Potential effects of the most prescribed drugs on the microbiota-gut-brain-axis: A review

The link between drug-induced dysbiosis and its influence on brain diseases through gut-residing bacteria and their metabolites, named the microbiota-gut-brain axis (MGBA), remains largely unexplored. This review investigates the effects of commonly prescribed drugs (metformin, statins, proton-pump-inhibitors, NSAIDs, and anti-depressants) on the gut microbiota, comparing the findings with altered bacterial populations in major brain diseases (depression, multiple sclerosis, Parkinson's and Alzheimer's). The report aims to explore whether drugs can influence the development and progression of brain diseases via the MGBA. Central findings indicate that all explored drugs induce dysbiosis. These dysbiosis patterns were associated with brain disorders. The influence on brain diseases varied across different bacterial taxa, possibly mediated by direct effects or through bacterial metabolites. Each drug induced both positive and negative changes in the abundance of bacteria, indicating a counterbalancing effect. Moreover, the above-mentioned drugs exhibited similar effects, suggesting that they may counteract or enhance each other's effects on brain diseases when taken together by comorbid patients. In conclusion, the interplay of bacterial species and their abundances may have a greater impact on brain diseases than individual drugs or bacterial strains. Future research is needed to better understand drug-induced dysbiosis and the implications for brain disease pathogenesis, with the potential to develop more effective therapeutic options for patients with brain-related diseases.

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).

Vonoprazan (Voquezna) for erosive esophagitis

The FDA has approved vonoprazan (Voquezna – Phathom), a potassium-competitive acid blocker, for healing and maintenance of healing of all grades of erosive esophagitis and relief of associated heartburn in adults. Vonoprazan is also available copackaged with amoxicillin (Voquezna Dual Pak) and with amoxicillin and clarithromycin (Voquezna Triple Pak) for treatment of Helicobacter pylori infection in adults.

Protein-protein interactions and related inhibitors involved in the NLRP3 inflammasome pathway

NOD-like receptor thermal protein domain-associated protein 3 (NLRP3) receptor serves as the central node of immune sensing in the innate immune system, and plays an important role in the initiation and progression of chronic diseases. Cryo-electron microscopy (cryo-EM) has provided insights into the conformation of various oligomers within the NLRP3 activation pathway, significantly advancing our understanding of the mechanisms underlying NLRP3 inflammasome activation. Despite the extensive network of protein-protein interactions (PPIs) involved in the assembly and activation of NLRP3 inflammasome, the utilization of protein-protein interactions has been relatively overlooked in the development of NLRP3 inhibitors. This review focuses on summarizing PPIs within the NLRP3 inflammasome activation pathway and small molecule inhibitors capable of interfering with PPIs to counteract the NLRP3 overactivation. Small molecule NLRP3 inhibitors have been gained significant attention owing to their remarkable efficacy, excellent safety profiles, and unique mechanisms of action.

Proton pump inhibitor prescribing patterns and utilization: A retrospective chart review analysis

Introduction

Proton pump inhibitors (PPIs) show a high level of efficacy and a high safety profile, and they have been increasingly prescribed in recent years. However, recent pharmacoepidemiological evidence has shown that PPI use has been associated with health risks and complications.

Objectives

This study aimed to assess the prescribing patterns of proton pump inhibitors and the prevalence of potential drug-drug interactions (DDIs) among patients who use PPIs.

Method

This was a retrospective analysis of electronic health records from the Ministry of National Guard Hospitals in Riyadh from January 2019 to June 2022. All adult patients who used PPIs were included to assess the prescribing patterns and drug utilization, including the number of prescriptions, duration of prescriptions, number of doses, and prescription indications. Potential DDIs were assessed based on concurrent use, which is defined as taking an interacting drug parallel to PPIs. The assessment includes complete or partial overlapping, with at least one day of overlapping.

Results

The total number of PPI prescriptions was 80,365 for a total of 9,930 patients with a mean age of 67.5. The majority of PPIs were prescribed in high doses (74%), without reporting appropriate indications (95%), and 17% were prescribed for long-term use. A total of 24,575 (33.6%) potential DDIs with PPIs were found.

Conclusion

The results showed that the majority of the PPI prescriptions were made with a high number of doses, without reporting appropriate indications, with some having potential DDIs. This might result in exposing patients to an increasing number of health risks. The findings highlight the importance of implementing a stewardship program for PPI prescription with periodic reassessments of patients' needs for these medications.

Gastro‑oesophageal reflux disease in liver cirrhosis: Possible pathogenesis and clinical intervention (Review)

Oesophageal variceal bleeding is a common complication of decompensated liver cirrhosis (LC). Some studies have reported that reflux oesophagitis (RE) is a risk factor for upper gastrointestinal bleeding, and greatly impacts the quality of life. However, the frequency and mechanism of gastro-oesophageal reflux disease (GERD) in LC remain unclear. The present review explored the possible pathogenesis, and analysed the advantages and disadvantages of the interventional measures and the need for implementation of these measures. By combining the comprehensive terms associated with LC, GERD and RE, EMBASE, Medline/PubMed and the Cochrane Library were systematically searched. The underlying pathological mechanism of GERD in LC was summarized: Transient relaxation of the lower oesophageal sphincter, delayed gastric emptying, increased intra-abdominal pressure, increased intragastric pressure and excessive nitric oxide production destroyed the 'anti-reflux barrier', causing gastric content reflux. Proton pump inhibitors (PPIs) have been widely used empirically to lower the risk of oesophageal venous rupture and bleeding. However, long-term use of acid inhibitors in patients with LC may induce complications, such as spontaneous bacterial peritonitis. The metabolic half-life of PPIs is prolonged in patients with severe liver function impairment. Therefore, the indications for using acid inhibitors lack clarity. However, after endoscopic oesophageal variceal eradication, additional benefits may be gained from the long-term use of PPIs in small doses.

A comparison of different symptomatic reflux esophagitis treatments: A real-world study

BACKGROUND

Proton pump inhibitors (PPIs) are currently the reference drugs for gastroesophageal reflux disease (GERD), but symptoms often recur after their withdrawal. Moreover, whether prokinetics or barrier drugs used alongside PPIs are more effective remains under debate.

OBJECTIVES

The aim of the study was to assess the efficacy of different therapeutic approaches to GERD treatment.

MATERIAL AND METHODS

We enrolled 211 grade A reflux esophagitis patients who consented to participate in this non-randomized, open-label trial. The study consisted of 6 sequentially administered medical treatments for GERD, lasting 2 months, with a 3-week washout period between each drug schedule: Group A: PPI (esomeprazole 40 mg/day before breakfast); Group B: mucosal protective drugs (a combination of hyaluronic acid, chondroitin sulfate and poloxamer 407, or a combination of hyaluronic acid, chondroitin sulfate and aluminum, 3 times daily after a meal); Group C: prokinetics (levosulpiride 25 mg or domperidone 10 mg, 3 times daily before a meal); Group D: barrier drug (alginate 3 times daily after a meal); Group E: PPI (esomeprazole 40 mg/day before breakfast) and mucosal protective drugs (a combination of hyaluronic acid, chondroitin sulfate and poloxamer 407, or a combination of hyaluronic acid, chondroitin sulfate and aluminum, before sleep); Group F: PPI (esomeprazole 40 mg/day before breakfast) and prokinetics (levosulpiride 25 mg or domperidone 10 mg before lunch and dinner). Symptoms were evaluated using the visual analogue scale (VAS) and global symptomatic score (GSS), as follows: heartburn: 0-3; retrosternal chest pain: 0-3; regurgitation: 0-3.

RESULTS

All but 2 treatments (groups C and D) significantly improved VAS and GSS, with group E showing the most significant GSS improvement. Group C had the highest number of dropouts due to treatment failure and reported more side effects.

CONCLUSION

Using PPIs and mucosal protective drugs resulted in significant symptom alleviation. However, the administration of prokinetics caused higher dropouts due to treatment failure.

