Journal
QSAR & COMBINATORIAL SCIENCE
Volume 28, Issue 11-12, Pages 1394-1404Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/qsar.200910054
Keywords
Drug design; Antibiotics; Docking; Binding free energy; D-Ala-D-Ala ligase
Categories
Funding
- Belgian Fonds pour la Recherche dans l'Industrie et l'Agriculture (FRIA)
- Maitres de Recherche and CD is Chercheur Qualifie of the Belgian Fonds de la Recherche Scientifique (F.R.S.-FNRS)
- Pole d'Attractions Interuniversitaires (PAI) Program of the Federal Belgian government [P5/33]
- University of Strasbourg, France
- French institutes CNRS (Centre National de la Recherche Scientifique)
- INSERM (Institut National de la Sante et de la Recherche Medicale)
- Belgian Fonds pour la Recherche Scientifique Medicale [3.4.597.06]
- Bioval program from the Region Wallonne
- Region Wallonne
- Belgian Program on Interuniversity Poles of Attraction [P5/33, PAI6/19]
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D-Alanyl - D-alanine ligase is an enzyme which catalyzes the dimerization of D-alanine, and, as such, has an essential role in bacterial cell wall biosynthesis. It has been shown that inhibition Of D-alanyl - D-alanine ligase prevents bacterial growth. D-Alanyl D-alanine ligase represents therefore a viable antimicrobial target. The 3D structure of this enzyme complexed with a phosphinophosphate inhibitor has been reported, which allows for structure-based design studies. Four softwares (LUDI, MCSS, Autodock, and Glide) developed either for fragment or full-molecule docking were compared and scored for their ability to position in the active site four prototypic ligands: two inhibitors, i.e. a phosphinophosphate derivative and D-cycloserine, D-alanine and D-alanyl - D-alanine. Best performances were obtained with Glide and MCSS. A short series of novel derivatives based on a 2-phenylbenzoxazole scaffold was designed de novo on the basis of computational data. The best compound was found to fully inhibit the D-alanyl D-alanine ligase of E. faecalis with an IC50 of 400 mu M.
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