Design, synthesis and molecular docking analysis of flavonoid derivatives as potential telomerase inhibitors

Article abstract of DOI:10.3390/molecules24173180

Based on the structural scaffolds of natural products, two series of flavonoid derivatives, for a total of twelve compounds, were designed and synthesized as potential human telomerase inhibitors. Using a modified TRAP-PCR assay, compound 5c exhibited the most potent inhibitory activity against human telomerase with an IC₅₀ value of less than 50 μM. In vitro, the results demonstrated that compound 5c had potent anticancer activity against five classes of tumor cell lines. The molecular docking and molecular dynamics analyses binding to the human telomerase holoenzyme were performed to elucidate the binding mode of active compound 5c. This finding helps the rational design of more potent telomerase inhibitors based on the structural scaffolds of natural products.

Full text of DOI:10.3390/molecules24173180

molecules
Article
Design, Synthesis and Molecular Docking Analysis of
Flavonoid Derivatives as Potential
Telomerase Inhibitors
Zhan-Fang Fan 1,†, Sai-Tim Ho 2,†, Rui Wen 1, Ya Fu 1, Lei Zhang 1, Jian Wang 1, Chun Hu 1,
Pang-Chui Shaw 2,*, Yang Liu 1,
*
and Mao-Sheng Cheng 1,
*
1
Key Laboratory of Structure-Based Drugs Design and Discovery (Ministry of Education),
School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
Correspondence: pcshaw@cuhk.edu.hk (P.-C.S.); y.liu@syphu.edu.cn (Y.L.);
mscheng@syphu.edu.cn (M.-S.C.)
2
*
†
These authors contributed equally to this work.
ꢀꢁꢂꢀꢃꢄꢅꢆꢇ
ꢀꢁꢂꢃꢄꢅꢆ
Received: 9 August 2019; Accepted: 31 August 2019; Published: 1 September 2019
Abstract: Based on the structural scaffolds of natural products, two series of flavonoid derivatives,
for a total of twelve compounds, were designed and synthesized as potential human telomerase
inhibitors. Using a modified TRAP-PCR assay, compound 5c exhibited the most potent inhibitory
activity against human telomerase with an IC50 value of less than 50
µM. In vitro, the results
demonstrated that compound 5c had potent anticancer activity against five classes of tumor cell
lines. The molecular docking and molecular dynamics analyses binding to the human telomerase
holoenzyme were performed to elucidate the binding mode of active compound 5c. This finding
helps the rational design of more potent telomerase inhibitors based on the structural scaffolds of
natural products.
Keywords: human telomerase holoenzyme; flavonoid; antiproliferative activity; molecular modeling
1. Introduction
Cancer is one of the leading causes of mortality worldwide. Approximately one-third of people
are affected by cancer during their lives [
cancer statistics 2018, which estimated that there will be about 18.1 million new cancer cases and
9.6 million cancer deaths worldwide [ ]. Lots of studies have indicated that telomerase activity can be
detected in approximately 80–90% cancer cells; however, in somatic cells, this enzyme is relatively
low [ ]. As the community of destiny of telomere, telomerase ensures the indefinite proliferation of
1]. In 2018, the American Cancer Society published the global
2
3,4
cancer cells and has been chosen as a hot target for drug development in cancer therapy [5].
Multiple telomerase inhibitors have been produced, including natural and synthetic products
and modified oligonucleotides, through targeting of the catalytic core [
binding agents, quadruplex ligands (G4) also play a significant role in inhibiting the activity of
telomerase [ ]. Due to the side effects of synthetic products, such as multidrug resistance, toxicity,
5]. In addition, as telomere
6–8
and poor bioavailability, it is preferred that telomerase inhibitors be isolated from natural plant
and marine materials, including secondary metabolites such as polyphenols, alkaloids, terpenoids,
xanthones, and sesquiterpenes [9–11]. Among them, flavonoids, as naturally occurring polyphenols,
are widely distributed in many field plants and exhibit multitudinous biological and pharmacological
properties, for instance, antitumor, cytotoxic, anti-inflammatory, antioxidant, cardiovascular and
antidiabetic effects. Several studies have demonstrated that flavonoids can treat and prevent cancer by
inhibiting telomerase activity and inducing apoptosis [12
–15]. However, few flavonoids compounds
Molecules 2019, 24, 3180; doi:10.3390/molecules24173180
www.mdpi.com/journal/molecules

Molecules 2019, 24, 3180
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have been developed into commercially available drugs due to their relatively weak anticancer potency
and the uncertain mechanism of action. To date, there is no inhibitor based on the flavonoid skeleton
that has been approved by the FDA. Therefore, to explore novel and potent telomerase inhibitors based
on the structural scaffolds of natural product flavonoids that have enhanced anticancer activity and
can reveal the particular mechanisms remains a challenging task.
