The main research activities of the Molecular Analysis team lay on 2 pillars.
In the field of drug development, the team applies Bio-NMR and Biomolecular Modeling approaches towards the design of novel bioactive compounds targeting diseases of high socioeconomic interest.
Moreover, the group applies metabolomics using high throughput analytical platforms as NMR and LC-MS in combination with biostatistics with applications in biofluids and added-value natural products.
M.Sc. Students
Mr. Paris Christodoulou
Mr. Constantinos Makris
Mrs. Dimitra Tagouli
Under Graduate Students
Ms. Vasiliki Tsoumari
Overview of Research Activities
Drug Design and bioNMR projects
AT1 antagonists and renin inhibitors
CYP51 inhibitors
A. gambiae OBPs modulators
Aspartic-Protease Inhibitors
Molecular recognition of novel DHEA neurosteroid analogs by the neurotrophin receptors
Metabolomics projects
Laurencia crude alga extracts
Wine and grape marc distillates
Embryonomics
Antihypertensive agents
Highlights:
Elucidation of conformational properties and binding modes of AT1 antagonists (Sartans class) and Renin inhibitors
Insights into AT1 receptor activation through AII binding and MD simulations
Drug-membrane interactions by applying various biophysical methods (NMR in liquid/solid phase, SAXS, DSC) and in silico approaches in membrane modeled systems.
Our research work focuses on the elucidation of the conformational features and the binding modes of AT1 antagonists and renin inhibitors. Lately, we have gained insight into AT1 receptor activation through AII binding and MD simulations. Moreover we have been focusing on drug-membrane interactions by applying various biophysical methods and in silico approaches in membrane modeled systems. Our studies have provided for the first time, strong evidence for the spontaneous insertion of losartan, the prototype of the sartan family, in the lipidic core thus probing to a membrane mediated pathway towards the AT1 receptor besides the random encounter at its extracellular part.
The major objectives of our research focus on the:
Mechanism of inhibition
Design of novel inhibitors
AT1 receptor activation elements
Drug –Membrane interactions
through the combination of techniques
NMR
BioMolecular modeling
Virtual Screening
SAXS
DSC
Combination of NMR, molecular docking and MD simulations revealed major activation elements of the AT1 receptor.
Membrane acting as a trap for the free drug molecules. MD simulations indicated spontaneous insertion of losartan, the prototype of the sartan family, in the lipidic core probing to a membrane mediated pathway towards the AT1 receptor besides the random encounter at its extracellular part.
Selected publications
Frontiers in Medicinal Chemistry,(2006) 3,, 87-111; J. Chem. Inf. Model., (2009)49 (3), 726-739; J. Chem. Inf. Model., (2011), 26 51(9), 2386-9; J. Chem. Inf. Model., (2013), 53 (11), 2798–2811; J. Phys. Chem. B, (2011), 115(19), 6180-92; Phys. Chem. Chem. Phys., (2012), 14, 4780-4788;Biophysical J. (2009), 96, 2227-2236; BBA-Biomembranes (2012), 1818, 3107–3120; BBA-Biomembranes (2013)doi: 10.1016/j.bbamem.2013.12.012;
Supporting grants
EURODESY:FP6 Marie Curie (EST) 2006-2009; ARCADE:FP7-REGPOT-2009-1, (2009-2013)
Novel antimicrobial agents
Highlights:
SAR studies
New hits for CYP51
Design of novel inhibitors targeting Aspergillus Fumigatus &Candida Albicans
This project focuses on antifungal compounds, inhibitors of 14-a lanosterol demethylase. Target fungi strains include aspergillus fumigatus and candida albicans. In this project we have performed structure activity relationship studies for azoles, while we seek for new CYP51 (cytochrome P51) inhibitors by applying NMR, pharmacophore modeling, virtual screening and molecular docking
Sequence specific NMR assignment of the Odorant Binding Protein 1
15N HSQC Chemical shift perturbation assay to guide in silico docking studies and locate the binding site and modes of new ligands from natural sources or synthesized compounds
Identification of new odorants / design of optimized compounds
This study applies biomolecular NMR to identify odorants interacting with the olfactory system of the malaria-transmitting mosquito Anopheles gambiae seeking for new repellents with enhanced potency and selectivity.
