Much research has focused on the inhibition of the cyclooxygenase (COX) enzyme as this protein is responsible for the first step in the pain pathway in the conversion of arachidonic acid into prostaglandins and thromboxanes. Changes to these initial compounds yielded two classes of compounds that investigated the impact of the substitutions on the docking and binding scores, the positions, and the ligand-protein interactions. Thirty of the 166 compounds designed were selected for synthesis and biological screening as these compounds illustrate the range of changes observed in the full complement of compounds.
Full NMR spectroscopic analysis was performed on all compounds, with diffusion-controlled spectroscopy used to determine the diffusion coefficients and hydrodynamic radii of the two compounds and illustrate the dependence of these measurements on the properties of the medium. Four of the six positions are responsible for >95% of the solute population, with one position comprising nearly 50%. All but one of the poses show root mean square deviation (RMSD) values of less than 2 Å compared to the predicted pose, indicating that any of these poses could bind to the protein.
Initial results from an inhibition screening of the unsubstituted parent benzenesulfonate compound appeared to show threefold selectivity for COX-2 over COX-1 at 100 nM. Testing of the substituted compounds revealed that these compounds are not COX-2 selective as desired, but many show promise as COX-1 selective compounds, with inhibition results above 40%, and several other compounds show potential as non-selective COX inhibitors.
VIII
IX List of Figures and Schemes
A schematic diagram of the "Lock and Key" model for enzymes, where the active site is complementary to the native ligand structure. A schematic diagram of the Induced-Fit model for the binding of a ligand to an active site. Diagram of the interaction of the celecoxib ligand with COX-2 showing the interactions of the p-sulfonamide group of celecoxib with the secondary pocket present in COX-2, taken from PDB file 3LN1.
13 The red line indicates the presence of a π-cation interaction between the ligand and the protein, the solid purple line the presence of H-bonds between the ligand and the protein backbone, and the dashed purple line the H-bond interaction between the ligand and the side chain. Generated pose of celecoxib with carbon atoms shown in red overlapping with the pose of celecoxib bound to COX-2 shown with green carbon atoms (PDB file 3LN1). The generated pose of celecoxib, carbon atoms shown in red, overlaps with the pose of celecoxib bound to COX-1, carbon atoms shown in green (PDB file 3KK6).
The “inversion” of the pose generated for compound 15, shown in purple, compared to the pose generated for the parent sulfonate 3, shown in blue. The rotation of the alkyl chain in the pose generated for 16, shown in green, compared to 97.
XIII
1H NMR spectrum of 62 showing the shift in the location of the methylene signals upon formation of the ether bond. Overlays of the methylene peak area from the 1H NMR spectrum of 6 showing the solvent dependence of these peaks. Overlay of the position generated for 6 when docked to COX-2 (shown in blue) with the NAMFIS-derived conformer 6-602 (shown in purple).
Overlay of the pose generated for 6 upon docking in COX-1 (shown in green) with the NAMFIS-derived conformer 6-602 (shown in purple). Overlay of the pose generated for 6 upon docking in COX-2 (shown in blue) with the NAMFIS-derived conformer 6-1360 (shown in red). Overlay of the pose generated for 6 upon docking in COX-1 (shown in green) with the NAMFIS-derived conformer 6-1360 (shown in red).
Overlay of the pose generated for 6 when bound to COX-2 (shown in blue) with the NAMFIS-derived 6-2492 conformer (shown in purple). Overlay of the pose generated for 6 when bound to COX-1 (shown in green) with the NAMFIS-derived conformer 6-2492 (shown in purple).
XVII List of Abbreviations
XVIII
XIX NMR Nuclear Magnetic Resonance
XX TrxR Thioredoxin reductase
Introduction
- The History of Medicine: From Antiquity to Modern Times
- The Machines Are Taking Over: The Role of Computers in Drug Design
- Indian Gold: The Story of Curcumin
- A World of Pain: The Role of Cyclooxygenase in How We Feel Pain
- Aims and Objectives
- Results and Discussion: Computational Design and Analysis of Potential COX-2 Selective
- Exploring the Possibilities: Computational Analysis of Curcumin and Celecoxib
- In the Beginning: Initial Design and Analysis of a Novel COX-2 Selective Compound
- Expanding the Horizon: Design and Analysis of Sulfonate Analogs
- Always Have a Backup Plan: Design and Analysis of Sulfonamide Analogs
- A Word to the Wise: Selection of Candidates for Synthesis
- What We Never Knew We Needed to Know: A Review
- Results and Discussion: Synthesis of Target Benzenesulfonates
- From the Bottom Up: Retrosynthesis and Initial Synthesis
- Assembling the Puzzle: Attempts towards the Synthesis of the Final Compounds
- Changing Directions: Pathway B as an Alternative Route
- What We Never Knew We Needed to Know: A Review
- Results and Discussion: Analysis and Identification of Compounds
- The Truth of the Matter: Structure Elucidation through NMR Spectroscopy
- Separate but Still Together: Diffusion-Ordered Spectroscopy as a Chromatography Technique
- Linking the Abstract with the Concrete: Putting NMR Analysis of Molecular Flexibility in Solution (NAMFIS) to Work
- What We Never Knew We Needed to Know: A Review
- Results and Discussion: Inhibition Screening and Selectivity Determination
- When Worlds Collide: Theory Vs. Experiment
- An Unexpected Turn of Events: When Experiment and Theory Clash
- Gazing into the Crystal Ball: The Future of Isoform-Selective Coxibs
- What We Never Knew We Needed to Know: A Review
- Conclusion
- Future Work
One of the main differences between FBDD and SBDD lies in the molecular weight limit set. The third strategy used in the fight to improve the bioavailability of curcumin is the structural modification of the curcumin molecule. But people have always been aware of the problem with starting things.
When binding compounds 5–10 into COX-1, compounds 5–10 show inversion and/or rotation of the poses compared to the pose generated for 3 . These common interactions again help explain the similar binding scores observed for compounds 17-22. Overlap of the positions generated for 4 (shown in blue) and 29 (shown in green) when docked into COX-2.
Overlay of images generated for 4 (shown in blue) and 29 (shown in green) when introduced into COX-1. Overlay of shots 4 (shown in blue) and 32 (shown in yellow) when inserted into COX-2. Overlay of images generated for 4 (shown in blue) with compound 38 (shown in purple) when introduced into COX-2.
Overlap of the pose generated for 38 when docked into COX-2 (depicted in light blue) with the X-ray crystal structure of celecoxib (depicted in green). Overlap of the positions of 4 (shown in blue) with 40 (shown in green) when bound into COX-2. Overlap of the positions of 24 (shown in purple) and 3 (shown in blue) when bound into COX-1.
Although this is primarily a qualitative observation, it does indicate a change in the solution mobility of the molecule. Even with the promising results obtained for 3, all the additional compounds show significant COX-1 inhibition (Table 6.3).
