Pyrimidine-based pyrazoles as cyclin-dependent kinase 2 inhibitors: Design, synthesis, and biological evaluation

Article abstract of DOI:10.1111/cbdd.13334

A series of new pyrimidine-pyrazole hybrid molecules were designed as inhibitors of cyclin-dependent kinase 2. Designed compounds were docked using Glide and the compounds showing good score values and encouraging interactions with the residues were selected for synthesis. They were then evaluated using CDK2-CyclinA2 enzyme inhibition by a luminescent ADP detection assay. We show that of the 26 compounds synthesized and evaluated, at least 5 compounds were found to be highly potent (IC₅₀?

Full text of DOI:10.1111/cbdd.13334

DR NISHA K. SHAH (Orcid ID : 0000-0003-0556-123X)
Article type : Research Article
Pyrimidine based pyrazoles as Cyclin-dependent kinase 2 inhibitors: Design,
Synthesis and Biological Evaluation
Mayur K. Vekariyaa, Rajesh H. Vekariyaa, Pathik S. Brahmkshatriyab, Nisha K.
Shaha*
aDepartment of Chemistry, Gujarat University, Ahmedabad, Gujarat 380009, India
bInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i.,
Flemingovo nám. 2, 16610 Prague 6, Czech Republic
* Corresponding author
Nisha K. Shah
Department of Chemistry,
Gujarat University, Ahmedabad, Gujarat 380009, India
Tel : (M) +91 9825312095, (O) +91 79 26300969
E-mail : nishchem2004@yahoo.in
Abstract
A series of new pyrimidine-pyrazole hybrid molecules were designed as inhibitors of cyclin-
dependent kinase 2. Designed compounds were docked using Glide and the compounds showing
good score values and encouraging interactions with the residues were selected for synthesis. They
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been through the copyediting, typesetting, pagination and proofreading process, which may
lead to differences between this version and the Version of Record. Please cite this article as
doi: 10.1111/cbdd.13334
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were then evaluated using CDK2-CyclinA2 enzyme inhibition by a luminescent ADP detection assay.
We show that of the 26 compounds synthesized and evaluated, at least 5 compounds were found to
be highly potent (IC50< 20 nM); which can be further optimized to have selectivity over other kinase
isoforms.
Keywords: structure-based design, docking, cyclin-dependent kinase 2, pyrazole
1. Introduction
Controlling cell cycle by inhibiting various enzymes that normalize its progression is a smart
strategy for treating cancer and other diseases accompanying with abnormal cellular production[1].
Cyclin-dependent kinases (CDKs) are one class of such serine/threonine protein kinases and are well
known for their vital roles in the regulation of cell divisions. Action of these CDKs is tightly regulated
at several levels: dealings with negative and positive regulatory partners, activation by
phosphorylation or dephosphorylation, and shifts in their subcellular localization, etc. Cell cycle
deregulation is often related with the CDK activity in many cancers[2]. For these reasons, CDKs have
been targeted by numerous experimental anticancer therapeutics[3]. For example, palbociclib, a dual
inhibitor of CDK4/CDK6, has recently been approved for the treatment of ER-positive and HER2-
negative breast cancer[3]. Of the CDKs, CDK2 has been one of the most extensively studied members.
Several small molecules inhibitors of CDK2 have entered clinical trials. (Fig. 1)[4]. Many of
them contain pyrimidine and pyrazole moieties in their backbone which interact with the key hinge
residues. Moreover, pyrimidine and pyrazole analogues constitute an important class of bioactive
molecules and as drugs also. In medicinal chemistry, both pyrimidine derivatives and pyrazole
derivatives have been very well known for their biological potency. They demonstrate various types
of pharmacological activities such as anti-cancer[5,6]
,
anti-viral[7,8]
,
anti-HIV[9,10]
,
anti-
hypertensive[11,12], anti-tubercular[13,14], diuretic [15,16], anti-bacterial[17,18], anti-fungal[19,20] and anti-
epileptic[21,22] properties, and many classes of chemotherapeutic agents containing pyrimidine and
pyrazolenucleus are in clinical trials.
