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Computational Chemical Biology

Group coordinators: Irene Kouskoumvekaki, Olivier Taboureau
Members: Grace Shema Nzabonimpa, Sonny Kim Kjærulff, 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

  • Nutritional systems biology
  • Prediction of side effects of drugs
  • Pharmacogenomics of psychoactive drugs
  • Effect of gut microbiome in human health
The group is involved in the following international collaborative projects:

Online services

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

Education

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".


Selected Publications

  • HExpoChem: a systems biology resource to explore human exposure to chemicals
    Taboureau O, Jacobsen UP, Kalhauge C, Edsgärd D, Rigina O, Gupta R, Audouze K, Bioinformatics., 2013

  • 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, ISME, 2012

  • 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 Kjærulff 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

Full length list of CBS publications

If you are interested in learning more about the group please contact Olivier Taboureau or Irene Kouskoumvekaki.