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Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design Karl Drlica, Arkady Mustaev, Tyrell R Towle, Gan Luan, Robert J. Kerns, and James M Berger ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/cb500629k • Publication Date (Web): 13 Oct 2014 Downloaded from http://pubs.acs.org on October 14, 2014

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ACS Chemical Biology

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Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design Karl Drlica‡*, Arkady Mustaev‡, Tyrell R. Towle¶, Gan Luan‡, Robert J. Kerns¶*, and James M. Berger#§*

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‡

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New Jersey Medical School, Rutgers Biomedical and Health Sciences, 225 Warren St.,

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Newark, NJ 07103

Public Health Research Institute and Department of Microbiology & Molecular Genetics,

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¶

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Sciences & Experimental Therapeutics, University of Iowa College of Pharmacy, 115 S.

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Grand Ave., Iowa City, IA 52246

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#

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University of California, Berkeley, CA 94720

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§

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of Medicine, 725 N. Wolfe St., Baltimore, MD 21205

Division of Medicinal & Natural Products Chemistry, Department of Pharmaceutical

Molecular and Cell Biology Department, Quantitative Biosciences Institute, Stanley Hall,

Present address: Biophysics and Biophysical Chemistry, Johns Hopkins University School

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* To whom correspondence should be addressed. (Karl Drlica [Tel 917 821 6847; Fax 973

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854 3101, Email [email protected]]; Robert J. Kerns [Tel 319 335 8800, Fax 319-

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335-8766, Email [email protected]]; James M. Berger [Tel: 410-955-7163; Fax: 410-

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955-0637; Email: [email protected]]), Drs. Drlica, Kerns, and Berger contributed equally

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to experimental design, obtaining funding, and manuscript preparation.

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School of Medicine, 725 N. Wolfe St., Baltimore MD 21205

Present address: Department of Biophysics and Biophysical Chemistry, The Johns Hopkins

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Short title: Bypassing quinolone resistance with diones

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Keywords: E. coli, moxifloxacin, cleaved complexes, docking, dione

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ACS Paragon Plus Environment


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ABSTRACT

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Widespread fluoroquinolone resistance has drawn attention to quinazolinediones (diones),

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fluoroquinolone-like topoisomerase poisons that are unaffected by common quinolone-

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resistance mutations. To better understand differences between quinolones and diones, we

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examined their impact on the formation of cleaved complexes (drug-topoisomerase-DNA

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complexes in which the DNA moiety is broken) with gyrase, one of two bacterial targets of

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the drugs. Formation of cleaved complexes, measured by linearization of a circular DNA

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substrate, required lower concentrations of quinolone than dione. The reverse reaction,

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detected as resealing of DNA breaks in cleaved complexes, required higher temperatures and

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EDTA concentrations for quinolones than diones. The greater stability of quinolone-

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containing complexes was attributed to the unique ability of the quinolone C3/C4 keto acid to

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complex with magnesium and form a previously-described drug-magnesium-water bridge

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with GyrA-Ser83 and GyrA-Asp87. A nearby substitution in GyrA (G81C) reduced activity

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differences between quinolone and dione, indicating that resistance due to this variation

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derives from perturbation of the magnesium-water bridge. To increase dione activity, we

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examined a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent, which is

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distal to the bridging C3/C4 keto acid substituent of quinolones. The 3-

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(aminomethyl)pyrrolidinyl group at position C-7 was capable of forming binding interactions

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with GyrB-Glu466, as indicated by inspection of crystal structures, computer-aided docking,

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and measurement of cleaved-complex formation with mutant and wild-type GyrB proteins.

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Thus, modification of dione C-7 substituents constitutes a strategy for obtaining compounds

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active against common quinolone-resistant mutants.

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INTRODUCTION

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Fluoroquinolones are important antimicrobials that trap two bacterial topoisomerases, gyrase

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and topoisomerase IV, on DNA as complexes in which the DNA is broken. The complexes,

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commonly called cleaved complexes,1, 2 are the primary lesions responsible for quinolone

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activity.3-5 The DNA ends in cleaved complexes are constrained by covalent linkage to the

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topoisomerase, which facilitates resealing of the DNA breaks after drug removal.

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Consequently, damage caused by the complexes, such as inhibition of DNA synthesis, is

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reversible when drug is removed.6 Reversibility may be clinically important, since treatment

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of infections often involves fluctuating drug concentrations that may drop low enough to

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allow resealing of cleaved DNA. Resealing may reduce quinolone efficacy and increase

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pathogen survival. Pathogen survival can also arise from expansion of resistant

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subpopulations containing topoisomerase mutations that reduce drug binding and thereby

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cleaved-complex formation. Thus, understanding how the structure of quinolone-class

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antimicrobials affects topoisomerase-mediated DNA cleavage and resealing is central to

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designing more effective drug candidates.

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Cleaved-complex formation can be assayed by incubating gyrase or topoisomerase IV

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with quinolone and circular DNA, followed by treatment with an ionic detergent, such as

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sodium dodecyl sulfate (SDS), to dissociate the complexes. Gel electrophoresis is then used

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to separate the DNA species; the appearance of linear DNA indicates complex formation.7, 8

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Reversal of complex formation is observed as DNA resealing, i.e., the disappearance of

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linear DNA arising prior to dissociation of the complex with SDS. Reversal conditions,

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which involve destabilization of drug-bound enzyme-DNA complexes, include: i) dilution,9 ii)

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incubation at high temperature,9 or iii) treatment with ethylenediamine tetraacetic acid



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(EDTA).7, 10 EDTA chelates polyvalent metal ions, and its action can be explained by

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participation of Mg2+ in quinolone binding. Indeed, X-ray crystallographic studies of drug-

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enzyme-DNA complexes reveal that the C3/C4 keto acid moiety of fluoroquinolones

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coordinates a Mg2+ ion and forms a previously described drug-magnesium-water bridge to

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amino acid residues in helix-4 of either GyrA (gyrase) or ParC (topoisomerase IV).11-14

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Additional magnesium coordination occurs within the topoisomerase active site,15 making it

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likely that multiple magnesium ions participate in cleaved-complex formation and reversal.