As a class of polyhydroxy products, carbohydrates are widespread and ubiquitous in nature and
have excellent water solubility and various bioactivities, which have made them a reliable and valuable
source for drug design [16]. In addition, the “click reaction”, namely the Cu(I)-catalyzed azide-alkyne
1,3-dipolar cycloaddition, has been widely used to construct the 1,2,3-triazoles fragment, which can play
an important role in drug design [17]. Moreover, numerous structures and drugs bearing a cinnamoyl
moiety have shown strong inhibition against various tumor cell lines [18–21]. Previously, based on
natural product design, our group reported a series of triterpenoid saponin derivatives containing a
triazole linkage and N-acetylglucosamine derivatives substituted with cinnamoyl groups and they all
had remarkable antitumor activity both in vitro and in vivo [22–25]. Inspired by these previous results,
two series of novel flavonoid derivatives with glycosyl fragments linked by a triazole and containing an
N-acetylglucosamine substituted with a cinnamoyl group were designed and synthesized to enhance
inhibitory ability and elucidate their pharmacological mechanism (Figure 1).
Figure 1. General molecular formulas of two series of flavonoid derivatives.
In this study, we synthesized two series of flavonoid derivatives, for a total of twelve compounds
according to the split principle. Telomerase inhibition activity in vitro and antiproliferative activity
against five cancer cells lines were assayed to evaluate the possibility of these compounds as potential
telomerase inhibitors. Compound 5c showed the most potent activities both in the telomerase inhibition
assay and against all tested cell lines.
To date, for the human telomerase holoenzyme, there is no cocrystallization of protein and ligand
complexes available [26]. In this report, the active site of the protein structure was confirmed via
alignment with a similar protein discovered from Tribolium castaneum (PDB:5CQG), whose structure is
in complex with the highly specific inhibitor BIBR1532 [27]. Then, molecular docking simulations were
performed to elucidate the binding mode of active compound 5c.
2. Results and Discussion
2.1. Chemistry
Six flavonoid derivatives bearing glycosyl and triazole moieties were synthesized. The general
synthetic strategy for the formation of the target compounds is shown in Scheme 1. Kaempferol
(
1
), as the starting material, was protected by acetylation to give compound
synthesized via selective deprotection with compound and then allylation to obtain compound
Three azidosaccharide donors D1 D3 were prepared by the azidation of compounds C1 3, which
were obtained by bromination of B1 B3 with HBr-AcOH. The cyclization of with D1 D3 through
the classic “click-reaction” produced compounds 5a 5c, which were per deacetylated with a catalytic
amount of NaOMe in CH3OH to give compounds 6a–6c.
2. Compound 3 was
2
4.
–
–C
–
4
–
–

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OAc
OAc
OAc
OH
O
O
O
AcO
O
O
HO
O
O
HO
O
a
c
b
OAc
OAc
OAc
OH
OAc
OAc
OAc
OH
O
4
1
2
3
OH
OAc
O
O
O
O
O
O
d
e
O
N
O
N
OH
N
N
HO
N
OAc
AcO
N
OH
OAc
6a - 6c
5a - 5c
g
O
O
O
O
f
h
N3
OH
OAc
AcO
OH
AcO
AcO
HO
Br
C1-C3
A1-A3
B1-B3
D1-D3
OH
OH
HO
OH
O
OH
HO
O
A1
O
A2=
OH
A3=
HO
HO
OH
OH
OH
OH
Scheme 1. The synthesis route of compounds 5a
Et3N, DCM, 1 h, (b) imidazole, DMF, 0.5 h, (c) propargyl bromide, DMF, 1 h, (d) D1
–
5c and 6a
–
6c. Reagent and conditions: (a) Ac2O,
3, CuI, Et3N,
–
D
acetonitrile, 1 h, (e) MeOH/MeONa, 0.5 h, (f) Ac2O, Et3N, pyridine, 4 h, (g) HBr-AcOH, DCM, 2 h,
(h) NaN3, DMF, 4 h.
