Clodronic Acid has Strong Inhibitory Interactions with the Urease Enzyme of Helicobacter Pylori: Computer-aided Design and in vitro Confirmation

Mohsen Karami Fath; Saeed Khalili; Masoud Mashhadi Akbar Boojar; Zahra Sadat Hashemi; Mahboubeh Zarei

doi:10.2174/0115734099271837231026064439

Clodronic Acid has Strong Inhibitory Interactions with the Urease Enzyme of Helicobacter Pylori: Computer-aided Design and in vitro Confirmation

Curr Comput Aided Drug Des. 2023 Nov 10. doi: 10.2174/0115734099271837231026064439. Online ahead of print.

Authors

Mohsen Karami Fath¹, Saeed Khalili², Masoud Mashhadi Akbar Boojar¹, Zahra Sadat Hashemi³, Mahboubeh Zarei⁴

Affiliations

¹ Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
² Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
³ ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research, Tehran, Iran.
⁴ Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.

PMID: 37957909
DOI: 10.2174/0115734099271837231026064439

Abstract

Background: Helicobacter Pylori (HP) infection could lead to various gastrointestinal diseases. Urease is the most important virulence factor of HP. It protects the bacterium against gastric acid.

Objective: Therefore, we aimed to design urease inhibitors as drugs against HP infection.

Methods: The DrugBank-approved library was assigned with 3D conformations and the structure of the urease was prepared. Using a re-docking strategy, the proper settings were determined for docking by PyRx and GOLD software. Virtual screening was performed to select the best inhibitory drugs based on binding affinity, FitnessScore, and binding orientation to critical amino acids of the active site. The best inhibitory drug was then evaluated by IC50 and the diameter of the zone of inhibition for bacterial growth.

Results: The structures of prepared drugs were screened against urease structure using the determined settings. Clodronic acid was determined to be the best-identified drug, due to higher PyRx binding energy, better GOLD FitnessScore, and interaction with critical amino acids of urease. In vitro results were also in line with the computational data. IC50 values of Clodronic acid and Acetohydroxamic Acid (AHA) were 29.78 ± 1.13 and 47.29 ± 2.06 μg/ml, respectively. Diameters of the zones of inhibition were 18 and 15 mm for Clodronic acid and AHA, respectively.

Conclusion: Clodronic acid has better HP urease inhibition potential than AHA. Given its approved status, the development of a repurposed drug based on Clodronic acid would require less time and cost. Further, in vivo studies would unveil the efficacy of Clodronic acid as a urease inhibitor.

Keywords: Helicobacter pylori; approved small molecule drugs; clodronic acid.; docking; urease.