Cryo-EM structure of Helicobacter pylori urease with a novel inhibitor in the active site at 2.0 Å resolution

AbstractInfection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickeldependent urease in the cytoplasm of the bacteria. Here, we report the 2.01 Å resolution structure of the 1.1 MDa urease in complex with a novel inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.45 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.

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Clinical Relevance of Helicobacter pylori Infection

Journal of Clinical Medicine ◽

10.3390/jcm10163473 ◽

2021 ◽

Vol 10 (16) ◽

pp. 3473

Author(s):

Irena Mladenova

Keyword(s):

Helicobacter Pylori ◽

Age Groups ◽

Acid Resistance ◽

Clinical Indication ◽

Clinical Aspects ◽

Gastric Disease ◽

Upper Gastrointestinal Endoscopy ◽

World Population ◽

Ulcer Disease ◽

H Pylori

Helicobacter pylori (H. pylori) is a Gram-negative helical, microaerophilic bacterium which colonizes the antrum and body of the stomach, surviving in its harsh environment through mechanisms of acid resistance and colonization factors. It infects approximately 50% of the world population. Although the prevalence of this infection varies from country to country, as well as between different ethnic, social or age groups, it is estimated that about 50% of the human population only carries this microorganism. While H. pylori has been found to play a major etiological and pathogenic role in chronic gastritis, peptic ulcer disease and gastric cancer, its importance for many types of extra-gastric disease needs to be further investigated. The choice of tests to diagnose H. pylori infection, defined as invasive or non-invasive, depends on the clinical indication as to whether to perform upper gastrointestinal endoscopy. Focusing on bacterial eradication, the treatment should be decided locally based on the use of antibiotics and documented antibiotic resistance. The author provides an overview of the current state of knowledge about the clinical aspects of H. pylori infection, especially its diagnostic and therapeutic management.

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Synthesis and In Vitro Enzymatic Studies of New 3-Aryldiazenyl Indoles as Promising Helicobacter pylori IMPDH Inhibitors

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190227212334 ◽

2019 ◽

Vol 19 (5) ◽

pp. 376-382 ◽

Cited By ~ 4

Author(s):

Sachin Jangra ◽

Gayathri Purushothaman ◽

Kapil Juvale ◽

Srimadhavi Ravi ◽

Aishwarya Menon ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Infections ◽

Immunosuppressive Drugs ◽

Multi Drug Resistance ◽

Metabolic Enzyme ◽

World Population ◽

Inhibitor Molecule ◽

Nucleotide Synthesis ◽

H Pylori

Background & Objective:Helicobacter pylori infection is one of the primary causes of peptic ulcer followed by gastric cancer in the world population. Due to increased occurrences of multi-drug resistance to the currently available antibiotics, there is an urgent need for a new class of drugs against H. pylori. Inosine 5′-monophosphate dehydrogenase (IMPDH), a metabolic enzyme plays a significant role in cell proliferation and cell growth. It catalyses guanine nucleotide synthesis. IMPDH enzyme has been exploited as a target for antiviral, anticancer and immunosuppressive drugs. Recently, bacterial IMPDH has been studied as a potential target for treating bacterial infections. Differences in the structural and kinetic parameters of the eukaryotic and prokaryotic IMPDH make it possible to target bacterial enzyme selectively.Methods:In the current work, we have synthesised and studied the effect of substituted 3-aryldiazenyl indoles on Helicobacter pylori IMPDH (HpIMPDH) activity. The synthesised molecules were examined for their inhibitory potential against recombinant HpIMPDH.Results:In this study, compounds 1 and 2 were found to be the most potent inhibitors amongst the database with IC50 of 0.8 ± 0.02µM and 1 ± 0.03 µM, respectively.Conclusion:When compared to the most potent known HpIMPDH inhibitor molecule C91, 1 was only four-fold less potent and can be a good lead for further development of selective and potent inhibitors of HpIMPDH.