ThesecondseriesofflavonoidderivativescontainingN-acetylglucosaminesubstitutedbyacinnamoyl
group were synthesized, and the general synthetic route is shown in Scheme 2. Here, compound
could be efficiently obtained from intermediate via benzyl protection, followed by deacetylation to
give compound . Subsequently, treatment of with glycosyl bromide [16] in the presence of molecular
sieve led to the formation of , followed by acetylation to give 10. Then, to a solution of compound 10
in acetic acid, zinc powder was added in batches to selectively remove the Troc group to liberate 11
Then, compound 12 was generated by the debenzylation of 11 catalyzed with H2-Pd/C, followed by
condensation with substituted cinnamoyl chloride to give compounds 13a 13f. Compounds 14a 14f
were obtained by deacetylation of compounds 13a–13f with 1 mol/L NaOCH3 in CH3OH.
7
3
8
8
9
.
–
–
Scheme 2. The synthesis route of compounds 14a–14f. Reagent and conditions: (a) PhCH2Br, DMF,
2 h, (b) EtOH, 2 h, (c) glycosyl bromide, K2CO3, DMF, 5 h, (d) Ac2O, Et3N, DCM, 1 h, (e) Zinc dust,
glacial AcOH, 2 h, (f) H2/Pd-C, MeOH, 1 h, (g) substituted cinnamoyl chloride, pyridine, dry DCM,
15 min, (h) MeOH/MeONa, 0.5 h.

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2.2. Biological Activity
2.2.1. Telomerase Inhibitory Assay
According to previous reports, the exposed hydroxy group of the flavonoid is a functional group
that enhances its anticancer potential [ 13 14]. Herein, compounds 6a 6c 14a 14f were screened for
5,
,
–
,
–
their in vitro telomerase inhibitory activity against HeLa human cervical cancer cells via the telomere
repeat amplification protocol–polymerase chain reaction (TRAP–PCR) assay, and compound 5c was
chosen as a control. The results are shown in Figure 2. Unexpectedly, among them, compounds 5c
and 14e showed potent inhibitory activity against telomerase compared with baicalin as a reference.
Surprisingly, compound 5c showed the most effective activity against telomerase with IC50 < 50
(baicalin: IC50 > 100 M). The structure–activity relationship (SAR) of these flavonoid derivatives
demonstrated that compounds with acetyl protection displayed potential inhibitory activity.
µM
µ
Figure 2. Inhibitory effects of the compounds against telomerase by TRAP-PCR assay. (
compounds under different concentrations, baicalin as reference. ( ) Compounds 5c and 14e under
different concentrations. ( ) Compound 5c under different concentrations. [D: DMSO (solvent control);
A) The 10
B
C
+: contain cell lysate; -: no cell lysate].
2.2.2. Antiproliferation Assay
To further explore the structure–activity relationship (SAR) of these compounds and discover
the most potent compound, four flavonoid derivatives, 5c 6c 14b and 14e were evaluated for their
,
,
antiproliferative activity against human lung cancer cells (A549), human hepatoma cells (HepG2),
human cervical cancer cells (HeLa), human gastric cancer cells (MGC-803), and human gastric cancer
cells (SGC-7901) by comparison with 5-fluorouracil. The results are summarized in Figure 3 and Table 1.
As shown in Figure 3, these results suggested that compound 5c was an excellent anticancer agent
with potential broad-spectrum anticancer activity compared with the positive control 5-fluorouracil.
The anticancer activity of compound 5c was consistent with the SAR of the telomerase inhibitory
activity. It has been demonstrated that the potent anticancer activity of the synthetic compound 5c is
correlated with its telomerase inhibitory activity.

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Figure 3. Antiproliferative activities of compounds 5c, 6c, 14b, and 14e against A549, HepG2, HeLa,
MGC-803, and SGC-7901 cell lines.
Table 1. IC50 values (µM) of compounds 5c, 6c, 14b and 14e against cancer cell lines.
