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Symmetry 2019, 11(8), 974;

Investigation of the Inhibition Potential of New Oxindole Derivatives and Assessment of Their Usefulness for Targeted Therapy
Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096 Bydgoszcz, Poland
Received: 29 June 2019 / Accepted: 27 July 2019 / Published: 1 August 2019


Oxindole derivatives are a large group of compounds that can play the role of Adenosine triphosphate (ATP) competitive inhibitors. The possibility of modification of such compounds by addition of active groups to both cyclic systems of oxindole allows the obtaining of derivatives showing significant affinity toward cyclin-dependent kinase (CDK) proteins. Overexpression of that enzyme is observed in the case of most cancers. The discovery of new efficient inhibitors, which could be used in the development of targeted therapies, is one of the current goals setting trends in recent research. In this research, an oxindole molecular core was used, which was modified by the addition of different substituents to both side chains. The realized procedure allowed the creation of a set of oxindole derivatives characterized by binding affinity values and molecular descriptors evaluated during docking procedures and QSAR calculations. The most promising structures characterized by best sets of parameters were used during the molecular dynamics stage. The analysis of structural and energetic properties of systems obtained during this stage of computation gives an indication of inhibitors creating the most stable complexes, characterized by the highest affinity. During this stage, two structures were selected, where affinity towards potential nanocarriers was evaluated. Realized calculations confirmed a significant role of stacking interactions in the stabilization of ligand complexes with fullerene molecules. Obtained data indicates that complexes of oxindole derivatives and considered nanocarriers exhibit significant potential in the creation of immobilized drugs, and can be used in the development of targeted therapies.
CDK-2; oxidoles; docking; molecular dynamics; MMPBSA; inhibition; C60 fullerene derivatives

1. Introduction

The process of cell proliferation is crucial for all living organisms. The regulation of the cell cycle is strictly related to the action of a set of SER/THR kinases classified as cyclin-dependent kinases (CDKs). All these proteins, after complexation with activate factors called cyclins, play the role of regulation of activity of other proteins involved in transcription and replication processes [1,2,3]. Among all CDK proteins the most crucial role in progression of the cell cycle is assigned to CDK2. Overexpression of that enzyme is often observed in the case of most cancers [2,4,5,6,7]. The search for the ATP competitive inhibitors of CDK2 is important in the context of creation of anticancer therapies. The example of a natural product exhibiting such properties is indirubin [8,9] the anticancer properties of this compound were widely known and used in traditional Chinese medicine. The chemical structure of the indirubin molecule consists of two conjugated oxindoles. The derivatives and analogs of indirubine represent a large group of new CDK2 inhibitors [10,11,12,13,14]. The oxindole core was repeatedly the basis of the creation of ATP competitive inhibitors. Luk et al showed that the addition of active groups to both cyclic systems of oxindole allows the obtaining of derivatives showing significant affinity toward the CDK2 active site, which can also exhibit selective potential in the context of interactions with proteins from the CDK family [15,16]. The CDK2 inhibitors analyzed in earlier works [17,18] confirm that the oxindole core with a carbonyl group substituted in C5 position exhibits high affinity toward the CDK2 active site. The presence of hydrogen-bond donors and acceptors in this structure provides strong anchorage in the space of the active site through characteristic interaction with Glu 81, Leu 83, and Lys 33 [17,18] (see Figure 1). In this work, it was proposed to use such a structure as the basic core of new oxindole derivatives created by the addition of a set of different active groups exhibiting diverse binding properties (see Figure 2). The screening of obtained structures, including binding affinity and molecular properties, allows for the prediction of new ATP competitive inhibitors well suited to the structural and binding properties of the CDK2 active site. An important aspect of drug development is also the finding of effective delivery methods. One commonly used technique in the creation of targeted therapies is immobilization of drugs with the use of different types of carriers [19,20,21], which ensures their direct delivery and release to the appropriate biological target. The use of such a method has other potential related effects, e.g., decreasing drug toxicity [22,23], and increasing its bioavailability and elongation of pharmacological action [24,25]. One of the most commonly used nanomolecules employed for such an aim is C60 fullerene and its derivatives [23,26,27,28,29]. Such a molecule exhibits high affinity towards biologically active molecules containing aromatic systems. This popular fullerene exhibits biological activity towards cells [27], its characteristic chemical structure enables good permeation trough cell membrane [30,31], and small concentrations of this compound are nontoxic for living organisms. The investigation of oxindole derivative binding potential relative to C60 and its derivatives allows evaluation of the possibilities of their use in the creation of targeted therapies.