Most of these inhibitors are designed either by structure-based drug design approach
employing virtual screening/docking a large library of compounds or screening a small sub-set of
focused library of compounds. In the present work, we combine both these strategies, i.e.
knowledge-based approach (identifying the known pharmacophores for CDK2 inhibition) and
structure-based drug design. To execute this, we identified novel CDK2 inhibitors with pyrazole and
pyrimidine moieties embedded in a single molecule. Molecular docking of thus obtained focused
virtual library of compounds led to identification of a series of new pyrimidine-pyrazole hybrid
molecules, which were synthesized and evaluated in vitro for their CDK2-Cyclin A2 inhibitory activity
using kinase system along with ADP-Glo Assay. We strongly feel that this approach is a better way to
identify potential lead compounds which are good candidates for further evaluation for kinase
selectivity profiling.
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2. Experimental protocols
2.1. Design
2.1.1. Structure preparation
Protein structure coordinates were obtained from the RCSB Protein Data Bank (PDB Code 2R3J)[3].
Protein structures were prepared using the Protein Preparation Wizard in Maestro (Maestro v.10.1).
Default settings were used, except that missing side chains were added, all crystallographic water
molecules were removed and at the protein structure refinement step, exhaustive sampling was
used in order to obtain a better H-bond assignment. Ligands were prepared using LigPrep tool with
an Optimized Potentials for Liquid Simulations (OPLS_2005) force field. Their ionization states were
generated at pH 7.0 ± 2.0 using Ionizer in LigPrep. Specific chiralities were retained during ligand
preparations and stereoisomers per ligand were retained at a minimum value of 1.
2.1.2. Grid generation
Docking receptor grid was generated using Glide’s Receptor Grid Generation module. Grids were
generated keeping the default parameters of van der Waals scaling factor as 1.00 and charge cutoff
as 0.25; which was subjected to OPLS 2005 force field. A cubic box of 10 × 10 × 10 dimension
centered around the inhibitor in the active site was generated for each protein.
2.1.3. Docking
Standard precision (SP) ligand docking was carried out in Glide of Schrödinger-Maestro v10.1 within
which penalties were applied to non-cis/trans amide bonds. Van der Waals scaling factor and partial
charge cutoff was selected to be 0.80 and 0.15, respectively for ligand atoms. Final scoring was
performed on energy-minimized poses and displayed as Glide score. Number of poses were limited
to 5 per ligand.
2.2. Synthesis
All the analytical grade reagents and raw materials used were obtained from known
marketable sources and were used without further purification. TLC was performed on silica gel 60
F254 plate (Merck, Germany) and visualization was done using iodine or UV light Column
chromatography was performed using silica gel (60-120 mesh) from HPLC Chemicals (Mumbai,
India). Melting points were determined in automatic melting point apparatus named Optimelt
MPA100 and were uncorrected. Mass spectra were recorded in Waters Acquity TQD model, Waters
USA where acetone was used as mobile phase with electron spray ionization (ESI) as ion source. 1H-
NMR and 13C-NMR spectra were recorded on Bruker AV 400 MHz and 125 MHz spectrometer,
respectively using DMSO-d6 as solvent and TMS as the internal reference. Spectral graphs obtained
were shown in supporting data.
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2.2.1. Ethyl 2-((dimethylamino)methylene)-3-oxobutanoate (Intermediate-A)
Ethylacetoacetate (26 g, 200 mmol) and DMF-DMA (26.2 g, 220 mmol) were heated at 80°C for 1 h in
100 ml three-necked flask. The reaction mixture was then quenched with n-pentane to remove
unreacted material. Formation of product was confirmed by boiling point analysis. Reaction mixture
was directly used for the next step without further purification to afford ethyl 2-
((dimethylamino)methylene)-3-oxobutanoate (Intermediate-A) as dark brown liquid. Yield 90%; b.p.
180°C.