IC50 Values (µM)
Compound
Hela
HepG2
A549
MGC-803
SGC-7901
5c
6c
86.183 ± 2.444
88.149 ± 0.761
95.842 ± 0.926
82.992 ± 3.149
83.421 ± 1.593
>200
>200
>200
>200
>200
14b
14e
5-FU
163.971 ± 2.253
>200
110.164 ± 1.147
172.18 ± 1.881
>200
110.013 ± 0.603
155.323 ± 6.627
>200
105.712 ± 1.905
169.063 ± 1.676
>200
95.172 ± 2.618
156.527 ± 0.914
>200
96.011 ± 1.785
(a) The data represented the mean of three experiments done in triplicate and were expressed as means
IC50 value was defined as the concentration at which 50% survival of cells was observed. (c) 5-fluorouracil used as a
positive control.
±
SD. (b) The
Next, compound 5c was estimated on two normal human cell lines (Hacat and BEAS-2B). As shown
in Table 2, the IC50 values of compound 5c against the two normal human cells were greater than
200 µM, which proves that compound 5c owns its selective effect.
Table 2. IC50 values (µM) of compound 5c against human normal cell lines.
IC50 values (µM)
Compound
Hacat
BEAS-2B
5c
>200
>200
Hacat: human immortalized keratinocyte cells; BEAS-2B: human bronchial epithelial cells. Cells were incubated
with indicated compound for 48 h (means ± SD, n = 3).
2.3. Molecular Simulation Analyses
In 2018, the Kathleen Collins group first presented the cryo-electron microscopy structure of the
substrate-bound human telomerase holoenzyme, as well as the PDB coordinates [25]. However, there
is no cocrystallization of protein and ligand complexes available. In this report, to evaluate the binding
mode of active compound 5c compared with the inactive compound 6c, the active site of the protein
structure was confirmed via alignment with a similar protein discovered from T. castaneum (PDB:
5CQG), whose structure is in complex with the highly specific inhibitor BIBR1532. Then, the docked
complexes (5c, 6c, and BIBR1532) were chosen and submitted to perform a 100 ns molecular dynamics
(MD) simulation. The dynamic properties of the three complexes were then subjected to analysis
of the trajectory data obtained from the 100 ns MD simulations. The root-mean-square deviation

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(RMSD), root-mean-square fluctuation (RMSF), and protein–ligand contacts were used to evaluate
each system in the molecular dynamics studies, as shown in Figures 4–6, respectively. Meanwhile, the
superimposition of 5c and 6c with BIBR1532 in the active site of telomerase is presented in Figure 7.
As shown in Figure 4, during the simulation, the RMSD value of the BIBR1532/telomerase
complex configuration kept increasing until it stabilized at approximately 6.3 Å after 50 ns. Similarly,
the RMSD value of the 5c/telomerase complex finally reached an RMSD plateau at approximately
6.2 Å after 60 ns, although the complex underwent small fluctuations during the periods between
30 50 ns. These results indicated that the BIBR1532/telomerase and 5c/telomerase complexes reached
−
a steady state at the end of the MD simulations. Regrettably, the RMSD value of the 6c/telomerase
complex underwent fluctuations by a large margin until it stabilized at approximately 8.2 Å after 90 ns.
The root-mean-square fluctuation (RMSF) plots for BIBR1532 and compounds 5c and 6c can explain
the local changes in the protein chain during the MD simulations, which are shown in Figure 5. It was
obvious that the overall trend of the polylines was substantially similar between BIBR1532 and 5c
indicating that the compound 5c and BIBR1532 had similar stability and mode of interaction.
,
Figure 4. The root-mean-square fluctuation (RMSD) curve of BIBR1532/telomerase (gray), 5c/telomerase
(pink) and 6c/telomerase (blue) complexes.
Figure 5. The root-mean-square fluctuation (RMSF) curve of BIBR1532/telomerase (gray), 5c/telomerase
(red) and 6c/telomerase (blue) complexes.
As shown in Figure 6, four types of protein ligand interactions were monitored throughout the
−
MD simulations: hydrogen bonds, hydrophobic interactions, ionic interactions, and water bridges.