2. Methods

Ligand structures were created by the addition of 20 different active groups to both side chains of the oxindole core. In the first step, only one side chain was replaced by an active group, while the second was represented by a methyl group. In this way, such active groups were determined, which increase binding affinity of ligand towards the CDK2 active site with the preservation of interactions characteristic for indoline derivatives identified in previous works [17,18]. A total of 84 different indoline derivatives were created with the use of seven active groups in R1 position and 14 in R2. The designation of the structures created in this procedure contains the prefix (Indol_) and the numbers of the bases used in positions R1 and R2. All considered structures were optimized during computations with the use of TURBOMOL at COSMO-BP-tzvpd-fine level of theory [32]. The toxicity of obtained molecules was simulated using a combination of the 3D/4D QSAR (Quantitative structure–activity relationship) BiS/MC and CoCon algorithms [33,34] with the use of the Chemosophia application [35]. The octanol–water partition coefficient (LogP) was determined with use of the COSMOTHERM application [36]. All docking procedures were realized with the use of AutoDockVina [37]. The C60 structure and cyclin-dependent kinase 2 (CDK2-PDB ID 1E9H) were downloaded from Brookhaven Protein Database PDB, while C60 functionalized derivatives were obtained from PubChem database [38]. All calculations were realized with the use of chemical structures of ligands, protein, and nanocarriers containing only polar hydrogen atoms. All initial steps were realized with the use of the AutoDock Tolls package [39]. To confirm the location of the active site and to exclude the presence of competitive interactions on the surface of the protein, blind docking was performed [40,41]. The size of the grid box was 72 × 84 × 66 Å and covered the entire surface of the protein. The realized preliminary calculations confirmed the localization of the active site and the dimensions of the grid box were fitted to the size of active site of CDK2 enzyme (16 × 14 × 22 Å). In the case of all nanoparticles, the grid box dimensions were established equal to 26 × 26 × 26 Å. During the molecular dynamics procedure, there were structures of complexes created by CDK-2 protein with chosen ligand molecules. Ligand structures were characterized using generalized amber force-field parameters. In the case of the CDK-2 protein, the ff14SB Force Field [42] was used and the atomic charges were calculated according to the Merz–Kollmann scheme via the RESP (Restrained electrostatic potential atomic partial charges) procedure at HF/6-31G* level [43]. Each system was neutralized with the use of three chloride anions and immersed in a periodic box (79 x 86 x 71 Å) consisting of 14,809 TIP3P water molecules. Considered systems were heated to 300K by 100 ps of initial MD simulation, while the temperature was controlled by Langevin thermostat [44]. The minimization and heating of systems was realized with constant-volume periodic boundaries (NTB = 1), while the proper production of molecular dynamics was realized with constant pressure (NTB = 2). The periodic boundary conditions and SHAKE algorithm were applied for 80 ns of molecular dynamic simulation; the first 20 ns of simulation time was used as equilibration interval, and the next 60 ns of the trajectory were used in the analysis of the interaction between the considered subunits. Structural analysis was performed with use of the VMD package [45]. The energetic characteristic of interaction between the ligand and the active site was obtained with the use of Molecular Mechanic/Poisson–Boltzmann Surface Area (MMPBSA) method [46]. In all molecular dynamics simulations, the AMBER 14 package was used [47]. During analysis of interactions in the active site, the hydrogen bonds were defined by the following criteria: the distance between donor (D) and acceptor (A) < 3.5 Å, angle D–H–A > 90°, and distance H–A < 3Å.