2.2.2. 4-chloro-6-hydrazinylpyrimidine (1)
4,6-Dichloropyrimidine (15 g, 100 mmol) in ethanol was charged in 250 ml three-necked flask and
was cooled to 5°C. Hydrazine hydrate (4.7 ml, 120 mmol) was charged to the above flask dropwise.
After complete addition of hydrazine hydrate, reaction mixture was stirred at room temperature for
90 minutes. The reaction mixture was filtered and washed with water to afford crude product which
was recrystallized in ethanol to obtain 4-chloro-6-hydrazinylpyrimidine (1) as pale yellow solid. Yield
95%; Rf = 0.5 (hexane:ethyl acetate, 4:1); m.p. 164°C; 1H NMR 8.83 (s, 1H), 8.17 (s, 1H), 6.76 (s, 1H),
4.50 (s, 2H); EI-MS (m/z): 145.02 (M+1).
2.2.3. Ethyl 1-(6-chloropyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylate (2)
To a solution of 1 (10.0 g, 69.2 mmol) in ethanol (100 mL) was added Intermediate-A (13.0 mL, 69.2
mmol) and the reaction mixture was stirred for 45 minutes. After that the reaction mixture was
refluxed for 1 h. The reaction mixture was cooled and poured on crushed ice to obtain white solid as
crude product which was filtered, dried and recrystallized from ethanol to obtain ethyl 1-(6-
chloropyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylate (2) as white crystals. Yield 75%; Rf = 0.8
1
(hexane:ethyl acetate, 4:1); m.p. 180°C; H NMR 9.936 (s, 1H), 8.492 (s, 1H), 8.238 (s, 1H), 4.216 (q,
2H), 2.782 (s, 3H), 1.312 (t, J=7.2 Hz, 3H). EI-MS (m/z): 268.07 (M+2).
2.2.4. Ethyl 1-(6-(benzylamino)pyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylate (3)
To a solution of 2 (20.0g, 74.9 mmol) in ethanol (100 mL) was added triethylamine (31.6 mL, 224
mmol) and benzylamine (8.2 mL, 75 mmol) and the mixture was stirred at 80oC for 3 h. After
complete consumption of both the reactants, reaction mixture was poured on ice-cold water.
Resultant white precipitates were filtered off, dried and recrystallized with ethanol to afford Ethyl 1-
(6-(benzylamino)pyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylate (3) as white solid. Yield 95%; Rf
= 0.35 (hexane:ethyl acetate, 5:5); m.p. 188-192°C; 1H NMR 9.912 (s, 1H), 8.432 (s, 1H), 8.212 (s, 1H),
7.32-7.22 (m, 5H), 4.204 (s, 2H), 4.106 (q, J=7.2 Hz, 2H), 2.122 (s, 3H), 1.312 (t, J=7.2 Hz, 3H); EI-MS
(m/z): 338.47 (M+1).
2.2.5. 1-(6-(benzylamino)pyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylic acid (4)
To a previously cooled solution of 3 (22.0g, 65.2 mmol) in methanol:water (2:1) at 0-50C, lithium
hydroxide (7.8g, 326 mmol) was added portion wise. After completion of addition, the reaction
mixture was stirred at room temperature for 24 h. After completion of reaction, reaction mixture
was poured on ice-cold water and acidified with 1N HCl. Precipitates formed were filtered, washed
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with water and dried to afford 1-(6-(benzylamino)pyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylic
1
acid (4) as white solid. Yield 96%; Rf = 0.30 (hexane:ethyl acetate, 3:7); m.p. 182°C; H NMR 10.824
(s,1H), 9.932 (s, 1H), 8.422 (s, 1H), 8.12 (s, 1H), 7.32-7.22 (m, 5H), 4.211 (s, 2H), 2.102 (s, 3H); EI-MS
(m/z): 310.04 (M+1).