Our initial NMR-based screening approaches (1H STD-NMR) monitored binding interactions between Agam OBP1 and compounds from natural sources or synthesized ones.
We proceeded with 15N/13C labelling of OBP1 protein and backbone residual assignment by 3D NMR. This enabled us to apply chemical shift mapping experiments (15N-HSQC) in order to recognize the binding regions and binding modes of the identified ligands.
This information can further assist the design of optimized compounds showing improved interactions with the protein target.
In collaboration with: Dr. S. Zographos (IBMCB/NHRF), Dr. S. Golic Grdadolnik and Dr. M. Podobnik, National Institute of Chemistry, Ljubljana, Slovenia , Prof. V. Roussis, School of Pharmacy, Laboratory of Pharmacognosy and Chemistry of Natural Products, Univeristy of Athens
Novel aspartic protease inhibitors
Highlights:
Dynamic formation of an acylhydrazone library
Enzymatic selection of the best inhibitors to endothiapepsin by 1H-STD-NMR
A series of hydrazides and aldehydes were used for the dynamic formation of an acylhydrazone library. Enzymatic selection of the best inhibitors to endothiapepsin, a model system for aspartic proteases, was implemented by 1H-STD-NMR analysis.
The potency of the identified by 1H STD acylhydrazones inhibitors was further verified from the HIV protease in vitro assay.
Publications: Angew Chem Int Ed, 2013 accepted
Supporting grant: ARCADE: FP7-REGPOT-2009-1
In collaboration with: Prof. A. Hirsh , Stratingh Institute for Chemistry, University of Groningen, The Netherlands
Assessment of Laurencia Crude alga extract metabolome
Highlights:
Targeted isolation of new bioactive metabolites
“In house” developed Laurencia focused library for Virtual screening against biological targets
Laurencia alga consists a prolific source of metabolites exhibiting antibacterial, insecticidal and cytotoxic activity.
In this project, the global metabolic profile of Laurencia crude algal extracts was addressed by applying high throughput analytical techniques, (UPLC-Orbitrap-MS) and (2D HSQC) NMR spectroscopy.
An integrated platform including sophisticated s/w tools and databases has been developed to mine the complex analytical data, identify known metabolites and trace the presence of new natural products.
This combined screening strategy can be effectively used as a tool for targeted isolation of new metabolites. Moreover, an in house library of Laurencia metabolites has been developed which can be used for virtual screening purposes against biological targets.
Supporting grants
SysTerp, Cooperation 2009, operational programme competitiveness and entrepreneurship (in collaboration with Prof. Roussis, School of Pharmacy, Laboratory of Pharmacognosy and Chemistry of Natural Products, Univeristy of Athens)
ARCADE: FP7-REGPOT-2009-1
Metabolomics applications on beverages
Highlights:
NMR-omics towards the authenticity of grape derived products
Metabolic markers associated with genotypic, environment or production procedures are highlighted
An NMR-omics integrated platform has been developed and applied to added-value alcoholic beverages as Greek and Cypriot wines and traditional grape mark spirits
NMR omics platform successfully classified Greek grape mark spirits according to their provenance, incorporating also varietal information and succeeded in recognizing characteristic metabolites associated with genotypic and environmental influence or production practices
In practice, such results could be applied to fortify the authenticity claim of a product.
