Institute of Chemical Biology - National Hellenic Research Foundation

About Group Structure Funding Publications

Overview

Mission

The group’s mission is to discover novel bioactive compounds and biomarkers, utilizing state-of-the-art techniques in the fields of computational chemistry and bioanalysis.

Research Focus

Discover/design novel antimicrobial hit compounds
Identify biomarkers for Intrauterine Growth Restriction in Neonatology

Main Scientific Directions

Structure Based Design of Bioactive Compounds with applications in Health

In this direction, in silico tools were applied (Virtual screening of chemo-libraries with pharmacophore models, Molecular docking to target proteins, Molecular Dynamics Simulation, Prediction of physicochemical properties and QSAR) with the main purpose (a) the identification of hit compounds with affinity over a specific biological target, (b) guiding the optimization of precursors to lead compounds (hit-to-lead optimization), and (c) explaining the mechanisms of action of specific endogenous bioactive molecules or drugs.

The main protein targets were: (a) 14a Lanosterol dimethylase for the design of compounds with antimicrobial properties. Emphasis was given on resistant strains of the fungi Aspergillus Fumigatus and Candida Albicans. At the same time, based on structure-action studies, analogs of heterocyclic compounds (e.g., thiadiazoles, triazoles and oxadiazoles) were designed and synthesized (with external collaborators) and studied on microbial strains. (b) P2X7 receptor, 5 Lipoxygenase and cyclooxygenase 2 for the identification / design of compounds with anti-inflammatory action.

Targeted Chemical Analysis and Metabolomics

This direction includes: (a) Extraction and determination of bioactive compounds from plant, animal substrates as well as human biological samples. During the period 2018-2021 the recovery of carotenoids from food byproducts was studied by implementing experimental design (DOE)-based high energy extraction techniques using conventional and innovative green extraction solvents (natural deep eutectic solvents, NADES), and high throughput LC-MS and NMR analytical techniques. (b) Metabolomics (targeted and holistic) with applications in health. Focus was given on the study of the effects of bioactive compounds as well as the identification of putative biomarkers of disease through clinical trials in collaboration with University hospitals.
One of the group’s flagship projects from 2018-2021 was the identification of the mechanisms underlying Intrauterine growth restriction (IUGR) pathology which refers to a condition in which a fetus is unable to achieve its genetically determined intrinsic growth potential. By applying metabolomics on umbilical cord and maternal blood specimens we managed to identify secondary metabolites that characterize IUGR pathology and could lead to the use of biomarkers in the blood of pregnant women in order to develop new diagnostic tools for IUGR. The emergence of potential biomarkers at an early stage of pregnancy could help halt the negative effects of IUGR either through medication or nutritional intervention for the mother.

Positioning and Role within the Institute and the Center

The Research Group is part of the Molecular Analysis Laboratory of the Institute of Chemical Biology of the National Hellenic Research Foundation. Its expertise in computational chemistry and chemical analysis has positioned it in the initial steps of the Institute’s Drug Discovery pipeline.
The group was also responsible for setting up and running the analytical chemistry services (mainly based on LC-MS and NMR) of ICB.

Major outcomes and achievements

Receiving funding from 7 competitive funded research projects (>0.5 M€ for the group).
Receiving funding from industry (75 k €)
Coordinator and/or scientific responsible in 6 funding projects.
Author or coauthor of 50 publications (2018-2021) from which the corresponding ones for the years 2020 and 2021 are reported in the M.Zervou group evaluation.
Expanded network of collaborating industries.
3 PhD students (I supervised) successfully defended their theses.
Moved to the private sector (research mobility, Greek law 4310) and practice soft skills / acquire relevant experience.
Elected Head of the Department of Food Science and Technology – University of West Attica.
Elected director of the University Established Laboratory of Chemistry, Analysis and Design of Food Processes

MEMBERSΗIPS & reviewing activities 2018-2019
2018, 2019	Evaluator, European Commission, H2020 – MSCA INDIVIDUAL FELLOWSHIPS
2018	Evaluator, HFRI (1st call for PostDoc Fellowships)

Targets and Strategic plan

In the recent two years (as a visiting researcher of NHRF), my research group’s interests have been further moved towards the exploration of the role of the intestinal microbiome in the absorption of nutrients and in the biological mechanisms associated with diseases of socioeconomic interest. The intestinal microbiome has been a very “hot target” since it has been shown to contribute to the prevention of pathological conditions thus the regulation of its variability and activity may improve overall human health. Research in this field has led to the design of new food products, nutritional supplements and more specialized foods for special medical purposes (medical food) utilizing ingredients such as pre- and prebiotics and specialized phytochemicals.