Analysis of the BIBR1532/telomerase complex trajectory data showed the existence of hydrogen bonds

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between Asn 421, Arg 433, Lys 437 of telomerase and the carbonyl and carboxylic acid groups of
BIBR1532. The hydrogen bonds in which Arg 433 participated accounted for 117% of the entire
MD trajectory, indicating that this residue formed more than one hydrogen bond. In addition, the
hydrogen bonds formed by Asn 421 and Lys 437 were found to account for 20% and 21% of the entire
MD trajectory. From the above analysis, we found that the hydrogen-bonding interactions between
the carbonyl group and Asn 421, Arg 433 and Lys 437 played significant roles in ligand binding.
For hydrophobic contacts, the interactions with Ala 438 were relatively stable and were observed in
72% of the MD simulations. Several weaker ionic contacts were also found in this complex with Arg
433 and Lys 437 (Figure 6A). From the trajectory analysis of the 5c/telomerase complex, we can see
that the kaempferol acetyl moiety of 5c can mimic the benzoic acid moiety of BIBR1532 and form
the key hydrogen bonds with Asn 421 and Lys 437, which accounts for 147% and 21%, respectively.
Meanwhile, Lys 437 and Phe 434 produced hydrophobic interactions with compound 5c, accounting
for 48% and 32%, respectively (Figure 6B). From the trajectory analysis of the 6c/telomerase complex,
it was not surprising to find that the binding mode changed substantially. Here, it was not hard to see
that the key binding interaction was hydrogen bonds between Lys 418 and Asn 424, which has much
imparity between the above results (Figure 6C).
Figure 6. Protein–ligand contact interaction over trajectory with respect to BIBR1532 (
(B) and compound 6c (C).
A), compound 5c
With deep analysis of the MD simulation results of 5c and 6c, compared with BIBR1532, the
interactions between 5c and the amino acid residues of telomerase were similar to those of BIBR1532.
Conversely, 6c showed substantial differences as discussed above. All of the above verified that the
docking results were accurate (Figures 7 and 8) and all the results were consistent with the active
in vitro data.

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Figure 7. Molecules interact with amino acids in the binding site. Docking of compounds BIBR1532
), 5c ) and 6c ) to the active site of telomerase. Superimposing of BIBR1532 (gray) and compound
5c (gold) (D) and 6c (blue) (E) in the active site of telomerase.
(A
(B
(C
Figure 8. Binding mode of compounds with telomerase. (
with telomerase. ( ) 3D ligand interaction diagram of compound 5c with telomerase. (
interaction diagram of compound 6c with telomerase. ( ) 2D ligand interaction diagram of BIBR1532
with telomerase. ( ) 2D ligand interaction diagram of compound 5c with telomerase. ( ) 2D ligand
A
) 3D ligand interaction diagram of BIBR1532
B
C
) 3D ligand
D
E
F
interaction diagram of compound 6c with telomerase.
3. Materials and Methods
3.1. Chemistry
Reagents (Energy Chemical, Shanghai, China) were used without further purification unless
otherwise specified. Solvents were dried and redistilled prior to use in the usual way. Analytical
TLC was performed using silica gel HF254 (Qingdao Haiyang Chemical, Qingdao, Shandong Province,
China). Preparative column chromatography was performed using silica gel H. Melting points were
obtained on a Büchi melting point B-540 apparatus. NMR spectra were recorded on a Bruker ARX

Molecules 2019, 24, 3180
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600 MHz spectrometer (Bruker, Zurich, Zürich, Swiss) with TMS as the internal standard. NMR spectra
were analyzed and interpreted using MestreNova (Mestrelab Research, Spain). HRMS were obtained
on a Bruker microTOF_Q spectrometer (Agilent, Santa Clara, CA, USA). The gel was stained with
SYBR Green I Nuclei A (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
A Telomerase PCR ELISA kit (Roche, Palo Alto, CA, USA) was used per the manufacturer’s instructions.
3.1.1. General Procedure for the Preparation of Compounds 5a–5c
To a solution of compound
4 (1 g, 2.22 mmol) and compounds D1–D3 (2.22 mmol) in 20 mL
of acetonitrile, cuprous iodide (0.845 g, 4.44 mmol) and triethylamine (0.925 mL, 6.66 mmol) were
added and the reaction mixture was stirred at room temperature for 1 h. The mixture was quenched
by the addition of saturated ammonium chloride solution, followed by extraction with ethyl acetate.
