eleni siapi - Academia.edu (original) (raw)

Papers by eleni siapi

Journal of Mass Spectrometry, Feb 1, 2012

Mass spectral libraries represent versatile tools for the identification of small bioorganic mole... more Mass spectral libraries represent versatile tools for the identification of small bioorganic molecules. Libraries based on electron impact spectra are rated robust and transferable. Tandem mass spectral libraries are often considered to work properly only on the instrument that has been used to build the library. An exception from that rule is the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’. In various studies with data sets from different kinds of tandem mass spectrometric instruments, the outstanding sensitivity and robustness of this tandem mass spectral library search approach was demonstrated. The instrumental platforms tested, however, mainly included various tandem‐in‐space instruments. Herein, the results of a multicenter study with a focus on upfront and tandem‐in‐time fragmentation are presented. Five laboratories participated and provided fragment ion mass spectra from the following types of mass spectrometers: time‐of‐flight (TOF), quadrupole–hexapole–TOF, linear ion trap (LIT), 3‐D ion trap and LIT–Orbitrap. A total number of 1231 fragment ion mass spectra were collected from 20 test compounds (amiloride, buphenin, cinchocaine, cyclizine, desipramine, dihydroergotamine, dyxirazine, dosulepin, ergotamine, ethambutol, etofylline, mefruside, metoclopramide, phenazone, phentermine, phenytoin, sulfamethoxazole, sulfamoxole, sulthiame and tetracycline) on seven electrospray ionization instruments using 18 different instrumental configurations for fragmentation. For 1222 spectra (99.3%), the correct compound was retrieved as the best matching compound. Classified matches (matches with ‘relative average match probability’ >40.0) were obtained for 1207 spectra (98.1%). This high percentage of correct identifications clearly supports the hypothesis that the tandem mass spectral library approach tested is a robust and universal identification tool. Copyright © 2012 John Wiley & Sons, Ltd.

Pharmaceutics, Jan 27, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Current Analytical Chemistry, Aug 19, 2016

Thermochimica Acta, 2005

The protein collagen is the most predominant and important protein of the skin and therefore its ... more The protein collagen is the most predominant and important protein of the skin and therefore its physicochemical and thermal properties are important to be known. DSC has been applied in order to study the thermal changes caused by using different concentrations of the gentamycin antibiotic in fibrous membranes FM, named AMATCOL at different scanning rates. The thermal effect consisting of several peaks of the fibrous collageneous membrane alone or with different percentages of drug is simplified to a broad peak after 24 h equilibration time. The 35-70 • C endothermic effect attributed to the collapse of the tripple-helical domain of collagen due to the dehydration is affected by the presence of gentamycin. The endothermic peaks due to vaporization of bound water at the temperatures of 90-120 • C are also affected by the presence of gentamycin. This region consists of two peaks at low percentage of gentamycin and at higher percentages the peak near 120 • C decreases in intensity and finally disappears. The re-absorption of the water is more significant in the preparations containing gentamycin after 24 h equilibration time indicating that antibiotic makes a more stable complex with collagen molecules aiding this process. A minimum of reabsorption occurs when the concentration of gentamycin is 2% w/w in accordance with pore size and nitrogen gas permeability measurements. The collagen denaturation occurs at higher temperature when gentamycin is incorporated in fibrous membranes FM. This is an evidence that gentamycin stabilizes the cross-linkings between structural units (covalent, hydrophobic links) due to its interactions with collagen and water. Data resulted from differential scanning calorimetry (DSC) have been corroborated with those resulted from the porosity analysis. Specific morphology of fibrous collageneous membranes FM structure, containing macro-, micro-, and nano-pores resulted from freeze drying, acts on the gas and water vapor permeability, as well as water absorption. These characteristics are important in trans-dermal carriage of gentamycin contained in FM membranes.

Molecules, Jun 11, 2020

Traditional extraction remains the method-of-choice for phytochemical analyses. However, the abse... more Traditional extraction remains the method-of-choice for phytochemical analyses. However, the absence of an integrated analytical platform, focusing on customized, validated extraction steps, generates tendentious and non-reproducible data regarding the phytochemical profile. Such a platform would also support the exploration and exploitation of plant byproducts, which are a valuable source of bioactive metabolites. This study deals with the incorporation of (a) the currently sub-exploited high energy extraction methods (ultrasound (UAE)-and microwave-assisted extraction (MAE)), (b) experimental design (DOE), and (c) metabolomics, in an integrated analytical platform for the extensive study of plant metabolomics and phytochemical profiling. The recovery of carotenoids from apricot by-products (pulp) is examined as a case study. MAE, using ethanol as solvent, achieved higher carotenoid yields compared to UAE, where 1:1 chloroform-methanol was employed, and classic extraction. Nuclear magnetic resonance (NMR)-based metabolomic profiling classified extracts according to the variations in co-extractives in relation to the extraction conditions. Extracts with a lower carotenoid content contained branched-chain amino acids as co-extractives. Medium carotenoid content extracts contained choline, unsaturated fatty acids, and sugar alcohols, while the highest carotenoid extracts were also rich in sugars. Overall, the proposed pipeline can provide different the phytochemical fractions of bioactive compounds according to the needs of different industrial sectors (cosmetics, nutraceuticals, etc.).