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Drug-mediated magnesium coordination has been characterized by comparison of

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fluoroquinolones and quinazolinediones (diones), quinolone-like compounds (Figure 1A)

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that lack the carboxylate group needed for magnesium coordination with drug.9, 11, 16-18

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Diones are potentially important clinically, because they exhibit striking activity against

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several types of fluoroquinolone-resistant mutant containing amino acid substitutions in

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gyrase and DNA topoisomerase IV.17, 19-21 For two of these substitution sites (equivalent to

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GyrA-83 and GyrA-87 in E. coli), an absence of drug-mediated magnesium coordination has

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been implicated in the biochemical behavior of diones.9, 16, 18 A third resistance site (GyrA-

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81) is not expected to directly participate in metal-ion coordination, but a GyrA-G81C

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resistance substitution has been proposed to interfere with ion binding indirectly by sterically

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perturbing the geometry of the gyrase acidic group at a distance.20 Such interference has not

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been examined biochemically. A consequence of the stabilizing magnesium bridge is that

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fluoroquinolones exhibit greater activity than diones with wild-type enzyme and cells.18, 19, 21

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Thus, a challenge is to find ways to stabilize dione-containing cleaved complexes, thereby

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increasing activity of an agent that may bypass existing resistance.

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The present work began with a set of C-8-methoxy diones active against

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fluoroquinolone-resistant bacterial mutants.19, 20 To better understand differences between

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diones and quinolones, we examined their effects on gyrase-mediated DNA breakage and


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resealing using EDTA, thermal treatments, and a GyrA-G81C substitution. We then sought

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ways to both stabilize dione-containing cleaved complexes and increase dione activity. A 3-

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(aminomethyl)pyrrolidinyl substituent (hereafter called an aminomethyl pyrrolidine group) at

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position C-7 afforded increased activity for both dione and fluoroquinolone derivatives.

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Investigation of extant X-ray structures, along with docking studies, revealed a potential

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interaction between GyrB-Glu466 and the aminomethyl pyrrolidine group that might account

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for increased activity through a slightly altered binding orientation. In accord with this

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observation, a GyrB-E466C substitution preferentially decreased dione activity, supporting a

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stabilizing role for the GyrB interaction with the C-7 aminomethyl pyrrolidine group.

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Overall, the work establishes the functional relevance of crystal structures of cleaved

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complexes, explains the action of the GyrA-G81C resistance substitution, addresses

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crossover activity of diones for human topoisomerase II, and provides a new approach for

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bypassing the protective activity of current quinolone-resistance mutations.

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RESULTS AND DISCUSSION Cleaved-complex formation with quinolone and dione pairs. Quinazolinediones and

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cognate fluoroquinolones having four different C-7 ring moieties (Figure 1A) were incubated

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at various concentrations with E. coli gyrase and plasmid DNA to form cleaved complexes

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that were assayed by the appearance of linear DNA (see Supplementary Figure S1 for an

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example of electrophoretic separation of plasmid species). For each compound pair, the

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quinolone was 10-100 times more active than the dione, as judged by the concentration

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required to linearize ~20% of the DNA (Figure 1B). These results parallel earlier studies

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with cultured bacterial cells.19, 20 The UING5-249/UING5-207 pair was the most active; thus,

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subsequent work focused on these two compounds.



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DNA resealing stimulated by EDTA differs for dione- and quinolone-containing

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complexes. Previous studies have shown that type II DNA topoisomerases act through a two-

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metal mechanism15, 22, 23 and that the metal chelator EDTA helps stimulate resealing of

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broken DNA in cleaved complexes.1, 2, 10, 17, 24 In an initial experiment, we formed cleaved

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complexes by incubating gyrase, plasmid DNA, and the fluoroquinolone UING5-249. Then

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we treated reaction mixtures with EDTA to reseal the DNA. Increasing EDTA concentration

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caused the recovery of linear DNA to drop, reach a broad minimum beginning at about 2 mM

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EDTA (the concentration of Mg2+ in the reaction mixture), and then increase (Figure 2A).

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Addition of Mg2+ after incubation with moderate concentrations of EDTA (2 mM) reversed

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the resealing stimulated by EDTA (Supplementary Figure S2); incubation with Mg2+ after

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treatment with a high concentration of EDTA (50 mM) restored resealing (Supplementary

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Figure S2). Thus, EDTA likely exerts its effects by sequestering Mg2+ ions away from the

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ternary drug-enzyme-DNA complex.

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We reasoned that DNA resealing in complexes formed with diones might differ from

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that of quinolone-containing complexes, because diones cannot participate in magnesium-

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mediated bridging of drug with GyrA. When we compared cognate dione (UING5-207) and

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quinolone (UING5-249) for EDTA-dependent effects on DNA resealing, the overall shapes

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of the curves were similar (Figure 2A). However, in the low EDTA concentration range,

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reversal of quinolone-mediated DNA cleavage occurred at a higher relative EDTA

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concentration than observed for the dione. This reduced susceptibility of quinolone-

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containing complexes to EDTA-mediated DNA resealing is consistent with quinolones

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having an additional magnesium-dependent interaction that stabilizes their participation in

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cleaved-complex formation.

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The response to EDTA concentration may arise from low concentrations of EDTA

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promoting quinolone dissociation from the complex, thereby shifting gyrase from a DNA-


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breaking mode to a resealing one; if so, high concentrations of EDTA would then largely

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eliminate the remaining Mg2+ and thereby disrupt Mg2+-dependent DNA resealing by gyrase.