Efficacy and safety of proton pump inhibitors and H2 receptor antagonists in the initial non‑eradication treatment of duodenal ulcer: A network meta‑analysis

The present network meta-analysis aimed to enhance the corresponding evidence with respect to the efficacy and safety of pharmaceuticals treatments. Frequentist network meta-analysis was used. Medical literature up to November 2022 was searched for randomized clinical trials assessing the efficacy and safety of these pharmaceuticals, either compared with each other or compared with placebo. With the exception of ranitidine (300 mg four times daily) and vonoprazan (20 mg once daily) having lower safety than placebo, the efficacy and safety of the remaining treatments were superior to placebo. Cimetidine (400 mg four times daily) and pantoprazole (40 mg once daily) were ranked first in terms of efficacy. The frequentist network meta-analysis shows that for cimetidine (except 400 mg once daily), famotidine, rabeprazole, ilaprazole, lansoprazole (except 7.5 mg once daily) and omeprazole (except 10 mg once daily or 30 mg once daily), the efficacy comparison between the different doses of each of the aforementioned pharmaceuticals did not indicate statistically significant differences. In conclusion, pantoprazole (40 mg once daily) was the best choice for the initial non-eradication treatment of patients with duodenal ulcer, and cimetidine (400 mg twice daily), omeprazole (20 mg once daily), lansoprazole (15 mg once daily), ilaprazole (5 mg once daily) and rabeprazole (10 mg once daily) could be used as the first choice. If the aforementioned pharmaceuticals cannot be prescribed, famotidine (40 mg twice daily) is recommended.

Proton Pump Inhibitors, Kidney Damage, and Mortality: An Updated Narrative Review

Since their approval by the Food and Drug Administration (FDA) in 1989, proton pump inhibitors (PPIs) have become one of the most highly utilized drugs in the United States, assuming a position as one of the top 10 most prescribed medications in the country. The purpose of PPIs is to limit the amount of gastric acid secreted by the parietal cells via irreversible inhibition of the H+/K+-ATPase pump, therefore maintaining an elevated gastric acid pH of greater than 4 for 15-21 h. Even though PPIs have many clinical uses, they are not without their adverse effects, mimicking achlorhydria. Besides electrolyte abnormalities and vitamin deficiencies, long-term use of PPIs has been linked to acute interstitial nephritis, bone fractures, poor COVID-19 infection outcomes, pneumonia, and possibly an increase in all-cause mortality. The causality between PPI use and increased mortality and disease risk can be questioned since most studies are observational. Confounding variables can greatly affect an observational study and explain the wide-ranging associations with the use of PPIs. Patients on PPIs are generally older, obese, sicker with a higher number of baseline morbidities, and on more medications than the compared PPI non-users. These findings suggest that PPI users are at a higher risk of mortality and complications based on pre-existing conditions. This narrative review aims to update readers on the concerning effects that proton pump inhibitor use can have on patients and give providers a resource to create informed decisions on appropriate PPI use.

Tegoprazan as a New Remedy for Gastrointestinal Diseases in Comparison with its Therapeutic Predecessors: A Mini-Review

BACKGROUND

Potassium-competitive acid blockers (P-CABs), such as tegoprazan, are a new and diverse class of drugs that can completely block the potassium-binding site of gastric H+/K+ ATPase, potentially overcoming the limitations of proton-pump inhibitors (PPIs). A number of studies have compared the effectiveness as well as the safety profile of tegoprazan to PPIs and other P-CABs for the treatment of gastrointestinal diseases.

OBJECTIVE

The current review study evaluates the published works of literature related to clinical pharmacology and clinical trials of tegoprazan for the treatment of diseases related to the gastrointestinal tract.

CONCLUSION

The findings of this study revealed that tegoprazan is safe and well-tolerated and can be used to treat a group of gastrointestinal diseases, including gastroesophageal reflux disease (GERD), non-erosive reflux disease (NERD), and H. pylori infection.

The correlates of post-surgical haematoma in older adults with proximal femoral fractures

BACKGROUND

Little is known about the incidence of haematoma, and clinical correlates among orthogeriatric patients.

AIMS

This study aims to describe the incidence of haematoma after surgical repair of hip fracture and to identify the clinical correlates of haematoma among orthogeriatric patients.

METHODS

Two orthopaedic surgeons and a dedicated operator using ultrasound technique, each other in blindness, evaluated 154 orthogeriatric patients during their hospital stay. All patients received a comprehensive geriatric assessment. We investigated the concordance between clinical diagnosis and ultrasound detection of haematoma, and then we explored the clinical correlates of the onset of post-surgical haematoma.

RESULTS

Blood effusion at the surgical site was detected in 77 (50%) patients using ultrasound technique; orthopaedic surgeons reached a clinical agreement about post-surgical haematoma in 18 (23%) patients. The sensitivity of clinical evaluation was 0.66, and the specificity was 0.70. Independent of age, clinical, pharmacological, and surgical confounders, proton pump inhibitors (PPIs) were associated with post-surgical haematoma (OR 2.28; 95% CI 1.15-4.49). A tendency towards association was observed between selective serotonin reuptake inhibitors and post-surgical haematoma (OR 2.10; 95% CI 0.97-4.54), CONCLUSIONS: Half of older patients undergoing surgical repair of proximal femoral fracture develop a post-surgical haematoma. Clinical assessment, even if made by senior orthopaedic surgeons, underestimates the actual occurrence of post-surgical haematoma compared to ultrasound detection. Ultrasound technique may help to detect haematoma larger than 15 mm better than clinical assessment. PPIs's use is a risk factor for post-surgical haematoma independent of several medical and surgical confounders.

Hypocalcemia after parathyroidectomy in patients taking proton pump inhibitors

PURPOSE

Long-term use of proton pump inhibitors is associated with metabolic derangements, including hypocalcemia. Hypocalcemia is also a known complication of parathyroidectomy. We sought to determine the rate of hypocalcemia following parathyroidectomy in patients on proton pump inhibitors.

MATERIALS AND METHODS

The TriNetX Research Network was queried to identify patients with a history of primary hyperparathyroidism treated with parathyroidectomy between 2012 and 2022. The incidence of short-term (0-6 months following parathyroidectomy) and permanent (6-12 months following parathyroidectomy) postoperative hypocalcemia was compared between patients using proton pump inhibitors and those who were not.

RESULTS

Of 34,595 total patients, 19.5 % (n = 6753) were taking proton pump inhibitors prior to surgery. Patients taking proton pump inhibitors were significantly more likely to experience both short-term (RR, 95 % CI, P) (1.5, 1.4-1.6, P < 0.001) and permanent (1.8, 1.6-2.1, P < 0.001) hypocalcemia, and were also more likely to be evaluated in the emergency department after surgery (1.5, 1.4-1.7, P < 0.001).

CONCLUSIONS

Our study is the first to indicate an increased risk of hypocalcemia after parathyroidectomy in patients on proton pump inhibitors.

Evaluation of Proton Pump Inhibitors Prescribing Among Hospitalized Patients: A Cross-Sectional Study

Background

Proton pump inhibitors (PPIs) are the most effective agents for managing acid-related disorders. However, inappropriate prescribing of PPIs is becoming an issue of concern.

Objective

This study aimed to assess the appropriate utilization of PPIs in terms of indication, dose, frequency, and route of administration during admission and discharge. Furthermore, direct costs associated with inappropriate PPI use were calculated.

Methods

A descriptive cross-sectional study was conducted at the internal medicine department of a tertiary hospital in Palestine from January 1, 2021, to June 30, 2021. The medical records of patients aged 18 years or older, hospitalized for 48 hours or more, and receiving oral or intravenous (IV) PPIs during their stay were collected and evaluated for the appropriateness of PPIs prescribed according to clinical guidelines.

Results

Of 262 patients, 80.2% had an appropriate indication for prophylaxis (67.6%) or treatment (12.6%). A total of 230 patients were prescribed IV pantoprazole.182 (79.1%) had an appropriate indication, whereas 122/182 (67%) received IV PPI instead of oral without an appropriate indication. Of the 32 patients who received 20 mg of oral omeprazole, 28 (87.5%) had an appropriate indication, dose, and route of administration, whereas 16/28 (57.1%) had an inappropriate frequency. At discharge, 32.5% of patients were discharged with unnecessary PPI prescriptions. The total direct cost of inappropriate PPI Indications and route of administration in 188 patients over six months was $1518.

Conclusion

This study showed that most patients received a PPI for an appropriate indication with the correct dose. However, a high prevalence of inappropriate IV pantoprazole administration was observed, resulting in the highest costs, demonstrating the importance of correctly ordering IV medications. Adherence to clinical guidelines, such as those of the American College of Gastroenterology (ACG), will improve the appropriateness of PPI prescribing, prevent complications, and reduce healthcare costs.

Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA)

In multicellular organisms, establishing the full body plane involves cell-cell signaling where protein associations are important for the diverse cellular functions within the cells. For the study of protein-protein interactions (PPI), bimolecular fluorescence complementation (BiFC) and luciferase complementation assays (LCA) have proven to be reliable tools that can be used to confirm the physical association of two proteins in a semi-in vivo environment. This chapter provides a detailed description of these two techniques using Nicotiana benthamiana as a semi-in vivo transient expression system. As an example, we will use the interaction of the two well-described transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR), which are known as regulators of asymmetric cell division and stem cell specification in the root meristem of the model plant Arabidopsis thaliana. While the BiFC assay provides subcellular information by displaying a fluorescence signal, nuclear in this case, resulting from the reconstituted fluorophore, the LCA generates a quantitative readout of the SCR-SHR interaction. The combination of both assays provides information on the localization and strength of the PPI.