Towards this direction we have initiated the study of the interaction of the infant intestinal microbiome with specialized infant formulas rich in synbiotic components (see SYNBIO project funded from private company), as well as the study of the role of the microbiome in bone remodeling with the aim to design innovative food supplements (see funded project OSTEOME). This research activity is a common vision for colleagues from both hosts, who are already involved in the abovementioned running funded projects.

Since my appointment as an Associate Professor at the University of West Attica, a personal goal is the establishment of a bi-institutional team (Institute of Chemical Biology / NHRF – Department of Food Science and Technology /University of West Attica) with complementarity in both know-how and equipment, which will support this “health through microbiome” research activity with multidisciplinary approaches. Towards this direction, two proposals have been already submitted (2021) for funding with the participation of researchers / faculty members from both organizations.

In parallel, necessary equipment to assist this research direction is acquired (i.e., gut simulating bioreactor) and will be up and running during 2022, while a careful selection of new Ph.D. candidates has been initiated.

Since networking with experts in the field is of outmost importance, first fruitful contacts are set (i.e., with Institute of Clinical Sciences - University of Birmingham, Engineering and Technology Group- KU Leuven).
Finally, we seek further funding through competitive Horizon-Europe, National and bilateral calls.

Group Structure and Personnel

Group Leader [until 2020]

Panagiotis Zoumpoulakis PhD, MBA, Associate Professor & Head of the department of
Food Science and Technology, University of West Attica
Collaborating Researcher of ICB since 2020
Senior Researcher ICB, Group Leader until 2020

Group members

Eftichia Kritsi, Chemist, MSc., Ph.D.
Dimitra Z. Lantzouraki, Chemist, MSc, PhD
Thalia Tsiaka, Postdoctoral Researcher, Chemist, Ph.D, MSc

Group Leader & members CVs [pdf]

Group Structure

During the period 2018-2019 the research group, led by Dr. Zoumpoulakis, consisted of three post-doctoral researchers, namely Dr. Thalia Tsiaka (from 2019) and Dr. Eftichia Kritsi (in collaboration with Dr. M. Zervou) as well as 2 Ph.D. students, namely Mrs. Dimitra Lantzouraki and Mr. George Moros. Each postdoctoral researcher was assigned to one research direction according to the technical expertise and know-how and was responsible to guide the Ph.D. students as shown in the following diagram. Consequently, individual research projects were allocated to postdoctoral researchers. Several postgraduate M.Sc. students were joining the group to perform the experimental part of their Mater thesis. In specific, 10 MSc theses are not included in the Personnel Table of the platform either because they were implemented remotely (in silico drug design using the computer infrastructure of our group) or implemented in collaboration with industrial partners (within the frame of BIOENTREPRENEURSHIP Post-graduate Programme) or were based on a literature review.
Meetings at several levels were taking place to secure the timelines of the projects and the fulfillment of deliverables. Specifically, meetings between postdoctoral researchers and PhD and MSc students were taking place twice a week while weekly meetings occurred between the group leader and the postdocs. One day group meetings were taking place monthly with presentations of each member regarding the status of the running projects, difficulties and problems that had been faced and future planning.

