glucopyranose (1) with silylated N 4-benzoyl cytosine, followed by selective deprotection and isopropylidenation afforded compound 2. Routine deoxygenation at position 2′, followed by a deprotection-selective reprotection sequence afforded the partially tritylated dideoxy nucleoside of cytosine 6, which upon oxidation of the free hydroxyl group at the 4′-position, furnished the desired tritylated 2,3-dideoxy-3-fluoro ketonucleoside 7a in equilibrium with its hydrated form 7b. Compound 2 was the starting material for the synthesis of the dideoxy fluoro ketopyranonucleoside 13a. Similarly, several subsequent protection and deprotection steps as well as routine deoxygenation at position 4′, followed by oxidation of the free hydroxyl group at the 2′-position of the partially tritylated dideoxy nucleoside 12, yielded the desired carbonyl compound 13a in equilibrium with its hydrated form 13b. Finally, trityl removal from 7a/b and 13a/b provided the unprotected 2,3-dideoxy-3-fluoro-4-keto and 3,4-dideoxy-3-fluoro-2-ketopyranonucleoside analogues 8a and 14a, in equilibrium with their gem-diol forms 8b and 14b. None of the compounds showed inhibitory activity against a wide variety of DNA and RNA viruses at subtoxic concentrations, except 7a/b that was highly efficient against rotavirus infection. Nucleoside 7a/b also exhibited cytostatic activity against cells of various cancers. BrdU-cell cycle analysis revealed that the mechanism of cytostatic activity may be related to a delay in G1/S phase and initiation of programmed cell death.

Synthesis, Antiviral and Cytostatic Evaluation of Unsaturated Exomethylene and Keto D-Lyxopyranonucleoside Analogues

This report describes the synthesis of unsaturated exomethylene lyxopyranonucleoside analogues as potential biologically active agents. Commercially available 1,2,3,4‐tetra‐O‐acetyl‐α‐D‐lyxopyranose 1 was condensed with silylated thymine and uracil, respectively, deacetylated and acetalated to afford 1‐(2,3‐O‐isopropylidene‐α‐D‐lyxopyranosyl)thymine 4a and 1‐(2,3‐O‐isopropylidene‐α‐D‐lyxopyranosyl)uracil 4b. The new derivatives 1‐(2,3,4‐trideoxy‐4‐methylene‐α‐pent‐2‐enopyranosyl)thymine 8a and 1‐(2,3,4‐trideoxy‐4‐methylene‐α‐pent‐2‐enopyranosyl)uracil 8b were prepared via two different key intermediates, 7a, b and 13a, b in order to elucidate the influence of 2′,3′‐unsaturation and to clarify the difference between the keto and exomethylene group on the biological activity of the target molecules. Compounds 7a, b, 8a, b, and 13a, b were evaluated for their antiviral and cytostatic activity using several virus strains and cell lines. Whereas no marked antiviral activity was noticed, 13a and 13b showed a cytostatic activity that ranged between 7 and 23 μM for 13a and 26 and 38 μM for 13b against murine leukemia L1210, human lymphocyte Molt4/C8 and CEM cells, and human breast carcinoma MCF7 cells.

An Integrated In Silico Approach to Design Specific Inhibitors Targeting Human Poly(A)-Specific Ribonuclease

Poly(A)-specific ribonuclease (PARN) is an exoribonuclease/deadenylase that degrades 3′-end poly(A) tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN’s catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A) amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A) inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.

Branched-chain C-cyano pyranonucleosides: Synthesis of 3'-C-cyano & 3'-C-cyano-3'-deoxy pyrimidine pyranonucleosides as novel cytotoxic agents

Abstract This report describes the total and facile synthesis of 3′-C-cyano & 3′-C-cyano-3′-deoxy pyrimidine pyranonucleosides. Reaction of 3-keto glucoside 1 with sodium cyanide gave the desired precursor 3-C-cyano-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose (2). Hydrolysis followed by acetylation led to the 1,2,3,4,6-penta-O-acetyl-3-C-cyano-D-glucopyranose (4). Compound 4 was condensed with silylated 5-fluorouracil, uracil, thymine and N 4-benzoylcytosine, respectively and deacetylated to afford the target 1-(3′-C-cyano-β-D-glucopyranosyl)nucleosides 6a–d. Routine deoxygenation at position 3′ of cyanohydrin 2, followed by hydrolysis and acetylation led to the 3-C-cyano-3-deoxy-1,2,4,6-tetra-O-acetyl-D-allopyranose (10). Coupling of sugar 10 with silylated pyrimidines and subsequent deacetylation yielded the target 1-(3′-C-cyano-3′-deoxy-β-D-allopyranosyl)nucleosides 12a–d. The new analogues were evaluated for their antiviral and cytostatic activities. It was found that 6a was endowed with a pronounced anti-proliferative activity that was only 2- to 8-fold less potent than that shown for the parental base 5-fluorouracil. None of the compounds showed activity against a broad panel of DNA and RNA viruses.

A Facile, One‐Step Conversion of 6‐O‐Trityl and 6‐O‐TBDMS Monosaccharides into the Corresponding Formate Esters

A convenient method has been developed for a facile and high‐yield conversion of 6‐O‐tert‐butyldimethylsilyl and 6‐O‐trityl protected monosaccharides to their formate esters, which may serve as useful intermediates for the replacement of the primary hydroxyl group of sugars by other functional groups.