Are Drugs Associated with Microscopic Colitis? A Systematic Review and Meta-Analysis

There is growing evidence of the association of Microscopic Colitis (MC) with the use of specific medications such as proton pump inhibitors (PPIs), Selective serotonin reuptake inhibitors (SSRIs), Non-Steroidal anti-inflammatory drugs (NSAIDs), Statins and H2-receptor antagonists (H2RA). In our study, we calculated the pooled odds of MC in patients using these drugs. We performed a detailed search of major databases, including PubMed/Medline, Scopus, web of science, and Embase, to include the studies in which odds of MC were reported after using above mentioned drugs. A random-effects model was used to pool the estimates. Thirteen studies were included in our analysis consisting of 304,482 patients (34,194 cases and 270,018 controls). In eight studies, the control group consisted of a random population selected based on age, gender and same birth year, whereas 3 studies recruited patients who presented with diarrhea and underwent colonoscopy and biopsy to rule out MC. Two studies reported odds of MC for both diarrhea and random control groups. Patients taking PPIs were more likely to develop MC, AOR 2.65 (95% CI 1.81-3.50, I² 98.13%). Similarly, higher odds of association were found in patients taking SSRIs (OR 2.12, 95% CI 1.27-2.96, I² 96.46%), NSAIDs (OR 2.02, 95% CI 1.33-2.70, I² 92.70%) and Statins (OR 1.74, 95% CI 1.19-2.30, I² 96.36%). No difference in odds of developing MC was seen in patients using H2RA compared to the control group (OR 2.70, 95% CI 0.32-5.08, I² 98.67%). We performed a subgroup analysis based on the control group and found higher odds of MC in patients on PPIs compared to the random control group (OR 4.55, 95% CI 2.90-6.19, I² 98.13%). Similarly, higher odds of MC were noted for SSRI (OR 3.23, 95% CI 1.54-4.92, I² 98.31%), NSAIDs (OR 3.27, 95% CI 2.06-4.48, I² 95.38%), and Statins (OR 2.23, 95% CI 1.41-3.06, I² 98.11%) compared to the random control group. Contrary lower odds of MC were seen in the PPI and H2RA group compared to the diarrhea control group (OR 0.68, 95% CI 0.48-0.88, I² 7.26%), (OR 0.46, 95% CI 0.14-0.78, I² 0%) respectively. We found no difference in odds of MC in patients on SSRIs (OR 0.96, 95% CI 0.49-1.42, I² 37.89%), NSAIDs (OR 1.13, 95% CI 0.49-1.76, I² 59.37%) Statins (OR 0.91, 95% 0.66-1.17, I² 0%) and H2RA (OR 3.48, 95% CI -0.41-7.36, I² 98.89%) compared to the diarrhea control group. We also analyzed the association use of PPIs and NSAIDs with the development of collagenous colitis (CC) and lymphocytic colitis. Only the use of NSAIDs was associated with increased odds of developing collagenous colitis (OR 1.61, 95% CI 1.50-1.72, I² 0%). No increased odds of CC and LC were seen in PPI users. PPIs, NSAIDs, SSRIs, and Statins are associated with an increased risk of MC compared to the random control group. On the contrary, the use of PPIs, NSAIDs, SSRIs, and Statins is not associated with an increased risk of MC when compared to the diarrhea control group.

Identifying novel interactions of the colon-cancer related APC protein with Wnt-pathway nuclear transcription factors

BACKGROUND

Colon cancer is often driven by mutations of the adenomatous polyposis coli (APC) gene, an essential tumor suppressor gene of the Wnt β-catenin signaling pathway. APC and its cytoplasmic interactions have been well studied. However, various groups have also observed its presence in the nucleus. Identifying novel interactions of APC in the Wnt pathway will provide an opportunity to understand APC's nuclear role better and ultimately identify potential cancer treatment targets.

METHODS

We used the all-vs-all sequencing (AVA-Seq) method to interrogate the interactome of protein fragments spanning most of the 60 Wnt β-catenin pathway proteins. Using protein fragments identified the interacting regions between the proteins with more resolution than a full-length protein approach. Pull-down assays were used to validate a subset of these interactions.

RESULTS

74 known and 703 novel Wnt β-catenin pathway protein-protein interactions were recovered in this study. There were 8 known and 31 novel APC protein-protein interactions. Novel interactions of APC and nuclear transcription factors TCF7, JUN, FOSL1, and SOX17 were particularly interesting and confirmed in validation assays.

CONCLUSION

Based on our findings of novel interactions between APC and transcription factors and previous evidence of APC localizing to the nucleus, we suggest APC may compete and repress CTNNB1. This would occur through APC binding to the transcription factors (JUN, FOSL1, TCF7) to regulate the Wnt signaling pathway including through enhanced marking of CTNNB1 for degradation in the nucleus by APC binding with SOX17. Additional novel Wnt β-catenin pathway protein-protein interactions from this study could lead researchers to novel drug designs for cancer.

The influence of different proton pump inhibitors and potassium-competitive acid blockers on indomethacin-induced small intestinal injury

BACKGROUND AND AIM

The influence of gastric acid inhibitors (GAIs) on nonsteroidal anti-inflammatory drug (NSAID)-induced enteropathy is controversial. Herein, the influences of different GAIs on NSAID-induced intestinal injury and the underlying mechanisms are clarified.

METHODS

Indomethacin (IND; 10 mg/kg/day) was administered to mice to induce small intestinal injury. Disease activity was examined macroscopically and histologically. The permeability of small intestine was evaluated by measuring plasma lipopolysaccharide levels. 16S rDNA sequencing was performed to determine the composition of intestinal flora.

RESULTS

Among the four GAIs, ilaprazole (IPZ) significantly attenuated IND-induced small intestinal injury and maintained the integrity of the mucosal barrier. Omeprazole (OPZ) and vonoprazan (VPZ) ameliorated ulceration without significant differences, while rabeprazole (RPZ) failed to protect against the injury. To explore the potential mechanism, we investigated changes in the gut microbiota mediated by GAIs. After 5-day administration, GAIs significantly altered the composition of the gut microbiota. The IND group had a significant decrease in alpha diversity compared with the control group, and this decrease was reversed by OPZ and IPZ treatment, respectively. After IPZ treatment, the community membership was more assembled in the control group than the IND group. Further, we found that Lactobacillus was significantly increased in the groups of OPZ, IPZ, and VPZ, while Bacteroides was significantly increased in the RPZ group.

CONCLUSION

Our results indicated that GAIs have different influences on the mucosal barrier, possibly by altering the composition of intestinal microbiota, and the impacts mediated by various GAIs in the IND-induced intestinal damage model seem different.

Structural Determinants of Yeast Protein-Protein Interaction Interface Evolution at the Residue Level

Interfaces of contact between proteins play important roles in determining the proper structure and function of protein-protein interactions (PPIs). Therefore, to fully understand PPIs, we need to better understand the evolutionary design principles of PPI interfaces. Previous studies have uncovered that interfacial sites are more evolutionarily conserved than other surface protein sites. Yet, little is known about the nature and relative importance of evolutionary constraints in PPI interfaces. Here, we explore constraints imposed by the structure of the microenvironment surrounding interfacial residues on residue evolutionary rate using a large dataset of over 700 structural models of baker's yeast PPIs. We find that interfacial residues are, on average, systematically more conserved than all other residues with a similar degree of total burial as measured by relative solvent accessibility (RSA). Besides, we find that RSA of the residue when the PPI is formed is a better predictor of interfacial residue evolutionary rate than RSA in the monomer state. Furthermore, we investigate four structure-based measures of residue interfacial involvement, including change in RSA upon binding (ΔRSA), number of residue-residue contacts across the interface, and distance from the center or the periphery of the interface. Integrated modeling for evolutionary rate prediction in interfaces shows that ΔRSA plays a dominant role among the four measures of interfacial involvement, with minor, but independent contributions from other measures. These results yield insight into the evolutionary design of interfaces, improving our understanding of the role that structure plays in the molecular evolution of PPIs at the residue level.