3. Results and Discussion

The structures of ligand molecules obtained by the addition of a single functional group to the oxindole core of the molecule were docked to the CDK2 active site. Each obtained complex preserved characteristic interactions between the oxindole core and the CDK2 active site, namely with LEU 83, GLU 81, and LYS 33. The binding affinities of considered structures toward protein are presented in Table 1. The modifications applied to the R1 position in 16 cases increased the binding affinity of the ligand toward the CDK2 active site. The highest observed increase of this value did not exceed 16% and only in seven cases exceeded 10%. All active groups exhibiting the best impact on binding properties of ligands contain in their structure aromatic or heterocyclic rings and chemical groups which can fulfil the role of hydrogen-bond donors or acceptors. Among all considered chemical groups, only in four cases was there observed a decrease of binding affinity of ligand toward protein, each of them being an aliphatic system with hydrogen-bond donors. The use of a similar set of active groups in the R2 position meant that for 18 ligand structures there was observed an increase of affinity toward the CDK2 active site. In 14 cases it exceeded 10% and the highest reported values indicated almost a 25% increase of binding properties. The highest impact on the increase of binding affinity has substitution of active groups number 10, 9, 15, 1, 11, 13, and 12 in R2 position. The comparison of energy values characterizing all modified structures indicates that substitutions in the R2 position have a greater impact on binding affinity than modification added to R1. The next step of docking proceedings used ligand structures created with the use of active groups, which ensured at least 10% increase of binding affinity (7 substitutions R1, 14 substitutions R2). The values describing binding affinity and basic molecular descriptors for the chosen ligand molecules are presented in Table 2, and the characteristics of all structures analyzed in this work are placed in the Appendix A Table A1. During ligand selection, the used criteria encompassed not only the values of binding affinity and related inhibition constant (IC), but also molecular descriptors such as LogP and toxicity of considered molecules. The toxicity of the analyzed compounds estimated during QSAR predictions is described by values in the range from 0 to 1. The compounds with very low toxicity adopt values from 0.0–0.2, the moderate toxic ones correspond to values 0.2–0.8, and highly toxic compounds to values 0.8–1.0, with the standard error for estimated values being 0.1. Among all considered oxindole derivatives, only 23 structures were characterized by values indicating nontoxic character. In the next stage, compounds characterized as medium toxic, with toxicity index below 0.4, were also used, which allowed an increase in the studied group to 40 compounds. The IC for ligand molecules was estimated based on the equation
K I = e x p ( Δ G b RT )
where ΔGb represents binding affinity, R gas constant, and T temperature. The analysis including all presented factors allows for selection of potential inhibitors characterized by small values of inhibition constant, slight toxicity, and potentially good permeability through cell membranes (LogP). The best obtained structures are characterized by ~30% increase of binding affinity toward the CDK2 binding site, which is also related to significant changes in IC, which decreased in best cases to values lower than 10 nM (IC for Indol_0_0 = 824.2 nM).
The interactions involved in the stabilization of complexes of five chosen ligands exhibiting best properties are presented in Figure 3; the summary presentation of all observed interactions is attached in Table 3. For all obtained ligand molecules, characteristic interactions of oxindole derivatives created by atoms from molecule core are observed. Considering geometric classification of hydrogen-bond strength, interactions with Leu 83, Glu 81, and Lys 33 can be classified as medium-strength impacts in the case of all chosen structures, while the bonds created with Asp 146 are weak. For all considered ligands, potential stacking interactions with aromatic system of Phe 80 were also observed, and in all cases similar distances between aromatic rings and their analogical mutual orientation were noticed. The addition of active groups in the R1 and R2 positions provided additional impacts, which are hydrogen bonds with Gln 85 (all), Glu 12 (Indol_4_9; Indol_4_10), Asp 86 (Indol_20_10, Indol_20_15, Indol_4_9), Lys 89 (Indol_4_10, Indol_20_15, Indol_9_15). In all cases they can be classified as medium- or weak-strength interactions.

