5BS3 image
Entry Detail
PDB ID:
5BS3
Title:
Crystal Structure of S.A. gyrase in complex with Compound 7
Biological Source:
PDB Version:
Deposition Date:
2015-06-01
Release Date:
2015-06-17
Method Details:
Experimental Method:
Resolution:
2.65 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 61
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA gyrase subunit A and B
Chain IDs:A (auth: B), B (auth: D)
Chain Length:692
Number of Molecules:2
Biological Source:Staphylococcus aureus
Polymer Type:polyribonucleotide
Description:DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)-R(P*AP*GP*GP*GP*CP*CP*C)-D(P*T)-R(P*AP*CP*GP*GP*C)-D(P*T)-3')
Chain IDs:C (auth: E), D (auth: F)
Chain Length:20
Number of Molecules:2
Biological Source:Staphylococcus aureus subsp. aureus ED98
Primary Citation
Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2).
Bioorg.Med.Chem.Lett. 25 1831 1835 (2015)
PMID: 25851938 DOI: 10.1016/j.bmcl.2015.03.044

Abstact

Novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. A series of novel oxabicyclooctane-linked NBTIs with new tricyclic-1,5-naphthyridinone left hand side moieties have been described. Compounds with a (R)-hydroxy-1,5-naphthyridinone moiety (7) showed potent antibacterial activity (e.g., Staphylococcus aureus MIC 0.25 μg/mL), acceptable Gram-positive and Gram-negative spectrum with rapidly bactericidal activity. The compound 7 showed intravenous and oral efficacy (ED50) at 3.2 and 27 mg/kg doses, respectively, in a murine model of bacteremia. Most importantly they showed significant attenuation of functional hERG activity (IC50 >170 μM). In general, lower logD attenuated hERG activity but also reduced Gram-negative activity. The co-crystal structure of a hydroxy-tricyclic NBTI bound to a DNA-gyrase complex exhibited a binding mode that show enantiomeric preference for R isomer and explains the activity and SAR. The discovery, synthesis, SAR and X-ray crystal structure of the left-hand-side tricyclic 1,5-naphthyridinone based oxabicyclooctane linked NBTIs are described.

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