This project is using highthroughput molecular dynamics for the evaluation of protein–ligand interactions. The information is used further for the structurebased drug design (the closest analogue www. GPUGRID.net), but on top of molecular dynamics, our project is expected to use different sorts of opensource drug discovery software for processing of the big chemical databases, including virtual chemical spaces, like GDB (http://www.gdb.unibe.ch/gdb/home.html) The presentation of the project you can download here .
Development of the dynamic pharmacophores. In this project we are going to couple the molecular dynamics simulation to pharmacophore models with selection of the most favourable pharmacophores. Ideally it would be to make a protein-ligand simulation in which the generalized pharmacophore model is simulated instead of the specific molecule and correspondingly this model affects inductedfit conformation of the protein, imitating not a single molecule, but more generalized action of specific class of the molecules (represented by the averaged pharmacophore model.
Averaged pharmacophore models
Development of the averaged pharmacophores models when shape, size of each pharmacophore is made as averaged, based on the analyzis of a number of protein-ligand complexes (X–ray data) for the specific binding site, rather than only one protein-ligand complex.
Tankyrase/PI3K dual inhibitors
Development of Tankyrase/PI3K dual inhibitors for the colorectal cancer. On top of this pair of the biotargets, we also consider other pairs of the targets, which participate both in Wnt/Betacatenin and EGFR/KRAS siganling pathways, important for the colorectal cancer treatment. My best track of records is for this topic.
Wnt/Frizzled small molecule activators
Development of the Wnt/Frizzled small molecule activators, acting on the extracellular side of Frizzled receptors as antiAlzheimer small molecules, which can be used also in other regenerative medicine applications, like osteoporosis.
TET1-TET3 small molecule inhibitors development
Development of the small molecule inhibitors for TET1–TET3 family of enzymes, which change gene expression in response to hypoxic conditions.
Development of methods for drug–drug synergy prognosis. This includes integration of the different genomics data: proteomics, transcriptomics, genomics, gene expression, chemical databases, protein-drug interaction databases.
Chromothripsis is a relatively newly discovered biological phenomenon, which represents sudden structural chromosomal rearrangements in a single event. It is involved in both cancer and congenital diseases. Chromothripsis opposes the theory of cancer as gradual acquisition of genomic rearrangements and somatic mutations over time. It was very recently found that chromothripsis can be curative – woman with WHIM (warts, hypogammaglobulinemia, infections and myelokathexis) was found to be curated through chromothripsis. Our work in this field explores the possible therapeutic applications of chromothripsis and analysis of its causes.
Our experience also includes
The research work for small molecules development is done for other organisations on the next biotargets:
MRSA pyruvate kinase
Gyrase B and hTopo2alpha inhibitors
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