Title: Carbohydrates_proteins_interactions
SNIC Project: SNIC 2021/23-155
Project Type: SNIC Small Storage
Principal Investigator: Alessandro Ruda <>
Affiliation: Stockholms universitet
Duration: 2021-03-02 – 2021-06-01
Classification: 10603


Molecular dynamics simulations for virtual screening of a set of ligand libraries and to investigate ligand/protein interactions will be employed on different systems. In the first project MD simulations will be carried out on a glycosyltransferase, WaaG. This enzyme is involved in the synthesis of the lipopolysaccharide (LPS) and is present in some Gram-negative bacteria, such as Escherichia coli. Three libraries will be investigated representing potential inhibitors of the enzyme based on previous biological essays. Different oligosaccharide moieties mimicking the structural composition of the inner core of LPS in E. coli K12 will also be employed to deepen the recognition processes and dynamics between LPS and WaaG. The second project concerns the inhibition of the vascular endothelial growth factor receptor (VEGFR), a tyrosine kinase receptor (TKR). One of its most effective inhibitors is represented by Axitinib (AG013736; trade name Inlyta). This drug has been approved for the treament of renal cell carcinoma (mRCC) and several other solid and haematological tumours. A new library of compounds structurally related to Axitinib has been created and will be screened by MD.