Change search
ReferencesLink to record
Permanent link

Direct link
NMR-based exploration of the acceptor binding site of human blood group B galactosyltransferase with molecular fragments
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Show others and affiliations
2010 (English)In: Glycoconjugate Journal, ISSN 0282-0080, E-ISSN 1573-4986, Vol. 27, no 3, 349-358 p.Article in journal (Refereed) Published
Abstract [en]

A substantial body of work has been devoted to the design and synthesis of glycosyltransferase inhibitors. A major obstacle has always been the demanding chemistry. Therefore, only few potent and selective inhibitors are known to date. Glycosyltransferases possess two distinct binding sites, one for the donor substrate, and one for the acceptor substrate. In many cases binding to the donor site is well defined but data for acceptor binding is sparse. In particular, acceptor binding sites are often shallow, and in many cases the dimensions of the binding pocket are not well defined. One approach to glycosyltransferase inhibitors is to chemically link donor site and acceptor site ligands to generate high affinity binders. Here, we describe a novel approach to identify acceptor site ligands from a fragment library. We have chosen human blood group B galactosyltransferase (GTB) as a biologically important model target. The approach utilizes a combination of STD NMR, spin-lock filtered NMR experiments and surface plasmon resonance measurements. Following this route we have identified molecular fragments from a fragment library that bind to the acceptor site of GTB with affinities of the order of a natural acceptor substrate. Unlike natural substrates these fragments allow for straightforward chemical modifications and, therefore will serve as scaffolds for potent GTB inhibitors. In general, the approach described is applicable to any glycosyltransferase and may assist in the development of novel glycosyltransferase inhibitors.

Place, publisher, year, edition, pages
Springer , 2010. Vol. 27, no 3, 349-358 p.
National Category
Organic Chemistry
URN: urn:nbn:se:su:diva-38507DOI: 10.1007/s10719-010-9282-5ISI: 000276168200005OAI: diva2:310712
Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2011-11-23Bibliographically approved
In thesis
1. Structure, dynamics and interactions of biomolecules: Investigations by NMR spectroscopy and computational methods
Open this publication in new window or tab >>Structure, dynamics and interactions of biomolecules: Investigations by NMR spectroscopy and computational methods
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, the structure, dynamics and interactions of proteins and carbohydrates are investigated using mainly NMR spectroscopy and computer simulations.

Oligosaccharides representing a Salmonella O-antigen have been synthesized and their dynamic behavior and interaction with the bacteriophage P22 tail-spike protein have been studied by NMR spectroscopy, MD and docking simulations. A binding mechanism between the protein and the O-antigen has been proposed.

Transient hydrogen bonds have been defined and examined in an E. coli polysaccharide and in a pentasaccharide representing the repeating unit, using MD simulation and NMR spectroscopy.

Conformational dynamics of a trisaccharide representing the repeating unit of an A. salmonicida O-antigen have been investigated by MD simulations. The simulation together with relaxation matrix calculations reveals a conformational exchange on a ns timescale and explains an unusual NOE.

A fragment-based screening for inhibitors of the glycosyltransferase GTB acceptor site has been performed using NMR spectroscopy and SPR. IC50 values of the binding fragments are reported. Complex structures of the fragments and GTB have been proposed using docking simulations.

A fragment-based screening for inhibitors of the WaaG glycosyltransferase donor site has been performed using NMR spectroscopy and three compounds were selected. Structures of the WaaG-fragment complexes have been suggested from docking simulations. Binding of natural substrates and activity has also been investigated by NMR spectroscopy. MD simulations have been carried out on WaaG with and without bound donor substrate. The simulation revealed a conformational change upon substrate binding.

Interactions between HEWL and carbohydrate ligands have been investigated, using a combination of weak affinity chromatography, NMR spectroscopy and computer simulations. KDs of the ligands have been presented as well as the solution structures of two HEWL-disaccharide complexes.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2009. 82 p.
NMR spectroscopy, MD simulation, carbohydrate synthesis, protein-ligand interaction, glycosyltransferase
National Category
Chemical Sciences
Research subject
Organic Chemistry
urn:nbn:se:su:diva-30120 (URN)978-91-7155-953-1 (ISBN)
Public defence
2009-11-13, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Submitted. Paper 5: In progress. Paper 6: In progress. Paper 7: Manuscript.Available from: 2009-10-22 Created: 2009-10-04 Last updated: 2011-11-23Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Widmalm, Göran
By organisation
Department of Organic Chemistry
In the same journal
Glycoconjugate Journal
Organic Chemistry

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 31 hits
ReferencesLink to record
Permanent link

Direct link