Programmes 2018-2019

Project Title: ΚΡIPIS II– Sthenos-β. "Targeted therapeutic approaches against degenerative diseases-conditions with emphasis in cancer and aging. Hit-to-lead optimization ". Grant num: ΟΠΣ (MIS) 5002398 Institutional Program. Funding Agency: NSRF 2014-2020. Budget for the Team: 22.000 €. Duration: 11/2017-06/2021
Project Title: DINNESMIN- “Pre-clinical development of innovative Neuroprotective & Neuroregenerative synthetic micro-neurotrophins for the treatment of Alzheimer disease”. Grant num: Τ1ΕΔΚ-03186Funding Agency: ΕΥΔΕ – ΕΤΑΚ, Programme: Research-Create-Innovate. Budget for the Team: 80.000 € (including supply of GPU computational facility) Duration: 9/2018-8/2021
Project Title: INSPIRED: A National Research Infrastructure on Integrated Structural Biology, Drug Screening efforts and Drug-target functional characterization. Grant num: MIS: 5002550 Funding Agency: EPAnEK 2014-2020 Operational Programme Competitiveness Entrepreneurship Innovation Budget for the Team:100.254 (including upgrade of the Varian 600MHz NMR with a triple channel cryoprobe). Duration: 2017-2022
Project Title: «Discovery of biomarkers related to Intrauterine Growth Restriction with the use of Metabolomics” Name of PhD Candidate: George Moros, Programme for PhD studies: Contract Number:109, Duration: 2017-2020, Funding Body: HFRI, Budget: 30.000 €, Role: Scientific Supervisor.
Project title: «Metabolomic profile of infants’ urine who are exclusively breast-fed comparatively to those exclusively fed with infant formural enriched in synbiotics», Duration: 2018-2020, Funding: Rontis Hellas S.A., Budget: 12.500 €, Role: Project Coordinator.
Project Title: “Nanoemulsions of natural oils with hydration and repellent properties”, Duration: 2018- 2022, Number: Τ1ΕΔΚ-00996, Funding Body: ΕΥΔΕ – ΕΤΑΚ, Programme: Research-Create-Innovate, Budget 289.900,35 €, Role: Research Team Member.
Project Title: “Valorization of agricultural by-products as new substrates for the production of Pleurotus mushrooms with high nutritional value – Development and clinical evaluation of an innovative polyvalent functional food (“mushroom snack”) with enhanced content in bioactive compounds (vitamin D and antioxidants)”, Funding Body: ΕΥΔΕ – ΕΤΑΚ, Programme: Research-Create-Innovate, Duration: 2018-2022, Number: Τ1ΕΔΚ-02560, Budget: 161.401,50 €, Role: Scientific Responsible for NHRF.