Tetrahedron Letters, 2013

ABSTRACT An aniline- and two pyridine-derived (R)-BINOL-based P,N-containing phosphite ligands ha... more ABSTRACT An aniline- and two pyridine-derived (R)-BINOL-based P,N-containing phosphite ligands have been synthesized via a one-pot procedure. Treatment of the aniline-derived ligand with 1 equiv of [Rh(COD)2]BF4 yielded a mixture of a P,N-chelate complex and a biligated P-monodentate complex (exclusively obtained by treatment of the ligand with rhodium in a ratio of 2:1), while the pyridine analogues led to the corresponding P,N-bidentate complexes as unique species. For the first time, such phosphites were studied for rhodium-catalyzed enantioselective olefin hydrogenation. At room temperature, the aniline-derived ligand was found to be more active and selective compared to the pyridine analogues, which can probably be attributed to its different coordination mode and the formation of a biligated P-monodentate complex.

Thermochimica Acta, May 1, 2005

Several steroidal esters of alkylating agents have been synthesized and tested in vitro and in vi... more Several steroidal esters of alkylating agents have been synthesized and tested in vitro and in vivo in various experimental cancer types. 3␤-Hydroxy-17␣-aza-D-homo-5-androsten-7,17-dione-N,N-bis(2-chloroethyl) aminophenylacetate (I) is a highly active compound. DSC scans show differences between the alkylating agent alone and in conjugation with the steroidal part in the broadening and lowering of the phase transition of DPPC bilayers. These differences may in part explain the better pharmacokinetic profile and lower toxicity of conjugated congener I versus the alkylating agent alone.

Molecules, Mar 24, 2021

Biomolecules, Mar 9, 2022

Metabolites

The accumulation of cell biomass is associated with dramatically increased bioenergetic and biosy... more The accumulation of cell biomass is associated with dramatically increased bioenergetic and biosynthetic demand. Metabolic reprogramming, once thought as an epiphenomenon, currently relates to disease progression, also in response to extracellular fate-decisive signals. Glioblastoma multiforme patients often suffer misdiagnosis, short survival time, low quality of life, and poor disease management options. Today, tumor genetic testing and histological analysis guide diagnosis and treatment. We and others appreciate that metabolites complement translational biomarkers and molecular signatures in disease profiling and phenotyping. Herein, we coupled a mixed-methods content analysis to a mass spectrometry-based untargeted metabolomic analysis on plasma samples from glioblastoma multiforme patients to delineate the role of metabolic remodeling in biological plasticity and, hence, disease severity. Following data processing and analysis, we established a bioenergetic profile coordinated ...

Biochimica Et Biophysica Acta - Biomembranes, Dec 1, 2011

Small-angle and wide angle X-ray scattering Raman spectroscopy Differential scanning calorimetry ... more Small-angle and wide angle X-ray scattering Raman spectroscopy Differential scanning calorimetry Solid state NMR spectroscopy It is proposed that AT 1 antagonists (ARBs) exert their biological action by inserting into the lipid membrane and then diffuse to the active site of AT 1 receptor. Thus, lipid bilayers are expected to be actively involved and play a critical role in drug action. For this reason, the thermal, dynamic and structural effects of olmesartan alone and together with cholesterol were studied using differential scanning calorimetry (DSC), 13 C magicangle spinning (MAS) nuclear magnetic resonance (NMR), cross-polarization (CP) MAS NMR, and Raman spectroscopy as well as small-and wide angle X-ray scattering (SAXS and WAXS) on dipalmitoylphosphatidylcholine (DPPC) multilamellar vesicles. 13 C CP/MAS spectra provided direct evidence for the incorporation of olmesartan and cholesterol in lipid bilayers. Raman and X-ray data revealed how both molecules modify the bilayer's properties. Olmesartan locates itself at the head-group region and upper segment of the lipid bilayers as 13 C CP/MAS spectra show that its presence causes significant chemical shift changes mainly in the A ring of the steroidal part of cholesterol. The influence of olmesartan on DPPC/cholesterol bilayers is less pronounced. Although, olmesartan and cholesterol are residing at the same region of the lipid bilayers, due to their different sizes, display distinct impacts on the bilayer's properties. Cholesterol broadens significantly the main transition, abolishes the pre-transition, and decreases the membrane fluidity above the main transition. Olmesartan is the only so far studied ARB that increases the gauche:trans ratio in the liquid crystalline phase. These significant differences of olmesartan may in part explain its distinct pharmacological profile.

