Susi Kusumaningrum, et al.
DOCKINGSTUDIES RHINACANTHIN DERIVATIVES
In this study, we carried out docking simulation of rhinachanthin derivatives to demonstrate inhibitory interaction activities toward Plk1 in silico (Figure 1). The binding interactions between these inhibitors and Plk1 were studied by molecular docking methods using MOE software [5].
The aims of this study is to get drug ligand that could inhibit interaction of Plk1, and to understand the interactions with in the inhibitor and the enzyme’s binding sites via computational docking methods. It is expected that result from this study will provide information about the design d e v e l o p m e n t ofanticancer drugs.
Fig 1. Structure of Rhinacanthin M, N, Q and 39 related naphthoquinone esters
1.Rhinacanthin-M Rhinacanthin-N 2. R=H
Rhinacanthin-Q 3. R=Me
4 R1=R2=Me, R3=OMe, R4=H 14 R1=R2=Me, R3=R4=H 5 R1=R2=Me, R3=OH, R4=H 15 R1=R2=Me, R3=OMe, R4=H 6 R1=R2=Me, R3=OMe, R4=OMe 16 R1=R2=Me, R3=OH, R4=H 7 R1=R2=Me, R3=OH, R4=OMe 17 R1=R2=Me, R3=R4=OH 8 R1=R2=Me, R3=R4=OH 18 R1=Me, R2=H, R3=R4=H 9 R1= Me, R2=H, R3=R4=H 19 R1=Me, R2=H, R3=OMe, R4=H 10 R1=Me, R2=H, R3=OMe, R4=H 20 R1=Me, R2=H, R3=OH, R4=H 11 R1=Me, R2=H, R3=OH, R4=H 21 R1=Me, R2=H, R3=OMe,R4=OMe 12 R1=Me, R2=H, R3=OMe,R4=OMe 22 R1=Me, R2=H, R3=OH,R4=OMe 13 R1=Me, R2=H, R3=OH,R4=OMe 23 R1= R2=R3= R4=H
24 R1=R2=H, R3=OMe,R4=H 25 R1=R2=H, R3=OH,R4=H 26 R1=R2=H, R3=OMe,R4=OMe 27 R1=R2=H, R3=OH,R4=H
28 R1=R2=Me, R3=R4=H 39 R=H 29 R1=R2=Me, R3=OMe, R4=H 40 R=OMe 30 R1=R2=Me, R3=OH, R4=H
31 R1=Me, R2=H, R3=R4=H 32 R1=Me,R2=H, R3=OMe, R4=H 33 R1= Me, R2=H, R3=OH, R4=H 34 R1=R2=H=R3= R4=H
35 R1=R2=H, R3=OMe, R4=H 36 R1=R2=H, R3=OH,R4=H 37 R1=R2=H, R3=OMe,R4=OMe
38 R1=R2=H, R3=OH,R4=OMe 41 R=H 42 R=OMe METHODOLOGY
Protein structure
Dockingstudies Rhinacanthin Derivatives………
Three dimensional (3D) structure of the polo-like kinase 1 complex was retrieved from RCSB (Research Collaboratory for Structural Bioinformatics)[6]. The 3D structure was feed to the MOE software with pdb file format.
Building ligand structures
In this study, 42 compounds were obtained from Kongkathip (2004). The ligands consist of Rhinanchanthin and naphthoquinone esters (Fig.1). The ligand structures were built and minimized optimation by using ChemBioDraw Ultra 12.0. Amino acid residues have been chosen from template box in database menu to draw the two dimensional structure of the ligands. The output is MDL Molfile.
And then, the output format was converted to MDL Mol format with VEGA ZZ software [7].
Docking
Docking files were prepared by using MOE 2008.10 software. In the MOE software, the default non-stochastic Triangle Matcher placement method, followed by molecular mechanics refinement and London dG scoring, GBVI, and no return poses 1000, was operated for the docking runs [8,9]. The default of MOE parameters was used for the other parameters in docking simulation.