2.2.6. 1-(6-(benzylamino)pyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxamide
derivatives (5a-5z)
To a stirred solution of 4 (1mmol) in DMF was added HOBT (0.7 mmol) under anhydrous conditions
at room temperature. EDC.HCl (1.5 mmol) was added to the above reaction mixture and stirred for
15 minutes. Triethylamine (3.0 mmol) was added and to the reaction mixture and it was further
stirred for 5 minutes. After this, the corresponding amine (1.0 mmol) was added and reaction
mixture was allowed to stir at room temperature for 1 to 2 h. Reaction was monitored on TLC. After
completion of reaction, the reaction mixture was poured in cold-water and extracted with ethyl
acetate twice. Combined organic layer was dried over sodium sulphate and concentrated to get
crude product which was purified by column chromatography using ethyl acetate: hexane mobile
phase and recrystallized from ethanol to obtain title compounds (5a-5z).Physical data of all targeted
compounds were available in supporting data.
2.2.Biology
The CDK2-CyclinA2 enzyme inhibition assay was measured by a luminescent ADP detection assay
using CDK2/CyclinA2 Kinase Enzyme System with ADP-Glo™ Kinase Assay kit (Promega Corporation,
USA)[23]. The assay was performed in a volume of 50 µL at room temperature in 384-well flat bottom
white polystyrene plates. The final concentrations of the assay ingredients were 25 ng CDK2-Cylin
A2, 100 µg histone substrate, and 50µMATP. The compounds were dissolved in DMSO and added to
the reaction mixture at eight different concentrations with the highest concentration of 20 µM for
Roscovitine and 100 µM for the rest of the targeted compounds. DMSO concentration was
maintained 1% in all the test concentrations irrespective of the dilutions. Continuous kinetic
monitoring of enzyme activity was performed on VICTOR Multilabel Luminescence Reader (Perkin
elmer, USA). The experiment was carried out in duplicate and the percent inhibition of enzyme
activity was calculated for all the compounds at each concentration. The IC50 values were obtained
from the non-linear curve fitting of the plot of percent inhibition versus inhibitor concentration [I]
using the equation, % inhibition = 100/{1+ (IC50/[I])k}, where k is the Hill slope in Graphpad Prism
software. Bio assay results of Roscovitine was briefly shown in supporting data.
3. Results and Discussion
3.1 Computational results
ADME properties were predicted using Qikprop (Shrodinger) for all targeted compounds and
the results obtained as shown in Table 1. All compounds showed drug like properties with no
violation of Lipinski’s rule of five. The Lipinski’s rule of five values for all compounds were also
tabulated in Table 1. All compound possess satisfactory pharmacokinetic properties (ADME). All
compound have shown good percentage (83.302–100%) of human oral absorption. The projected
aqueous solubility (QP log S) parameter directs all compounds possess permissible scores except
some compound 5k, 5p, 5r, 5x. Similarly all compound exhibit good blood–brain barrier permeability
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(QP log BB) values. The predicted IC50 value of HERG K+ channel blockage (QP logHERG) depicted
admirable range of values.
Cyclin-dependent kinase 2 protein (PDB Code 2R3J) was used for docking the designed compounds
into the active site of the protein. An in-house database of 100 compounds, which were designed
based on the common pharmacophoric requirements for CDK2 inhibition, was used for docking. All
compounds were docked using Glide-SP protocol and rescored using Glide-XP. Encouragingly, some
of the compounds showed very good scores and showed favourable interactions with the
neighbouring residues. It was also encouraging to see a satisfactory correlation between Glide score
and pIC50 (r = 0.73, Table 2). Compounds which showed favourable interactions and good Glide score
along with pharmacokinetic properties were then selected for synthesis. All compounds were found
to have good glide score vary from -6.235 to -9.014. Fig. 2 shows docked poses of few representative
molecules which were part of the synthesized target compounds. It was encouraging to see that
most of the docked poses consistently showed interactions with the hinge residue (Leu83) with two
strong hydrogen bonds. Along with this the compounds also interacted with Leu134, Ile10 and
Phe82 with dispersion interactions.
