DBDD - Research teams

The Department of Biothermodynamics and Drug Design (DBDD) was established in 2006 based on the former Laboratory of Recombinant Proteins. The DBDD designs novel chemical compounds for therapeutic purposes. The efficiency of both naturally occurring and synthetic compounds is evaluated by structural biothermodynamics and molecular mode
ling methods.
The laboratory’s personnel consist of five teams according to their research goals and activities:

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 The Team of Molecular and Cellular Biology,

headed by Dr. Jurgita Matulienė (Ph. D. in cell biology from the University
of Minnesota, USA, 2003), makes target proteins by gene cloning, expression in E.coli, insect, or mammalian cells, and chromatografic purification of large quantities of active proteins sufficient for biothermodynamic measurements of compound binding. Several projects involve the design of mutants and
truncated protein domain constructs. Live human cancer cells are cultured for the evaluation of compound anticancer activity. Dr. Vilma Petrikaitė has a Ph.D. in pharmacy and performs compound testing in mice xenografts. The team collaborates with the Department of Immunology and Cell Biology in antibody design and diagnostic markers.

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The Team of Organic Synthesis,

headed by Dr. Virginija Dudutienė (Ph. D. in organic synthesis from the Vilnius University, 2005), synthesizes compounds that are designed to bind carbonic anhydrases and other drug target proteins. Compounds are designed by computer docking, molecular modeling, and comparison with naturally occurring or previously
synthesized compound functional groups. Compound identity and purity is verified by NMR and HPLC-HRMS.

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The Team of Biophysics,

headed by Prof. Daumantas Matulis (Ph. D. in biochemistry, molecular biology and biophysics from the University of Minnesota, USA, 1998), measures compound binding to target proteins by isothermal titration calorimetry (ITC), fluorescent thermal shift assay (DSF, ThermoFluor®), pressure shift assay (PSA), and conventional enzyme inhibition methods. The team determines intrinsic Gibbs free energies, enthalpies, entropies, heat capacities and volume of binding and measures protein stability in the presence of various excipients.

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The Team of Molecular Modelling,

headed by Dr. Vytautas Petrauskas (Ph. D. in physics from the Vilnius University, 2008), is responsible for the application of computational methods, database management, in silico docking of large compound libraries and the analysis of X-ray crystal structures of synthetic compound – protein complexes solved in collaboration with Dr. Saulius Gražulis group at the Department of
Protein – DNA interactions. Molecular modelers collaborate with the Department of Bioinformatics and use their methods to model protein structures that are not solved by X-ray crystallogphy. The group, together with several collaborating scientists is developing the software that estimates the energies of compound binding to a protein when only the crystal structure of the free protein is available.

bvts vs 2015 1The Team of Amyloid Research.

Recently a new team has started upon the return of Dr. Vytautas Smirnovas (Ph. D. from the Technical University of Dortmund, 2007) to Lithuania in 2011. The main interests and research of his team lie in the protein aggregation and amyloidogenesis that are involved in a number of diseases, including such neurodegenerative disorders as Alzheimer’s and Parkinson’s.


 

Collaborations
The DBDD has ongoing collaborations with a number of research laboratories and industry worldwide, including:

Institute of Medical Technology, University of Tampere, Finland
University of Florence, Italy
University of Nice, France
Centre for Structural Biochemistry, Montpellier, France
International Institute of Molecular and Cell Biology, Warsaw,
Poland
Polish Medical Research Centre, Polish Academy of Sciences,
Warsaw, Poland
University of Geneve, Geneve, Switzerland
TA Instruments, Stockholm, Sweden
Linköping University, Sweden
Jensen Pharmaceuticals, Johnson&Johnson, USA
Houston Methodist Research Institute, USA
Genome Damage and Stability Centre, University of Sussex,
Falmer, Brighton, UK
St. Andrews University, UK
Sygnature Discovery, Nottingham, UK
Cancer Research Centre, University of Edinburgh, UK
University of Latvia, Riga, Latvia
Institute of Organic Synthesis, Riga, Latvia
Institute of Organic Chemistry, University of Tubingen, Germany
Bellvitge Biomedical Research institute, Barcelona, Spain
Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
Center for Physical Sciences and Technology, Vilnius, Lithuania
National Cancer Institute, Vilnius University, Lithuania
National Centre of Pathology, Vilnius, Lithuania
Faculty of Chemistry, Vilnius University, Lithuania
Faculty of Natural Sciences, Vilnius University, Lithuania
Institute of Biochemistry, Vilnius, Lithuania
Lithuanian University of Health Sciences, Kaunas, Lithuania
AB “Amilina”, Panevėžys, Lithuania
Nature Research Centre, Institute of Botany, Vilnius, Lithuania
   

Memberships

Lithuanian Biophysical Society