alzheimer 's disease is the most common form of neurodegenerative disorders   characterized by the formation of extracellular deposits composed of amyloid beta peptide ( a )   and masses of paired , helically wound protein filaments in the cytoplasm of neuronal cell bodies and neuritic processes called neurofibrillary tangles . the tau proteins are phosphoproteins whose levels of phosphorylation are regulated by tau kinases and phosphatases . substantial evidence reveals the increased activity of glycogen synthase kinase 3 ( gsk3 ) ( also known as human tau protein kinase i ) during ad . similarly , p25/cyclin - dependent kinase 5 ( cdk5 ) , dual - specific tyrosine [ y ] regulated kinase 1a ( dyrk1a ) , and mitogen - activated protein kinases ( mapk ) also possess higher activity in ad brain . thus , our work focuses on the chosen 10 kinases involved in hyperphosphorylation of tau and elevated responses in ad . . developments of discriminating inhibitors are a key task in drug discovery and development , and appreciating the basis of kinase inhibitor selectivity is critical to the design of effective drugs . gsk3 is composed of three domains : an n - terminal domain consisting of a closed -barrel structure , a c - terminal domain containing a kinase fold  structure , and a small extradomain subsequent to the c - terminal domain . the catalytic site is between the two major domains and has an atp analogue molecule in its atpbinding site . the adenine ring is buried in the hydrophobic pocket and interacts specifically with the main - chain atoms of the hinge loop . the structure of gsk3 is known to have a catalytically active dimer conformation that progressively phosphorylates substrates with ser / thr penta repeats . it is known that the inhibitors compete with the atp binding sites of gsk3 [ 10 , 11 ] . realizing the need to design the inhibitors for these kinases , with the hope that it could affect the hyperphosphorylation of tau , the investigations have been undertaken . the studies reveal shared conservations across sequences , structural homologies , and atp binding site geometries across the ten tau kinases . interestingly , the inhibitor 3-aminopyrrolidine scaffold exhibits high preferential affinity with gsk3. though the literature on ad indicates overexpression and activity of gsk3 during pathogenesis of ad , surprisingly , the pdb does not contain the structural details of gsk3 with these specific inhibitors . consequently , our explorations provide vital clues towards design of novel off - target drugs for ad . the analysis of the structures of the 10 tau kinases , along with their respective ligands , was carried out as illustrated in the flow chart ( figure 1 ) . to begin with , the structures of the 10 tau kinases , along with their respective ligands , were retrieved from the pdb and their details are provided in table 1 . a phylogenetic tree was generated for the amino acid sequences of 10 tau kinases using clustalw   and is illustrated in figure 2 . the dendrogram reveals that gsk3 , cdk5 , mapk such as p38 , extracellular signal - regulated kinases 1 & 2 ( erk 1/2 ) , c - jun n - terminal kinase ( jnk ) , and dual - specificity tyrosine-[y]-phosphorylation - regulated kinase 1a ( dyrk1a ) are closely related ( as in cluster 1 ) ; protein kinase a ( pka ) , protein kinase b ( akt / pkb ) , and protein kinase c ( pkc ) form the closely related second cluster . interestingly , casein kinase 1 delta ( ck1d ) stands out as an independent taxis , indicating characteristic sequence variations from the group .   to observe the conservation of residues in the atp binding region , a multiple sequence alignment was carried out amongst the 10 kinases , using the tool multalin . the alignment is depicted in figure 3(a ) , which reveals that the sequences differ significantly at the positions of gate - keeper residues and the surface residues , while they are well conserved at the subsites that interact directly with atp . the atp binding amino acids lys 85 & asp 200 , asp 133 & val 135 and glu 185 are conserved across these kinases , and lie in the phosphate binding region , adenine binding region and in the sugar binding regions respectively ( refer to figure 3(b ) ) . overall sequence identity and similarity amongst the sequences and rmsd between the 3d geometries are highlighted in table 2 . the identity ( and similarity ) amongst the kinase sequences lies in the broad range of 22.8% ( 48.1% ) and 49% ( 77.4% ) . the closest set appears between erk1/2 and p38 , which share the highest identity of 49% , while the least values of 22.8% exist between 2 sets , namely , ck1d and cdk5 and akt and erk1/2 , respectively . it is interesting to note that the rmsd between all pairs of 10 tau kinases for c atoms