Limiting Rheumatoid Arthritis through the designing PI 3 K protein inhibitors

Rheumatoid arthritis (RA) is a chronic autoimmune disease that often causes inflammation of the synovial joints resulting in severe pain, bone erosion, and joint deformity which affects more than 2 million Americans. Current treatments for RA are based on anti-inflammatory treatments including steroids, non-steroidial antiinflammatory drugs (NSAIDs), disease-modifying antirheumatic drugs (DMARDs), immunosuppressants, and TNF-alpha inhibitors. Side effects of current treatments can lead to heart problems, liver and kidney damage, bone marrow suppression, and severe lung infections. Improved pharmaceutical targeting of inflammatory proteins such as phosphphatidylinositol 3-kinase (PI3K) should yield drugs with increased efficacy and decreased side effects.1-9 This research sought to understand the pharmaceutical blockade of the PI3K kinase functionality to inhibit its function in the inflammatory pathway. 16 crystal structures of the tyrosine kinase of the PI3K protein were docked using IGEMDock to FDA approved pharmaceupticals, Alkaloids, Lactams, Lactones, Flavinoids, Sulfanilamide, Cyclic Imides, and NSAIDs drugs to determine structural correlation for the most effective binders. Structural similarities were determined with IGEMDock and partition coefficient was determined using DRAGON program. This data found a cluster of approximately 10 drugs to preferentially bind to the PI3K kinase for use as targeted antiinflammatory treatments. This work will be used in the engineering of improved PI3K kinase inhibitors.


Introduction
This project was designed on the structural understanding and pharmaceutical engineering of the PI3K inhibitors.Rheumatoid arthritis like many inflammatory diseases has the ability to be acute or chronic with few targeted treatments.Often treatments are based on wide spectrum antiinflammatories, such as steroids, that show efficacy however do maintain some detrimental effect including heart problems and liver and kidney damage.A new understanding in pharmaceutical treatments is based on selective targeting of the immune pathways for decreased toxicity.This research sought to understand the PI3K for targeted treatment of Rheumatoid arthritis.

Specific and Overall Goal
The overall goal of this research is to investigate the interaction of multiple drug candidates to find the best drug candidates for targeted inhibition of the PI3K moiety.This research will first determine the binding and chemical properties of the PI3K active site molecules as a control group.Secondly, a group of select drug candidates whose properties are more effective at binding to the active site versus the control molecules will be chosen.Drug classification analysis will indicate preferences to improved active site binding.Finally, quantitative structure and activity relationship (QSAR) analysis will be done on both the control and experimental molecules to identify similar trends and values.

Methods and Materials
16 isoforms of PI3K that contained active site molecules were selected from the RCSB protein databank.The PI3K active site molecules were considered as controls versus drug candidates.1172 drug candidates were chosen which included, 715 FDA approved, 197 Alkaloids, 73 Imides, 40 Lactams, 36 Lactones, 50 NSAIDs, 25 Sulfanilamide and 37 Flavonoids pharmaceuticals were selected and computationally bound to the PI3K kinase protein using IGEMDock.The 16 protein values were averaged for all 1172 drug candidates and control molecules.IGEMDock used two independent docking with the average of both bindings factoring into binding selectivity.An ANOVA was done to determine if any discrepancies in binding were seen between proteins.Additionally grouping of the molecular functionalities was determined to find if any statistical difference in drug type were found.The best 10 grouping based on binding energies was selected and structural data such as molecular weight and partition coefficient was collected using Dragon and compared to control molecules.4AOF Selective small molecule inhibitor discovered by …reveals regulation by PI3Kgamma 4DK5 Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine inhibitor 10 4F1S Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine-sulfonamide inhibitor 11 4FJY Crystal structure of PI3K-gamma in complex with quinoline-indoline inhibitor 24f 12 4FJZ Crystal structure of PI3K-gamma in complex with pyrrolo-pyridine inhibitor 63 13 4FLH Crystal structure of human PI3K-gamma in complex with AMG511

Discussion
Upon analysis of the data, 10 compounds were identified as effective based upon their interactions with each protein.Specifically an average energy of -121.453 was found for the drug candidates compared to -97.6334 for the control molecules.10 drugs were chosen due to their low binding energies (for both binding interactions).An ANOVA determination of differences between the 16 proteins analyzed indicated no statistical differences were seen with an F value of 0.53873 compared to an F critical value of 1.66665.The data indicated that there were no statistical differences between all drug types with all averages with the standard deviations.Structural analysis found that many of these molecules are relatively small with similar partition coefficient (-0.009 to 0.3.72) of the top binders.

Conclusion
By using the computational techniques we were able to identify several molecule that show improved binding efficacy over currently used PI3K inhibitors.These PI3K drug candidates indicated a diverse pool of PI3K binders with improved efficacy.This work can be used to engineer these motifs into novel PI3K inhibitors for improved drug efficacy.
Summary of 1172 Drug Candidates vs Proteins (IGEMDock Data).
Crystal Structure of 4AOF (UCSF Chimera)Active Site Structure of 4AOF (UCSF Chimera)