4. Molecular Dynamics of Chosen Complexes

The molecular dynamics stage of simulations covered five complexes of CDK2 protein with selected ligands characterized by best binding and molecular properties. The dynamic and structural stability of the considered systems was evaluated with the use of root mean square deviation (RMSD) values, which where estimated for protein and inhibitor molecules. The appropriate values describing each element of the analyzed complexes are presented in Figure 4 and Table 4. Each presented system reached structural equilibrium in the first 20 ns stages of the molecular dynamics simulation. The distributions and averaged values presented in the table show that CDK2 protein exhibits similar structural and dynamic properties in each considered system. The behavior of the analyzed inhibitor molecules in the protein active site is more varied. The highest structural stiffness is observed in the case of Indol_4_9 and Indol_20_10 molecules; small average values and uniform distributions indicate stabile structural conformations of both inhibitors. The differences in standard deviations describing both populations are related to incidental structural fluctuations observed in the case of Indol_20_10. The rest of the considered ligand molecules are characterized by more diverse distributions. In the case of Indol_4_10, values presented on the chart indicate the potential presence of a second conformation, which appears after 30 ns of simulation time. The structures containing sulfonamide group in R2 position (Indol_9_15, Indol_20_15) exhibit higher structural flexibility than the rest of considered inhibitors, which confirms the observed fluctuations and higher standard deviations of RMSD values. The observed general trends of ligands molecule dynamic properties are also reflected in the durability of interactions involved in the stabilization of the analyzed complexes. The data presented in Table 5 describes the quantity and quality of the interactions reported for complexes during molecular dynamics simulations. Not all interactions identified during the molecular docking stage proved to be stable; however, in some cases new impacts appeared to be created with other amino acids. All realized molecular dynamics simulations revealed that interactions with Leu 83 and Glu 81 play a crucial role in the stabilization of inhibitor-CDK2 complexes. Such hydrogen bonds were observed for all conformations collected for each ligand during computations; the bond distances indicate that most can be classified as medium-strength interactions (~80% for Leu 83, ~75% for Glu 81). The third interaction created by atoms from the molecular core of the considered ligands, namely with Lys 33, is characterized by a much larger diversity, which manifests in the quantity and strength of created bonds alike. The most stable interactions are observed in the case of the Indol_4_9 molecule; however, the largest share of interactions with the highest impact energy (~40%) was recorded for Indol_9_15 and Indol_20_15 molecules. The weak interactions reported for Asp 146 disappeared during the molecular dynamics simulation. Much more important discrepancies in relation to initial complex conformations are observed for interactions of groups placed in the side chains of considered ligands. The first considered ligand, namely Indol_4_9, creates a stabile interaction with oxygen from aspartic acid ASP 86; such a hydrogen bond is observed in 98% of conformations obtained during molecular dynamics simulation. The other impacts identified during the docking procedure have changed, namely weak interactions with GLU 12 are observed only for 45% of collected conformations, while hydrogen bonds with GLN 85 have disappeared. In the case of Indol_4_10, two hydrogen bonds created by groups from side chains were observed. The first of them, created with GLU12, is observed for 46.4% of conformations, while the second impact, namely the hydrogen bond with GLU8 (69.1%), does not occur in the complex obtained during the docking phase. The appearing of this new interaction is a consequence of the change of R2 side chain conformation, which is also related to the disappearance of hydrogen bonds with LYS 98 and GLN 85. All the hydrogen bonds found for active groups from the side chains of Indol_9_15 during docking stage disappeared. The analysis of possible interactions for conformers obtained during molecular dynamics stage indicates only one hydrogen bond with GLY13; however, the quantity and distances indicate a weak stabilizing impact of this bond. The next molecule, namely Indol_20_10, interacts with the active site by hydrogen bonds created by both side chains. The hydrogen bond identified between the amino group of side chain R1 and ASP 86 is observed for 50% of conformations obtained during molecular dynamics calculations. The structural mobility of this part of ligand molecule caused the occurrence of a second competitive interaction created with the oxygen atom of ILE10 (61.3%). The active group from the second side chain also creates a bond, namely with GLU 8 (85.7%); the quantity and distance of this hydrogen bond clearly indicate a significant stabilizing impact for the complex structure. In the case of the last considered ligand, namely Indol_20_15, during the molecular dynamics stage the presence of two hydrogen bonds observed in initial complex and one new impact was identified and confirmed. Both oxygens from the sulfonamide group are involved in interactions with LYS89 (73.6%); the rotation of this group relative to the aromatic ring allowed for the appearance of a new bond observed between amide hydrogens and oxygen from HIE 84 (56.7%). The activity of the second side chain is much less significant; the hydrogen bond between amine group and ASP 86 is observed only for 48% of the conformations. The values of binding enthalpies (ΔH) obtained for complexes considered during the molecular dynamic stage strictly correspond to the dynamic properties of ligands described by RMSD values, as well as the quantity and quality of interactions involved in the stabilization of complexes. Values presented in Table 6 clearly show that the most stable complexes during molecular dynamics stage were created by two inhibitors, namely Indol_4_9 and Indol_20_10, with very similar values of enthalpy (~40 kcal/mol) and standard deviations indicating a similar inhibiting potential of these two compounds. The next group of ligands are Indol_4_10 and Indol_20_15, which are characterized by enthalpy values about 6 kcal/mol smaller than those obtained for the best inhibitors. The worst inhibiting potential among all structures analyzed during the molecular dynamics stage is shown by the Indol_9_15 molecule.