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Nicked DNA was recovered at high EDTA concentration (Figure 2B), consistent with these

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conditions partially inhibiting gyrase-mediated resealing of DNA breaks. Partial resealing

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associated with high concentrations of EDTA (35 mM) has been observed previously with

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Streptococcus pneumoniae gyrase-containing complexes.17 However, in that work, 35 mM

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EDTA failed to induce DNA resealing for an 8-methyl dione complexed with topoisomerase

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IV.17 The difference at high EDTA concentration seen between the 8-methyl dione and the 8-

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methoxy derivative used here may derive from tighter binding of the methyl derivative, since

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formation of cleaved complexes with the methoxy compound requires higher concentrations

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than its cognate methyl analog.18, 21

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Since high salt concentration can reverse DNA cleavage induced by some quinolones,17

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sodium ions present in EDTA solutions could, in principle, contribute to DNA resealing

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during EDTA treatment. However, we saw no stimulation of DNA resealing by sodium

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acetate (up to 250 mM, Supplementary Figure S3). Likewise, 200 mM sodium acetate failed

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to reduce resealing temperature, in contrast to the effects of EDTA treatment (Supplementary

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Figure S4). Thus, salt effects are probably not responsible for DNA resealing stimulated by

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low EDTA concentration.

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A variety of divalent cations, such as Co2+, Ni2+, Pb2+, and Mn2+, can satisfy the

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requirement for a non-catalytic metal ion in formation of cleaved complexes with both

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quinolone and dione.9 However, several metal ions, including Ca2+, Cd2+, Zn2+, and Ba2+,

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also preferentially form complexes with dione-type compounds.9 While the basis for these

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metal ion differences is not known, the data fit with the idea that in cleaved complexes the

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metal dependencies of quinolones and diones differ.



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Temperature-promoted DNA resealing differs between dione- and quinolone-

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containing complexes. In addition to the effects on EDTA-induced resealing, we reasoned

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that an additional stabilizing magnesium interaction might also increase the reversal

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temperature of complexes formed with fluoroquinolones relative to cognate diones. When

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cleaved complexes, formed by incubation of drug, gyrase, and plasmid DNA, were subjected

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to 5-min incubations at various temperatures, the production of linear DNA showed a distinct

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decrease over the same temperature range at which supercoiled DNA increased

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(Supplementary Figure S5; the fraction of nicked DNA grew slightly as temperature

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increased). For comparison of dione and quinolone, we determined the temperature at which

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the proportion of linear DNA had decreased by 50%: dione-containing complexes exhibited

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overall lower DNA resealing temperatures than complexes formed with cognate quinolones

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(Figure 3A; Supplementary Table S1). In general, compounds having a greater stimulatory

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effect on DNA cleavage tended to exhibit higher DNA resealing temperature (Figure 3B).

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The lower thermal stability of cleaved complexes formed with diones was observed over a

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broad concentration range in which raising dione concentration raised resealing temperature

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(Supplementary Figure S6). These data suggest that DNA resealing is facilitated by

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dissociation of quinolone/dione from the complexes. Overall, the results of thermal resealing

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experiments are consistent with a role for drug-enzyme stability in favoring cleaved-complex

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formation, a result that accords with the observed stabilizing effects of water-magnesium ion

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bridging between fluoroquinolones and GyrA/ParC.

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In previous work, a thermal resealing difference was not observed during comparison

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of an 8-methyl dione with several commercial quinolones.16 In those experiments complexes

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were formed with wild-type topoisomerase IV followed by incubation for various times at

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only a single temperature, 75oC. The present work suggests that 75oC is likely to be above


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the transition temperature, which could make that particular test insensitive to compound

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structure.

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Dione-containing complexes are less sensitive than quinolone-containing complexes

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to a GyrA-G81C substitution. X-ray analysis of crystal structures for cleaved complexes

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suggests that drug binding occurs close enough to GyrA-Gly81 for a Cys substitution to

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sterically perturb quinolone-mediated magnesium bridging.11, 20 Thus, cleaved complexes

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formed with GyrA-G81C gyrase and quinolones were expected to have properties similar to

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those of complexes formed with diones. Indeed, when dione UING5-207 and its cognate

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quinolone (UING5-249) were compared for complex formation with wild-type gyrase, 10- to

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20-times more dione was required to generate the same amount of linear DNA (Figure 4Ai).

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By contrast, the difference was only 2-fold when GyrA-G81C was used (Figure 4Aii).

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Similarly, examination of DNA resealing by GyrA-G81C gyrase at various EDTA

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concentrations revealed no difference between dione- and fluoroquinolone-containing

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complexes at low EDTA concentration (Figure 4B) (unlike the result obtained with wild-type

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gyrase, Figure 2A). The GyrA-G81C substitution also lowered DNA resealing temperature

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more for the fluoroquinolone than for the dione, bringing them to similar levels (Figure 4C).

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Overall, these results are consistent with the GyrA-G81C substitution exerting a destabilizing

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effect on the fluoroquinolone-mediated magnesium linkage that is absent in dione-containing

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complexes. Thus, the GyrA-G81C substitution joins substitutions at GyrA-83 and GyrA-87

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in acting by impeding the formation of the quinolone-magnesium-water-enzyme bridge.9, 16

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Although substitution at GyrA-81 can be strongly protective with cultured cells6, 19, 20

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and with purified gyrase (Figure 4A), it is seldom associated with clinical resistance,25

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perhaps due to loss of mutant fitness in human hosts. Interestingly, at high EDTA

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concentrations, GyrA-G81C gyrase exhibited a reduced ability to reseal dione-containing

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complexes (Figure 4B). While additional work is required to understand this phenomenon, it



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is likely that GyrA-G81C gyrase may still allow tighter binding of the quinolone than the

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dione (Fig. 4Aii).

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C-7 ring substituents interact with GyrB. Comparison of diones having various C-7

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rings identified UING5-207 as the most active at forming cleaved complexes (Figure 1B).

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This result is consistent with UING5-207 being more active than other 8-methoxy diones as

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determined with B. anthracis topoisomerase IV.18 To better understand this elevated activity,

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we examined published X-ray structures derived from compounds similar to UING5-249 and

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UING5-207 in complex with type-II topoisomerases and DNA.11-14 When we substituted

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dione UING5-207 and UING5-249 for moxifloxacin in X-ray structure PDB 2XKK

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(moxifloxacin complexed with Acinetobacter baumannii topoisomerase IV; a comparable

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gyrase structure is not presently available), we noticed during manual docking that the

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primary amine of the C-7 aminomethyl pyrrolidine group is in a position where it could

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potentially form a salt bridge/hydrogen bond with Glu466 of GyrB (Figure 5A, 5B).

