Active Site Of Casein Kinase 2 And E- Pharmacophore Modeling
Before developing an e-pharmacophore hypothesis for casein kinase 2 inhibitory activity, the binding site and interaction patterns of silmitasertib (a clinical trial candidate) were thoroughly examined (Fig. 1). The examination revealed that the active site comprises a hydrophobic core, as well as H-bond donor and acceptor regions. It was found that the carboxylic moiety of CX-4945 facilitated H-bond interactions with amino acid residues Lys68, Asp175, and Trp176, and two thermodynamically stable water molecules. The naphthalidine moiety interacted with Val116 and Hie160, while the chlorophenyl amino moiety's NH group created considerable water-mediated H-bond interaction with Asn118. It was further deduced that the chlorophenyl group mediated the salt-bridge interaction with Hie160. According to previous research, the interaction between Val116 and Lys68 is a critical hotspot residue for casein kinase inhibitory activity, and the Benzo Naphthyridine moiety occupies the hydrophobic core of casein kinase-2's active site. These results show that H-bond interaction with amino acid residues Lys68 and Val116, as well as maximal occupancy of the hydrophobic core, is critical for casein kinase inhibitory activity.
The 3D coordinates of CK-2 with CX-4945 (PDB ID-3PE1) were chosen for an e-pharmacophore generation and submitted to the protein production wizard. Based on the previously indicated collective inhibitory activity insights, six pharmacophore characteristics (three aromatic rings [(RRR), two H-bond acceptors (AA), and one negatively charged group (N)] hypotheses were generated and utilized for database screening (Fig. 2).
Database Screening And Molecular Docking
For hypothesis testing, 2D structures of FDA-approved drugs were acquired from "DrugBank" and submitted to "Phase Database generation." Pharmacophore analysis of the FDA database using four of six matching criteria yielded 453 structurally different FDA drugs. Prior to the molecular docking procedure, the algorithm's accuracy was tested by computing the RMSD value of the superimposition of redocked (CX-4945) ligands (Supplementary Fig. 1). The RMSD value was less than one (0.0701), indicating that further molecular docking might anticipate a stronger intramolecular framework between the produced CK-2 protein and evaluated FDA drugs. Molecular docking was used to separate actives and inactives from the 453 screened ligands mentioned above. The forty-seven active ligands were found to be docked with the active site of casein kinase-2 protein as a consequence of XP docking. After carefully analyzing the scoring and binding interactions of the top five ligands Supplementary Fig. 2 and (Table 1), it was observed that bromazepam, an antipsychotic medication, had the most favorable H-bond interactions at Lys68 and Asp175 with a docking score of -10.298 kcal/mol and ligand efficacy score of -0.542. Ataluren, a medication used to treat Duchenne muscular dystrophy, had H-bond interactions at Lys68, Asp175, and Trp176, as well as Pi-Pi stacking with Hie160, with a docking score of -9.82 kcal/mol and ligand efficacy score of -0.468. Masoprocol had Leu45, Asn118, Asp175, and Trp176 mediating H-bond interaction and Pi-Pi stacking with Hie160, with a docking score of -9.223 kcal/mol and ligand efficacy of -0.419. Deferasirox, an ion chelator used to treat chronic iron overload in thalassemia disorders, then mediated H-bond interactions with Lys68, Val116, Asp175, and Trp176 with a docking score of -9.662 kcal/mol and ligand efficacy score of -0.345.
Table 1
Details on the top-ranking FDA-approved drugs against CK2 Docking results of Set-1 analogue t-SNE visualization
Compound Name
|
Docking Score
|
Glide ligand efficiency
|
Amino acid Residue
|
Nature of Interaction
|
Fitness Score
|
Align Score
|
Silmitasertib
|
-11.074
|
-0.563
|
GLY 46
|
Water mediated H bond
|
|
|
|
|
|
LYS 68
|
Salt bridge, H bond
|
|
|
|
|
|
VAL 116
|
H bond
|
|
|
|
|
|
ASN 118
|
Water mediated H bond
|
|
|
|
|
|
HIE 160
|
Pi-Pi Stacking
|
|
|
|
|
|
ASP 175
|
H bond
|
|
|
|
|
|
TRP 176
|
Water mediated H bond
|
|
|
Ataluren
|
-9.82
|
