High‐throughput tandem‐microwell assay for ammonia repositions FDA‐Approved drugs to inhibit Helicobacter pylori urease

Abstract

To date, little attempt has been made to develop new treatments for Helicobacter pylori (H. pylori), although the community is aware of the shortage of treatments for H. pylori. In this study, we developed a 192-tandem-microwell-based highthroughput assay for ammonia that is a known virulence factor of H. pylori and a product of urease. We could identify few drugs, that is, panobinostat, dacinostat, ebselen, captan, and disulfiram, to potently inhibit the activity of ureases from bacterial or plant species. These inhibitors suppress the activity of urease via substrate-competitive or covalent-allosteric mechanism, but all except captan prevent the antibiotic-resistant H. pylori strain from killing human gastric cells, with a more pronounced effect than acetohydroxamic acid, a well-known urease inhibitor and clinically used drug for the treatment of bacterial infection.This study offers several bases for the development of new treatments for ureasecontaining pathogens and to study the mechanism responsible for the regulation of urease activity.

Using Machine Learning and Molecular Docking to Leverage Urease Inhibition Data for Virtual Screening

“…This indicates that the model performance should be "recalibrated" periodically as new scaffolds are being published. Previous in vitro screening efforts for sets of 84 and 3904 compounds were able to discover new urease inhibitors with different mechanisms of action [6,7]. Screening a large number of compounds is, however, usually costly, and for this reason, there has been an interest in predicting urease inhibition for virtual screening.…”

“…Recently, using machine learning classification and regression models such as associative neural networks, k-nearest neighbors, XGBOOST, and WEKA-RF (RF model in WEKA), with cross-validation on a small dataset containing 647 compounds (518/129 split) showed the potential of predicting activity [8]. Even though the experimental compounds (thiazole based scaffold) were Previous in vitro screening efforts for sets of 84 and 3904 compounds were able to discover new urease inhibitors with different mechanisms of action [6,7]. Screening a large number of compounds is, however, usually costly, and for this reason, there has been an interest in predicting urease inhibition for virtual screening.…”

“…However, so far, these compounds have had limited translation to the clinical setting due to issues of cost, potency, solubility, and chemical and metabolic stability as well as toxicity due to promiscuous binding to other enzymes. Recently, high-throughput screening of FDA-approved drugs as a re-purposing strategy was carried out to find inhibitors of urease, but the most potent compounds were found to be anti-cancer drugs and consequently not appropriate for this application [7]. Therefore, there is still much interest and potential in developing new inhibitors, but the de novo design of lead molecules is still a difficult challenge.…”