5. The Immobilization of Chosen Ligands with the Use of C60 Fullerene Derivatives

In the last stage of research, two ligand molecules were used which exhibit the highest affinity towards active site during molecular dynamics stage, namely Indol_4_9 and Indol_20_10. The affinity of the mentioned molecules towards C60 fullerene and its derivatives was evaluated during docking calculations. The data presented in Table 7 and Table 8 show that both considered ligands exhibit similar affinity toward native C60 fullerene; however, slightly higher values are denoted for the Indol_20_10 molecule. Both considered ligand molecules contain in each of their side chains one cyclic system, aromatic or heterocyclic, and such a chemical structure allows an occurrence of stacking interactions. The graphic representations of these complexes included in Figure 5 confirm that all cyclic systems of both inhibitors are involved in such a type of interaction. The planar orientation of all cyclic systems relative to fullerene surface and relatively small distances placed in the range from 3.36 to 3.77 Å indicate an occurrence of strong stacking interactions stabilizing the considered complexes. The rest of the values presented in Table 7 and Table 8 concerns functionalized derivatives of C60 fullerene. Each of these structures was created by a single or multiple addition of functional groups to the fullerene surface. Among all used substituents there can be found aliphatic chains with halogen, methoxy, ester, and amide groups, and aromatic systems such as unsubstituted benzene rings and more complex aromatic systems. The description of all used nanosystems is presented in Table A2. All the structural modifications observed in the considered nanocarriers contributed to an increase of binding affinities towards both ligand molecules. In the case of Indol_4_9, the observed differences are placed in a range from −0.7 to −1.8 kcal/mol while for Indol_20_10 from −0.8 to −2 kcal/mol. Much more evident discrepancies are observed in the case of binding constant for the complex creation. The comparison of the best obtained complexes relative to the reference system (C60 fullerene) indicates an increase in the yield of the complex formation reaching as much as 2824%. The Indol_4_9 exhibits the highest binding affinity toward FF_12 fullerene, and the increase of yield of this complex formation relative to the reference system is equal to 1986.5%. The complex obtained during the docking stage is maintained by several stacking interactions occurring between all cyclic systems of ligand and surface of fullerene; observed distances are placed in the range from 3.26 to 3.58 Å. Also, the orientation of both cyclic systems from side chains towards aromatic substituents placed on the fullerene surface indicates the presence of additional stabilizing impacts. The next interesting complexes of this ligand are created with FF_5 and FF_11 nanomolecules; both are characterized by similar affinity values. In both complexes, all cyclic systems are involved in the creation of stacking interactions. In the case of complexes with the FF_5 molecule, a new stabilizing impact appears, namely the hydrogen bond between the hydrogen from the amine group and oxygen from the phosphoryl group with the distance of 1.96 Å, indicating the medium strength of this impact. The complexes created by Indol_20_10 are characterized by higher affinity values in relation to the previously discussed inhibitor. The most stable complexes are created with FF_12 and FF_11 nanomolecules and the value of binding affinity equals −9.2 kcal/mol, causing the yield of these complexes creation to be higher by 2824% relative to the reference system. The graphic representations presented in Figure 5 confirm that in both complexes all aromatic systems of the considered ligand create stacking interactions with fullerene surface, and in some cases also with aromatic substituents placed on the fullerene surface. The next interesting group of complexes created by Indol_20_10 are systems containing FF_3, FF_5, and FF_9 nanocarriers, all of which are characterized by similar affinity values (−8,9 kcal/mol). The increase of yield relative to the reference system in this case reaches a value of 1662.4%. The observed ligand conformations in all cases supports the occurrence of stacking interactions between all aromatic systems of ligand and the surface of considered nanomolecules; denoted distances are placed in the range from 3.27 to 3.8 Å.