Identification of novel inhibitors targeting TIRAP interactions with BTK and PKCδ in inflammation through an in silico approach

Advanced computational tools focusing on protein-protein interaction (PPI) based drug development is a powerful platform to accelerate the therapeutic development of small lead molecules and repurposed drugs. Toll/interleukin-1 receptor (TIR) domain-containing adapter protein (TIRAP) and its interactions with other proteins in macrophages signalling are crucial components of severe or persistent inflammation. TIRAP activation through Bruton's tyrosine kinase (BTK) and Protein Kinase C delta (PKCδ) is essential for downstream inflammatory signalling. We created homology-based structural models of BTK and PKCδ in MODELLER 9.24. TIRAP interactions with BTK and PKCδ in its non-phosphorylated and phosphorylated states were determined by multiple docking tools including HADDOCK 2.4, pyDockWEB and ClusPro 2.0. Food and Drug Administration (FDA)-approved drugs were virtually screened through Discovery Studio LibDock and Autodock Vina tools to target the common TIR domain residues of TIRAP, which interact with both BTK and PKC at the identified interfacial sites of the complexes. Four FDA-approved drugs were identified and found to have stable interactions over a range of 100 ns MD simulation timescales. These drugs block the interactions of both kinases with TIRAP in silico. Hence, these drugs have the potential to dampen downstream inflammatory signalling and inflammation-mediated disease.

Estrogen Receptor 1 Inhibition of Wnt/β-Catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis

Background

Hepatocellular Carcinoma (HCC) is a sexually dimorphic cancer, with female sex being independently protective against HCC incidence and progression. The aim of our study was to understand the mechanism of estrogen receptor signaling in driving sex differences in hepatocarcinogenesis.

Methods

We integrated 1,268 HCC patient sample profiles from publicly available gene expression data to identify the most differentially expressed genes (DEGs). We mapped DEGs into a physical protein interaction network and performed network topology analysis to identify the most important proteins. Experimental validation was performed in vitro on HCC cell lines, in and in vivo, using HCC mouse model.

Results

We showed that the most central protein, ESR1, is HCC prognostic, as increased ESR1 expression was protective for overall survival, with HR=0.45 (95%CI 0.32-0.64, p=4.4E-06), and was more pronounced in women. Transfection of HCC cell lines with ESR1 and exposure to estradiol affected expression of genes involved in the Wnt/β-catenin signaling pathway. ER-α (protein product of ESR1) agonist treatment in a mouse model of HCC resulted in significantly longer survival and decreased tumor burden (p<0.0001), with inhibition of Wnt/β-Catenin signaling. In vitro experiments confirmed colocalization of β-catenin with ER-α, leading to inhibition of β-catenin-mediated transcription of target genes c-Myc and Cyclin D1.

Conclusion

Combined, the centrality of ESR1 and its inhibition of the Wnt/β-catenin signaling axis provide a biological rationale for protection against HCC incidence and progression in women.

Pharmacist-structured review of proton pump inhibitor utilisation in primary care: A nonrandomised control study

INTRODUCTION

In the primary care setting, proton pump inhibitor (PPI) overutilisation often stems from the failure to discontinue prophylaxis treatment prior to tertiary care discharge and consider step-down therapy following discharge. Long-term PPI use can result in potential drug-related problems and unnecessary drug expenditure. This study aimed to evaluate the effectiveness of pharmacist-structured review in reducing inappropriate PPI prescriptions and estimate the potential cost saving.

METHODS

This non-randomised controlled study was conducted for 16 weeks at 17 government health clinics in Selangor, Malaysia. Eligible patients attending the outpatient pharmacies of intervention clinics were recruited consecutively and their consent was obtained. A structured review of PPIs was performed in which pharmacists identified patient demographics, indications and the length of PPI therapy using a PPI intervention form. Recommendations were discussed with physicians before prescription changes were made and documented. Moreover, standard management was conducted in the control clinics.

RESULTS

A total of 568 patients with prescriptions containing PPIs were sampled, with a total of 284 patients being placed into the control and intervention groups, respectively. Compared to the control group, inappropriate PPI utilisation in the intervention group significantly decreased from 79.9 to 30.4% (p<0.05). The changes to PPI prescriptions observed in the intervention group included: stop PPI therapy (30.8%), step-down therapy (22.9%), start substitution therapy (15.9%) and no change (30.4%). The physicians' acceptance rate for pharmacist intervention was 67.8%. A 66.1% reduction in monthly PPI pill count and a 72.0% reduction in monthly medication expenditure (RM44.85/patient/year) were observed.

CONCLUSION

The pharmacist-structured review was effective in increasing appropriate PPI utilisation and led to substantial cost savings.

Non-steroidal anti-inflammatory drugs and the gastrointestinal tract

Non-steroidal anti-inflammatory drugs (NSAIDs) are used commonly but can cause foregut symptoms, peptic ulcer disease and small bowel enteropathy. Such iatrogenic injury can be complicated by gastrointestinal bleeding and perforation. Limiting NSAID use or co-administration with proton pump inhibitors (PPIs) reduce dyspepsia, peptic ulcer disease and rates of complications. Selective cyclo-oxygenase (COX)-2 inhibitors are as effective as adding PPIs in preventing upper and lower gastrointestinal complications. COX-2 inhibitors are suggested in those with high cardiovascular risk and the addition of PPI in those with high risk of bleeding. Where required, COX-2 inhibitor monotherapy may be preferred in unexplained iron deficiency anaemia.

Cognition, oxidative stress and vitamin B12 levels evaluation on patients under long-term omeprazole use

OBJECTIVES

To evaluate the differences concerning cognitive performance, oxidative stress and vitamin B12 levels in omeprazole users under treatment for longer than six months.

METHODS

A case-control study was developed with 44 omeprazole users (OU; 81.8 % female, 66 ± 8.7 years old) and 35 nonusers (NOU; 88.6 % female, 62 ± 8.7 years old). The cognitive ability was assessed through tests approaching attention, memory and executive functions. The vitamin B12 was dosage using a chemiluminescent immunoassay and oxidative stress analysis, based on the evaluation of malondialdehyde, enzymatic activity of extracellular superoxide dismutase, glutathione peroxidase, catalase and the ferric reducing antioxidant power in plasma.

KEY FINDINGS

A significant increase of the ferric reducing antioxidant power [omeprazole users (OU) group = 1690 µM ± 441 and nonusers (NOU) group = 1308 ± 616; P value=0.002] and a decrease on glutathione peroxidase levels [OU group = 0.534 (0.27-10.63) and NOU group = 71.86 (14.36-173.1); P value=0.006] were found on omeprazole users group, as well as differences on cognitive performance, with impairments on executive functions, automatic and attentional processing.

CONCLUSIONS

Long-term use of omeprazole is suggested to induce an oxidative stress condition, which causes neurotoxicity and cognitive decline.

Comparison of quinazoline and benzoylpyrazoline chemotypes targeting the CaVα-β interaction as antagonists of the N-type CaV2.2 channel

Structural studies with an α subunit fragment of voltage-gated calcium (CaV) channels in complex with the CaVβ subunits revealed a high homology between the various CaVα-β subunits, predicting that targeting of this interface would result in nonselective compounds. Despite this likelihood, my laboratory initiated a rational structure-based screening campaign focusing on "hot spots" on the alpha interacting domain (AID) of the CaVβ2a subunits and identified the small molecule 2-(3,5-dimethylisoxazol-4-yl)-N-((4-((3-phenylpropyl)amino)quinazolin-2-yl)methyl)acetamide ( IPPQ ) which selectively targeted the interface between the N-type calcium (CaV2.2) channel and CaVβ. IPPQ (i) specifically bound to CaVβ2a; (ii) inhibited CaVβ2 's interaction with CaV.2-AID; (iii) inhibited CaV2.2 currents in sensory neurons; (iv) inhibited pre-synaptic localization of CaV2.2 in vivo; and (v) inhibited spinal neurotransmission, which resulted in decreased neurotransmitter release. IPPQ was anti-nociceptive in naïve rats and reversed mechanical allodynia and thermal hyperalgesia in rodent models of acute, neuropathic, and genetic pain. In structure-activity relationship (SAR) studies focused on improving binding affinity of IPPQ , another compound (BTT-369), a benzoyl-3,4-dihydro-1'H,2 H-3,4'-bipyrazole class of compounds, was reported by Chen and colleagues, based on work conducted in my laboratory beginning in 2008. BTT-369 contains tetraaryldihydrobipyrazole scaffold - a chemotype featuring phenyl groups known to be significantly metabolized, lower the systemic half-life, and increase the potential for toxicity. Furthermore, the benzoylpyrazoline skeleton in BTT-369 is patented across multiple therapeutic indications. Prior to embarking on an extensive optimization campaign of IPPQ , we performed a head-to-head comparison of the two compounds. We conclude that IPPQ is superior to BTT-369 for on-target efficacy, setting the stage for SAR studies to improve on IPPQ for the development of novel pain therapeutics.