3.2. Chemistry
The synthetic methodology for the pyrimidine pyrazole hybrid molecules is shown in Scheme
1. Synthesis of Enaminone intermediate throughN,N-Dimethylformamide dimethyl acetal (DMF-
[24]
DMA) approach
was a primary step towards the formation of key scaffold i.e. ethyl 1-(6-
chloropyrimidin-4-yl)-5-methyl-1H-pyrazole-4-carboxylate (Intermediate-A). Reaction of 1 with
Intermediate-A under refluxing condition in ethanol afforded ethyl 1-(6-chloropyrimidin-4-yl)-5-
methyl-1H-pyrazole-4-carboxylate (2) by a facile formation of pyrazole ring, which then underwent
nucleophilic substitution using by benzylamine to afford ethyl 1-(6-(benzylamino)pyrimidin-4-yl)-5-
[25]
methyl-1H-pyrazole-4-carboxylate (3). Hydrolysis of 3 using lithium hydroxide
yielded the
corresponding acid (4) which then was coupled with respective amines using 1-hydroxybenzotriazole
hydrate (HOBT) and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC HCl)
[26]
reagent
to afford the target compounds in moderate to high yields involving facile workup
procedures.
3.3. Biology
Synthesized target compounds were screened for their potential to inhibit CDK2/CyclinA2
enzymatic activity in vitro. Table 2 shows the results of the biochemical evaluation and Glide score
values. While many compounds were found to be inactive (IC50>100 µM), few compounds were
found to be significantly potent as compared to the activity of roscovitine (IC50 = 0.32 µM). Of these,
compounds 5b, 5i, 5j, 5l and 5m were found to be significantly active with IC50< 20 nM. In general,
good agreement was found between Glide score and IC50 values. For example, compounds 5b, 5i,
and 5j which were found to have IC50 <15 nM had the highest scores amongst the predicted
compounds. A closer analysis of structure-activity relationship suggests that both aromatic and
aliphatic substituents were tolerated at the R1 position. In general, irrespective of the positions at
the aromatic ring (ortho/meta/para), polar groups and groups with H-bond donors (e.g. OH and NH)
were found to decrease the activity. From the poses, it was expected that the activity would be
mostly governed by dispersion interactions. Indeed, as seen from the activity of 5d, 5i, 5j, 5m, 5o,
5p, this was found to be the case.
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Structure–activity relationship (SAR)
The substitution pattern of the aryl amine ring at the different position was observed to
affect biological activity. The electronic nature of the substituents led to significant variation for
disparity in activity. Compounds possessing electron-donating substituents Except -F (-OH, -OCH3) at
4th position of phenyl ring led to an increase in the CDK2-Cyclin A inhibition activity. The methyl
group (weak electron donating) at 2nd, 3rd and 4th position of phenyl ring was found to be a less
active. In particular, it was found that 5k occupied a different position of R group than its close
analogues: 5i, 5j and 5l. As seen from Fig. 3a, 4-methylphenyl analog (5k) faces towards solvent
while in 5i, 5j and 5l, corresponding aryl moieties align well and interact with protein residues by
dispersion interactions. This could be one of the reasons of 5k being less scored and less active in
vitro. Similarly, we tried to also hypothesize the differential activities between structurally close
homologs; 5o, 5p, 5q and 5r. It was evident to see that bulky substitution was not tolerated at C-3
position of the phenyl ring at R group. Indeed, as seen from Fig. 3b, compound 5o with 3-F
substitution fit well in the protein allowing the aryl ring to have dispersion (CH-π) interactions with
neighbouring residues. Increasing the bulk from fluoro to chloro (5p), methoxy (5q), methyl (5r) and
acetyl (5u) moved the phenyl ring slightly out of the hydrophobic pocket facing the solvent side on
account of steric clashes. Indeed, this was reflected in the reduced/loss of activity of 5q, 5r and 5u.
While 5p did retain activity, we think that this may have resulted because of reasons which couldn’t
be explained by simple protein-ligand interactions (for example, entropic considerations or protein
conformational change).