6. Conclusions

The proposed procedure of oxindole derivative preparation allows indication of a group of compounds exhibiting an inhibiting potential towards the CDK2 active site. The realized calculations unambiguously show that both proposed additions to the oxindole core considerably affect the binding affinity towards the active site. The use of similar groups of substituents in both side chains allows a conclusion that modifications made in the R2 position contribute to a much greater increase of binding affinity than modifications in the R1 position. Such an observation clearly shows that this part of the active site created by amino acids LEU83, HIE84, GLN85, ASP86, LYS89, and GLU8 exhibits much more activity in the creation of interactions with ligand molecules. The greatest impact on the values of binding affinity was exerted by substituents, which were heterocyclic or aromatic systems with hydrogen-bond donors and acceptors. Among all the created structures, a significant part was compounds exhibiting not only high binding affinity toward the active site but also an acceptable level of toxicity and a satisfactory ability to penetrate cell membranes expressed by LogP values. The oxindole derivatives chosen based on these factors were evaluated during the molecular dynamics stage and almost all of them confirmed their inhibitory abilities. Two of the analyzed structures, namely Indol_4_9 and Indol_20_10, are characterized by the highest enthalpy values describing their affinities relative to the active site. The energetic aspects correlate also with structural analysis of conformers collected during the molecular dynamics stage. The stable interactions during simulation time, created not only by active groups from molecule core but also for both side chains, together with uniform distribution of RMSD values characterizing these ligands, indicate a significant stability of the considered complexes. Slightly worse but also satisfactory properties exhibit complexes formed by Indol_4_10 and Indol_20_15. Only in the case of Indol_9_15 molecular dynamics analysis was there a total disappearance of interactions created by active groups from side chains identified during the docking stage. This phenomenon is not related to the appearance of new competitive interactions. Such structural observations also confirm a significant decrease of binding enthalpy. The realized calculations show that the best oxindole derivatives exhibit significant affinity towards C60 fullerene and functionalized derivatives of this nanomolecule. The three cyclic systems in each of the molecules consist of aromatic or heterocyclic groups which can participate in π–π stacking interactions with fullerene surface. The obtained data shows that the most significant increase of binding affinity is related to the presence of additional aromatic substituents on the fullerene surface as confirmed by values characterizing ligand complexes with FF_12 and FF_11 fullerene. The obtained data shows that one of the most important factors stabilizing such complexes is stacking and hydrophobic interactions; the presence of hydrogen-bond donors or acceptors does not play such an important role in the stabilization of such complexes. The presented data clearly shows that the created complexes of oxindole derivatives and considered nanocarriers exhibit significant potential in the creation of immobilized drugs, and can be used in the development of targeted therapies.


This research received no external funding.


This research was supported by PL-Grid Infrastructure (

Conflicts of Interest

The author declares that there are no conflicts of interest.