Geographical and genotypic discrimination of Greek traditional beverages tsipouro and tsikoudia
Supporting grants:Framework Programme for Research, Technological Development and Innovation of the Cypriot Research Promotion Foundation. Wine-omics. “Metabolic, isotopic, Antioxidant and elemental profiling to characterize Cypriot wines of specific geographical and varietal origin” . (2011-2013)
Metabolomics applications on food products
Highlights:
A combined methodology to detect γ-irradiated food items
This project refers to the application of NMR techniques and NMR based metabolomics on irradiated food. Currently, there is a need for the development of efficient and reliable techniques to detect imported food items processed with gamma irradiation but which do not bring the appropriate labeling.
1H DOSY as well as fast NMR profiling of the lipid fraction of food items have provided very promising results for the future development of a detection methodology even at low irradiation doses.
Under this project, several high energy extraction techniques (Microwave Assisted Extraction –MAE and Ultrasound Assisted Extraction-UAE) have been applied towards the fast isolation of the lipid fraction from selected food products.
1H DOSY NMR of sesame seeds fat content can provide evidence for the formation of gamma irradiation induced radiolytic products
NMR food-omics on lipid fraction of macadamia nuts has been proposed as a fast discrimination methodology between irradiated samples at high (>5kGy) doses.
«Functional and Potentially Hazardous Food Constituents. Impact of Electromagnetic Treatments for Quality Products» Programme ARHIMIDES 2012-2015, SECTORAL OPERATIONAL PROGRAMME, EDUCATION AND LIFELONG LEARNING –ESPA 2007-2013 (Member of the main research team).
Initiated Activities
Design of novel ligands for :
BRAF V600E (colorectal cancer)
GR (Inflammation and breast cancer)
using modern in silico techniques:
Pharmacophore modeling
Virtual Screening
Molecular Docking
Molecular Dynamics Simulations
In silico ADMET
This project refers to the institute’s STHENOS funded proposal. Molecular Analysis contribution is focusing on the implementation of modern in silico techniques towards the design of novel inhibitors of the mutated oncoprotein kinase BRAF and modulators of the glucocorticoid receptor, GR
Financial Support
"STHENOS-KRIPIS: Targeted therapeutic approaches against degenerative diseases, with emphasis on cancer and aging", NSRF 2007-2013.
NMR based Embryo-metabolomics
Highlights:
Identification of biomarkers related to fetal malformations and preterm delivery
Discrimination between term infants with normal (Appropriate for Gestational Age) and increased (Large for Gestational Age) fetal growth.
using the following template biofluids:
Maternal blood serum
Umbilical cord blood serum
Human amniotic fluid
Financial Support
«Metabolomics as a tool for the assessment of embryo growth and viability in in-vitro fertilization» Programme THALIS 2012-2015,SECTORAL OPERATIONAL PROGRAMME, EDUCATION AND LIFELONG LEARNING –ESPA 2007-2013
Computational Chemistry
Experimental determination of dipole moments and polarizabilities in ground and excited electronic states
Theoretical prediction of linear and nonlinear optical (NLO) properties of molecules, nanomaterials and condensed phases. In an effort to develop efficient methods to compute the NLO properties of materials, we have developed and implemented an approach for the computation of the NLO properties of molecular crystals, liquids and polymers. We are trying to extend these methods to novel materials, like nanomaterials, which show very promising NLO properties. I’m also working on developing methods for the accurate determination of the vibrational contributions to NLO properties, with special emphasis on molecules exhibiting large-amplitude motions, such as the umbrella motion in ammonia.
Application of accurate ab-initio methods to large-scale problems involving bioactive compounds. Examples include the application of the effective fragment potential (EFG) approach to the elucidation of the binding mechanism of renin, or the use of the fragment molecular method (FMO) to the investigation of the interaction between fullerenes and human serum albumin.
Drug Design and bioNMR projects
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NMR-omics towards the authenticity of grape derived products
Highlights:
1H DOSY NMR of sesame seeds fat content can provide evidence for the formation of gamma irradiation induced radiolytic products 
Design of novel ligands for :
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