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Manually rotating the C-7 group of moxifloxacin to make this same binding contact revealed

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that the secondary amine of the moxifloxacin C-7 group was unlikely to extend far enough to

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form a similar binding interaction with GyrB Glu466. Thus, the C-7 aminomethyl

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pyrrolidine substituent appeared to afford an additional binding contact with GyrB.

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We next turned to computer-aided docking and fitting. The 20 best binding poses for

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each fluoroquinolone and dione were obtained by first docking with the 2XKK topoisomerase

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IV crystal structure of cleaved complexes formed with moxifloxacin. The poses were then

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overlaid and examined for differences in the relative orientations of functional groups and for

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binding contacts with DNA and protein (see Supplemental Figures S7, S8, and Supplemental

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Table S2 for the 20 docked poses). Docking of moxifloxacin into the fluoroquinolone-

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binding site of the 2XKK crystal structure revealed that the C-7 group preferentially adopts a

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conformation that creates a hydrogen bond to the deoxyribose oxygen of dA-20 (see Figure


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6A for top-scoring binding pose). In contrast, many of the top binding poses for the UING5-

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249 fluoroquinolone docked into this site exhibited a 180˚ rotation of the C-7 aminomethyl

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pyrrolidine group, such that the primary amine of this moiety could form a hydrogen bond

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with both ParE-Glu437 (corresponding to E. coli GyrB-466) and the backbone carbonyl of

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nearby ParE-Arg418 (Figure 6B). Indeed, docked poses for UING5-249 revealed that the C-

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7 aminomethyl pyrrolidine group is capable of simultaneously forming hydrogen bonds with

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multiple residues. In the rigid C-7 ring system of moxifloxacin, however, the amine group is

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directly linked to the pyrrolidine and cannot reach ParE-Glu437. A similar difference

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between binding contacts of the C-7 groups was seen with the cognate diones, UING5-157

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and UING5-207 (Figure 6C and 6D).

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In addition to the preferred binding contacts between the primary amine of the

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aminomethyl pyrrolidine group with ParE-Glu437 (E. coli GyrB-Glu466), the dione UING5-

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207 also adopted several poses in which the primary amine of the aminomethyl pyrrolidine

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formed single hydrogen bonding interactions with ParE-Glu437 and the backbone carbonyl

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of ParE-Arg418 (Figure 6D). An interaction of the moxifloxacin C-7 group with ParE-

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Arg418 was also observed, but only in a few of the lower-scoring poses (Supplemental Table

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S2). Thus, the fluoroquinolone and dione derivatives containing a C-7 aminomethyl

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pyrrolidine appear capable of forming binding interactions with GyrB residues, while the C-7

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group of moxifloxacin and the cognate dione, UING5-157, preferentially interact with dA-20.

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As expected from crystal structures, docking the fluoroquinolone required the C-3/C-4

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ketoacid-magnesium interaction to anchor the fluoroquinolones to helix-4. To observe dione

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docking, the compounds needed to be anchored through their C-2 carbonyl group to ParC-

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Arg123, as seen in the PDB 3LTN structure of Streptococcus pneumoniae topoisomerase IV

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bound to dione and DNA.11



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We next performed docking with the GyrB-E466C substitution by introducing the

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equivalent change (ParE-E437C) into the 2XKK crystal structure of cleaved complexes

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formed with A. baumannii topoisomerase IV. With moxifloxacin, the top 20 binding poses

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were similar to the top 20 binding poses generated using wild-type enzyme (Figure 7A, see

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Supplementary Figures S7 and S8 for visualization of all 20 binding poses), as expected from

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moxifloxacin lacking a contact with GyrB-Glu466. Thus, the ParE-E437C (GyrB-E466C)

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substitution appears to have little effect on the preferred interaction of the C-7 group of

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moxifloxacin. In contrast, the top 20 binding poses of the fluoroquinolone UING5-249 with

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the ParE-E437C variant showed greater variation for C-7 group orientation and binding

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contacts: the primary amine of the C-7 aminomethyl pyrrolidine group formed hydrogen

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bonds to dA-20, to dT-19, to the backbone carbonyl of ParE-Arg418, or simply failed to form

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any polar or electrostatic interaction (two DNA contacts are exemplified in Figures 7B and

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7C). Thus, the Cys substitution severely disrupts interaction with GyrB-466. Similar

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differences were seen with the cognate diones (Figure 7D and 7E), indicating that the C-7

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aminomethyl pyrrolidine group might interact with wild-type GyrB and thus provide a

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stabilizing effect with GyrB that is not seen with the C-7 diazabicylco compounds (i.e.,

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moxifloxacin and UING5-157). Finally, a consistent observation throughout comparison of

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the top binding poses was that, as compared to the fluoroquinolone, the positioning and

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orientation of the dione core structures were highly conserved in all binding poses due to the

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restriction imposed by the hydrogen bond between the dione C-2 carbonyl group and Arg123

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of ParC (see overlapping structures in Supplementary Figures S7 and S8).

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To provide an experimental test for an interaction between the C-7 aminomethyl

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pyrrolidine group and GyrB-Glu466, we compared cleaved-complex-forming activity of

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diones UING5-207 and UING5-157 using a GyrB-E466C mutant available from other work.6

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With wild-type gyrase, UING5-207 was about 10-fold more active than the moxifloxacin-like


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302

dione UING5-157 (Figures 8A and 8B). Replacement of the anionic glutamate with the

303

shorter, uncharged cysteine side-chain reduced the activity more for UING5-207 than for

304

UING5-157, presumably due to a loss of C-7 ring interactions between UING5-207 and

305

GyrB-Glu466 (the core portions of diones position similarly in mutant and wild-type protein,

306

Supplementary Figures S7 and S8). The differences shown in Figures 8A, 8B, and 8E are

307

consistent with the GyrB-E466C substitution removing a preferred binding contact for the C-

308

7 aminomethyl pyrrolidine group of dione UING5-207. The unique binding interactions

309

between the aminomethyl pyrrolidine and GyrB thus appears to improve the ability of diones

310

with this substituent to poison gyrases bearing helix-4 substitutions compared to derivatives

311

having other C-7 groups that have been examined to date.