Submitted by Eιρήνη Κοτσίκου (eirhnhkot@ekt.gr) on 2016-04-13T09:29:43Z No. of bitstreams: 1 D3_P... more Submitted by Eιρήνη Κοτσίκου (eirhnhkot@ekt.gr) on 2016-04-13T09:29:43Z No. of bitstreams: 1 D3_PUBL_4_poster_EΙE_2.doc: 689664 bytes, checksum: 440f8f3f43997ac3ec60e7a7ec57bcf2 (MD5)

Current Research in Nutrition and Food Science Journal, 2016

Diketopiperazines (DKPs) are cyclic dipeptides which have been detected in a variety of natural p... more Diketopiperazines (DKPs) are cyclic dipeptides which have been detected in a variety of natural products, especially in thermally treated or fermented foods and beverages, providing a metallic bitter taste. DKPs, mainly due to their characteristic heterocyclic system, have been reported to exhibit a broad spectrum of biological activities including antimicrobial, antiviral, antitumor, antihyperglycaemic and antimutagenic. In the present study, several DKPs were identified in seven different Greek varieties of processed olives using HR-LC-MSn. The identification of DKPs in olive samples was achieved by comparison of their retention time and fragmentation pattern with reference DKP standards. The MSn spectra were identical to confirm the presence of specific compounds because their results associate both fragmentation pattern and fragments’ intensity. Nine compounds were found out of a total of 19 standard DKPs. The most prominent diketopiperazine was the cyclo(Phe-Phe) followed by an...

Current Analytical Chemistry, 2016

Journal of Chromatography B, 2017

Introduction: In the case of the MS-based metabolomics, the large number of false positives remai... more Introduction: In the case of the MS-based metabolomics, the large number of false positives remains a fundamental issue. Objective: The aim of this study was to develop a new strategy, which highlights the number of the reliable features i.e. the detected features that correspond to a consistent peak according to chromatographic and mass spectrometric criteria. Method: For the analysis blood samples from 20 chickens, which were administrated with naringin and 9 samples from control, were analyzed by UHPLC-HRMS (Orbitrap Velos). Two methodologies have been compared for data processing. In the first one (classical approach), all data in the 100-900 m/z mass-to charge range were included for the data processing procedure whereas for the newly developed methodology, the data were shred in 100 Da slices generating 8 datasets, which have been then subjected to the downstream MS data processing. Each dataset was treated separately and the m/z t R features obtained by either VIP's or t-test values were merged and used as the input for the construction of the general model. Results: The new methodology resulted to a 4-fold increase of the peaks that could be considered chromatographically and mass spectrometrically valid. Conclusion: A new strategy was reported on the detection of chromatographically reliable features during a metabolomic approach. The shredding of the LC-MS chromatograms into multiple m/z ranges increased the number of the identified chromatographically reliable features.

Peptides Across the Pacific: The Proceedings of the Twenty-Third American and the Sixth International Peptide Symposium, 2013

We extend to you a warm and sunny Aloha in celebration of the 23 rd American Peptide Symposium an... more We extend to you a warm and sunny Aloha in celebration of the 23 rd American Peptide Symposium and the 6 th International Symposium. The meeting theme, Peptides Across the Pacific, embraced the spirit of the scientific and social program. Peptides Across the Pacific encompassed the important role that peptide science currently plays in so many disciplines and explored the potential impact peptides can make in scientific fields that have yet to realize the utility of these wonderful molecules. The scientific program for 2013 was framed by distinguished lectures delivered by two renowned peptide chemists.

Journal of Natural Products, 2003

Two new sesterterpene metabolites, 16-acetoxy-dihydrodeoxoscalarin (1) and astakolactin (2), were... more Two new sesterterpene metabolites, 16-acetoxy-dihydrodeoxoscalarin (1) and astakolactin (2), were isolated from the sponge Cacospongia scalaris, collected from the gulf of Astakos, Greece, along with furoscalarol (3) and deoxoscalarin (4), which have not been reported from C. scalaris in the past. The unpalatability of the sponge to fish was traced by field feeding assays to the fractions containing dihydrofurospongin-2. The structures of the new metabolites were elucidated by interpretation of their NMR data and highresolution mass spectral measurements.

... Centre under the framework of "Digital Greece" (www.psifiakiellada.gr) and is co-fu... more ... Centre under the framework of "Digital Greece" (www.psifiakiellada.gr) and is co-funded by the European Union - European Regional Development Fund (80%) and by the Hellenic State (20%) through the Operational Programme Information Society (3rd CSF 2000-2006).