ΙΝΣΤΙΤΟΥΤΟ ΒΙΟΛΟΓΙΑΣ, ΦΑΡΜΑΚΕΥΤΙΚΗΣ ΧΗΜΕΙΑΣ & ΒΙΟΤΕΧΝΟΛΟΓΙΑΣ

 
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Molecular Analysis

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.

Members

Research Staff
Maria Zervou, PhD, M.Sc, Researcher B'
Panagiotis Zoumpoulakis PhD, MBA, Researcher C'

Collaborating Faculty Member
Prof. Thomas M. Mavromoustakos, Uni of Athens

Special Functional Scientist
George Bonas, PhD,  SFS A'

Scientific Technical Staff
Eleni Siapi, MSc., Scientific Technical Staff

Postdoctoral Fellows
Costantinos Potamitis, PhD, M.Sc
Charalambos Fotakis, PhD, MSc.

PhD Students
Katerina Kokkotou, MSc.
Eftychia Kritsi, MSc.
Thalia Tsiaka, MSc

M.Sc. Students
Mr. Paris Christodoulou
Ms Elina Dima

Under Graduate Students
Ms. Vasiliki Tsoumari
Mr. Constantinos Makris

 

Overview of Research Activities

Drug Design and bioNMR projects

  1. AT1 antagonists and renin inhibitors
  2. CYP51 inhibitors
  3. A. gambiae OBPs modulators
  4. Aspartic-Protease Inhibitors
  5. Molecular recognition of novel DHEA neurosteroid analogs by the neurotrophin receptors

Metabolomics projects

  1. Laurencia crude alga extracts
  2. Wine and grape marc distillates
  3. 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

Selected publications

Bioorg. Med. Chem., (2008), 16, 1150-1161; Chem. Pharm. Bull., (2010), 58(2), 160-7; Bioorg. Med. Chem. 18, (2010), 426-432; Bioorg. Med. Chem., (2012), 20 1569–1583.


Supporting grants

ARCADE: FP7-REGPOT-2009-1,  (2009-2013)

 

Agents for control of vector-borne diseases

Highlights:

  • 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.

 

Supporting grant: ARCADE: FP7-REGPOT-2009-1,  (2009-2013)

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

 

Selected publications:
Food Chemistry (2013), 138,1837–1846; Food Res. Int.(2013), 54, 1184-1194; Anal.Lett. (2012),  45 (5-6), 581-591; J Agric Food Chem(2005); 53, 5293-5303

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.

 

 

 

 

 

 

Selected publications

Food Chemistry, 131 (2012) 713–721
Food Research International, (2014),DOI:10.1016/j.foodres.2014.01.015

 

Supporting grants

«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

 

 

 

 

 

 

 

 
 

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