The phenyl ring without any electron donating or withdrawing group also showed weaker
CDK2-Cyclin A inhibitory activity. Furthermore, compounds having electron-donating substituents (-
Me, -OMe, -OH) at 3rd position of phenyl ring to a decrease in the CDK2-Cyclin A inhibition activity,
except halogenated groups (-Cl & -F). In addition, compound possessing -COCH3 group at 3rd
position of phenyl ring led to a decrease in the CDK2-Cyclin A inhibition activity. In contrast,
compounds bearing electron donating groups (–Cl, -OMe, -Me, -OH, -F) at 2nd position of phenyl
ring possessed weaker activity. It can be noted that among the halogenated compounds with the
lowest lipophilicity (Lowest Log P) showed highest activity.
Compounds having aliphatic amines also showed excellent CDK2-Cyclin A inhibitory activity.
Compounds possessing piperidine, morpholine & ethanolamine led to more potent CDK2-Cyclin A
inhibitory activity. While compounds containing piperidone and piperazine afforded weaker CDK2-
Cyclin A inhibitory activity. Furthermore, CDK2-Cyclin A inhibitory activity was observed, when
compound possess N-methylpiperazine. While ethyl substituted compounds showed lesser activity.
Compounds possessing benzyl amine, isoniazid and phenyl hydrazine as substituents were also
found to lesser CDK2-Cyclin A inhibitory activity. This concept has been explained graphically in fig. 4.
4. Conclusions
In conclusion, a series of novel pyrimidine-pyrazole hybrid molecules as potent CDK2-CyclinA2
enzyme inhibitors has been studied. Molecular docking of these novel molecules on CDK2-CyclinA2
enzyme (PDB: 2R3J) exhibited very good docking score values which was also confirmed by the
biochemical assay using a luminescent ADP detection method. On the basis of SAR, it has been
observed that compounds having electron donating fluoro and chloro groups on aryl amine as well
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as piperidine and morpholine show increased CDK2-Cyclin A inhibitory activities. Out of total 26
compounds synthesized and screened, at least 5 compounds were found to be highly potent (IC50 <
20 nM); which are very good candidates for further optimization of drug likeliness and selectivity
over other kinase isoforms.
Conflicts of interest
The authors declare that they have no competing interests.
Acknowledgement
This work was supported by the Gujarat Council on Science and Technology (GUJCOST/MRP/14-
15/1138), Department of Science and Technology, Gandhinagar, Gujarat, India. Mayur K. Vekariya is
also thankful to the UGC, India for providing financial support under UGC-BSR Fellowship (Grant No:
F./25-1/2013- 14 (BSR) / 7-74/2007 (BSR) dated 30-05- 2014).
List of Figure legends
Fig. 1: Examples of CDK2 inhibitors in clinical evaluation
Fig. 2: Interactions of the target compounds 5i (panel a) and 5j (panel b) with CDK2 protein (PDB
Code 2R3J). Color coding: carbon in cyan (protein) or yellow (ligand), nitrogen in blue, oxygen in red.
The numbers represent distances in Å.
Fig. 3: Panel a) Poses of target compounds 5i, 5j, 5k and 5l in CDK2. Color coding: carbon in cyan (5j),
green (5l), orange (5i) and yellow (5k); nitrogen in blue, oxygen in red, fluorine in off-white; Panel b)
Poses of target compounds 5o, 5p, 5q and 5r in CDK2. Color coding: carbon in green (5o), orange
(5p), yellow (5q) and pink (5r), nitrogen in blue, oxygen in red, fluorine in off-white.
Fig. 4: Structure–activity relationship
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Fig. 1 Examples of CDK2 inhibitors in clinical evaluation
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Fig. 4 Structure–activity relationship
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Scheme 1. Reagents and conditions: (a) NH2NH2.H2O, EtOH, 1.5 h, rt; (b) Intermediate-A, EtOH, 1 h,
reflux; (c) Benzylamine, TEA, EtOH, 3 h, reflux; (d) LiOH, MeOH, H2O, 24 h, reflux; (e) various amines,
HOBt, EDC.HCl, DIPEA, DMF, 1-2 h, reflux.
