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Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design.

Drlica K, Mustaev A, Towle TR, Luan G, Kerns RJ, Berger JM - ACS Chem. Biol. (2014)

Bottom Line: To increase dione activity, we examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is distal to the bridging C3/C4 keto acid substituent of quinolones.The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking, and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins.Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds active against common quinolone-resistant mutants.

View Article: PubMed Central - PubMed

Affiliation: Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences , 225 Warren Street, Newark, New Jersey 07103, United States.

ABSTRACT
Widespread fluoroquinolone resistance has drawn attention to quinazolinediones (diones), fluoroquinolone-like topoisomerase poisons that are unaffected by common quinolone-resistance mutations. To better understand differences between quinolones and diones, we examined their impact on the formation of cleaved complexes (drug-topoisomerase-DNA complexes in which the DNA moiety is broken) with gyrase, one of two bacterial targets of the drugs. Formation of cleaved complexes, measured by linearization of a circular DNA substrate, required lower concentrations of quinolone than dione. The reverse reaction, detected as resealing of DNA breaks in cleaved complexes, required higher temperatures and EDTA concentrations for quinolones than diones. The greater stability of quinolone-containing complexes was attributed to the unique ability of the quinolone C3/C4 keto acid to complex with magnesium and form a previously described drug-magnesium-water bridge with GyrA-Ser83 and GyrA-Asp87. A nearby substitution in GyrA (G81C) reduced activity differences between quinolone and dione, indicating that resistance due to this variation derives from perturbation of the magnesium-water bridge. To increase dione activity, we examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is distal to the bridging C3/C4 keto acid substituent of quinolones. The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking, and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins. Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds active against common quinolone-resistant mutants.

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Docking of quinolones and diones withwild-type enzyme. Representativecleaved complex interactions were taken from the top 20 binding posesobtained from docking moxifloxacin (A), UING5-249 (B), UING5-157 (C),and UING5-207 (D) into the 2XKK (wild-type) crystal structure. Hydrogen bonds areshown as dashed yellow lines. The top scoring and most consistentpose for moxifloxacin and UING5-157 shows a hydrogen bond to the deoxyriboseoxygen of dA-20; top pose of UING5-249 and UING5-207 shows hydrogenbonds from the C-7 aminomethyl pyrrolidine primary amine to E437 andR418. Both diones were anchored to ParC-Arg123 through a hydrogenbond with their C-2 carbonyl group.
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fig6: Docking of quinolones and diones withwild-type enzyme. Representativecleaved complex interactions were taken from the top 20 binding posesobtained from docking moxifloxacin (A), UING5-249 (B), UING5-157 (C),and UING5-207 (D) into the 2XKK (wild-type) crystal structure. Hydrogen bonds areshown as dashed yellow lines. The top scoring and most consistentpose for moxifloxacin and UING5-157 shows a hydrogen bond to the deoxyriboseoxygen of dA-20; top pose of UING5-249 and UING5-207 shows hydrogenbonds from the C-7 aminomethyl pyrrolidine primary amine to E437 andR418. Both diones were anchored to ParC-Arg123 through a hydrogenbond with their C-2 carbonyl group.

Mentions: We next turned to computer-aideddocking and fitting. The 20 bestbinding poses for each fluoroquinolone and dione were obtained byfirst docking with the 2XKK topoisomerase IV crystal structure of cleaved complexesformed with moxifloxacin. The poses were then overlaid and examinedfor differences in the relative orientations of functional groupsand for binding contacts with DNA and protein (see Supporting Information Figures S7, S8, and Table S2 for the20 docked poses). Docking of moxifloxacin into the fluoroquinolone-bindingsite of the 2XKK crystal structure revealed that the C-7 group preferentially adoptsa conformation that creates a hydrogen bond to the deoxyribose oxygenof dA-20 (see Figure 6A for top-scoring bindingpose). In contrast, many of the top binding poses for the UING5-249fluoroquinolone docked into this site exhibited a 180° rotationof the C-7 aminomethyl pyrrolidine group such that the primary amineof this moiety could form a hydrogen bond with both ParE-Glu437 (correspondingto E. coli GyrB-466) and the backbonecarbonyl of nearby ParE-Arg418 (Figure 6B).Indeed, docked poses for UING5-249 revealed that the C-7 aminomethylpyrrolidine group is capable of simultaneously forming hydrogen bondswith multiple residues. However, in the rigid C-7 ring system of moxifloxacin,the amine group is directly linked to the pyrrolidine and cannot reachParE-Glu437. A similar difference between binding contacts of theC-7 groups was seen with the cognate diones, UING5-157 and UING5-207(Figure 6C,D).


Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design.