312

The fluoroquinolone comparison (UING5-249 vs. moxifloxacin) with GyrB E466C

313

was more complex, because the substitution could perturb both GyrB-C-7 ring interactions

314

and formation of the magnesium-water bridge at the other end of the fluoroquinolone. When

315

the top 20 poses for each docking run were considered as a whole (Supplementary Figures S7

316

and S8), both moxifloxacin and the UING5-249 fluoroquinolone docked in a generally less-

317

ordered fashion to GyrB-E466C gyrase than to the wild-type enzyme, and the docking

318

orientation around the magnesium ion was less ordered with mutant gyrase. In addition,

319

UING5-249 was unable to form a hydrogen bond to GyrB-466 when it was cysteine. These

320

observations suggest that both fluoroquinolones would exhibit lower activity with GyrB-

321

E466C gyrase and that the reduction for UING5-249 would be slightly greater. Such was the

322

case when cleaved-complex forming activity was measured (Figure 8C, 8D, 8E). Efforts are

323

now being made to obtain crystal structures of cleaved complexes formed with gyrase and

324

either UING5-249 or UING5-207 to confirm and extend conclusions derived from docking

325

and DNA cleavage studies. Dione-resistant mutants are also being examined for the location

326

of GyrB substitutions and impact on drug susceptibility.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

327

Cross-over activity with human topoisomerase II. For reasons that were previously

328

unclear, the C-7 aminomethyl pyrrolidine group confers crossover activity for

329

fluoroquinolones and diones with human topoisomerase II.18 When we compared spatial

330

orientation of amino acid residues in the cleaved complex region of the crystal structures for

331

A. baumannii topoisomerase IV (2XKK)14 with that of human topoisomerase IIβ (3QX3),26

332

we found that human topoisomerase II has glutamic acid (E522) and arginine (R503) residues

333

in its TOPRIM domain that are conserved with respect to ParE-Glu437 and ParE-Arg418 in

334

topoisomerase IV. While the amino acid sequences adjacent to the glutamate residue

335

(DEVLASQEV and KQIMENAEI in A. baumannii topoisomerase IV and human

336

topoisomerase II, respectively) are not highly conserved, spatial positioning of the glutamate

337

residue relative to DNA and drug binding is highly conserved (3-dimensional conservation).

338

Moreover, the nearby arginine-containing sequences are highly conserved (PIRGKILN vs.

339

PLRGKILN). These similarities suggest that anchoring of the drug to the cleavage site

340

through the conserved binding interaction between the C-7 aminomethyl pyrrolidine group

341

and the TOPRIM domain glutamic acid and/or arginine (as observed with topoisomerase IV,

342

Figures 6B and 6D) contributes to the poisoning activity with helix-4 variants of B. anthracis

343

topoisomerase IV and wild-type human topoisomerase II. Indeed, the binding contacts

344

formed by the C-7 aminomethyl pyrrolidine group that impart activity against helix-4 variants

345

of bacterial type-II topoisomerases are likely to be the same features and contacts that impart

346

C-7 aminomethyl pyrrolidine fluoroquinolone and dione activity against human

347

topoisomerase II.

348

Concluding remarks.

The traditional response to antibiotic resistance has been

349

creation of new compounds to which bacteria are not yet resistant. The present work focused

350

on just such a strategy for quinolone-like quinazolinediones. Judicious choice of C-7 ring

351

substituents, and likely many other substituents yet to be explored, can provide the


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352

stabilization needed to generate quinolone-class derivatives that have activity against

353

fluoroquinolone-resistant type II topoisomerases. Diones bypass much of the protective

354

effect of common GyrA-mediated resistance mutations because they do not form the drug-

355

magnesium-water-GyrA bridge characteristic of fluoroquinolones. We found that dione

356

activity can be increased through a specific C-7 ring interaction with E. coli GyrB-466. Since

357

the most active compounds with purified E. coli gyrase were generally the most active with

358

cultured cells (supplementary Table S1), biochemical studies of the type described are likely

359

to be useful for finding more effective agents. In the course of the present work, the Osheroff and Kerns laboratories found that

360 361

quinolone/dione C-7 substituents that facilitate action with bacterial topoisomerase helix-4

362

variants also facilitate action with human topoisomerase II,18 a result explained by the

363

findings reported here. While such activity may cause topoisomerase II-based toxicity in

364

mammalian hosts, other aspects of dione/quinolone structure, such as substituents at the C-8

365

position, can be altered to discriminate activity between human and bacterial enzymes.18 We

366

expect the experimental and computational modeling approach presented above to provide a

367

platform for designing new quinolone-class antibacterials having both elevated activity with

368

wild-type and fluoroquinolone-resistant bacteria, along with reduced activity against human

369

topoisomerase II.

370 371

METHODS GyrA and GyrB subunits of E. coli gyrase, including those with GyrA-G81C and

372 373

GyrB-E466C substitutions, were expressed and purified separately as described previously,6,

374

27

375

Healthcare; gatifloxacin was from Bristol-Meyers-Squibb; PD161148 was from Parke-Davis

376

Division of Pfizer Corp. Other fluoroquinolones and quinazolinediones were synthesized as

and in Supplemental Materials. Moxifloxacin and ciprofloxacin were obtained from Bayer



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

377

described previously.19 Formation and detection of cleaved complexes was as described

378

previously6 and in Supplemental Materials. In all cases, a quinolone or dione was used to

379

form cleaved complexes.

