Molecular docking analysis of Indole based diaza-sulphonamides with JAK-3 protein

JAK-3 gene is a part of an important signalling pathway in oral cancer. Therefore, it is of interest to evaluate the inhibitory properties of new indole based diaza-sulphonamides compounds against JAK3 gene. Molecular docking analysis showed that among the selected compounds (1-9), the compounds 1-4 turned out to be the most potentially capable ones to be used as ant-cancer drugs. Also, they are proved to be non-toxic.


Materials and Methods: Protein preparation:
The 3D crystal structure of the JAK-3 protein (PDB ID: 1YVJ) of Homo sapiens was downloaded from the protein data bank (Figure 1).As per standard protocol, protein preparation was done using the software Biovia Discovery Studio and Mgl tools 1.5.7.Water molecules and cofactors were chosen for elimination.The previously connected ligands were removed, and the protein was produced by adding polar hydrogens and Kollmans charges with Auto Prep.

Ligand preparations:
The 2D structures of the literature derived indole based diazasulphonamide compounds (1-9) are drawn using the ChemDraw 16.0 software (Figure 2).During the optimization method, the software Chem3D was employed and all parameters were selected in order to achieve a stable structure with the least amount of energy.The structural optimization approach was used to estimate the global lowest energy of the title chemical.Each molecule's 3D coordinates (PDB) were determined using optimized structure.

Auto dock Vina analysis:
The graphical user interface Auto Dock vina was used for Ligand-Protein docking interactions (Fig: 3).Auto Dock Tools (ADT), a free visual user interface (GUI) for the AutoDock Vina software, was used for the molecular docking research.The grid box was built with dimensions 39.4753, 27.4692, 33.2939A pointing in the x, y, and z axes.The central grid box for 1YVJ was 1.4065, -11.5737, -13.9655 A. For each ligand, nine alternative conformations were created and ranked based on their binding energies utilizing Auto Dock Vina algorithms.

Drug likeness and toxicity predictions:
In the present study, in-silico pharmacokinetic properties (ADME), drug-likeness, toxicity profiles are examined using SwissADME, and ProTox-II online servers.The SwissADME, a web tool from Swiss Institute of Bioinformatics (SIB) is used to convert the twodimensional structures into their simplified molecular input line entry system (SMILES).The physicochemical properties (molar refractivity, topological polar surface area, number of hydrogen bond donors/ acceptors); pharmacokinetics properties (GI absorption, BBB permeation, P-gp substrate, cytochrome-P enzyme inhibition, skin permeation (log Kp)) which are critical parameters for prediction of the absorption and distribution of drugs within the body, and drug likeness (Lipinski's rule of five) were predicted using SwissADME.The toxicological endpoints (hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity) and the level of toxicity (LD50, mg/Kg) are determined using the ProTox-II server.

Statistical analysis:
One way ANOVA was used for statistical analysis.The clinically proven drugs are used as a control and the results are compared.The significance of the results was found to be p< 0.05

Results: Interaction of indole based diaza-sulphonamide compounds with JAK-3 protein from Homo sapiens:
All the compounds (1-9) are run against the target JAK-3 protein of Homo sapiens and it shows the range between -8.8 to -9.7 (Table 1).The compounds show hydrogen molecules interaction similar to clinically proven drug Doxorubicin (-9).All the compounds show similar binding affinity as the lead molecules are within the binding site.

Toxicity profiling:
The compounds show class 4 toxicity (Table 4).All the compounds (1-9) show a similar LD50 value (720 mg/kg).Compounds (1-4) are inactive in hepatotoxicity, carcinogenicity, immunotoxicity, mutagenicity and cytotoxicity.However, compounds (5-9) are hepatotoxic.Discussion: JAK-3, a cancer protein, also known as the JAK3 gene is a stable well-binding protein of the ginkgetin which has a well confirmed stereochemistry and is a high-quality structure with 90% residue in its most favored region.A leading drug that specifically suppresses JAK3 activity is NSC114792.Therefore, this JAK3 small molecule inhibitor may be a good place to start when creating a new class of medications that target JAK3 activity and may be useful in treating a variety of disorders that are brought on by aberrant JAK3 activity.
After evaluation of the results, all the newly formed compounds showed high negative log kp value hence proving the fact that they are skin permeable.All the compounds can be absorbed in the gastrointestinal tract and none of them are blood-brain barrier permeable.The compounds (1-4) are non-toxic while compounds 5-9 are hepatotoxic.The compounds 1, 2, 3 and 4 are better in terms of toxicity than the clinically proven drugs.The selected ligands (1-4) show better interactions with module protein within the binding sites.Ligands 1, 2, 3 and 4 obey Lipinski's rule of five with no toxicity profile.Lipinski's rule of five is a rule of thumb that describes the druggability of a determinate molecule.It states that there should be No more than 5 hydrogen bond donors.No more than 10 hydrogen bond acceptors.Molecular mass should not be less than 500Da and partition coefficient should not be greater than 5.The violation of 2 or more of these conditions predicts a molecule as a non-orally available drug.To sum it up, the compounds 1, 2, 3 and 4 have the potential to be used against cancer as they show better interaction than the clinical proven drugs, and are non-toxic.Furthermore, despite the fact that their mode of action needs to be defined, other oxadiazole ligands have been discovered with promise anticancer activity.It should be noted that oxadiazoles with significant cytotoxicity share a number of structural characteristics.In particular, the molecules described here have bioactive compound modifications, extended aromatic surfaces, or sulfur-based functional groups.

Conclusion:
The selected compounds (1)(2)(3)(4) show better interaction than the clinically proven drugs.Among the 9 compounds, 1, 2, 3 and 4 are potential to be lead molecules as they obey Lipinski's rule of five and are non-toxic.Therefore, these compounds are potential inhibitors for cancer protein JAK-3.It should be noted that further validation is required using in vitro studies.