Pharmacologic treatment of GERD: Where we are now, and where are we going?

The introduction of acid inhibition in clinical practice has revolutionized the management of acid-related diseases, leading to the virtual abolition of elective surgery for ulcer disease and relegating antireflux surgery to patients with gastroesophageal reflux disease (GERD) not adequately managed by medical therapy. Proton pump inhibitors (PPIs) are the antisecretory drugs of choice for the treatment of reflux disease. However, these drugs still leave some unmet clinical needs in GERD. PPI-refractoriness is common, and persistent symptoms are observed in up to 40-55% of daily PPI users. Potassium-competitive acid blockers (P-CABs) clearly overcome many of the drawbacks and limitations of PPIs, achieving rapid, potent, and prolonged acid suppression, offering the opportunity to address many of the unmet needs. In recent years, it has been increasingly recognized that impaired mucosal integrity is involved in the pathogenesis of GERD. As a consequence, esophageal mucosal protection has emerged as a new, promising therapeutic avenue. When P-CABS are used as add-on medications to standard treatment, a growing body of evidence suggests a significant additional benefit, especially in the relief of symptoms not responding to PPI therapy. On the contrary, reflux inhibitors are considered a promise unfulfilled, and prokinetic agents should only be used on a case-by-case basis.

Gastrointestinal pharmacology: practical tips for the esophagologist

Gastroesophageal reflux disease (GERD) is primarily a motor disorder, and its pathogenesis is multifactorial. As a consequence, treatment should be able to address the underlying pathophysiology. Proton pump inhibitors (PPIs) are the mainstay of medical therapy for GERD, but these drugs only provide the control of symptoms and lesions without curing the disease. However, continuous acid suppression with PPIs is recommended for patients with Barrett's esophagus because of their potential chemopreventive effects. In addition to the antisecretory activity, these compounds display several pharmacological properties, often overlooked in clinical practice. PPIs can indeed affect gastric motility, exert a mucosal protective effect, and an antioxidant, anti-inflammatory, and antineoplastic activity, also protecting cancer cells from developing chemo- or radiotherapeutic resistance. Even in the third millennium, current pharmacologic approaches to address GERD are limited. Reflux inhibitors represent a promise unfulfilled, effective and safe prokinetics are lacking, and antidepressants, despite being effective in selected patients, give rise to adverse events in a large proportion of them. While waiting for new drug classes (like potassium-competitive acid blockers), reassessing old drugs (namely alginate-containing formulations), and paving the new avenue of esophageal mucosal protection are, at the present time, the only reliable alternatives to acid suppression.

Proton Pump Inhibitors: The Good, Bad, and Ugly

Proton pump inhibitors (PPIs) continue to be the medication of choice for treatment of acid-related disease, with few if any overt side effects seen with daily use. They are often prescribed empirically, often in high doses and with many patients being treated with multiple PPIs without an objective diagnosis. Therefore, they are believed to be overprescribed and used without indication. In this article we discuss the appropriate clinical indications for PPIs, review in detail the major associated adverse events, and put in perspective key issues in balancing benefits and risk of this exceptional (and safe) class of drug.

Long-term proton pump inhibitor usage and the association with pancreatic cancer in Sweden

BACKGROUND

The long-term safety of proton pump inhibitors (PPIs) is increasingly questioned. The aim of our study was to assess the risk of pancreatic cancer among long-term PPI users in Sweden.

METHODS

This population-based nationwide Swedish cohort study including 796,492 adult long-term PPI users has been used to calculate the standardized incidence rate ratios (SIRs) and 95% confidence intervals (CI) for pancreatic cancer, stratifying by indications of use, age, sex, and duration of use. The risk among all 20,210 long-term H2-receptor antagonist users was assessed as comparison.

RESULTS

Pancreatic cancer was found in 1733 long-term PPI users, and 25 H2-receptor antagonist users. For PPI users, the risk of pancreatic cancer was increased overall (SIRs = 2.22; 95% CI 2.12-2.32) and in all subgroup analyses, with the highest risk among PPI-users younger than 40 years (SIR = 8.90, 95% CI 4.26-16.37), and among individuals with a history of Helicobacter pylori (SIR = 2.99, 95% CI 2.54-3.49). After the first year after enrolment (during which PPI use may be because of early symptoms of pancreatic cancer), the risk remained increased over time, with SIR = 1.57 (95% CI 1.38-1.76) after 5 years. No associations were found for H2-receptor antagonists (SIR = 1.02, 95% CI 0.66-1.51).

CONCLUSIONS

This large study showed an increased risk of pancreatic cancer in long-term users of PPIs in Sweden, in particular among the youngest users.

The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection

Influenza (flu) is a contagious viral disease, which targets the human respiratory tract and spreads throughout the world each year. Every year, influenza infects around 10% of the world population and between 290,000 and 650,000 people die from it according to the World Health Organization (WHO). Influenza viruses belong to the Orthomyxoviridae family and have a negative sense eight-segment single-stranded RNA genome that encodes 11 different proteins. The only control over influenza seasonal epidemic outbreaks around the world are vaccines, annually updated according to viral strains in circulation, but, because of high rates of mutation and recurrent genetic assortment, new viral strains of influenza are constantly emerging, increasing the likelihood of pandemics. Vaccination effectiveness is limited, calling for new preventive and therapeutic approaches and a better understanding of the virus-host interactions. In particular, grasping the role of influenza non-structural protein 1 (NS1) and related known interactions in the host cell is pivotal to better understand the mechanisms of virus infection and replication, and thus propose more effective antiviral approaches. In this review, we assess the structure of NS1, its dynamics, and multiple functions and interactions, to highlight the central role of this protein in viral biology and its potential use as an effective therapeutic target to tackle seasonal and pandemic influenza.

N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists

Recently, it was reported that tetrapeptides cyclized via lactam bond between the amino terminus and a glutamic residue in position 4 (termed here N-lock) can nucleate helix formation in longer peptides. We applied such strategy to derive N-locked covalent BH3 peptides that were designed to selectively target the anti-apoptotic protein Bfl-1. The resulting agents were soluble in aqueous buffer and displayed a remarkable (low nanomolar) affinity for Bfl-1 and cellular activity. The crystal structure of the complex between such N-locked covalent peptide and Bfl-1 provided insights on the geometry of the N-locking strategy and of the covalent bond between the agent and Bfl-1.

The Dual Interactions of p53 with MDM2 and p300: Implications for the Design of MDM2 Inhibitors

Proteins that limit the activity of the tumour suppressor protein p53 are increasingly being targeted for inhibition in a variety of cancers. In addition to the development of small molecules, there has been interest in developing constrained (stapled) peptide inhibitors. A stapled peptide ALRN_6924 that activates p53 by preventing its interaction with its negative regulator Mdm2 has entered clinical trials. This stapled peptide mimics the interaction of p53 with Mdm2. The chances that this peptide could bind to other proteins that may also interact with the Mdm2-binding region of p53 are high; one such protein is the CREB binding protein (CBP)/p300. It has been established that phosphorylated p53 is released from Mdm2 and binds to p300, orchestrating the transcriptional program. We investigate whether molecules such as ALRN_6924 would bind to p300 and, to do so, we used molecular simulations to explore the binding of ATSP_7041, which is an analogue of ALRN_6924. Our study shows that ATSP_7041 preferentially binds to Mdm2 over p300; however, upon phosphorylation, it appears to have a higher affinity for p300. This could result in attenuation of the amount of free p300 available for interacting with p53, and hence reduce its transcriptional efficacy. Our study highlights the importance of assessing off-target effects of peptide inhibitors, particularly guided by the understanding of the networks of protein-protein interactions (PPIs) that are being targeted.

New classifications of gastroesophageal reflux disease: an improvement for patient management?

Introduction: Gastroesophageal reflux disease (GERD) is a very common and often debilitating disease. In the broad spectrum of GERD phenotypes, three main groups may be traditionally distinguished: 1) patients only affected by esophageal and/or extra-esophageal symptoms; 2) patients with erosive esophagitis and 3) patients with further complications. Areas covered: This review provides an overview on the current classifications of GERD patients, and their impact on their management. Expert opinion: In 2017, the GERD Consensus Working Group focused the attention on patients unresponsive to PPIs. In this scenario, a diagnosis of GERD might be confirmed by evident signs of erosive esophagitis and the finding of pH or multichannel intraluminal impedance-pH tests, such as more than 6%. The 'Lyon Consensus' panel of experts confirmed that positive indices of reflux-symptom association, without other altered parameters, represent reflux hypersensitivity. GERD requires a customized management; it is crucial to assess frequency and severity of symptoms and their response to an optimal course of therapy as well as to explore the endoscopic alterations and consider other diagnoses responsible for persistent symptoms.

Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population

Background

Tick-borne encephalitis (TBE) is a viral infectious disease caused by tick-borne encephalitis virus (TBEV). TBEV infection is responsible for a variety of clinical manifestations ranging from mild fever to severe neurological illness. Genetic factors involved in the host response to TBEV that may potentially play a role in the severity of the disease are still poorly understood. In this study, using whole-exome sequencing, we aimed to identify genetic variants and genes associated with severe forms of TBE as well as biological pathways through which the identified variants may influence the severity of the disease.

Results

Whole-exome sequencing data analysis was performed on 22 Russian patients with severe forms of TBE and 17 Russian individuals from the control group. We identified 2407 candidate genes harboring rare, potentially pathogenic variants in exomes of patients with TBE and not containing any rare, potentially pathogenic variants in exomes of individuals from the control group. According to DAVID tool, this set of 2407 genes was enriched with genes involved in extracellular matrix proteoglycans pathway and genes encoding proteins located at the cell periphery. A total of 154 genes/proteins from these functional groups have been shown to be involved in protein-protein interactions (PPIs) with the known candidate genes/proteins extracted from TBEVHostDB database. By ranking these genes according to the number of rare harmful minor alleles, we identified two genes (MSR1 and LMO7), harboring five minor alleles, and three genes (FLNA, PALLD, PKD1) harboring four minor alleles.

When considering genes harboring genetic variants associated with severe forms of TBE at the suggestive P-value < 0.01, 46 genes containing harmful variants were identified. Out of these 46 genes, eight (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) were additionally found among genes containing rare pathogenic variants identified in patients with TBE; and five genes (WDFY4,ALK, MAP4, BNIPL, EPPK1) were found to encode proteins that are involved in PPIs with proteins encoded by genes from TBEVHostDB. Three genes out of five (MAP4, EPPK1, ALK) were found to encode proteins located at cell periphery.

Conclusions

Whole-exome sequencing followed by systems biology approach enabled to identify eight candidate genes (MAP4, WDFY4, ACTRT2, KLHL25, MAP2K3, MBD1, OR10J1, and OR2T34) that can potentially determine predisposition to severe forms of TBE. Analyses of the genetic risk factors for severe forms of TBE revealed a significant enrichment with genes controlling extracellular matrix proteoglycans pathway as well as genes encoding components of cell periphery.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0503-x) contains supplementary material, which is available to authorized users.

Long-term use of proton-pump inhibitors and risk of gastric cancer: a review of the current evidence

Gastric cancer remains one of the leading cancers in the world with a high mortality, particularly in East Asia. Helicobacter pylori infection accounts for the majority of the noncardia gastric cancers by triggering gastric inflammation and subsequent neoplastic progression. Eradication of H. pylori can reduce, but not totally eliminate, subsequent risk of developing gastric cancer. Proton-pump inhibitors (PPIs) are one of the most widely prescribed medications worldwide. With their profound gastric-acid suppression, there are concerns about a possible carcinogenic role in gastric cancer, due to induced hypergastrinemia, gastric atrophy and bacterial overgrowth in the stomach. While randomized clinical trials to establish causality between long-term PPI use and gastric cancer are lacking, current evidence based on observational studies suggests PPIs are associated with an increased gastric cancer risk. However, opinions on causality remain divergent due to unmeasured and possible residual confounding in various studies. Our recent study has showed that even after H. pylori eradication, long-term PPI use is still associated with an increased risk of gastric cancer by more than twofold. Hence, long-term PPIs should be used judiciously after considering individual's risk-benefit profile, particularly among those with history of H. pylori infection. Further well-designed prospective studies are warranted to confirm the potential role of PPIs in gastric cancer according to baseline gastric histology and its interaction with other chemopreventive agents like aspirin, statins and metformin.

The Spectrum of Small Intestinal Lesions in Patients with Unexplained Iron Deficiency Anemia Detected by Video Capsule Endoscopy

Background and objectives: Video-capsule endoscopy (VCE) has shown a large range (38⁻83%) of diagnostic yield in unexplained iron deficiency anemia (IDA) and obscure-occult bleeding. Therefore, we retrospectively investigated the VCE-detected spectrum and the prevalence of small bowel injuries and associated risk factors in inpatients with both of the above reported conditions. Methods: We selected inpatients with IDA (hemoglobin <12 g/dL in women, <13 g/dL in men) and obscure-occult bleeding. We excluded VCE indications other than IDA. Complete medical histories and laboratory tests were collected. All subjects underwent PillCam SB2/SB3. The VCE feature Lewis score was calculated when appropriate. We used the t-test and Fisher's exact test for continuous and categorical variables, respectively, in univariate analysis. For multivariate analysis, we used binomial logistic regression. Results: We retrieved 109 patients (female:male ratio of 53:56; age 63.4 ± 18.9 years). Eighty patients (73.4%) showed ≥1 small bowel lesions. The Lewis score was calculated in 41 patients: 13 (31.7%) showed a mild (<135) and 28 (68.3%) a moderate-severe (135⁻790 and >790, respectively) score. In univariate analysis, the small bowel transit time (6.2 ± 2.9 versus 5.2 ± 2.1 h; p = 0.049) and non-steroidal anti-inflammatory drug use for at least two weeks (17.5% versus 0%; p = 0.01) were significantly higher in subjects with injuries. These associations were not confirmed at multivariate analysis. The severity of a lesion directly correlated with proton pump inhibitor (PPI) use and duration (not confirmed in multivariate analysis). VCE can reveal the source of obscure-occult bleeding in a high percentage of unexplained IDAs. A wide spectrum of endoscopic pictures may be found. Known as well as supposed risk factors for small bowel lesions may be detected.

Omeprazole prevents CDX2 and SOX9 expression by inhibiting hedgehog signaling in Barrett's esophagus cells

Activation of hedgehog (Hh) signaling contributes to the progression of Barrett's esophagus (BE), which increases the risk of esophageal adenocarcinoma. Recent clinical studies revealed that proton-pump inhibitors (PPIs) but not H2 receptor antagonists (H2RAs) were associated with a decreased risk of esophageal adenocarcinoma. We would like to know whether PPIs interfere with BE progression during BE treatment. Here, we explored the role of omeprazole on Hh signaling and expression of two crucial biomarkers of BE, SOX9 and CDX2. We demonstrated that bile acids elevated expression of Hh pathway target genes, such as GLI1 and PTCH1, and induced SOX9 and CDX2 up-regulation in both CP-A and CP-B cells. Omeprazole, but not famotidine, down-regulated these genes induced by bile acids. In addition, omeprazole-induced down-regulation of SOX9 and CDX2 was mediated by Hh signaling. To explore the mechanisms by which omeprazole inhibits Hh signaling, we performed luciferase assay but did not find any effects of omeprazole on the activity of GLI1 promoter, the critical transcription factor of Hh signaling. Therefore, we used miRNA sequencing and a bioinformatics tool in our study to identify the differently expressed miRNAs in BE organoids treated with or without omeprazole, and we identified miR-2116-3p was involved in omeprazole-mediated inhibition of Hh signaling and subsequent down-regulation of SOX9 and CDX2. Collectively, our data indicate omeprazole inhibits Hh signaling and subsequent SOX9 and CDX2 expression via up-regulating miR-2116-3p. We have demonstrated a novel acid-independent mechanism of omeprazole that might yield valuable insight into clinical management of BE progression, irrespective of acid reflux symptoms.

Advances in inhibition of protein-protein interactions targeting hypoxia-inducible factor-1 for cancer therapy

Hypoxia is a common characteristic of many types of solid tumors and is associated with tumor propagation, malignant progression, and resistance to anti-cancer therapy. HIF-1 pathway is one of the survival pathways activated in tumor in response to hypoxia. In hypoxic condition, hypoxia-inducible factor-1α (HIF-1α) is stabilized and translocated into nucleus where it forms heterodimer with HIF-1β and regulates the expression of a plethora of genes involved in different processes, such as cell proliferation, differentiation, apoptosis, vascularization/angiogenesis, tumor invasion and metastasis. Recruitment of co-activator p300 or CBP to HIF-1α is critical to the transactivation activity of HIF-1 dimer, therefore, small molecules which can block the dimerization of HIF-1α and HIF-1β or inhibit the interaction between HIF-1α and p300 can function as inhibitors of HIF-1 and have the potential to be developed as novel therapies for the treatment of human cancers. In this review, recent progress of small molecular inhibitors of protein-protein interactions targeting HIF-1 is summarized, the mechanism of functions of these compounds and their potential usage as anti-cancer agents have also been discussed.