380

Resealing of plasmid DNA was accomplished in two ways. In one, reaction mixtures,

381

prepared and incubated to obtain cleaved complexes, were incubated in EDTA at 37oC for 30

382

min before SDS (1% w/v) and proteinase K (100 µg ml-1) were added for an additional 15-

383

min incubation. In the other, aliquots of reaction mixtures, incubated as described for

384

complex formation, were incubated at various temperatures for 5 min followed by incubation

385

in 1% SDS and 100 µg ml-1 proteinase K for another 15 min at 37oC. In both reaction

386

schemes, EDTA concentration was brought to 50 mM prior to applying reaction mixtures to

387

agarose gels. Plasmid species were separated by gel electrophoresis and quantified.

388

For modeling studies, an initial, manual analysis and manipulation of

389

fluoroquinolone-gyrase cleaved complexes was performed using structures obtained from

390

PBD access numbers 2XKK for A. baumannii topoisomerase IV14 and 3LTN for S.

391

pneumoniae topoisomerase IV11 using WebLab ViewerLight. For computer-aided docking,

392

SYBYL-X 1.3 was used to prepare the 2XKK crystal structure for ligand docking.28

393

Standard Tripos procedures were followed for SYBYL-X 1.3 (Certara, L.P.). Briefly, metal

394

bonds were removed, atom types in the ligands were fixed, missing side chains were added,

395

protein termini were charged, hydrogen atoms were added, and a staged minimization of the

396

entire complex was performed. Details are provided in Supplementary Materials. The

397

quinazoline-2,4-dione ligands were docked in two steps. In the first step, dione UING5-157,

398

the cognate of moxifloxacin, was docked according to the procedure in Supplementary

399

Materials except that the magnesium ion of the magnesium-water bridge was removed prior

400

to docking. After docking, the top 20 binding poses were examined, and the highest scoring

401

pose that showed a hydrogen bond interaction between the dione C-2 carbonyl and ParC-


Page 16 of 33

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402

Arg123 was used as the template for subsequent docking of UING5-157 and UING5-207.

403

The parameters of the second docking run were identical to the first, except that deviation

404

from the ParC-Arg123 hydrogen-bond-forming binding pose template was required to exceed

405

5 pKd/Å2 to be scored. This very small "penalty" had the effect of fixing the dione core in

406

the position revealed by the 3LTN crystal structure11 while allowing the C-7 substituents to

407

sample various binding interactions with GyrB and DNA. Binding poses were examined and

408

visualized using the SYBYL-X 1.3 software.

409 410

SUPPLEMENTARY INFORMATION

411

Supporting tables and figures plus detailed descriptions of methods. This information is

412

available free of charge via Internet at http://pubs.acs.org

413

AUTHOR INFORMATION

414

Corresponding authors

415

*Email: :[email protected]; [email protected]; [email protected]

416

417

Note:

418

The authors declare no competing financial interest.

419

ACKNOWLEDGEMENTS

420

We thank members of the Berger laboratory, especially K. Jude, for technical advice, M.

421

Malik for preparing figures, and the following for many experimental suggestions and critical

422

comments on the manuscript: M. Gennaro, K. Jude, M. Malik, R. Pine, and X. Zhao. KD

423

was a Visiting Scholar, University of California, Berkeley, CA.



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424

425

FUNDING

426

This work was supported by the National Institutes of Health [R01AI073491 to K.D.,

427

R01AI87671 to R.K., R01CA077373 to J.B.]. Funding for open access charge: National

428

Institutes of Health.

429

430

REFERENCES

431

[1] Osheroff, N., and Zechiedrich, E. (1987) Calcium-promoted DNA cleavage by eukaryotic

432

topoisomerase II: trapping the covalent enzyme-DNA complex in an active form.,

433

Biochemistry 26, 4303-4309.

434

[2] Howard, M. T., Neece, S. H., Matson, S. W., and Kreuzer, K. N. (1994) Disruption of a

435

topoisomerase-DNA cleavage complex by a DNA helicase, Proc. Natl. Acad. Sci.

436

U.S.A. 91, 12031-12035.

437 438 439 440

[3] Snyder, M., and Drlica, K. (1979) DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid., J. Mol. Biol. 131, 287-302. [4] Drlica, K., Malik, M., Kerns, R. J., and Zhao, X. (2008) Quinolone-mediated bacterial death, Antimicrob Agents Chemother 52, 385-392.

441

[5] Kreuzer, K. N., and Cozzarelli, N. R. (1979) Escherichia coli mutants thermosensitive for

442

deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication,

443

transcription, and bacteriophage growth, J. Bacteriol. 140, 424-435.

444

[6] Mustaev, A., Malik, M., Zhao, X., Kurepina, N., Luan, G., Oppegard, L., Hiasa, H.,

445

Marks, K., Kerns, R., Berger, J., and Drlica, K. (2014) Fluoroquinolone-gyrase-DNA

446

complexes: two modes of drug binding, J Biol Chem 289, 12300-12312.


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[7] Gellert, M., Mizuuchi, K., O'Dea, M. H., Itoh, T., and Tomizawa, J.-L. (1977) Nalidixic

448

acid resistance: a second genetic character involved in DNA gyrase activity., Proc.

449

Natl. Acad. Sci. U.S.A. 74, 4772-4776.

450

[8] Sugino, A., Peebles, C., Kruezer, K., and Cozzarelli, N. (1977) Mechanism of action of

451

nalidixic acid: purification of Escherichia coli nalA gene product and its relationship

452

to DNA gyrase and a novel nicking-closing enzyme., Proc. Natl. Acad. Sci. U.S.A. 74,

453

4767-4771.

454

[9] Aldred, K., McPherson, S., Turnbough, C., Kerns, R., and Osheroff, N. (2013)

455

Topoisomerase IV-quinolone interactions are mediated through a water-metal ion

456

bridge: mechanistic basis of quinolone resistance, Nucleic Acids Res. 41, 4628-4639.

457

[10] Pan, X., Dias, M., Palumbo, M., and Fisher, L. (2008) Clerocidin selectively modifies

458

the gyrase-DNA gate to induce irreversible and reversible DNA damage., Nucleic

459

Acids Res. 36, 5516-5529.

460

[11] Laponogov, I., Pan, X., Veselkov, D., McAuley, K., Fisher, L., and Sanderson, M.

461

(2010) Structural basis of gate-DNA breakage and resealing by type II

462

topoisomerases, PLoS One 5, e11338.