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Identification of Markers for Helicobacter pylori Strains Isolated from Children with Peptic Ulcer Disease by Suppressive Subtractive Hybridization

Infection and Immunity ◽

10.1128/iai.00123-06 ◽

2006 ◽

Vol 74 (7) ◽

pp. 4064-4074 ◽

Cited By ~ 34

Author(s):

Mónica Oleastro ◽

Lurdes Monteiro ◽

Philippe Lehours ◽

Francis Mégraud ◽

Armelle Ménard

Keyword(s):

Helicobacter Pylori ◽

Peptic Ulcer ◽

Peptic Ulcer Disease ◽

Subtractive Hybridization ◽

Suppressive Subtractive Hybridization ◽

Ulcer Disease ◽

Lipopolysaccharide Biosynthesis ◽

The Difference ◽

H Pylori

ABSTRACT Peptic ulcer disease (PUD) occurs after a long-term Helicobacter pylori infection. However, the disease can develop earlier, and rare cases have been observed in children, suggesting that these H. pylori strains may be more virulent. We used suppressive subtractive hybridization for comparative genomics between H. pylori strains isolated from a 5-year-old child with duodenal ulcer and from a sex- and age-matched child with gastritis only. The prevalence of the 30 tester-specific subtracted sequences was determined on a collection of H. pylori strains from children (15 ulcers and 30 gastritis) and from adults (46 ulcers and 44 gastritis). Two of these sequences, jhp0562 (80.0% versus 33.3%, P = 0.008) and jhp0870 (80.0% versus 36.7%, P = 0.015), were highly associated with PUD in children and a third sequence, jhp0828, was less associated (40.0% versus 10.0%, P = 0.048). Among adult strains, none of the 30 sequences was associated with PUD. However, both jhp0562 and jhp0870 were less prevalent in adenocarcinoma strains than in PUD strains from children and adults, the difference being statistically significant for jhp0870. In conclusion, two H. pylori genes were identified as being strongly associated with PUD in children, and their putative roles as an outer membrane protein for jhp0870 and in lipopolysaccharide biosynthesis for jhp0562, suggest that they may be novel virulence factors of H. pylori.

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A resolution record for cryoEM

Faculty Reviews ◽

10.12703/r-01-000002 ◽

2021 ◽

Vol 10 ◽

Author(s):

Jonathan Ashmore ◽

Bridget Carragher ◽

Peter B Rosenthal ◽

William Weis

Keyword(s):

Electron Microscopy ◽

Image Analysis ◽

Structure Determination ◽

Test Specimen ◽

Structural Information ◽

Atomic Resolution ◽

Fast Growing ◽

Cryo Electron Microscopy ◽

New Instrument ◽

Resolution Structure

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

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Prevalence of Helicobacter pylori infection among patients undergoing upper gastrointestinal endoscopy

Asian Journal of Health Sciences ◽

10.15419/ajhs.v3i1.405 ◽

2015 ◽

Vol 3 (1) ◽

Author(s):

Vudumula Vijaya Lakshmi

Keyword(s):

Duodenal Ulcer ◽

Helicobacter Pylori ◽

Normal Population ◽

Gastric Ulcers ◽

Upper Gastrointestinal Endoscopy ◽

Contributing Factors ◽

Duodenal Ulcers ◽

Female Ratio ◽

Ulcer Disease ◽

H Pylori

Helicobacter pylori (H. pylori) has a role in the multifactorial etiology of peptic ulcer disease. A link between H. pylori infection and duodenal ulcer disease is now established. Other contributing factors and their interaction with the organism may initiate the ulcerative process. The fact that eradication of H. pylori infection leads to a long-term cure in the majority of duodenal ulcer patients and the fact that the prevalence of infection is higher in ulcer patients than in the normal population are cogent arguments in favor of it being the primary cause of the ulceration. This study was under taken at the Department of surgery, Narayana medical college, Nellore from January 2007 to July 2008. A total of 150 patients with duodenal ulcers, gastric ulcers, antral gastritis, gastric carcinoma and dyspepsia of any kind were studied. Maximum number of cases were in the age group of 31 years to 50 years among both sexes and number of cases gradually decreased after 50 years of age in males and females. Males were more in number and male to female ratio is (2.75:1) approximately 3:1.