Proton pump inhibitors use and risk of chronic kidney disease in diabetic patients

AIMS

Chronic kidney disease consumes a huge amount of medical resources and proton pump inhibitors may be a potential factor for the increasing prevalence. This population-based cohort study investigates the risk of chronic kidney disease in a diabetic population using proton pump inhibitors in Taiwan.

METHODS

This study is based on a specific diabetic database obtained from the National Health Insurance Research Database. Individuals with a new diagnosis of diabetes from 2002 to 2013 were enrolled. "Exposure" to proton pump inhibitors was defined as at least one prescription and dosage over 180 DDD (defined daily dose) in one year after the index date. A multivariable Cox proportional hazard model and competing-risk regression model were applied.

RESULTS

There were 5994 patients in the final cohort of proton pump inhibitor users and 23,976 patients in the matched controlled cohort based on 1:4 propensity score matching. Compared with no exposure users, PPIs exposure group had more anemia prevalence, anti-hypertension medication and NSAIDs prescriptions. The multivariable Cox proportional hazard model showed that the adjusted hazard ratio of chronic kidney disease was 1.52 (95% CI 1.40-1.65) in diabetic individuals with PPIs exposure, compared with no exposure users.

CONCLUSIONS

Proton pump inhibitors use is associated with 1.52-fold increased risk of chronic kidney disease in diabetic patients when the dosage is over 180 DDD in one year in Taiwan.

A 12-Week Maintenance Therapy with a New Prepared Viscous Budesonide in Pediatric Eosinophilic Esophagitis

BACKGROUND

A new prepared oral viscous budesonide (PVB) has been effective in inducing clinical and histological remission in pediatric eosinophilic esophagitis (EoE).

AIMS

To evaluate the efficacy of a 12-week maintenance therapy on clinical, endoscopic, and histological remission using half of the dose used in the induction therapy.

METHODS

We prospectively enrolled pediatric patients with active EoE. After 12 weeks of induction therapy with PVB (< 150 cm: 2 mg/day; ≥ 150 cm: 4 mg/day) patients received a maintenance dose of half of the dose used in the induction therapy (1 mg or 2 mg) for another 12 weeks. A 12-week follow-up was then performed in all patients after the end of therapy. Endoscopy was performed at weeks 0, 12, 24, and 36. Symptoms, endoscopy, and histology scores were also calculated. Serum cortisol was evaluated during the treatment period.

RESULTS

We enrolled 20 children (15 males; median age 10 years; range 4-17). After the 12-week induction therapy 18 patients (90%) were in remission, with a significant decrease in the median peak of eosinophil count/HPF as well as a marked reduction in clinical, endoscopic, and histological scores (p < 0.01). At the end of the maintenance therapy (week 24), 17 patients (85%) were still in remission, while there were only 9 at week 36 (45%). No significant changes in cortisol levels were observed during the study period.

CONCLUSIONS

The 12-week maintenance treatment with the half the dose of PVB was effective in sustaining remission at week 24; however, no reduction in the rate of relapse after suspension of treatment occurred.

The risks of long-term use of proton pump inhibitors: a critical review

Proton pump inhibitors (PPIs) are among the most frequently prescribed medications. Their use is likely even higher than estimated due to an increase in the number of PPIs available without a prescription. Appropriate indications for PPI use include Helicobacter pylori infection, erosive esophagitis, gastric ulcers, and stress ulcer prevention in high-risk critically ill patients. Unfortunately, PPIs are often used off-label for extended periods of time. This increase in PPI usage over the past two decades has called into question the long-term effects of these medications. The association between PPI use and infection, particularly Clostridium difficile and pneumonia, has been the subject of several studies. It’s proposed that the alteration in gastrointestinal microflora by PPIs produces an environment conducive to development of these types of infections. At least one study has suggested that long-term PPI use increases the risk of dementia. Drug interactions are an important and often overlooked consideration when prescribing any medication. The potential interaction between PPIs and antiplatelet agents has been the subject of multiple studies. One of the more recent concerns with PPI use is their role in the development or progression of chronic kidney disease. There is also some literature suggesting that PPIs contribute to the development of various micronutrient deficiencies. Most of the literature examining the potential adverse effects of PPI use is composed of retrospective, observation studies. There is a need for higher quality studies exploring this relationship.

Attitude and knowledge of Saudi community pharmacists towards use of proton pump inhibitors

Introduction

Proton pump inhibitors (PPIs) effectively suppress acid secretion and play an important role in peptic ulcer disease and gastroesophageal reflux disease. There is a real concern about the overutilization of PPIs, which will lead to significant high cost and undesirable outcomes. Despite that most of PPIs are classified as prescribed medications, yet most of their users take them without prescription in Saudi Arabia. Therefore, it was important to understand community pharmacists practice in dealing with PPIs and to evaluate their despising pattern of these medications.

Method

A cross-sectional survey-based study that was carried out between September and December 2017. The survey intended to evaluate the knowledge and attitude of CPs towards use of proton pump inhibitors and was built as an online survey.

Results

The results of this study showed that almost all CPs prescribe anti-ulcer drugs for their patients. Most of the participants (68.4%) have prescribed PPI for acute gastritis (68.4%), prophylaxis for stress ulcers (17.7%) and stress ulcer (11.1%). 54.9 percent of the participants recommend using acid suppression drugs for 1 to 2 weeks when they prescribe them to their patients. Thirty-two percent of the respondents had reported adverse events with PPIs. The study showed a significant association between length of work experience in community pharmacy and reporting adverse events.

Conclusion

Community pharmacists in Saudi Arabia usually recommend and prescribe PPIs to their patients. Most of them have some knowledge on PPIs indications and side effects. Managing OTC PPI use in the community pharmacy setting is necessary to promote both patient and medication safety.

Proton pump inhibitors not associated with hypomagnesemia, regardless of dose or concomitant diuretic use

BACKGROUND AND AIM

Proton pump inhibitors (PPIs) are among the most commonly prescribed medications worldwide, with dramatic efficacy for upper gastrointestinal acid-related disorders. In recent years, however, the safety of long-term PPI use has been questioned. One issue based on scant and conflicting literature is the possibility of PPI-related hypomagnesemia. Our purpose was to assess for any clinically significant alteration in serum magnesium levels in large groups of patients taking different PPIs in varying doses, with or without diuretics.

METHODS

This was a retrospective review of patient records at time of hospitalization, from February 2012 to December 2014. Two thousand four hundred patients were randomly selected from a pool of 12 058 magnesium levels performed at or within 24 h of hospital admission. Patients were categorized in six groups based on outpatient PPI and/or diuretic use. The main outcome studied was hypomagnesemia, defined as serum magnesium level < 1.6 mg/dL.

RESULTS

Mean magnesium levels were normal in PPI users (1.84 ± 0.29 mg/dL [normal 1.6 to 2.5 mg/dL]) and PPI nonusers (1.85 ± 0.30 mg/dL), P = 0.40, and there was no statistical difference in the prevalence of hypomagnesemia (14.7% vs 15.1%, P = 0.77). In separate groups, there were also no significant differences in serum magnesium levels between those taking PPIs of varying doses, with or without concomitant diuretics, and those not taking PPIs or diuretics.

CONCLUSION

Regardless of PPI dosage or concomitant diuretics prescribed, magnesium levels were unaffected. Routine screening of serum magnesium in PPI patients appears unnecessary.

Bimolecular Fluorescence Complementation to Visualize Protein-Protein Interactions in Human Cells Based on Gateway Cloning Technology

Bimolecular fluorescence complementation (BiFC) is a powerful and sensitive tool to discover new protein-protein interactions (PPIs). It enables visualization and localization of protein-protein interactions (PPIs) in living cells. The idea behind BiFC is to split a fluorescent protein, for example yellow fluorescent protein (YFP), into two parts that are unable to emit fluorescent signal on their own. Therefore, in order to regain fluorescence the split protein fragments must establish close proximity. This is accomplished by fusing the split fragments to proteins that are postulated to interact, and expressing them in living cells. Subsequently, detection of fluorescence indicates interaction of given proteins. Since complementation is practically irreversible it can capture weak and transient interactions. Using suitable vectors for human protein expression, thus avoiding viral cell transfection, we introduced Gateway-based cloning features to the BiFC system, thereby enabling time efficient vector construction in order to maximize the full potential of the BiFC approach to investigate many protein-protein interactions in a high-throughput fashion. This protocol explains steps in a typical protein-protein interaction survey, from the vector selection, cell transfection, and visualization of the fluorescent signal.