Drlica K, Mustaev A, Towle TR, Luan G, Kerns RJ, Berger JM - ACS Chem. Biol. (2014)

Docking of quinolones and diones withwild-type enzyme. Representativecleaved complex interactions were taken from the top 20 binding posesobtained from docking moxifloxacin (A), UING5-249 (B), UING5-157 (C),and UING5-207 (D) into the 2XKK (wild-type) crystal structure. Hydrogen bonds areshown as dashed yellow lines. The top scoring and most consistentpose for moxifloxacin and UING5-157 shows a hydrogen bond to the deoxyriboseoxygen of dA-20; top pose of UING5-249 and UING5-207 shows hydrogenbonds from the C-7 aminomethyl pyrrolidine primary amine to E437 andR418. Both diones were anchored to ParC-Arg123 through a hydrogenbond with their C-2 carbonyl group.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4273985&req=5

fig6: Docking of quinolones and diones withwild-type enzyme. Representativecleaved complex interactions were taken from the top 20 binding posesobtained from docking moxifloxacin (A), UING5-249 (B), UING5-157 (C),and UING5-207 (D) into the 2XKK (wild-type) crystal structure. Hydrogen bonds areshown as dashed yellow lines. The top scoring and most consistentpose for moxifloxacin and UING5-157 shows a hydrogen bond to the deoxyriboseoxygen of dA-20; top pose of UING5-249 and UING5-207 shows hydrogenbonds from the C-7 aminomethyl pyrrolidine primary amine to E437 andR418. Both diones were anchored to ParC-Arg123 through a hydrogenbond with their C-2 carbonyl group.
Mentions: We next turned to computer-aideddocking and fitting. The 20 bestbinding poses for each fluoroquinolone and dione were obtained byfirst docking with the 2XKK topoisomerase IV crystal structure of cleaved complexesformed with moxifloxacin. The poses were then overlaid and examinedfor differences in the relative orientations of functional groupsand for binding contacts with DNA and protein (see Supporting Information Figures S7, S8, and Table S2 for the20 docked poses). Docking of moxifloxacin into the fluoroquinolone-bindingsite of the 2XKK crystal structure revealed that the C-7 group preferentially adoptsa conformation that creates a hydrogen bond to the deoxyribose oxygenof dA-20 (see Figure 6A for top-scoring bindingpose). In contrast, many of the top binding poses for the UING5-249fluoroquinolone docked into this site exhibited a 180° rotationof the C-7 aminomethyl pyrrolidine group such that the primary amineof this moiety could form a hydrogen bond with both ParE-Glu437 (correspondingto E. coli GyrB-466) and the backbonecarbonyl of nearby ParE-Arg418 (Figure 6B).Indeed, docked poses for UING5-249 revealed that the C-7 aminomethylpyrrolidine group is capable of simultaneously forming hydrogen bondswith multiple residues. However, in the rigid C-7 ring system of moxifloxacin,the amine group is directly linked to the pyrrolidine and cannot reachParE-Glu437. A similar difference between binding contacts of theC-7 groups was seen with the cognate diones, UING5-157 and UING5-207(Figure 6C,D).

Bottom Line: To increase dione activity, we examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is distal to the bridging C3/C4 keto acid substituent of quinolones.The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking, and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins.Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds active against common quinolone-resistant mutants.

View Article: PubMed Central - PubMed

Affiliation: Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences , 225 Warren Street, Newark, New Jersey 07103, United States.

ABSTRACT
Widespread fluoroquinolone resistance has drawn attention to quinazolinediones (diones), fluoroquinolone-like topoisomerase poisons that are unaffected by common quinolone-resistance mutations. To better understand differences between quinolones and diones, we examined their impact on the formation of cleaved complexes (drug-topoisomerase-DNA complexes in which the DNA moiety is broken) with gyrase, one of two bacterial targets of the drugs. Formation of cleaved complexes, measured by linearization of a circular DNA substrate, required lower concentrations of quinolone than dione. The reverse reaction, detected as resealing of DNA breaks in cleaved complexes, required higher temperatures and EDTA concentrations for quinolones than diones. The greater stability of quinolone-containing complexes was attributed to the unique ability of the quinolone C3/C4 keto acid to complex with magnesium and form a previously described drug-magnesium-water bridge with GyrA-Ser83 and GyrA-Asp87. A nearby substitution in GyrA (G81C) reduced activity differences between quinolone and dione, indicating that resistance due to this variation derives from perturbation of the magnesium-water bridge. To increase dione activity, we examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is distal to the bridging C3/C4 keto acid substituent of quinolones. The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking, and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins. Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds active against common quinolone-resistant mutants.

Show MeSH
Related in: MedlinePlus