463

[12] Laponogov, I., Sohi, M., Veselkov, D., Pan, X., Sawhney, R., Thompson, A., McAuley,

464

K., Fisher, L., and Sanderson, M. (2009) Structural insight into the quinolone-DNA

465

cleavage complex of type IIA topoisomerases., Nat Struct Mol Biol. 16, 667-669.

466

[13] Bax, B., Chan, P., Eggleston, D., Fosberry, A., Gentry, D., Gorrec, F., Giordano, I.,

467

Hann, M., Hennessy, A., Hibbs, M., Huang, J., Jones, E., Jones, J., Brown, K., Lewis,

468

C., May, E., Saunders, M., Singh, O., Spitzfaden, C., Shen, C., Shillings, A.,

469

Theobald, A., Wohlkonig, A., Pearson, N., and Gwynn, M. (2010) Type IIA

470

topoisomerase inhibition by a new class of antibacterial agents., Nature 466, 935-940.



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471

[14] Wohlkonig, A., Chan, P., Fosberry, A., Homes, P., Huang, J., Kranz, M., Leydon, V.,

472

Miles, T., Pearson, N., Perera, R., Shillings, A., Gwynn, M., and Bax, B. (2010)

473

Structural basis of quinolone inhibition of type IIA topoisomerases and target-

474

mediated resistance. , Nat Struct Mol Biol. 17, 1152-1153.

475 476 477

[15] Deweese, J., and Osheroff, N. (2010) The use of divalent metal ions by type II topoisomerases., Metallomics 2, 450-459. [16] Aldred, K., McPherson, S., Wang, P., Kerns, R., Graves, D., Turnbough, C., and

478

Osheroff, N. (2012) Drug interactions with Bacillus anthracis topoisomerase IV:

479

biochemical basis for quinolone action and resistance., Biochemistry 51, 370-381.

480

[17] Pan, X., Gould, K., and Fisher, L. M. (2009) Probing the differential interactions of

481

quinazolinedione PD 0305970 and quinolones with gyrase and topoisomerase IV.,

482

Antimicrob Agents Chemother 53, 3822-3831.

483

[18] Aldred, K., Schwanz, H., Li, G., McPherson, S., CL Turnbough, J., Kerns, R., and

484

Osheroff, N. (2013) Overcoming target-mediated quinolone resistance in

485

topoisomerase IV by introducing metal ion-independent drug-enzyme interactions:

486

implications for drug design, ACS Chem Biol 8, 2660-2668.

487

[19] German, N., Malik, M., Rosen, J., Drlica, K., and Kerns, R. (2008) Use of gyrase

488

resistance mutants to guide selection of 8-methoxy-quinazoline-2,4-diones,

489

Antimicrob Agents Chemother 52, 3915-3921.

490

[20] Malik, M., Marks, K., Mustaev, A., Zhao, X., Chavda, K., Kerns, R., and Drlica, K.

491

(2011) Fluoroquinolone and quinazolinedione activities against wild-type and gyrase

492

mutant strains of Mycobacterium smegmatis, Antimicrob Agents Chemother 55, 2335-

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2343.


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[21] Oppegard, L. M., Streck, K., Rosen, J., Shwanz, H. A., Drlica, K., Kerns, R. J., and

495

Hiasa, H. (2010) Comparison of in vitro activities of fluoroquinolone-like 2,4- and

496

1.3-diones., Antimicrob Agents Chemother 54, 3011-3014.

497

[22] Noble, C., and Maxwell, A. (2002) The role of GyrB in the DNA cleavage-religation

498

reaction of DNA gyrase: a proposed two metal-ion mechanism., J. Mol. Biol. 318,

499

361-371.

500

[23] Pitts, S., Liou, G., Mitchenall, L., Burgin, A., Maxwell, A., Neuman, K., and Osheroff,

501

N. (2011) Use of divalent metal ions in the DNA cleavage reaction of topoisomerase

502

IV., Nucleic Acids Res. 39, 4808-4817.

503 504 505

[24] Sander, M., and Hsieh, T. (1983) Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster, J. Biol. Chem. 258, 8421-8428. [25] Maruri, F., Sterling, T., Kaiga, A., Blackman, A., vanderHeijden, Y., Mayer, C.,

506

Cambau, E., and Aubry, A. (2012) A systematic review of gyrase mutations

507

associated with fluoroquinolone-resistant Mycobacterium tuberculosis and a proposed

508

gyrase numbering system, J Antimicrob Chemother 67, 819-831.

509

[26] Wu, C., Li, T., Farh, L., Lin, L., Lin, T., Yu, Y., Yen, T., Chiang, C., and Chan, N.

510

(2011) Structural basis of type II topoisomerase inhibition by the anticancer drug

511

etoposide. , Science 333, 459-462.

512

[27] Schoeffler, A., May, A., and Berger, J. (2010) A domain insertion in Escherichia coli

513

GyrB adopts a novel fold that plays a critical role in gyrase function, Nucleic Acids

514

Res. 38, 7830-7844.

515 516

[28] Jain, A. (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. , J Med Chem 46, 499-511.

517

518



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

519

FIGURE LEGENDS

520

Figure 1. Structure and activity differences between quinolones and diones. A. Compounds

521

used in the present work. Structures of the C-7 substituents (R1) are above the dashed line as

522

a-f. Below the dashed line are fluoroquinolones (left) and quinazolinediones (right).. The

523

report focuses on the 3-(aminomethyl)pyrrolidinyl C-7 group (boxed). B. Formation of

524

cleaved complexes occurs at lower concentrations of fluoroquinolone (empty bars) than

525

quinazolinedione (filled bars). Cleaved complex formation was assayed as in Methods to

526

determine the concentration of quinolone or dione required to linearize 20% of the plasmid

527

DNA. Error bars represent standard deviation for independent experiments.