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Features of the endoscopic picture in paediatric gastroduodenal diseases caused by Helicobacter pylori

Russian Journal of Infection and Immunity ◽

10.15789/2220-7619-fot-1249 ◽

2020 ◽

Vol 10 (3) ◽

pp. 543-550

Author(s):

Sh. T. Turdieva ◽

E. A. Shamansurova

Keyword(s):

Helicobacter Pylori ◽

Inflammatory Diseases ◽

Gastric Wall ◽

Duodenogastric Reflux ◽

Chronic Atrophic Gastritis ◽

Endoscopic Examination ◽

Ulcer Disease ◽

Functional Studies ◽

H Pylori ◽

Endoscopic Picture

The aim of the study was to examine the features of the endoscopic picture in the upper digestive tract mucosa in paediatric chronic gastroduodenal pathology (CGDP) associated with Helicobacter pylori. Materials and methods. There were examined 286 patients, aged 6–15 years. Diagnostic criteria for chronic gastroduodenal pathology were anamnestic as well as instrumental and functional studies data: gastric fractional intubation, esophagogastroduodenoscopy (EPGDS) with endoscopic pH-metry without biopsy, and ultrasound examination of abdominal organs. H. pylori testing was carried out by two unrelated methods such as respiratory test and a immunochromatographic fecal test. Results. Detection of H. pylori in children with CGDP peaked in patients with peptic gastric and duodenal ulcer (up to 87.5%, p < 0.05). The main endoscopic signs were edema, hyperaemia and contact bleeding, as well as local haemorrhage were the major endoscopic signs of inflammation in the stomach and duodenum mucosa. Atrophic mucosal lesions were characterized by thinning, pale colour together with transilluminated submucosal vessels. Non-atrophic antral gastritis was featured with delayed gastric emptying, antral stasis and pyloric spasm. In contrast, hypotension of the gastric wall, duodenogastric reflux and decreased motility were more typical to chronic atrophic gastritis. Major endoscopic feature in patients with H. pylori infection was presented by dominant atrophic changes combined with gastroduodenal reflux (77.6%, p < 0.05) compared to patients without H. pylori infection. Conclusion. Detection of HP infection was peaked in children with CGDP coupled to peptic ulcer disease compared to patients with inflammatory diseases (p < 0.05). Endoscopic examination in HP-positive patients showed that atrophic changes were found by 4-fold more frequently together with gastroduodenal reflux compared to patients without HP infection (p < 0.05).

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Mutational Analysis of Metronidazole Resistance in Helicobacter pylori

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.3.1236-1237.2005 ◽

2005 ◽

Vol 49 (3) ◽

pp. 1236-1237 ◽

Cited By ~ 14

Author(s):

Jill M. Moore ◽

Nina R. Salama

Keyword(s):

Helicobacter Pylori ◽

Mutational Analysis ◽

Transposon Mutagenesis ◽

Human Stomach ◽

Metronidazole Resistance ◽

H Pylori ◽

Chromosomal Loci

ABSTRACT Metronidazole is one of a few antibiotics effective in eliminating Helicobacter pylori infection of the human stomach. Several chromosomal loci have been implicated in resistance to this drug. Saturation transposon mutagenesis of the H. pylori genome revealed inactivation of the rdxA gene as uniquely able to confer metronidazole resistance.

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Atypical presentation at acute gastritis: significant gastric wall thickening as a presentation of a primary Helicobacter pylori infection in children

BMJ Case Reports ◽

10.1136/bcr-2021-243912 ◽

2021 ◽

Vol 14 (7) ◽

pp. e243912

Author(s):

Kiyokuni Nakamura ◽

Ryo Tamura ◽

Yoshitomi Yasui ◽

Hideaki Okajima

Keyword(s):

Helicobacter Pylori ◽

Epigastric Pain ◽

Gastric Wall ◽

Malignant Tumour ◽

Wall Thickening ◽

Atypical Presentation ◽

Negative Consequences ◽

Ulcer Disease ◽

Acute Gastritis ◽

H Pylori

Helicobacter pylori infection could cause chronic inflammation in the stomach and induce peptic ulcer disease or even malignant tumour. The initial infection of the organism happens in childhood but most of cases are latent. We had a case of 10-year-old girl who presented with acute epigastric pain and significant thickening of the stomach wall on CT. The finding seemed atypical for acute gastritis so oesophagogastroduodenoscopy and serology examination were added and the primary infection of H. pylori was confirmed with the exclusion of other possible diagnoses like eosinophilic gastritis and IgA vasculitis. Acute gastritis is one of the most common sickness in children, however, it would be worthwhile considering further investigation including H. pylori infection in a case of atypical presentation to prevent negative consequences derived from chronic H. pylori infection.

