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OJBTM
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
ABSTRACT
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.
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