range between 1.07 and 1.82   ( refer to table 2 ) . interestingly , these lowest and highest values of rmsd are related to the molecule pkc . however as expected , for the molecule ck1d which stands out in the phylogeny , the identities with all other kinases are less than 30% . similarly , the rmsd values of all the kinases with ck1d lie in the higher range of 1.57 to 1.76   . further , the structural alignments revealed that the active site occurs between two lobes of kinases showing the conserved overlap of the atp binding regions . thus , the rmsd values for the entire atp binding region amongst the kinases lie between 0.63 and 1.25   . however , the rmsd values for the phosphate binding region lie between 0.23 and 0.46   , and the nucleotide binding region is in - between 0.16 and 1.25   respectively . hence , docking the binding site of kinases with atp was attempted to appreciate the nature of interactions . table 3 provides the molecular details and properties of the various inhibitors used in the study . their relative binding affinities in terms of ic50 and k 
 i values are also indicated for each inhibitor ( table 3 ) . the set of chosen inhibitors does contain two small molecules which are deposited in the drug bank , that is , inhibitor 2 ( drug bank i d db07794 ) and inhibitor 5 ( drug bank i d db07919 ) . in order to appreciate the structural similarity of these inhibitors with atp , the outcome of these structural comparisons revealed that the rmsd between atp and the 7 ligands lie between 0.37 and 0.67   , while the inhibitor - to - inhibitor rmsd values are in the range of 0.32 to 0.67   . table 5 lists the various residues forming the atp binding pocket and exhibiting favorable interactions with atp . in order to appreciate the conservation of this atp binding site across all 10 tau kinases , docking studies were carried out using the discovery studio software version 3.5 ( accelrys software inc . , it is clear from table 5 that g63 , a83 , k85 , e97 , d / e133 , n186 , and d200 form the set of well - conserved residues in the atp binding pocket and interact with atp in all the 10 kinases . though the molecules jnk and erk1/2 exhibit less number of interactions with atp , key contacts of conserved residues are indeed present . residue corresponding to v110 exhibits least number of interactions across kinases . though the residue corresponding to r141 appears changed in all the kinases , its interactions with atp , across the receptors , are well conserved . our aim to study the efficacies of select inhibitors with gsk3 triggered the need to dock these ligands to the key tau kinase gsk3. identifying the atp binding site , the molecular docking studies of kinase inhibitors were carried out using the discovery studio software version 3.5 and lead it tool of flexx 2.1.2 . gsk3 receptor structure was docked to all of the seven ligands to the atp binding pocket by the rigid receptor - flexible ligand docking competencies of flexx and the interactions are tabulated in table 6 . the docking examination revealed that the inhibitor-3-aminopyrrolidine scaffold exhibits high preferential affinity with gsk3. while all inhibitors appear to sit in the atp pocket of gsk3 , the most favorable is inhibitor 6 and the least probable is inhibitor 5 . in the present study , the analysis of 10 tau kinases implicated in ad has been performed to elucidate the conservation of the binding site and selectivity of the 7 inhibitors . multiple sequence alignment , 3d structural alignment , catalytic active site overlap , and docking studies of inhibitors with gsk3 have been carried out to fingerprint the interactions with the key / gatekeeper residues in the atpbinding pocket . the results highlight that tau protein kinases share common structural elements for the binding of the inhibitors and atp . comparatively , the inhibitor 3-aminopyrrolidine ( inhibitor 6 ) exhibits high preferential affinity with gsk3. interestingly , the literature on ad indicates the overexpression and activity of gsk3 during pathogenesis of ad , and surprisingly , the pdb does not contain the structural details of gsk3 with this specific inhibitor . our studies disclose that regions of the active site which found high conservation across tau kinases may form the determinants for binding to the ligand . interactions of 7 inhibitors with the remaining 9 tau kinases in ad are also being explored . our results indicate that the binding pocket of the 10 tau kinases is structurally conserved and offer a common feature of determinants with the 7 inhibitors investigated . this study highlights that suitable therapeutics can be successfully developed from the available chemical space , thus facilitating inhibitor design and off - target effects for ad .