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Table 1 : Pharmacokinetic properties of compounds 5a-5z
Lipinski’s rule of five factors
Pharmacokinetic properties
Percent
human oral
absorption
(>80 high,
<25 poor)
100
QP log
Po/w
(<5)
QP
QP log Sa
Comp
Mol_MW
(<500)
Donor
Acceptor
HB (<10)
Molar
Rule of
five
QPlog BBc
(-3 to 1.2)
logHERGb
HB (<5)
Refractivity
(-6.5 to 0.5)
(below -5)
5a
5b
5c
5d
5e
5f
384
378
398
376
378
390
428
352
402
414
398
400
392
406
402
2
1
2
1
3
1
3
3
2
2
2
3
2
2
2
6
7
6
6
6
7
9
7
6
7
6
7
6
6
6
4.559
3.199
4.932
4.202
2.618
3.068
3.465
2.526
4.788
4.653
4.861
3.793
2.994
3.429
4.791
112.2
104.54
115.43
107.57
105.38
107.96
116.99
97.24
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
-6.575
-4.867
-6.913
-6.261
-4.643
-5.622
-6.181
-4.625
-6.914
-6.795
-7.133
-6.251
-4.276
-5.012
-6.932
-7.852
-6.068
-7.899
-6.556
-7.214
-6.619
-7.66
-0.788
-0.48
100
100
-0.811
-0.609
-0.516
-1.21
100
83.302
92.556
88.9
5g
5h
5i
-1.805
-1.336
-0.673
-0.871
-0.814
-1.477
-0.186
-0.34
89.715
100
-6.444
-7.705
-7.714
-7.732
-7.703
-7.04
112.17
118.76
116.95
113.88
110.34
114.96
112.17
5j
100
5k
5l
100
95.584
90.569
92.625
100
5m
5n
5o
-7.506
-7.716
-0.682
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5p
5q
5r
418
414
398
400
427
426
402
414
418
398
400
2
2
2
3
3
2
2
2
2
2
3
6
7
6
7
8
7
6
7
6
6
7
5.045
4.606
4.862
3.75
122.06
118.76
116.95
113.88
119.19
122.22
112.17
118.76
122.01
116.95
113.88
0
0
0
0
0
0
0
0
1
0
0
100
100
100
96.44
100
100
100
100
100
100
100
-7.294
-6.545
-7.127
-6.017
-6.851
-6.581
-6.966
-6.891
-7.175
-6.935
-5.981
-7.732
-7.467
-7.727
-7.454
-7.862
-7.533
-7.789
-7.765
-7.728
-7.638
-7.447
-0.631
-0.768
-0.812
-1.363
-1.49
5s
5t
4.407
3.999
4.812
4.71
5u
5v
5w
5x
5y
5z
-1.399
-0.688
-0.883
-0.6
5.026
4.825
3.826
-0.773
-1.256
a Predicted aqueous solubility in mol/l , b Predicted IC50 value of HERG K+ channels blockage, c Predicted blood–brain barrier permeability
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Table 2: Inhibition of CDK2-Cyclin A activity by the target compounds
CDK2/CyclinA2
CDK2/CyclinA2
IC50 (µM)
Compound
R
Glide-XP Score
-6.896
Compound
R
Glide-XP Score
-6.599
IC50 (µM)
5a
5b
5c
5d
5e
>100
5n
5o
5p
5q
5r
>100
0.067 ± 0.014
0.074 ± 0.001
>100
-8.966
0.008 ± 0.014
>100
-7.649
-6.765
-6.449
-8.759
0.022 ± 0.022
>100
-6.235
-6.586
-6.556
>100
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5f
-6.445
-6.836
>100
>100
5s
5t
-8.645
-6.300
>100
>100
5g
5h
-7.234
0.1 ± 0.002
5u
-6.412
>100
5i
5j
-8.783
-9.014
-6.932
-7.704
0.015 ± 0.015
0.015 ± 0.010
>100
5v
5w
5x
5y
5z
-7.828
-7.850
-7.818
-7.986
-7.123
>100
>100
>100
>100
>100
5k
5l
0.01 ± 0.002
5m
-7.739
-8.866
0.018 ± 0.012
0.34 ± 0.035
Roscovitine
---
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