Appendix A

Table A1. The characteristics of affinities and molecular descriptors of analyzed oxindole derivatives. (ΔG—ligand binding affinity; IC—Inhibition constant; Tox—index of toxicity; LogP—octanol/water coefficient; MW—molecular weight; n HbA—number of hydrogen-bond acceptors; n HbD—number of hydrogen-bond donors.).
Table A1. The characteristics of affinities and molecular descriptors of analyzed oxindole derivatives. (ΔG—ligand binding affinity; IC—Inhibition constant; Tox—index of toxicity; LogP—octanol/water coefficient; MW—molecular weight; n HbA—number of hydrogen-bond acceptors; n HbD—number of hydrogen-bond donors.).
n HbAn HbD
Table A2. Description of functionalized C60 fullerene derivatives (FF_X) used during docking stage.
Table A2. Description of functionalized C60 fullerene derivatives (FF_X) used during docking stage.
methyl 9-(2-trimethylsilylethyl)(C60-Ih)[5,6]fullerene-1-carboxylate


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Figure 1. The hydrogen bonds and stacking interactions characteristic for oxindole core with amino acids from CDK2 active site.
Figure 1. The hydrogen bonds and stacking interactions characteristic for oxindole core with amino acids from CDK2 active site.
Symmetry 11 00974 g001
Figure 2. The graphic representation of oxindole core and active groups used during the creation of ligands.
Figure 2. The graphic representation of oxindole core and active groups used during the creation of ligands.
Symmetry 11 00974 g002aSymmetry 11 00974 g002b
Figure 3. The graphic representations of interactions of chosen oxindole derivatives with CDK2 active site identified during docking stage.
Figure 3. The graphic representations of interactions of chosen oxindole derivatives with CDK2 active site identified during docking stage.
Symmetry 11 00974 g003
Figure 4. Distributions of RMSD (Å) values. Black distributions refer to ligand molecules while gray distributions refer to CDK-2 protein.
Figure 4. Distributions of RMSD (Å) values. Black distributions refer to ligand molecules while gray distributions refer to CDK-2 protein.
Symmetry 11 00974 g004aSymmetry 11 00974 g004b
Figure 5. Graphic representation of chosen ligand complexes with functionalized derivatives of C60 fullerene characterized by highest binding affinity.
Figure 5. Graphic representation of chosen ligand complexes with functionalized derivatives of C60 fullerene characterized by highest binding affinity.
Symmetry 11 00974 g005aSymmetry 11 00974 g005b
Table 1. The values of biding affinity of oxindol mono derivatives towards CDK2. Increase of binding affinity estimated relative to the value for Indol_0_0 equals −8.3 kcal/mol.
Table 1. The values of biding affinity of oxindol mono derivatives towards CDK2. Increase of binding affinity estimated relative to the value for Indol_0_0 equals −8.3 kcal/mol.
NameBinding Affinity
Increase of Binding Affinity (%)NameBinding Affinity
Increase of Binding Affinity (%)
Table 2. The values of biding affinity and molecular parameters for the structures exhibiting the best properties.
Table 2. The values of biding affinity and molecular parameters for the structures exhibiting the best properties.
NameLogPToxicityBinding Affinity
Increase of
Binding Affinity (%)
Inhibition Constant
Table 3. Interactions stabilizing oxindole derivatives complexes with CDK2 active site, estimated during docking simulation stage.
Table 3. Interactions stabilizing oxindole derivatives complexes with CDK2 active site, estimated during docking simulation stage.
Amino AcidHydrogen-Bond Length/Distance Between Aromatic Systems * (Å)
Glu 122.572.64------------
