Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.

The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.

Molecular insights into antibiotic resistance - how a binding protein traps albicidin.

The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. The drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to cooperatively clamp albicidin, which is unusual for drug-binding proteins of the MerR family. Structure-guided NMR binding studies employing synthetic albicidin derivatives give valuable information about ligand promiscuity of AlbAS. Our findings thus expand the general understanding of antibiotic resistance mechanisms and support current drug-design efforts directed at more effective albicidin analogs.

Synthesis of Albicidin Derivatives: Assessing the Role of N-terminal Acylation on the Antibacterial Activity.

The peptide antibiotic albicidin, which is synthesized by the plant pathogenic bacterium, Xanthomonas albilineans, represents the most prominent member of a new class of antibacterial gyrase inhibitors. It shows remarkable antibacterial activities against Gram-positive and Gram-negative microorganisms. Its unique structure potentially represents a new lead structure for the development of an antibacterial drug. Here we report the synthesis of 14 albicidin derivatives with structural variations at the N-terminus, primarily investigating the effects of variation of cinnamoyl, phenylpropanoyl, and benzoyl residues. Gyrase inhibition in vitro and determination of minimal inhibitory concentrations were assessed in parallel. Activities in a nanomolar range and the importance of N-acylation were demonstrated.

Synthesis and Antimicrobial Activity of Albicidin Derivatives with Variations of the Central Cyanoalanine Building Block.

To investigate the pharmacophore regions of the antibiotic albicidin, derivatives with variations on the central amino acid were synthesized. Charged as well as uncharged residues were chosen to explore the influence of charge, chirality, and steric bulk. The bioactivity of the newly synthesized derivatives was determined by a microdilution technique to obtain minimum inhibitory concentrations (MIC) values. The compounds were also tested in a cell-free system to obtain information about their ability to inhibit their primary target, DNA gyrase. It was then shown that derivatives with uncharged side chains retain antibacterial activity, whereas incorporation of charged amino acid residues decreases the antibacterial activity dramatically, possibly due to restricted cell penetration of these derivatives. From the newly synthesized derivatives, the threonine derivative shows the most promising results in both tests. The information will help to develop the features of albicidin toward more drug-like structures.

A field model of learning: 2. Long-term memory in the crab Chasmagnathus granulatus.

In the previous companion paper, the possibility of learning by Chasmagnathus in field conditions was demonstrated. Here, we study long-term memory inquiring to what extent an internal representation could be maintained in a complex environment. Two 45-min training sessions, each of 15 visual danger stimulus presentations with 3-min intertrials, were given at a 24-h interval. Throughout the first training session and during the first 22.5 min of re-training on day 2, crabs kept the same hiding response level but then, during the second phase of re-training, the re-emerging increased up to the point that 32% of surface crabs ignored the stimulus. Each session was followed by a 22.5-min testing without stimulation. At testing on day 2 after re-training, crabs showed a change in the usual exploring strategy. Results reveal long persistency in responding despite a rest interval of 24 h followed by a gradual decrease in response until it vanishes. The statistical analysis was performed by comparing performances at day 2 (Rescorla in Am Psychol 43:151-160, 1988) and then confirmed through comparisons between day 1 and day 2. However, it is not possible to identify separate and taxonomically well-defined learnings but rather a tangled collection of processes that influence each other blurring some of the diagnostic features of each learning.

A field model of learning: 1. Short-term memory in the crab Chasmagnathus granulatus.

Learning and memory studies have been performed for more than two decades using the crab Chasmagnathus in our laboratory. Here, our research was aimed at disclosing some instances of learning in field conditions. Three experiments were performed non-simultaneously, all with a 22.5-min pre-training preceding the first visual-danger-stimulus, an opaque rectangle passing overhead. In Experiment 1, crabs received a single stimulus followed by 22.5-min testing without stimulation, where the re-emerging latency was considered the basic latency response. In Experiment 2, training consisted of 15 stimulus 3-min apart, followed by 22.5-min testing without stimulation. Throughout training crabs were underground but re-emerged at testing with latencies longer than the basic latency response. Both at pre-training and testing the usual strategy of exploring was the short-near excursions. In Experiment 3, training included three stimulus 22.5-min apart, followed by 22.5-min testing. Crabs left their burrows before the end of each inter-trial, showing a mean latency like the basic latency response, but a sensitization to the stimulus and a preponderance of the fast-far excursions over the usual slow-near. In brief: through 15-3 training, crabs learn that the stimulus is iteratively presented; through 3-22.5 training, crabs acquire sensitization to the stimulus and a different strategy of exploration.