Computational Chemical Biology
Group coordinators: Irene Kouskoumvekaki, Olivier Taboureau
Members: Grace Shema Nzabonimpa, Ulrik Plesner Jacobsen
Guest member: Damian Rafal Plichta
Catalog of previous student projects.
About the group
The Computational Chemical Biology group at CBS focuses on the study of the interplay between small molecules and biological systems. The group holds expertise in molecular modeling, machine learning (QSAR, Neural Networks, Support Vector Machines), chemoinformatics and systems chemical biology.
A small molecule with biological activity (drug, phytochemical, enviromental chemical - or any xenobiotic compound in general) rarely acts on only one biological target but rather follows a complex interaction pattern with a number of proteins.This multi-targeting can be beneficial in drug discovery (polypharmacology), but it may also lead to disturbance of the metabolism, adverse effects or toxicity effects. Although many questions still remain, systems biology has already led to great advances in our understanding of the biology of complex diseases and drug targets. Thus, the field has now reached a state that allows the integration of large-scale data across multiple levels of information (drug-protein interaction data, protein-protein interaction data, gene expression data, side effect data) that can provide a more holistic picture of the effect of a small molecule on the human body. Such efforts of "systems chemical biology" are gradually emerging with the aim to explain how small molecules modulate biological pathways and how they can be most effectively used for disease prevention and treatment.
Current research areas
The group is involved in the following international collaborative projects:
- Nutritional systems biology
- Prediction of side effects of drugs
- Pharmacogenomics of psychoactive drugs
- Effect of gut microbiome in human health
pHSol: Predictor of pH-dependent aqueous solubility of druglike small molecules
ChemProt: Resource of annotated and predicted chemical-protein interactions
HExploChem: Resource of chemicals from diverse sources (drugs, food, cospetics, industrial chemicals, human metabolites) for exploring human health risk from chemical exposure
The group runs the MSc and PhD course Chemoinformatics in Drug Discovery and gives lectures at CBS courses "Biological Sequence Analysis", "Introduction to Systems Biology" and "Health, Diseases and Technology".
Full length list of CBS publications
- HExpoChem: a systems biology resource to explore human exposure to chemicals
Taboureau O, Jacobsen UP, Kalhauge C, EdsgÃ¤rd D, Rigina O, Gupta R, Audouze K,
- The chemical interactome space between the human host and the genetically defined gut metabotypes
Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G,
- Mapping the Genome of Plasmodium falciparum on the Druglike Chemical Space Reveals Novel Anti-malarial Targets and Potential Drug Leads
Jensen K, Plichta D, Panagiotou G, Kouskoumvekaki I,
Mol. BioSyst., 2012
- Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures
Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Audouze K, Brunak S, Main KM,
Int J Androl., 2012
- ChemProt-2.0: visual navigation in a disease chemical biology database
Kim KjÃ¦rulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O,
Nucleic Acids Res., 2012
- Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer- Aided Drug Repurposing
Oprea TI, Nielsen SK, Ursu O, Yang JJ, Taboureau O, Mathias SL, Kouskoumvekaki I, Sklar LA, Bologa C,
Molecular Informatics, 2011
If you are interested in learning more about the group please contact Olivier Taboureau or Irene Kouskoumvekaki.