Lys 332.
Leu 831.941.911.811.811.92
Glu 812.332.322.142.102.23
Gln 852.752.44
Asp 861.90--------2.412.52
Lys 89----2.922.54----2.42
Phe 80 *3.873.873.843.763.84
Table 4. The averaged values of RMSD (Å) for ligands and enzyme for all steps used during structural analysis. The values in italics represent standard deviations.
Table 4. The averaged values of RMSD (Å) for ligands and enzyme for all steps used during structural analysis. The values in italics represent standard deviations.
Table 5. Distribution of the most frequently created hydrogen bonds between ligands molecule and selected amino acids from CDK-2 active site. The hydrogen bonds in the table represent median values of intervals with a width of 0.25 Å.
Table 5. Distribution of the most frequently created hydrogen bonds between ligands molecule and selected amino acids from CDK-2 active site. The hydrogen bonds in the table represent median values of intervals with a width of 0.25 Å.
Hydrogen BondPopulation %
1.5 Å1.75 Å2.0 Å2.25 Å2.5 Å2.75 Å3.0 Å
Ligand (O2) … (HN) LEU 83100.
Ligand (H3) … (O) GLU 81100.
Ligand (O3) … (H) LYS 3398.70.024.444.416.
Ligand (H1) … (O) ASP 8698.
Ligand (H4) … (O) GLU 1245.
Ligand (O2) … (HN) LEU 83100.
Ligand (H3) … (O) GLU 81100.00.019.557.
Ligand (O3) … (H) LYS 3382.90.126.935.812.
Ligand (H2) … (O) GLU 869.115.443.
Ligand (H4) … (O) GLU 1246.
Ligand (O3) … (HN) LEU 83100.00.124.555.
Ligand (H5) … (O) GLU 81100.
Ligand (O4) … (H) LYS 3394.30.244.340.
Ligand (F) … (H) GLY 1331.
Ligand (O1) … (HN) LEU 831000.125.757.314.
Ligand (H5) … (O) GLU 811000.027.956.613.
Ligand (O4) … (H) LYS 3392.50.138.935.313.
Ligand (NHX) … (O) ASP 8650.70.218.822.
Ligand (H4) … (O) GLU 885.721.354.
Ligand (NHX) … (O) ILE 1061.30.010.925.
Ligand (O3) … (HN) LEU 83100.
Ligand (H6) … (O) GLU 81100.00.024.361.413.
Ligand (O4) … (H) LYS 3389.60.338.439.
Ligand (H3) … (O) ASP 8648.00.011.420.
Ligand (H1) … (O) HIE 8456.70.120.925.
Ligand (O1/2) … (H) LYS 8973.60.16.723.517.611.88.55.4
Table 6. The values of binding enthalpy (kcal/mol) estimated for all complexes considered during molecular dynamics stage (EVDWAALS = van der Waals contribution from MM.; EEL = electrostatic energy; EPB = the electrostatic contribution to the solvation free energy calculated by PB; ECAVITY = nonpolar contribution to the solvation free energy; ΔH = final estimated binding enthalpy).
Table 6. The values of binding enthalpy (kcal/mol) estimated for all complexes considered during molecular dynamics stage (EVDWAALS = van der Waals contribution from MM.; EEL = electrostatic energy; EPB = the electrostatic contribution to the solvation free energy calculated by PB; ECAVITY = nonpolar contribution to the solvation free energy; ΔH = final estimated binding enthalpy).
Table 7. Values of binding affinity (kcal/mol) of Indol_4_9 molecule relative to functionalized C60 fullerene derivatives (FF_X) obtained during docking stage.
Table 7. Values of binding affinity (kcal/mol) of Indol_4_9 molecule relative to functionalized C60 fullerene derivatives (FF_X) obtained during docking stage.
Nanostructure NameΔG (kcal/mol)Binding Constant (Kmax)Difference of Kmax Relative to C60 (%)
Table 8. Values of binding affinity (kcal/mol) of Indol_20_10 molecule relative to functionalized C60 fullerene derivatives (FF_X) obtained during docking stage.
Table 8. Values of binding affinity (kcal/mol) of Indol_20_10 molecule relative to functionalized C60 fullerene derivatives (FF_X) obtained during docking stage.
Nanostructure NameΔG (kcal/mol)Binding Constant (Kmax)Difference of Kmax Relative to C60 (%)

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