Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations

doi:10.1016/j.bmcl.2007.01.052

Bioorganic & Medicinal Chemistry Letters

Volume 17, Issue 7, 1 April 2007, Pages 1966-1970

https://doi.org/10.1016/j.bmcl.2007.01.052 Get rights and content

Abstract

Results of an in silico screening of a freely accessible database encompassing 50,000 commercial compounds on bacterial glucosamine-6P synthase (Glms) are described. Each product was docked with the GOLD software in a region of 20 Å surrounding the sugar binding site and ranked according to its score. Among the 14 best-scored molecules, three molecules exhibited good experimental inhibition properties (IC₅₀ = 70 μM) giving a high hit rate (H.R.: 0.23). Interestingly, these molecules are predicted to interact with a protein region that forms a pocket at the interface between the two enzyme monomers, opening the route to dimerization inhibitors.

Graphical abstract

Results of an in silico screening of a freely accessible database encompassing 50,000 commercial compounds on bacterial glucosamine-6P synthase (Glms) are described. 3 molecules predicted to bind at the interface between the two enzyme monomers exhibited good experimental inhibition properties (IC50 = 70 μM) opening the route to dimerization inhibitors.

Section snippets

Acknowledgements

Financial support from ICSN to NF and CR is gratefully acknowledged. This work has been supported in part by the Indo-French program IFC/3003-A.

References and notes (28)

R.R. Traxinger et al.
J. Biol. Chem.
(1991)
M.A. Denisot et al.
Arch. Biochem. Biophys.
(1991)
A. Teplyakov et al.
J. Mol. Biol.
(2001)
A.M. Janiak et al.
Bioorg. Med. Chem.
(2003)
S.C. Bobzin et al.
J. Chromatogr. B. Biomed. Sci. Appl.
(2000)
S. Mouilleron et al.
J. Biol. Chem.
(2006)
L. Kalé et al.
J. Comp. Phys.
(1999)
G. Jones et al.
J. Mol. Biol.
(1997)
A. Teplyakov et al.
Structure
(1998)
G. Obmolova et al.
J. Mol. Biol.
(1994)

D.A. McClain et al.

Diabetes

(1996)

B. Badet et al.

Biochemistry

(1987)

C. Leriche et al.

J. Am. Chem. Soc.

(1996)

L. Yaouancq et al.

J. Org. Chem.

(2002)

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Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations

Abstract

Graphical abstract

Section snippets

Acknowledgements

J. Biol. Chem.

Arch. Biochem. Biophys.

J. Mol. Biol.

Bioorg. Med. Chem.

J. Chromatogr. B. Biomed. Sci. Appl.

J. Biol. Chem.

J. Comp. Phys.

J. Mol. Biol.

Structure

J. Mol. Biol.

Diabetes

Biochemistry

J. Am. Chem. Soc.

J. Org. Chem.