RESULTS AND DISCUSSIONS
Crystal structures of the Plk1 PBD in complex with artificial phosphopeptides optimized for PBD binding have revealed that the PB1 and PB2 motifs have identical β6α folds and form a heterodimericphosphopeptide binding module. The phosphopeptide binds to a cleft formed between PB1 (residues 411-489), PB2 (residues 511-592) and interacts with key amino acid residues from both polo boxes, His 538 and Lys 540 from PB2 are pivotal for electrostatic interactions with the negatively charged phosphate group of phosphorylated serine or threonine residues, whereas Trp 414 from PB1 is crucial for the selection of serine. Molecular surface of the Plk1 crystal structure had the hydrophobic surface and hydrogen bonds (Fig. 2). Hydrophobic is represented in green, hydrogen bond in pink, and polar interaction is in blue.
Figure 2. Crystal structures of the Plk1 PBD.
Parameters Docking
The protein structure was prepared for docking as described previously. This included the addition of missing hydrogens. During docking, series of poses (ligand-protein complexes) were generated for each molecule. The quality of each pose was further assessed by the London dG (LdG) scoring function (SF) which estimated the binding free energy of the ligand and a set of the highest score poses were chosen for each molecule (pose) docked [10,11]. In this study, MMFF94 and MMFF94x were used for forcefield minimization. MMFF94x was reported as the efficient forcefield for minimizing ligand-protein complexes [12,13], furthermore, the MMFF94 variant ensures planar geometry of the peptide bonds [14]. Triangle Matcher [15,16] was applied to orient the ligands in the active site based on charge groups and spatial fit. Triangle Matcher performs a random walk with the ligand in the active site to define the optimal binding orientations. Docking simulations carried out on
the pocket, which is composed of Trp 414, Arg 516, His 538, and Lys 540 residues. This hydrophobic pocket give contribution to the interaction of Plk1 PBD [1]. Based on docking simulation result, naphthoquinone derivatives, could be proposed as a potential inhibitor to the interaction of of Plk1 PBD 8-{[2-methoxy-5-(4-methylpiperazin-1-yl)phenyl]amino}-1-methyl-4,5-dihydro-1H-pyrazolo[4,3- h]quinazoline-3-carboxamide (071), which became as comparative ligands, have already designed earlier by other research group.
Estimated docking energy
The calculated free binding energy (∆Gbind) of flexible-ligand docking simulation from the best ligand is shown in Table 1. Free energy of binding for all the designed ligands were lower than the comparative ligand. The free energy of all the designed ligands was negative value. The negative and low value of ∆Gbind indicated the strong favorable bond between enzyme and ligand.
Table1.The ligand free energy of binding and Ki results calculated using MOE.
Ligand Estimated ∆G (kcal/mol) Estimated Ki (µM)
071 -9.1434 0.578
Rhinacanthin-M -16.4709 6.53x10-7
Rhinacanthin-N -15.9464 9.84x10-8
Rhinacanthin-Q -15.1760 1.44x10-5
(13) -19.7035 1.63x10-7
(4) -18.4780 1.01x10-6
(25) -18.2865 1.39x10-7
These ∆Gbind values are parallel to the Ki values observed in Table 1. All the designed ligands showed the lowest Ki value, it could be estimated that the reaction equilibrium shifted to the complex formation. In general, all calculated Ki values were small (within micromolar range), indicating the formation of stable enzyme-ligand complexes. Every ligands showed reasonably low internal energy. It indicates that the docked conformation of the ligands were in their most favourable conformations. In this docking simulation, we utilized gas phase solvation.
a b c
D
Figure 3. Interaction plots illustrating between ligand and the respective amino acid residues, rhinacanthins-M (a), rhinacanthin–N (b),rhinacanthin –Q(c), 071(d).
Dockingstudies Rhinacanthin Derivatives………
(a) (b)
(c)
Figure 4 Interaction plots illustrating between ligand and the respective amino acid residues13 (a),4 (b),[25 (c).
Binding interaction between enzyme and ligand
We presented residue contact of naphthoquinone derivativesligands. All ligands have residue contact with Trp 414, His 538, and Lys 540 residues.
If we compare all of the ligand, compound [13] are the best ligand. Hopefully, this ligand can block the interaction of Plk1 PBD.In Fig. 3 and Fig. 4, we presented the ligand-receptor interaction diagrams.This is a depiction of relatively strong connections among hydrogen bonds as well as electrostatic or charge-transfer interaction between a ligand and the protein residue.
CONCLUSION
Rhinacantihn M, N, Q, naphthoquinone esters (13,14,25) could be proposed as a potential inhibitor of Plk1 PBD.
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