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Online Journal of Bioinformatics©
Volume 21(2): 154-167, 2020.
In silico ligand docking human AlkB proteins hABH6 and 7 to inhibit cancer.
Karumuri S MSc, Vidyarthi AS PhD, Shankaracharya A MSc.
1Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi – 835215, India
Karumuri S, Vidyarthi AS, Shankaracharya A., In silico ligand docking human AlkB proteins hABH6 and 7 to inhibit cancer, Onl J Bioinform., 21(2): 154-167, 2020. AlkB proteins from 2-oxoglutarate are DNA repair proteins. In humans homologues hABH 1 to 8 can induce cancer. Analogues of 2-OG and quercetin inhibit docking Human AlkB protein homologues 6 and 7. Our dockings using iGEMDOCK created 3D ligand binding poses and energy values with most negative values representing most stable binding. We found that ligand 31706609 provided most negative energy values. SMILES notation revealed it had a –SO3H group unlike other ligands and we assumed that this group enhanced binding. We then added the –SO3H group to ligand with less docking energy 14821299 but resulting in maximum binding with hABH7. Basically we showed that removing SO3H from the ligand reduced binding/docking. Analogues of Quercetin and 2-Oxoglutarate showed least interaction quality. Of the 100’s of ligands only 3 binded, illustrating the functional variability of the proteins. The results suggest that ligand 14821299 could inhibit protein hABH7. However, binding with hABH6(1) and hABH6(2) was not as strong However, –SO3H in these ligands enhances binding to protein but reduces total binding energy through –CH3 groups.
Keywords: AlkB, Homologues, Docking, analogues, inhibitors, hABH proteins.