This suggests that the binding sites are similar as reported for other drugs, thereby bringing about similar mode of inhibition. investigation. Since piroxicam has already been reported to inhibit N-methyl-D-aspartate (NMDA) receptor and matrix metalloproteinases (MMPs), which are also linked to CI-induced neurodegeneration, we hereby propose piroxicam to be a gold-standard drug in preventing neurodegeneration in CI. format. We searched for 3-D structures of the receptors, and have selected one best fit structure of each based on the completeness of the structure, bound ligand and the resolution. format. The structures of ethoxolamide and hydroxamic acid were available with the respective receptors ? AQ-4 and ASIC-1a respectively, and were used for reference of binding site and comparison of inhibitory potential, while AA – the natural substrate of COXs ? was used for the same purpose in case of COXs. em Molecular Docking /em : Flips, rotations and protonations in the receptor molecules were corrected before docking by using FlexX, following Mazumder em et al /em . [12]. The enzymes were docked using FlexX with their natural substrate and/or known inhibitors as well as with the NSAIDs under investigation. Known inhibitors of the receptors were used for reference of binding sites; and amino acids within a region of 20? were included in the simulation following Mazumder and Borah [13]. The best poses, in terms of free energy of binding, were compared following Mazumder em et al /em . [12, 14]. Results Interactions of ligands with COX-1: A total of 2 hydrogen bonds and 19 weak interactions are being formed between AA and COX-1. Aspirin forms 2 Rabbit polyclonal to USP20 hydrogen bonds Zonampanel and 3 weak interactions; nimesulide forms 3 hydrogen bonds and 6 weak interactions (Supplementary Figure 1) while piroxicam forms 2 hydrogen bonds and 8 weak interactions (Figure 1A). Open in a separate window Figure 1 Docking pose of Zonampanel Piroxicam with (A) COX-1; (B) COX- 2; (C) AQ-4 and (D) ASIC-1a, developed using FlexX. The dotted lines represent hydrogen bonds formed between the respective ligands and the receptors; the green lines represent weak interactions. Docking Zonampanel scores (free energy of binding), in kcal/mol, for each are shown against respective poses. Interactions of ligands with COX-2: AA forms 1 hydrogen bond and 13 weak interactions with COX-2; aspirin forms two hydrogen bonds and five weak interactions; nimesulide forms four hydrogen bonds and seven weak interactions (Supplementary Figure 2); while piroxicam forms six hydrogen bonds and eight weak interactions (Figure 1B). Interactions of Aquaporin-4: With the inhibitor ethoxolamide, AQ-4 forms 2 hydrogen bonds and 2 weak interactions; with aspirin, Zonampanel it forms 1 hydrogen bond and 3 weak interactions; with nimesulide, 1 hydrogen bond and 5 weak interactions are formed (Supplementary Figure 3); while with piroxicam, 2 hydrogen bonds and 3 weak interactions (Figure 1C). Interactions of ligands with ASIC-1a: The ASIC-1a inhibitor ? sinomenine ? forms 3 hydrogen bonds and 4 weak interactions with the receptor; aspirin forms 4 hydrogen bonds and 3 weak interactions; nimesulide forms 2 hydrogen bonds and 3 weak interactions (Supplementary Figure 4); while piroxicam forms 2 hydrogen bonds and 6 weak interactions (Figure 1D). em Inhibition of the receptor activities /em : From our study, we find that piroxicam has highest free energy of binding with both COX-1 and COX-2 as well as with Aquaporin ?4 as compared to the other NSAIDs in question and the natural substrate AA. In case of ASIC-1a, aspirin shows highest free energy of binding and Piroxicam has the second highest score Table 1 (see supplementary material). When a ligand binds with the active site of a receptor with higher free energy of binding as compared to the natural substrate and/or other inhibitors, the activity of the receptor is inhibited [12, 14]. Discussion From our study, we find that the active site residues of COX-1 and COX-2 with which piroxicam interacts Zonampanel are those which were reported to be responsible for catalytic activity of COX-1 [15] and COX-2 [16]. The catalytic domain of COX-1 and COX- 2 comprises of the residues 117-587 [17] with which piroxicam, aspirin and nimesulide have been found to interact directly (Figure 1, Supplementary Figure.