2018

Baira, E., Dagla, I., Siapi, E., Zoumpoulakis, P., Simitzis, P., Goliomytis, M., Deligeorgis, S.G., Skaltsounis, A.-L., Gikas, E., UHPLC–HRMS-based tissue untargeted metabolomics study of naringin and hesperidin after dietary supplementation in chickens. (2018) Food Chemistry, 269, pp. 276-285.
DOI: 10.1016/j.foodchem.2018.06.146
Deraos, G., Kritsi, E., Matsoukas, M.-T., Christopoulou, K., Kalbacher, H., Zoumpoulakis, P., Apostolopoulos, V., Matsoukas, J., Design of linear and cyclic mutant analogues of dirucotide peptide (MBP 82–98 ) against multiple sclerosis: Conformational and binding studies to MHC class II. (2018) Brain Sciences, 8 (12), art. no. 213.
DOI: 10.3390/brainsci8120213
Fotiou, M., Fotakis, C., Tsakoumaki, F., Athanasiadou, E., Kyrkou, C., Dimitropoulou, A., Tsiaka, T., Chatziioannou, A.C., Sarafidis, K., Menexes, G., Theodoridis, G., Biliaderis, C.G., Zoumpoulakis, P., Athanasiadis, A.P., Michaelidou, A.-M., 1H NMR-based metabolomics reveals the effect of maternal habitual dietary patterns on human amniotic fluid profile. (2018) Scientific Reports, 8 (1), art. no. 4076.
DOI: 10.1038/s41598-018-22230-y
Sinanoglou, V.J., Zoumpoulakis, P., Fotakis, C., Kalogeropoulos, N., Sakellari, A., Karavoltsos, S., Strati, I.F. On the characterization and correlation of compositional, antioxidant and colour profile of common and balsamic vinegars, (2018) Antioxidants, 7 (10), art. no. 139.
DOI: 10.3390/antiox7100139
Strati, I.F., Kostomitsopoulos, G., Lytras, F., Zoumpoulakis, P., Proestos, C., Sinanoglou, V.J., Optimization of polyphenol extraction from allium ampeloprasum var. porrum through response surface methodology. (2018) Foods, 7 (10), art. no. 162.
DOI: 10.3390/foods7100162
Tsiaka, T., Lantzouraki, D.Z., Siapi, E., Sinanoglou, V.J., Heropoulos, G.A., Calokerinos, A.C., Zoumpoulakis, P., Macular carotenoids in lipid food matrices: DOE-based high energy extraction of egg yolk xanthophylls and quantification through a validated APCI(+) LC-MS/MS method, (2018) Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences, 1096, pp. 160-171.
DOI: 10.1016/j.jchromb.2018.08.010
Goliomytis, M., Kostaki, A., Avgoulas, G., Lantzouraki, D.Z., Siapi, E., Zoumpoulakis, P., Simitzis, P., Deligeorgis, S.-G., Dietary supplementation with orange pulp (Citrus sinensis) improves egg yolk oxidative stability in laying hens. (2018) Animal Feed Science and Technology, 244, pp. 28-35.
DOI: 10.1016/j.anifeedsci.2018.07.015
Sinanoglou, V.J., Cavouras, D., Xenogiannopoulos, D., Proestos, C., Zoumpoulakis, P., Quality assessment of pork and Turkey hams using FT-IR spectroscopy, colorimetric, and image analysis. (2018) Foods, 7 (9), art. no. 152.
DOI: 10.3390/foods7090152
Giannakourou, M., Strati, I.F., Manika, E.-M., Resiti, V., Tataridis, P., Zoumpoulakis, P., Sinanoglou, V.J., Assessment of phenolic content, antioxidant activity, colour and sensory attributes of wood aged “tsipouro”. (2018) Current Research in Nutrition and Food Science, 6 (2), pp. 318-328.
DOI: 10.12944/CRNFSJ.6.2.07
Igoumenidis, P.E., Zoumpoulakis, P., Karathanos, V.T., Physicochemical interactions between rice starch and caffeic acid during boiling. (2018) Food Research International, 109, pp. 589-595.
DOI: 10.1016/j.foodres.2018.04.062
Lazaridou, A., Vouris, D.G., Zoumpoulakis, P., Biliaderis, C.G., Physicochemical properties of jet milled wheat flours and doughs. (2018) Food Hydrocolloids, 80, pp. 111-121.
DOI: 10.1016/j.foodhyd.2018.01.044
Andreou, V., Strati, I.F., Fotakis, C., Liouni, M., Zoumpoulakis, P., Sinanoglou, V.J., Herbal distillates: A new era of grape marc distillates with enriched antioxidant profile. (2018) Food Chemistry, 253, pp. 171-178.
DOI: 10.1016/j.foodchem.2018.01.162
Tratrat, C., Haroun, M., Paparisva, A., Geronikaki, A., Kamoutsis, C., Ćirić, A., Glamočlija, J., Soković, M., Fotakis, C., Zoumpoulakis, P., Bhunia, S.S., Saxena, A.K., Design, synthesis and biological evaluation of new substituted 5-benzylideno-2-adamantylthiazol[3,2-b][1,2,4]triazol-6(5H)ones. Pharmacophore models for antifungal activity. (2018) Arabian Journal of Chemistry, 11 (4), pp. 573-590.
DOI: 10.1016/j.arabjc.2016.06.007
Smiljkovic, M., Matsoukas, M.-T., Kritsi, E., Zelenko, U., Grdadolnik, S.G., Calhelha, R.C., Ferreira, I.C.F.R., Sankovic-Babic, S., Glamoclija, J., Fotopoulou, T., Koufaki, M., Zoumpoulakis, P., Sokovic, M., Nitrate Esters of Heteroaromatic Compounds as Candida albicans CYP51 Enzyme Inhibitors. (2018) ChemMedChem, 13 (3), pp. 251-258.
DOI: 10.1002/cmdc.201700602
Proestos, C., Zoumpoulakis, P., Sinanoglou, V.J., Isolation and Characterization of Phenolic Compounds From Selected Foods of Plant Origin Using Modern Spectroscopic Approaches. (2018) Studies in Natural Products Chemistry, 57, pp. 203-220.
DOI: 10.1016/B978-0-444-64057-4.00007-7

