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Title of Thesis

Muhammad Arif Lodhi
Institute/University/Department Details
H.E.J. Research Institute of Chemistry/ University of Karachi
Number of Pages
Keywords (Extracted from title, table of contents and abstract of thesis)
urease, enzyme inhibitors, gastric ulcers, cytotoxicity

Many drug molecules are enzyme inhibitors. Their discovery and development is an active area of research in the fields of medicinal chemistry, biochemistry and molecular and clinical pharmacology. Research in the field of enzyme inhibition has enormous potential to introduce new drug candidates against different clinical conditions. Keeping in view the therapeutic importance of ureases, we have selected them as potential targets to discover new lead molecules for the treatment of gastric ulcers, and other urease associated disorders.

Over 2,000 natural and synthetic compounds were screened against the urease enzyme by using high-throughput mechanism-based assays. As a result, five new classes of urease inhibitors were discovered.

New urease inhibitors identified through the initial high-throughput screening were subjected to mechanism-based kinetic studies. Lineweaver-Burk and Dixon plots and their secondary replots were constructed to determine the type of inhibition, inhibition constants and other kinetic parameters. Evaluation of cytotoxicity of the most potent urease inhibitors were performed through cell-based human neutrophils and fibroblast viability assays. Most of the urease inhibitors were found to be non-toxic in these assays. Molecular docking, 3-D QSAR (CoMF A, CoMSIA), mechanism-based protection experiments and time dependent inhibition studies were also conducted in order to identify the interactions of leading compounds with urease. These studies showed that chelation, hydrogen bonding and hydrophobic interactions were the main stabilizing factors in urease-inhibitor complexes. Saturation Transfer Difference NMR (STD) and Transferred Nuclear Overhauser Effect NMR (TrNOE) studies on selected enzyme-inhibitor complex provided further insight into the interactions of inhibitors and enzyme at atomic resolution.

Download Full Thesis
4109.76 KB
S. No. Chapter Title of the Chapters Page Size (KB)
1 0 Contents
230.57 KB
2 1 General Introduction Of Enzymes
195.63 KB
  1.1 Enzymes: Basic Concepts 1
  1.2 Mechanism Of Enzyme Action 2
  1.3 Inhibition Of Enzymes By Small Molecules 3
  1.4 Importance Of Enzyme Inhibitors 6
3 2 Ureases - Structure And Function
431.83 KB
  2.1 Urease Structure And Its Mechanism Of Action 8
  2.2 Molecular Pathogenesis Associated With Ureases 11
  2.3 Structure Of Ureases 15
  2.4 Known Urease Inhibitors 19
  2.5 Objectives Of Current Study 25
4 3 Experimental Techniques
300.61 KB
  3.1 Urease Inhibition Assays 26
  3.2 Methodology For Mechanism-Based Protection Experiments 28
  3.3 Time Dependent Inhibition Protocol 28
  3.4 UV Spectral Interaction Studies Protocol 29
  3.5 Evaluation Of Phytotoxicity 29
  3.6 Synthesis Of Urease Inhibitors 30
  3.7 Methodology For The Evaluation Of Free Radical Scavenging Potential 31
  3.8 3d QSAR ( CoMF A) Studies 32
  3.9 3d QSAR ( CoMSIA ) Studies 33
  3.10 Saturation Transfer Difference (STD) And TRNOE (Transfer Nuclear Overhauser Enhancement) NMR Experimental 34
  3.11 Methodologies For Evaluation Of Cytotoxicity 35
  3.12 Molecular Docking Methodologies 37
5 4 Results And Discussion 40
2852.19 KB
  4.1 Urease Inhibition And Free Radical Scavenging Studies 40
  4.2 Urease Inhibition Studies 43
6 5 References
315.6 KB
  5.1 List Of Publication