528

Figure 2. EDTA-mediated resealing of DNA in cleaved complexes formed with quinolone

529

and dione. Incubations containing gyrase, DNA, and either fluoroquinolone (UING5-249 at

530

2 µM, empty circles) or dione (UING5-207 at 20 µM, filled circles) generated similar

531

amounts of cleaved complexes for both compounds. Parallel reaction mixtures were

532

incubated at the indicated concentration of EDTA for an additional 30 min before treatment

533

with SDS and proteinase K. The fraction of total DNA in linear (Panel A) or nicked (Panel B)

534

forms was determined by gel electrophoresis. Data were normalized to a zero-EDTA control,

535

which was similar for quinolone and dione. Replicate experiments gave similar results; error

536

bars indicate standard deviation.

537

Figure 3. Thermal reversal of cleaved complexes formed with quinolones and diones. A.

538

Comparison of quinolones and cognate diones. Cleaved complexes were formed as

539

described in Methods and then incubated at various temperatures to determine the

540

temperature causing 50% resealing of DNA. B. Relationship between drug concentration

541

required for complex formation and thermal resealing of DNA. Concentrations of

542

fluoroquinolone (empty circles) or quinazolinedione (filled circles) required to trap 20% of


Page 22 of 33

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543

the plasmid DNA in a linear form were determined as in Figure 1B, and temperatures at

544

which 50% of the linear DNA was resealed were determined. Letters indicate paired

545

fluoroquinolones and diones (a = UING5-249/207; b = moxifloxacin/UING5-157; c =

546

UING5-248/159; d = PD161148/UING5-209); cip, ciprofloxacin; gat, gatifloxacin. Error

547

bars indicate standard deviation of means.

548

Figure 4. Effect of GyrA-G81C gyrase on dione and quinolone activity. A. Compound

549

concentration effects on complex formation. Panel i. Wild-type gyase. Panel ii. GyrA-G81C

550

gyrase. Symbols: empty circles, fluoroquinolone UING5-249; filled circles, dione UING5-

551

207. Similar results were obtained with four replicate experiments. B. DNA resealing

552

stimulated by EDTA. Reaction mixtures containing cleaved complex were treated with the

553

indicated concentrations of EDTA and analyzed as in Figure 2. Linear DNA was quantified

554

and expressed as a percent of the zero-EDTA control. Symbols: filled circles, dione UING5-

555

207 at 80 µM; empty circles, fluoroquinolone UING5-249 at 40 µM. Similar results were

556

obtained with three independent replicate experiments. C. DNA resealing stimulated by high

557

temperature. Reaction mixtures containing cleaved complexes were treated and analyzed as

558

in Figure 3. Panel i. Complexes formed with fluoroquinolone UING5-249. Panel ii.

559

Complexes formed with dione UING5-207. Symbols; empty symbols wild-type gyrase;

560

filled symbols GyrA81C gyrase. Similar results were obtained with four replicate

561

experiments.

562

Figure 5. Location of C-7 ring substitutents relative to amino acid 466 of GyrB in cleaved

563

complexes. A potential salt bridge and hydrogen bond between the C-7 ring systems and

564

GyrB-466E are shown. Panel A. Dione binding. The C-7 ring system of UING5-157 is

565

shown in light gray, while that of UING5-207 is in dark gray. Panel B. Quinolone binding.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

566

The C-7 ring system of moxifloxacin is shown in light gray, while that of UING5-249 is in

567

dark gray.

568

Figure. 6. Docking of quinolones and diones with wild-type enzyme. Representative

569

cleaved-complex interactions were taken from the top 20 binding poses obtained from

570

docking moxifloxacin (A), UING5-249 (B), UING5-157 (C), and UING5-207 (D) into the

571

2XKK (wild-type) crystal structure. Hydrogen bonds are shown as dashed yellow lines. The

572

top scoring and most consistent pose for moxifloxacin and UING5-157 show a hydrogen

573

bond to the deoxyribose oxygen of dA-20; top pose of UING5-249 and UING5-207 show

574

hydrogen bonds from the C-7 amine to E437 and R418. Both diones were anchored to ParC-

575

Arg123 through a hydrogen bond with their C-2 carbonyl group.

576

Figure 7. Docking of quinolones and diones with ParE/GyrB mutant enzyme. Representative

577

ternary complex interactions were taken from the top 20 binding poses obtained from

578

docking moxifloxacin (A), UING5-249 (B, C), UING5-157 (D), and UING5-207 (E) into the

579

2XKK crystal structure modified from ParE-Glu437 to Cys437. Hydrogen bonds are shown

580

as dashed yellow lines. The top pose for moxifloxacin (A) showed formation of the same

581

hydrogen bond to dA-20 as found with the wild-type structure. However, when UING5-249

582

was docked into the E437C mutant structure (B, C), the top scoring poses no longer showed

583

hydrogen bonds to the 437 position or to R418. Instead, the C-7 amine rotated about 180

584

degrees to form hydrogen bond interactions with DNA (dA-20 or dT-19). In the case of

585

docking UING5-157 (D) into the mutant enzyme, the top two poses (shown) either form a

586

hydrogen bond to R418 or form no electrostatic/hydrogen bond interaction. When UING5-

587

207 (E) was docked, its top pose displayed hydrogen bonds from the C-7 amine to both the

588

R418 side chain and to the deoxyribose oxygen of dG-17.


Page 24 of 33

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589

Figure 8. C-7 ring substituent affects GyrB-466C-mediated reduction in complex-forming

590

activity. Cleaved complexes were formed at the indicated concentrations of fluoroquinolone

591

or dione. Percent linear DNA was determined by gel electrophoresis. Panel A, dione

592

UING5-207; Panel B, dione UING5-157; Panel C, fluoroquinolone UING5-249; Panel D,

593

moxifloxacin. Symbols: empty circles (wild-type gyrase), filled circles (GyrB-466C gyrase).

594

Panel E. Comparision of cleavage activities. Compound concentration required to achieve

595

20% linear DNA for GyrB-466C gyrase was divided by that value for wild-type gyrase,

596

determined for each test compound (average values from multiple experiments; error bars

597

represent standard deviation). Arrows indicate 20% linear DNA.

598



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93x63mm (300 x 300 DPI)


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