Structural and Functional Characterisation of Novel Potential Drug Targets in Helicobacter pylori

<i>Helicobacter pylori</i> colonises the human gastric mucosa. <i>H</i>. <i>pylori </i>infection may cause diseases of the upper gastrointestinal tract, such as chronic gastritis, ulcers and gastric cancer. The success rate of the current <i>H. pylori</i> treatment regimen has declined over time, mainly due to antibiotic resistance. Therefore, there is a clear need for identification of novel targets that can be used in the development of alternative treatment strategies for <i>H</i>. <i>pylori </i>infections. To address this, the present study focuses on two enzymes from <i>H. pylori</i> that represent novel potential targets for drug design: M17 aminopeptidase (HpM17AP) and α-carbonic anhydrase (HpαCA). HpM17AP plays a role in bacterial defence against human innate immune response and contributes to the mechanism of drug resistance, whereas HpαCA is important for buffering periplasmic pH of <i>H. pylori</i> close to neutral as a means of survival in the harsh acidic environment of human stomach. Due to their crucial role in colonisation and survival within the host, HpM17AP and HpαCA need to be evaluated as potential drug targets.<br> <br>    In order to understand the structural basis of catalysis and inhibition of HpM17AP, the crystal structures of HpM17AP and its complex with its inhibitor have been determined and analysed. In addition, the specificity of HpM17AP towards the N-terminal amino acid of its peptide substrates has been established. The inhibitor-bound structure of HpM17AP revealed that the D-phenylalanine moiety of the inhibitor binds in the S1 subsite of the enzyme. At the end of the S1 subsite, HpM17AP was found to harbor a hydrophilic pocket, which is a unique feature of the enzyme compared to very similar homologues from other bacteria. This pocket is flanked by a sodium ion and its coordinating water molecules. Furthermore, structural analysis revealed that variable loops at the entrance to and in the middle of the substrate-binding channel are important determinants of the substrate specificity of M17 aminopeptidases. In fact, the study has demonstrated that HpM17AP has broad substrate specificity and, in contrast to most characterised M17 aminopeptidase, HpM17AP displays preference for L-Arg over L-Leu residues in the peptide substrate.<br> <br>    In order to understand the molecular details of catalysis and the structural basis for the inhibition of HpαCA by sulfonamides, the crystal structures of HpαCA in complex with a series of sulfonamide inhibitors have been determined and analysed. This study revealed that HpαCA and human carbonic anhydrase likely follow the same catalytic mechanism, where HCO₃- is generated from CO₂ via a nucleophilic attack on CO₂ by the zinc-bound hydroxide ion. In addition, the study has demonstrated that sulfonamides act as site-directed inhibitors by mimicking the transition state of the CO₂ hydration reaction. Analysis of the structures revealed that the binding mode of sulfonamide correlates well with their inhibitory activities. Furthermore, the study has identified two pockets near the active site in HpαCA that are distinctly different from the corresponding regions in the structure of human carbonic anhydrase II. Thus, our analysis identified major structural features that can be exploited in the design of selective and more potent inhibitors of HpαCA that may lead to novel antimicrobials.<br> <br>    Finally, this study has shown that sulfonamides RSO₂NH₂ kill <i>H. pylori</i> via mechanisms that are different from the mechanisms of action of common antibiotics used to treat <i>H. pylori</i> infections. Despite having been chosen for this study due to their known activity as inhibitors of carbonic anhydrases, whose function is essential at acidic pH, these compounds also displayed bactericidal activity at neutral pH. As neutral pH approximates the conditions under which <i>H. pylori</i> persists in the stomach, we have analysed the mechanisms by which spontaneous mutations give rise to sulfonamide resistance at pH close to 7.0. The carbonic anhydrase inhibitors acetazolamide, methazolamide and ethoxzolamide produce a complex phenotype, likely involving the combination of different mechanisms which involve modifications in cellular proteins and systems other than α- and β-carbonic anhydrases themselves. The frequency of spontaneous mutations resulting in <i>H. pylori</i> resistance to sulfonamides was 2.5×10-8 or less, indicating that resistance does not develop easily. Furthermore, this and other studies have shown that the antimicrobial activity of sulfonamides is specific to <i>H. pylori</i> and several other bacteria, including <i>Streptococcus pneumoniae</i>, <i>Neisseria</i> spp. <i>Brucella suis</i>. This suggests that this class of sulfonamides can be developed into selective anti-<i>H. pylori</i> agents with a novel mechanism of action, which can be used for <i>H. pylori </i>infections management

Anti-Helicobacter pylori activity of ethoxzolamide

Ethoxzolamide (EZA), acetazolamide, and methazolamide are clinically used sulphonamide drugs designed to treat non-bacteria-related illnesses (e.g. glaucoma), but they also show antimicrobial activity against the gastric pathogen Helicobacter pylori. EZA showed the highest activity, and was effective against clinical isolates resistant to metronidazole, clarithromycin, and/or amoxicillin, suggesting that EZA kills H. pylori via mechanisms different from that of these antibiotics. The frequency of single-step spontaneous resistance acquisition by H. pylori was less than 5 × 10-9, showing that resistance to EZA does not develop easily. Resistance was associated with mutations in three genes, including the one that encodes undecaprenyl pyrophosphate synthase, a known target of sulphonamides. The data indicate that EZA impacts multiple targets in killing H. pylori. Our findings suggest that developing the approved anti-glaucoma drug EZA into a more effective anti-H. pylori agent may offer a faster and cost-effective route towards new antimicrobials with a novel mechanism of action

Laboratory Methods for Determining Etiology of Neonatal Infection at Population-based Sites in South Asia: The ANISA Study

Background: The Aetiology of Neonatal Infection in South Asia (ANISA) study aims to determine the etiology of neonatal infections in 5 population-based sites in Bangladesh, India and Pakistan.Methods: The main laboratory challenges in ANISA were selection and consistent implementation of laboratory methods at participating sites with varied infrastructure. The other specific challenges included (1) specimen collection and transport to designated study laboratories and timely processing in rural settings; (2) minimal or nonexistent laboratory facilities at the field sites; (3) obtaining sufficient volumes of blood from enrolled infants aged 0-59 days and (4) caregivers\u27 concerns about collection of clinical specimens from young infants. An additional challenge was selecting an appropriate molecular platform from multiple available options, all with limited field validation, for use in determining infection in young infants.CONCLUSIONS: This article describes how the challenges of specimen collection, transport and processing and implementation of laboratory methods have been addressed in the ANISA study. It also describes the measures taken to improve detection of microorganisms causing young infant infections by enhancing the sensitivity of existing laboratory methods for pathogen detection