2019

Koutsoukos, S., Tsiaka, T., Tzani, A., Zoumpoulakis, P., Detsi, A., Choline chloride and tartaric acid, a Natural Deep Eutectic Solvent for the efficient extraction of phenolic and carotenoid compounds. (2019) Journal of Cleaner Production, 241, art. no. 118384.
DOI: 10.1016/j.jclepro.2019.118384
Sinanoglou, V.J., Kavga, A., Strati, I.F., Sotiroudis, G., Lantzouraki, D., Zoumpoulakis, P., Effects of Infrared Radiation on Eggplant (Solanum melongena L.) Greenhouse Cultivation and Fruits’ Phenolic Profile. (2019) Foods, 8 (12), art. no. 630.
DOI: 10.3390/foods8120630
Karetsi, V.A., Banti, C.N., Kourkoumelis, N., Papachristodoulou, C., Stalikas, C.D., Raptopoulou, C.P., Psycharis, V., Zoumpoulakis, P., Mavromoustakos, T., Sainis, I., Hadjikakou, S.K., An efficient disinfectant, composite material {SLS@[Zn3(CitH)2]} as ingredient for development of sterilized and non infectious contact lens. (2019) Antibiotics, 8 (4), art. no. 213.
DOI: 10.3390/antibiotics8040213
Charitos, G., Trafalis, D.T., Dalezis, P., Potamitis, C., Sarli, V., Zoumpoulakis, P., Camoutsis, C., Synthesis and anticancer activity of novel 3,6-disubstituted 1,2,4-triazolo-[3,4-b]-1,3,4-thiadiazole derivatives. (2019) Arabian Journal of Chemistry, 12 (8), pp. 4784-4794.
DOI: 10.1016/j.arabjc.2016.09.015
Sakellari, A., Karavoltsos, S., Tagkouli, D., Rizou, C., Sinanoglou, V.J., Zoumpoulakis, P., Koutrotsios, G., Zervakis, G.I., Kalogeropoulos, N., Trace Elements in Pleurotus Ostreatus, P. Eryngii, and P. Nebrodensis Mushrooms Cultivated on Various Agricultural By-Products. (2019) Analytical Letters, 52 (17), pp. 2692-2709.
DOI: 10.1080/00032719.2019.1594865
Giannakourou, M., Strati, I.F., Kriebardis, A.G., Mantanika, V., Poulis, S., Zoumpoulakis, P., Sinanoglou, V.J., Shelf Life Extension and Quality Improvement of Cucumber Slices Impregnated in Infusions of Edible Herbs. (2019) Analytical Letters, 52 (17), pp. 2677-2691.
DOI: 10.1080/00032719.2019.1589476
Kollia, E., Proestos, C., Zoumpoulakis, P., Markaki, P., Capsaicin, an inhibitor of Ochratoxin A production by Aspergillus section Nigri strains in grapes (Vitis vinifera L.). (2019) Food Additives and Contaminants - Part A Chemistry, Analysis, Control, Exposure and Risk Assessment, 36 (11), pp. 1709-1721.
DOI: 10.1080/19440049.2019.1652771
Baira, E., Dagla, I., Siapi, E., Zoumpoulakis, P., Tsarbopoulos, A., Simitzis, P., Goliomytis, M., Deligeorgis, S.G., Skaltsounis, A.-L., Gikas, E., Development of a Validated UHPLC-ESI (-)-HRMS Methodology for the Simultaneous Quantitative Determination of Hesperidin, Hesperetin, Naringin, and Naringenin in Chicken Plasma. (2019) Food Analytical Methods, 12 (5), pp. 1187-1196.
DOI: 10.1007/s12161-018-01420-4
Potamitis, C., Siakouli, D., Papavasileiou, K.D., Boulaka, A., Ganou, V., Roussaki, M., Calogeropoulou, T., Zoumpoulakis, P., Alexis, M.N., Zervou, M., Mitsiou, D.J., Discovery of New non-steroidal selective glucocorticoid receptor agonists. (2019) Journal of Steroid Biochemistry and Molecular Biology, 186, pp. 142-153.
DOI: 10.1016/j.jsbmb.2018.10.007
Kavga, A., Strati, I.F., Sinanoglou, V.J., Fotakis, C., Sotiroudis, G., Christodoulou, P., Zoumpoulakis, P., Evaluating the experimental cultivation of peppers in low-energy-demand greenhouses. An interdisciplinary study. (2019) Journal of the Science of Food and Agriculture, 99 (2), pp. 781-789.
DOI: 10.1002/jsfa.9246
Kritsi, E., Matsoukas, M.-T., Potamitis, C., Detsi, A., Ivanov, M., Sokovic, M., Zoumpoulakis, P., Novel hit compounds as putative antifungals: The Case of Aspergillus fumigatus. (2019) Molecules, 24 (21), art. no. 3853.
DOI: 10.3390/molecules24213853