The organic layer was washed with brine, dried over anhydrous Na2SO4, filtered, and the solvent
was removed in vacuo. The residue was purified by silica gel column chromatography (petroleum
ether: ethyl acetate = 2:1) to afford compounds 5a–5c, the NMR spectrums of compounds 5a–5c were
contained in Supplementary Materials.
7-O-((1-(2,3,4,6-tetra-O-acetyl-
(
β
-d-glucopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-3,5,40-tri-O-acetyl-kaempferol
8.64 (s, 1H), 7.95
5a): Yellow solid, 87% yield, m.p. 173.5–175.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
(d, J = 8.5 Hz, 2H), 7.43 (d, J = 2.4 Hz, 1H), 7.40 (d, J = 8.5 Hz, 2H), 6.93 (d, J = 2.4 Hz, 1H), 6.39
(d, J = 9.1 Hz, 1H), 5.68 (t, J = 9.3 Hz, 1H), 5.56 (t, J = 9.5 Hz, 1H), 5.39 (d, J = 2.6 Hz, 2H), 5.19 (t,
J = 9.7 Hz, 1H), 4.38 (ddd, J = 10.2, 5.3, 2.3 Hz, 1H), 4.16–4.07 (m, 2H), 2.32 (d, J = 4.6 Hz, 9H), 2.03 (s, 3H),
1.99 (s, 3H), 1.96 (s, 3H), 1.76 (s, 3H). HRMS (ESI): calcd. for [M + H]+ C38H38N3O18+: 824.2150, found
824.2159.
7-O-((1-(2,3,4,6-tetra-O-acetyl-
5b): Yellow solid, 87% yield, m.p. 173.7–175.8 C; H-NMR (600 MHz, DMSO-d6)
β
-d-galactopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-3,5,40-tri-O-acetyl-kaempferol
◦
1
(
δ 8.63 (s, 1H),
7.95 (d, J = 8.8 Hz, 2H), 7.43 (d, J = 2.5Hz, 1H), 7.40 (d, J = 8.8 Hz, 2H), 6.92 (d, J = 2.5 Hz, 1H), 6.41
(d, J = 9.5 Hz, 1H), 5.69 (t, J = 9.5 Hz, 1H), 5.57 (t, J = 9.7 Hz, 1H), 5.39 (d, J = 2.6 Hz, 2H), 5.19 (t, J = 9.7 Hz,
1H), 4.38 (dd, J = 4.4, 2.3 Hz, 1H), 4.09 (m, 2H), 2.32 (d, J = 4.6 Hz, 9H), 2.03 (s, 3H), 1.99 (s, 3H), 1.96
(s 3H), 1.76 (s, 3H). HRMS (ESI): calcd. for [M + H]+ C38H38N3O18+: 824.2150, found 824.2201.
7-O-((1-(2,3,4-tri-O-acetyl-a-L-arabinopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-3,5,40-tri-O-acetyl-kaempferol
◦
1
(
5c): Yellow solid, 85% yield, m.p. 175.8–176.2 C; H-NMR (600 MHz, DMSO-d6) δ 8.55 (s, 1H),
8.00–7.91 (m, 2H), 7.45 (d, J = 2.4 Hz, 1H), 7.41–7.37 (m, 2H), 6.93 (d, J = 2.4 Hz, 1H), 6.18 (d, J = 9.2 Hz,
1H), 5.60 (t, J = 9.6 Hz, 1H), 5.41 (dd, J = 10.2, 3.6 Hz, 1H), 5.37 (s, 2H), 5.32 (dt, J = 3.4, 1.5 Hz, 1H),
4.21–4.16 (m, 1H), 4.05 (dd, J = 13.2, 1.9 Hz, 1H), 2.39–2.24 (m, 9H), 2.16 (s, 3H), 1.95 (s, 3H), 1.78 (s, 3H).
HRMS (ESI): calcd. for [M + H]+ C35H34N3O16+: 752.1939, found 752.1953.