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Helicobacter pylori causes gastrointestinal hemorrhage in patients with congenital bleeding disorders

Thrombosis and Haemostasis ◽

10.1055/s-0037-1613581 ◽

2003 ◽

Vol 89 (04) ◽

pp. 741-746 ◽

Cited By ~ 7

Author(s):

Ann-Sofie Rehnberg ◽

Marju Hein ◽

Olga Hegedus ◽

Per Lindmarker ◽

Per Hellström ◽

...

Keyword(s):

Helicobacter Pylori ◽

Gastrointestinal Hemorrhage ◽

Breath Test ◽

Eradication Therapy ◽

Urea Breath Test ◽

Von Willebrand Disease ◽

Bleeding Disorders ◽

Ulcer Disease ◽

H Pylori ◽

One Year

Summary Helicobacter pylori (H. pylori) infection is associated with peptic ulcer disease and gastric cancer. The eradication of H. pylori is of special interest in patients with congenital bleeding disorders, for whom treatment of gastrointestinal hemorrhage with factor concentrates is costly. The prevalence of H. pylori varies between different populations and identification of high-risk subgroups may allow for more targeted screening and eradication of the infection. We performed a 5-year retrospective study of gastrointestinal bleeding, combined with screening and treatment for H. pylori and a long-term prospective follow-up in 168 Swedish and 23 Estonian patients with hemophilia or von Willebrand disease. The prevalence of seropositivity was lower in Sweden than in Estonia (28 versus 48%, p = 0.03), lower in native Swedes than in non-Nordic immigrants to Sweden (20 versus 76%, p = 0.0001) and lower in patients less than 40 years of age than older patients (16 versus 38%, p = 0.002). The incidence of gastrointestinal hemorrhages among the 35 Swedish patients with active H. pylori infection, confirmed by a urea breath test, was 6.0 per 100 patient-years before eradication therapy versus 1.7 during the prospective followup. A negative urea breath test one month after therapy always remained negative after one year. Screening, followed by treatment of all infected patients, yielded a reduction of direct costs over a 5-year period of 130 US-$ per screened patient. We conclude that screening and eradication therapy for infection with H. pylori in patients with congenital bleeding disorders is an effective and economic strategy.

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Phenotypic and Genotypic Analysis of Resistant Helicobacter pylori Strains Isolated from Children with Gastrointestinal Diseases

Diagnostics ◽

10.3390/diagnostics10100759 ◽

2020 ◽

Vol 10 (10) ◽

pp. 759

Author(s):

Monika Maria Biernat ◽

Aldona Bińkowska ◽

Łukasz Łaczmański ◽

Paweł Biernat ◽

Paweł Krzyżek ◽

...

Keyword(s):

Helicobacter Pylori ◽

Antibiotic Resistance ◽

Point Mutations ◽

Gastrointestinal Diseases ◽

Drug Susceptibility Testing ◽

Test Method ◽

Ulcer Disease ◽

Genotypic Analysis ◽

Clinical Diagnoses ◽

H Pylori

Antibiotic resistance of Helicobacter pylori is currently a global issue. The aim of this study was to analyze actual antibiotic resistance rates of H. pylori strains isolated from children with primary infections and to compare the incidence of mutations that determine resistance to clarithromycin (CH) and metronidazole (MET) in children with different clinical diagnoses. A total of 91 H. pylori strains were isolated from 108 children with primary infections. Drug susceptibility testing of the strains was performed using E-test method. Classical sequencing of DNA fragments was used to detect point mutations for CH and MET resistance. Resistance to CH was detected in 31% of isolated strains (28/91), while resistance to MET and CH was detected in 35% (32/91) of strains. A2143G was the most frequently detected mutation and was dominant among strains isolated from children with peptic ulcer disease (80%). Mutations in the rdxA gene were found significantly more frequently among MET-resistant strains than MET-sensitive strains (p = 0.03, Chi2 = 4.3909). In children, a higher frequency of H. pylori multiresistant strains was observed compared with the previous study in the same area. Differences were found in the occurrence of point mutations among H. pylori strains resistant to CH isolated from children with different clinical diagnoses.

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