Protonated peptides containing histidine or arginine residues and a free carboxyl group (His-Ala-Ile, His-Ala-Leu, Ala-His-Leu, Ala-Ala-His-Ala-Leu, His-Ala-Ala-Ala-Leu, and Arg-Ala-Ile) form stable anions upon collisional double electron transfer from Cs atoms at 50 keV kinetic energies. This unusual behavior is explained by hidden rearrangements occurring in peptide radical intermediates formed by transfer of the first electron. The rearrangements occur on a approximately 120 ns time scale determined by the radical flight time. Analysis of the conformational space for (His-Ala-Ile + H)(+) precursor cations identified two major conformer groups, 1a(+)-1m(+) and 5a(+)-5h(+) , that differed in their H-bonding patterns and were calculated to collectively account for 39% and 60%, respectively, of the gas-phase ions. One-electron reduction in 1a(+) and 5a(+) triggers exothermic hydrogen atom migration from the terminal COOH group onto the His imidazole ring, forming imidazoline radical intermediates. The intermediate from 5a is characterized by its charge and spin distribution as a novel cation radical-COO(-) salt bridge. The intermediate from 1a undergoes spontaneous isomerization by imidazoline N-H migration, re-forming the COOH group and accomplishing exothermic isomerization of the initial (3H)-imidazole radical to a (2H)-imidazole radical. An analogous unimolecular isomerization in simple imidazole and histidine radicals requires activation energies of 150 kJ mol(-1), and its occurrence in 1a and 5a is due to the promoting effect of the proximate COOH group. The rearrangement is substantially reduced in Ala-Leu-His due to an unfavorable spatial orientation of the imidazole and COOH groups and precluded in the absence of a free carboxyl group in His-Ala-Leu amide. In contrast to His-Ala-Ile and Arg-Ala-Ile, protonated Lys-Ala-Ile does not produce stable anions upon double electron transfer. The radical trapping properties of histidine residues are discussed.

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.

Structural studies of topoisomerase-fluoroquinolone-DNA ternary complexes revealed a cavity between the quinolone N-1 position and the active site tyrosine. Fluoroquinolone derivatives having positively charged or aromatic moieties extended from the N-1 position were designed to probe for binding contacts with the phosphotyrosine residue in ternary complex. While alkylamine, alkylphthalimide, and alkylphenyl groups introduced at the N-1 position afforded derivatives that maintained modest inhibition of the supercoiling activity of DNA gyrase, none retained ability to poison DNA gyrase. Thus, the addition of a large and/or long moiety at the N-1 position disrupts ternary complex formation, and retained ability to inhibit supercoiling is likely through interference with the strand breakage reaction. Two derivatives were found to possess inhibitory effects on the decatenation activity of human topoisomerase II.