3.1.2. General Procedure for the Preparation of Compounds 6a–6c
To a solution of compounds 5a–5c (1 g) in 30 mL of DCM-CH3OH (1:1), freshly prepared NaOMe
in MeOH solution (1.0 mol/L, 2.5 eq.) was added dropwise with stirring. After 0.5 h, the mixture
was neutralized with Dowex H+ resin to pH 7 and then filtered. The filtrate was concentrated and
purified by silica gel column chromatography (DCM:MeOH = 8:1) to afford compounds 6a
NMR spectrums of compounds 6a–6c were contained in Supplementary Materials.
–6c, the
7-O-((1-(
β
-d-glucopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-kaempferol (6a): Yellow solid, 45% yield, m.p.
12.49 (s, 1H), 10.16 (s, 1H), 9.51 (s, 1H), 8.49 (s, 1H),
175.8–176.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
8.08 (d, J = 8.9 Hz, 2H), 6.95 (d, J = 8.9 Hz, 2H), 6.92 (d, J = 2.2 Hz, 1H), 6.45 (d, J = 2.2 Hz, 1H), 5.57
(d, J = 9.2 Hz, 1H), 5.42 (d, J = 5.9 Hz, 1H), 5.29 (s, 1H), 5.28 (s, 2H), 5.16 (d, J = 5.2 Hz, 1H), 4.62
(t, J = 5.5 Hz, 1H), 3.78 (td, J = 9.1, 5.8 Hz, 1H), 3.69 (dd, J = 9.9, 5.7 Hz, 1H), 3.49–3.35 (m,4H). HRMS
(ESI): calcd. for [M + H]+ C24H24N3O11+: 530.1411, found 530.1423.

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7-O-((1-(
β
-d-galactopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-kaempferol (6b): Yellow solid, 47% yield, m.p.
12.49 (s, 1H), 10.13 (s, 1H), 9.51 (s, 1H), 8.43 (s, 1H),
175.8–176.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
8.09 (d, J = 8.5 Hz, 2H), 6.95 (d, J = 8.9 Hz, 2H), 6.92 (d, J = 2.8 Hz, 1H), 6.46 (d, J = 2.2 Hz, 1H), 5.52
(d, J = 9.1 Hz, 1H), 5.29 (s, 2H), 5.26 (d, J = 7.6 Hz, 1H), 5.02 (d, J = 5.7 Hz, 1H), 4.06 (td, J = 9.3, 5.9 Hz,
+
1H), 3.75 (dt, J = 20.0, 5.1 Hz, 2H), 3.59–3.43 (m,3H). HRMS (ESI): calcd. for [M + H]+ C24H24N3O11
:
530.1411, found 530.1364.
7-O-((1-(a-L-arabinopyranosyl)-1H-1,2,3-triazol-4-yl)-methyl)-kaempferol (6c): Yellow solid, 42% yield, m.p.
175.8–176.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
12.48 (s, 1H), 10.12 (s, 1H), 9.51 (s, 1H), 8.41 (s, 1H),
δ
8.08 (d, J = 8.9 Hz, 2H), 6.94 (d, J = 8.9 Hz, 2H), 6.91 (d, J = 2.2 Hz, 1H), 6.45 (d, J = 2.2 Hz, 1H), 5.45
(d, J = 9.1 Hz, 1H), 5.29 (s, 2H), 5.01 (d, J = 5.8 Hz, 1H), 4.79 (d, J = 4.5 Hz, 1H), 4.05 (td, J = 9.2, 5.8 Hz,
1H), 3.85–3.71 (m, 3H), 3.56 (ddd, J = 9.2, 5.6, 3.3 Hz, 1H), 3.16 (d, J = 4.7 Hz, 1H). HRMS (ESI): calcd.
for [M + H]+ C23H22N3O10+: 500.1305, found 500.1298.
3.1.3. General Procedure for the Preparation of Compounds 14a–14f
To a solution of compound 12 (0.4 g, 0.6 mmol) and pyridine (2.5 mL) in 10 mL dry DCM,
substituted cinnamoyl chloride (1.32 mmol) was added dropwise at room temperature, and the reaction
mixture stirred for 15 min. The organic layer was washed with water, saturated sodium hydrogen
carbonate, and brine, dried over anhydrous Na2SO4, filtered, and the solvent was removed in vacuo.