-0.468
|
LYS 68
|
Salt bridge
|
1.69
|
0.438
|
|
|
|
HIE 160
|
Water mediated H bond
|
|
|
|
|
|
ASP 175
|
Water mediated H bond
|
|
|
|
|
|
TRP 176
|
Water mediated H bond
|
|
|
|
|
|
HIE 160
|
Pi-Pi Stacking
|
|
|
Bromazepam
|
-10.298
|
-0.542
|
LYS 68
|
Halogen bond
|
1.026
|
0.942
|
|
|
|
ASP 175
|
Halogen bond, Water mediated H bond
|
|
|
Cromoglicic acid
|
-11.747
|
-0.345
|
No interactions
|
-
|
1.18
|
0.828
|
Mascoprocol
|
-9.223
|
-0.419
|
LEU 45
|
H bond
|
0.642
|
1.344
|
|
|
|
ASN 118
|
Water mediated H bond
|
|
|
|
|
|
HIE 160
|
Pi-Pi Stacking
|
|
|
|
|
|
ASP 175
|
H bond
|
|
|
|
|
|
TRP 176
|
Water mediated H bond
|
|
|
Deferasirox
|
-9.662
|
-0.345
|
LYS 68
|
Salt bridge, H bond
|
1.17
|
1.188
|
|
|
|
VAL 116
|
H bond
|
|
|
|
|
|
ASP 175
|
H bond
|
|
|
|
|
|
TRP 176
|
Water mediated H bond
|
|
|
Docking Results Of Set-1 Analogue T-sne Visualization
To get the first level of analogues, we loaded five FDA-approved medications into the "DrugSpaceX" database. From the top five FDA-approved medications, 1,589 analogues (Set-1) were generated. A similar docking approach was used to evaluate the Set-1 compounds. Table 2 displays the top five analogues examined in terms of docking score, interaction pattern, and synthetic accessibility score. Furthermore, the top five FDA-approved medications, their analogues (Set-1), and the top five Set-1 analogues' of t-distributed stochastic neighbor embedding (t-SNE) structural diversity distribution maps were encoded as 512-bit ECFP4 vectors. According to the t-SNE analysis, transformations focusing on deferasirox (DE1213) and masoprocol (DE67) are more promising for developing CK-2 inhibitors Fig. 3. DE153270 had a docking score of -10.854 kcal/mol and preserved the important contacts at Hie160, Asp175, and Lys68 with a SA score of 2.7, followed by DE153526, DE153269, DE15079, and DE153268 (docking score − 10.852, -10.617, -10.608, -9.543 kcal/mol) Supplementary Fig. 3 & Table 2, In addition to docking score, logP, molecular weight, number of H-bond donors, acceptors, rotors, and TPSA are depicted in the supplementary table 1.
Table 2
Details on the top-ranking Set 1 analogues against CK2
Title
|
Docking score
|
Glide ligand Efficacy
|
Amino Acid Residue
|
Nature of Interactions
|
DE150709
|
-10.608
|
-0.493
|
LYS 68
|
Halogen bond
|
|
|
|
GLU 114
|
H bond
|
|
|
|
VAL 116
|
H bond
|
|
|
|
ASN 118
|
Water mediated H bond
|
|
|
|
HIE 160
|
Pi- Pi Stacking
|
|
|
|
ASP 175
|
Halogen bond, Water mediated H bond
|
DE153269
|
-10.617
|
-0.356
|
LYS 68
|
H bond
|
|
|
|
GLU 81
|
Water mediated H bond
|
|
|
|
VAL 116
|
H bond
|
|
|
|
HIE 160
|
Water mediated H bond
|
|
|
|
ASP 175
|
H bond
|
|
|
|
TRP 176
|
Water mediated H bond
|
DE153270
|
-10.854
|
-0.356
|
LYS 68
|
Salt Bridge
|
|
|
|
HIE 160
|
Water mediated H bond, Pi-Pi Stacking
|
|
|
|
ASP 175
|
H bond, Water mediated H bond
|
DE153268
|
-9.543
|
-0.316
|
LYS 68
|
Salt Bridge, H bond
|
|
|
|
GLU 81
|
Water mediated H bond
|
|
|
|
VAL 116
|
H bond
|
|
|
|
HIE 160
|
Pi-Pi Stacking, Water mediated H bond
|
|
|
|
ASP 175
|
H bond
|
|
|
|
TRP176
|
Water mediated H bond
|
DE153526
|
-10.852
|
-0.402
|
LYS 68
|
Salt Bridge, H bond
|
|
|
|
GLU 81
|
Water mediated H bond
|
|
|
|
GLU 114
|
H bond
|
|
|
|
VAL 116
|
H bond
|
|
|
|
HIE 160
|
Pi-Pi Stacking, Water mediated H bond
|
|
|
|
ASP 175
|
H bond
|
|
|
|
TRP 176
|
Water mediated H bond
|
Molecular Dynamics Simulation Study
MD simulation was used to assess the stability of the complexes CX-4945 and DE153270 complexed with CK2 for 200 nanoseconds. The protein and ligand RMSDs were visually depicted, and the results are shown in Figs. 4 & 5. The protein RMSD for DE153270-CK2 complex was with in the region of 3Å during the 200-nanosecond simulation duration. The ligand RMSD fluctuated in the range of 2–3Å at 50 and 170 nanoseconds, indicating that the compound is stable and equilibrated. The "LigFitProt" shows that the ligand is firmly coupled to the CK-2 active site residues. The protein-ligand connections demonstrate that critical interactions such as Lys68, Asp175, and Trp176 have been retained. These data suggest that DE153270 has the potential to inhibit casein kinase-2.