Studies on new urease inhibitors by using biochemical, STD-NMR spectroscopy, and molecular docking methods
Discovery of new urease inhibitors is an important approach towards the treatment of diseases caused by ureolytic bacteria. Urease has an important role in several pathologies, such as urolithiasis, peptic and duodenal ulcers, etc. In this regard, urease inhibitory activity of heterocyclic synthetic compounds 1–14, belonging to different chemical classes was evaluated by employing in vitro biochemical assay, and saturation transfer difference-NMR technique. Compounds 1, 3–5, 7, 10, and 12 have shown urease inhibitory potential in vitro. Among them, compound 1 was found to be more potent (IC50 of 12.90 ± 0.63 µM) than a clinical drug, acetohydroxamic acid (IC50 = 41.5 ± 1.50 µM) (Standard). Compounds 3 (IC50 = 15.0 ± 1.10 µM), 4 (IC50 = 24.67 ± 2.87 µM), and 5 (IC50 = 25.50 ± 0.63 µM) were also identified as potent inhibitors of urease enzyme. These compounds showed strong interactions with the urease enzyme (receptor) in saturation transfer difference-NMR spectra. Specifically, aromatic protons of active compounds received maximum Rf saturation from the receptor protein, thus were inferred to be as in close proximity to the protein. New inhibitors identified through biochemical assay and saturation transfer difference-nuclear magnetic resonance techniques were then subjected to kinetic and molecular docking studies to investigate their mode of inhibition, and production of their interactions with the protein at atomic level, respectively. Active compounds were found to be non-cytotoxic against mouse fibroblast (3T3) cell line MTT assay. Present study thereby identifies new inhibitors of urease enzyme in vitro as leads for further investigation towards the development of novel mechanism-based urease inhibitors.
KeywordsUrease inhibition Ligand-based screening STD-NMR Molecular docking Urolithiasis
This project was funded by the Deanship of Scientific Research (DSR) at the King Abdulaziz University, Jeddah, Saudi Arabia, under grant no. (21-130-35-RG). The authors, therefore, acknowledge with thanks DSR for technical, and financial support.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
- Atia-tul-Wahab, Khan A, Marasini BP, Lodhi MA, Atta-ur-Rahman, Choudhary MI (2013) Discovery and study of the bindingepitopes of novel urease inhibitors by STD-NMR spectroscopy and biochemical analyses. Lett Drug Des Discov 10:515–521Google Scholar
- Chen Y, Liao J, Chen M, Huang Q, Lu Q (2015) Gossypol: New class of urease inhibitors, molecular docking and inhibition assay. J Chem Pharm Res 7(1):10–15Google Scholar
- Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shaw DE, Shelley M, Perry JK, Francis P, Shenkin PS (2004) Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739–1749CrossRefPubMedGoogle Scholar
- Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: A new approach for rapid, accurate docking and scoring. 2. Chapter 1: introduction 6 Schrödinger software release 2015-4 enrichment factors in database screening. J Med Chem 47:1750–1759CrossRefPubMedGoogle Scholar
- Khan KM, Rahim F, Khan A, Taha M, Saad SM, Ali S, Khan M, Najeebullah, Shaikh A, Perveen S, Choudhary MI (2015) Synthesis of benzophenone hydrazone analogs and their DPPH radical scavenging, and urease inhibitory activities. J Chem Soc Pak 37:157–161Google Scholar
- Mobley HL, Hausinger RP (1998) Microbial ureases: significance, regulation, and molecular characterization. Microbiol Rev 53:85–108Google Scholar
- Modolo LV, de Fatima A, França MGC, Horta LP, Faria CVN, da Silva DL, Morais VSS (2013) National Institute for industrial property (INPI), Patent # BR1020130173568, BrazilGoogle Scholar
- Schrödinger (2015a) LigPrep, version 3.6, LLC, New York, NYGoogle Scholar
- Schrödinger (2015b) LLC, New York, NY. Glide, version 6.9Google Scholar
- Schrödinger (2015c) Prime, version 4.2, LLC, New York, NY.Google Scholar
- Schrödinger (2015d) Protein Preparation Wizard 2015-4; Epik version 2.4, Schrödinger, LLC, New York, NY, 2015; Impact version 5.9, Schrödinger, LLC, New York, NY, 2015; Prime version 3.2, Schrödinger, LLC, New York, NY, 2015Google Scholar
- Scopes RK (2002) Enzyme activity and assays. eLSGoogle Scholar
- Taleb-Contini SH, Salvador MJ, Watanabe E, Ito IY, de Oliveira DCR (2003) Antimicrobial activity of flavonoids and steroids isolated from two Chromolaena species. Braz J Pharm Sci 39(4):403–408Google Scholar