Manufacturing Multienzymatic Complex Reactors In Vivo by Self-Assembly To Improve the Biosynthesis of Itaconic Acid in Escherichia coli

The self-assembly of multienzyme into bioreactors is of extensive interest to spatially regulate valuable reactions. Despite the important progresses achieved, methods to precisely manufacture multienzymatic complex reactors (MECRs) are still poorly proposed both in vivo and in vitro, particularly for more than three biocatalytically relevant enzymes. Here, we developed a sequential self-assembly system to form multitude MECRs involving three enzymes in the itaconic acid (IA) pathway with two pairs of protein-peptide interactions. The MECRs were identified as nanoscale particle-like structures when self-assembled in vitro and produced higher IA production than the unassembled and linearly assembled systems when applied in vivo coupling with CRISPR-Cas9 based metabolic engineering. This work provides novel insights into the construction of multifarious multienzyme complex into bioreactors by the self-assembly strategy for multistep cascades to sequentially control metabolic fluxes inside cells.

Proton Pump Inhibitors Intake and Iron and Vitamin B12 Status: A Prospective Comparative Study with a Follow up of 12 Months

BACKGROUND

Proton pump inhibitors (PPIs) represent the most widely prescribed antisecretory agents, but their prolonged use, may influence iron and vitamin B12 status, which could have important implications for clinical practice.

AIM

We undertook this study aiming to investigate the association between PPIs use for 12 months and potential changes in iron and vitamin B12 status, as well as whether this potential association varies among four specific PPI drugs used in the study.

METHODS

A total of 250 adult subjects were recruited into this study, of which 200 subjects were PPIs users while 50 subjects belonged to the control group. Serum iron, ferritin, vitamin B12, and homocysteine (Hcy) levels were measured before the start of the study and after 12 months. Mann - Whitney U test and Kruskal - Wallis test was used to compare the baseline characteristics of the study groups, while Wilcoxon test was used to analyse post - pre differences.

RESULTS

Statistical analysis showed significant changes within PPIs group and specific PPIs subgroups between the two-time points in serum ferritin and vitamin B12 levels, respectively, while no significant changes in serum iron and homocysteine levels were shown. However, subsequent diagnosis of hypoferremia and hypovitaminosis B12 in the whole study sample at 12 months was established in only 3.8% and 2.9% of the subjects, respectively.

CONCLUSION

PPIs use for 12 months did not result in clinically significant iron and/or vitamin B12 deficiency; thus, these findings argue routine screening under normal circumstances, although monitoring in elderly and malnourished may be of precious value.

Coprescribing proton-pump inhibitors with nonsteroidal anti-inflammatory drugs: risks versus benefits

Nonsteroidal anti-inflammatory drugs (NSAIDs) are often coadministered with proton-pump inhibitors (PPIs) to reduce NSAID-induced gastrointestinal (GI) adverse events. This coadministration is generally regarded as safe, and is included in many of the guidelines on NSAID prescription. However, recent evidence indicates that the GI risks associated with NSAIDs can be potentiated when they are combined with PPIs. This review discusses the GI effects and complications of NSAIDs and how PPIs may potentiate these effects, options for prevention of GI side effects, and appropriate use of PPIs in combination with NSAIDs.

Physician preference items: what factors matter to surgeons? Does the vendor matter?

Background

The USA devotes roughly $200 billion (6%) of annual national health expenditures to medical devices. A substantial proportion of this spending occurs during orthopedic (eg, hip and knee) arthroplasties – two high-volume hospital procedures. The implants used in these procedures are commonly known as physician preference items (PPIs), reflecting the physician’s choice of implant and vendor used. The foundations for this preference are not entirely clear. This study examines what implant and vendor characteristics, as evaluated by orthopedic surgeons, are associated with their preference. It also examines other factors (eg, financial relationships and vendor tenure) that may contribute to implant preference.

Methods

We surveyed all practicing orthopedic surgeons performing 12 or more implant procedures annually in the Commonwealth of Pennsylvania. The survey identified each surgeon’s preferred hip/knee vendor as well as the factors that surgeons state they use in selecting that primary vendor. We compared the surgeons’ evaluation of multiple characteristics of implants and vendors using analysis of variance techniques, controlling for surgeon characteristics, hospital characteristics, and surgeon–vendor ties that might influence these evaluations.

Results

Physician’s preference is heavily influenced by technology/implant factors and sales/service factors. Other considerations such as vendor reputation, financial relationships with the vendor, and implant cost seem less important. These findings hold regardless of implant type (hip vs knee) and specific vendor.

Conclusion

Our results suggest that there is a great deal of consistency in the factors that surgeons state they use to evaluate PPIs such as hip and knee implants. The findings offer an empirically derived definition of PPIs that is consistent with the product and nonproduct strategies pursued by medical device companies. PPIs are products that surgeons rate favorably on the twin dimensions of technology and sales/service.

A database of human genes and a gene network involved in response to tick-borne encephalitis virus infection

BACKGROUND

Tick-borne encephalitis is caused by the neurotropic, positive-sense RNA virus, tick-borne encephalitis virus (TBEV). TBEV infection can lead to a variety of clinical manifestations ranging from slight fever to severe neurological illness. Very little is known about genetic factors predisposing to severe forms of disease caused by TBEV. The aims of the study were to compile a catalog of human genes involved in response to TBEV infection and to rank genes from the catalog based on the number of neighbors in the network of pairwise interactions involving these genes and TBEV RNA or proteins.

RESULTS

Based on manual review and curation of scientific publications a catalog comprising 140 human genes involved in response to TBEV infection was developed. To provide access to data on all genes, the TBEVhostDB web resource ( http://icg.nsc.ru/TBEVHostDB/ ) was created. We reconstructed a network formed by pairwise interactions between TBEV virion itself, viral RNA and viral proteins and 140 genes/proteins from TBEVHostDB. Genes were ranked according to the number of interactions in the network. Two genes/proteins (CCR5 and IFNAR1) that had maximal number of interactions were revealed. It was found that the subnetworks formed by CCR5 and IFNAR1 and their neighbors were a fragments of two key pathways functioning during the course of tick-borne encephalitis: (1) the attenuation of interferon-I signaling pathway by the TBEV NS5 protein that targeted peptidase D; (2) proinflammation and tissue damage pathway triggered by chemokine receptor CCR5 interacting with CD4, CCL3, CCL4, CCL2. Among nine genes associated with severe forms of TBEV infection, three genes/proteins (CCR5, IL10, ARID1B) were found to have protein-protein interactions within the network, and two genes/proteins (IFNL3 and the IL10, that was just mentioned) were up- or down-regulated in response to TBEV infection. Based on this finding, potential mechanisms for participation of CCR5, IL10, ARID1B, and IFNL3 in the host response to TBEV infection were suggested.

CONCLUSIONS

A database comprising 140 human genes involved in response to TBEV infection was compiled and the TBEVHostDB web resource, providing access to all genes was created. This is the first effort of integrating and unifying data on genetic factors that may predispose to severe forms of diseases caused by TBEV. The TBEVHostDB could potentially be used for assessment of risk factors for severe forms of tick-borne encephalitis and for the design of personalized pharmacological strategies for the treatment of TBEV infection.

Non-guideline-recommended prescribing of proton pump inhibitors: implications for the future and reducing over usage

Drs Godman and Fadare review the paper by Mares-Garcia and colleagues in Spain regarding the extent of non-guideline recommended prescribing (NGRP) of proton pump inhibitors (PPIs) in ambulatory care. NGRP of PPIs is an increasing public health concern given the implications of overuse of PPIs on infection rates, osteoporosis and chronic kidney disease as well as increasing polypharmacy rates. Costs are less of an issue especially where there are low prices for generic PPIs; the main focus is on improving the quality of PPI prescribing. Encouragingly, Mares-Garcia and colleagues identified key factors associated with NGRP, providing direction to others.

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

The family Tectiviridae comprises a group of tailless, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria. In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing knowledge about the viral proteome, we carried out a comprehensive yeast two-hybrid analysis of all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprised 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggest that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, with the latter finding also being supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving nonstructural proteins, such as the DNA-binding protein P1 and the genome terminal protein (P4), which was confirmed by coimmunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle.IMPORTANCE Tailless viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function. Comprehensive protein-protein interaction (PPI) analysis of viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins determined using multivector yeast two-hybrid screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological role of the localization of some viral ORFan proteins within the viral particle that will be helpful for understanding the biology of tectiviruses infecting Gram-positive bacteria.