Christos Kiritsis

The σ-hole phenomenon of halogen atoms forms the structural basis of the strong inhibitory potency of C5 halogen substituted glucopyranosyl nucleosides towards glycogen phosphorylase b.

C5 halogen substituted glucopyranosyl nucleosides (1‐(β‐D‐glucopyranosyl)‐5‐X‐uracil; X=Cl, Br, I) have been discovered as some of the most potent active site inhibitors of glycogen phosphorylase (GP), with respective Ki values of 1.02, 3.27, and 1.94 μM. The ability of the halogen atom to form intermolecular electrostatic interactions through the σ‐hole phenomenon rather than through steric effects alone forms the structural basis of their improved inhibitory potential relative to the unsubstituted 1‐(β‐D‐glucopyranosyl)uracil (Ki=12.39 μM), as revealed by X‐ray crystallography and modeling calculations exploiting quantum mechanics methods. Good agreement was obtained between kinetics results and relative binding affinities calculated by QM/MM‐PBSA methodology for various substitutions at C5. Ex vivo experiments demonstrated that the most potent derivative (X=Cl) toward purified GP has no cytotoxicity and moderate inhibitory potency at the cellular level. In accordance, ADMET property predictions were performed, and suggest decreased polar surface areas as a potential means of improving activity in the cell.

The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment.

C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides have been synthesized and studied as inhibitors of glycogen phosphorylase b (GPb). Kinetic experiments have shown that most of these compounds were low micromolar inhibitors of the enzyme. The best inhibitor was 1-(β-D-glucopyranosyl)-5-ethynyluracil (K(i)=4.7 μM). Crystallographic analysis of these compounds in complex with GPb revealed that inhibitors with a long C5-alkynyl group exploited interactions with β-pocket of the active site and induced significant conformational changes of the 280s loop compared to GPb in complex with compounds with a short C5-alkynyl group. The results highlight the importance in the length of the aliphatic groups used to enhance inhibitory potency for the exploitation of the hydrophobic β-pocket. The best of the inhibitors had also a moderate effect on glycogenolysis in the cellular lever with an IC(50) value of 291.4 μM.

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.

Study of the interaction among Notch pathway receptors, correlation with stemness, as well as their interaction with CD44, dipeptidyl peptidase-IV, hepatocyte growth factor receptor and the SETMAR transferase, in colon cancer stem cells

Abstract Context: The Notch signaling pathway is one of the most important pathways during normal development and implicated in self-renewal of adult stem cells and differentiation of progenitor cells. Abnormal expression of Notch receptors has been associated with many epithelial metaplastic and neoplastic lesions. Objective-materials and methods: In this particular study, it was determined the relative gene expression of Notch receptors after knockdown experiments in colon cancer stem cells (CSCs) and the gene expression changes in stemness transcription factors (Oct4, Sox2, Nanog), as well in dipeptidylpeptidase-4, CD44 antigen, Met proto-oncogene and in Metnase transposase. Results: In control CSCs Notch-2 had the higher expression, followed by Notch-1, Notch-3. Notch-4 demonstrated the lower gene expression among the receptors. The suppression of Notch-1 led to increased expression of Oct4 and Sox2, but in decreased gene expression of cMET, Setmar and CD44. The CD26 expression remained unchanged. The knockdown of Notch-2 led to decreased expression of all transcription factors. Notch-3 down regulation caused increased Oct4 gene expression, but decreased levels for the rest of the genes. Finally, the suppression of Notch-4 had the same effect as in receptor Notch-3. Discussion and conclusion: The above experimental data suggest the possible interaction between the four different receptors of Notch signaling pathway. The expression of CD26, cMET and N-methyltransferase Setmar was also changed. Finally, the stemness phenotype was changed in a different way each time, according to the receptor that was down regulated. All Notch receptors and particularly Notch-2 seem to play an important role in cancer stem cells.

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.

Rapid microwave-enhanced synthesis of C5-alkynyl pyranonucleosides as novel cytotoxic antitumor agents

A microwave-assisted, one-pot, coupling reaction for the synthesis of C5-alkynyl-uracil and cytosine glucopyranonucleosides has been developed. The reaction is carried out under standard Sonogashira coupling conditions from glucopyranonucleosides of 5-iodouracil or 5-iodocytosine and various terminal alkynes. All compounds were evaluated for their cytostatic and antiviral activity. The 5-phenylethynyluracil pyranonucleoside derivative 6a showed the most promising cytostatic activity (50% inhibitory concentration in the lower micromolar range). No meaningful antiviral activity was recorded.

Stereocontrolled Facile Synthesis and Biological Evaluation of (3′S) and (3′R)-3′-Amino (and Azido)-3′-Deoxy Pyranonucleosides

This article describes the synthesis of (3 ′S) and (3 ′R)-3 ′-amino-3 ′-deoxy pyranonucleosides and their precursors (3 ′S) and (3 ′R)-3 ′-azido-3 ′-deoxy pyranonucleosides. Azidation of 1,2:5,6-di-O-isopropylidene-3-O-toluenesulfonyl-α-D-allofuranose followed by hydrolysis and subsequent acetylation afforded 3-azido-3-deoxy-1,2,4,6-tetra-O-acetyl-D-glucopyranose, which upon coupling with the proper silylated bases, deacetylation, and catalytic hydrogenation, obtained the target 3 ′-amino-3 ′-deoxy-β-D-glucopyranonucleosides. The desired 1-(3 ′-amino-3 ′-deoxy-β-D-allopyranosyl)5-fluorouracil was readily prepared from the suitable imidazylate sugar after azidation followed by a protection/deprotection sequence and reduction of the unprotected azido precursor. No antiviral activity was observed for the novel nucleosides. Moderate cytostatic activity was recorded for the 5-fluorouracil derivatives.

Comparison of the Growth Curves of Cancer Cells and Cancer Stem Cells

A fundamental problem in cancer research is identification of the cells responsible for tumor formation. The latest field of cancer research has revealed the existence and role of cancer stem cells (CSCs). These findings support the idea that malignancies originate from a small fraction of cancer cells that show self-renewal and multi- or pluripotency. Identification of this CSC population has important implications for the management of cancer patients, including diagnostic and predictive laboratory assays as well as novel therapeutic strategies that specifically target CSCs. In this study, we investigated the growth rates of CSC populations for comparison with cancer cell lines. To construct the growth curves, blood-derived CSCs were isolated from patients with breast, colon, or lung cancer and cultured in vitro. Quantitative real-time PCR was then performed to identify CSCs in the samples. We found that CSCs did not follow the common pattern of a typical growth curve of mammalian cells in contrast to the cancer cell lines. This observation of rapidly growing CSCs indicates their involvement in tumor formation.