The residue was concentrated and purified by silica gel column chromatography (petroleum ether:
ethyl acetate = 5:1) to obtain compounds 13a–13f. To a solution of 13a–13f in 20 mL DCM-CH3OH
(1:1), a 1.0 mol/L of NaOMe in MeOH solution (2.5 eq) was added dropwise with stirring. After
0.5 h, the mixture was neutralized with Dowex H+ resin to pH 7 and then filtered. The filtrate was
removed in vacuo and the residue was purified by silica gel column chromatography (DCM:MeOH
= 8:1) to afford compounds 14a–14f, the NMR spectrums of compounds 14a–14f were contained in
Supplementary Materials.
3-O-(2-deoxy-2-((3-(4-fluorophenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14a): Yellow
: 12.65 (s, 1H), 11.11 (s, 1H),
solid, 45% yield, m.p. 175.8–176.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
10.38 (s,1H), 8.29 (d, J = 8.8 Hz, 1H), 8.11 (d, J = 8.8 Hz, 2H), 7.62 (dd, J = 8.5, 5.8Hz, 2H), 7.41
(d, J = 15.7 Hz, 1H), 7.25 (t, J = 8.9 Hz, 2H,), 6.92 (d, J = 7.5 Hz, 2H), 6.62 (d, J = 15.6 Hz, 1H), 6.49
(s, 1H), 6.23 (s, 1H), 5.70 (d, J = 8.4 Hz, 1H), 5.16 (d, J = 3.1 Hz, 2H), 4.42–4.34 (m, 1H), 3.89 (m, 1H),
3.57 (m, 1H), 3.43 (dd, J = 9.9, 6.1 Hz, 2H), 3.16 (d, J = 5.2 Hz, 2H). HRMS (ESI): calcd. for [M + H]+
C30H27FNO11+: 596.1568, found 596.1549.
3-O-(2-deoxy-2-((3-(4-chlorophenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14b): Yellow
12.66 (s, 1H), 10.93 (s, 1H),
solid, 35% yield, m.p. 198.2–199.7 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
10.25 (s, 1H), 8.28 (d, J = 9.2 Hz, 1H), 8.12 (d, J = 9.0 Hz, 2H), 7.60 (d, J = 8.6 Hz, 2H), 7.48 (d, J = 8.6 Hz,
2H), 7.41 (d, J = 15.8 Hz, 1H), 6.94–6.89 (m, 2H), 6.68 (d, J = 15.8 Hz, 1H), 6.46 (d, J = 2.1 Hz, 1H), 6.20
(d, J = 2.1 Hz, 1H), 5.71 (d, J = 8.4 Hz, 1H), 5.10 (t, J = 4.6 Hz, 2H), 4.32 (t, J = 5.6 Hz, 1H), 3.95–3.84
(m, 1H), 3.59–3.55 (m, 1H), 3.46–3.42 (m, 1H), 3.36 (s,1H), 3.13 (td, J = 6.6, 5.5, 3.5 Hz, 2H). HRMS (ESI):
calcd. for [M + H]+ C30H27ClNO11+: 612.1273, found 612.1306.
3-O-(2-deoxy-2-((3-(3-fluorophenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14c): Yellow
solid, 30% yield, m.p. 181.8–183.2 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ
: 12.66 (s, 1H), 10.42 (s, 2H),
8.30 (d, J = 9.6 Hz, 1H), 8.11 (d, J = 6.9 Hz, 2H), 7.47 (d, J = 1.4 Hz, 1H), 7.43 (d, J = 4.9 Hz, 2H), 7.40
(s, 1H), 7.21 (d, J = 16.3 Hz, 1H), 6.90 (d, J = 6.7 Hz,2H), 6.70 (d, J = 16.4 Hz, 1H), 6.42 (s, 1H), 6.17
(s, 1H), 5.71 (d, J = 8.0 Hz, 1H), 5.07 (d, J = 18.5 Hz, 2H), 4.35 (s, 1H), 3.89 (dd, J = 18.5, 9.7Hz, 1H), 3.58
(d, J = 11.3 Hz, 1H), 3.43 (s, 2H), 3.11 (s, 2H). HRMS (ESI): calcd. for [M
found 594.1418.
−
H]- C30H27FNO11−: 594.1412,

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3-O-(2-deoxy-2-((3-(3-hydroxyphenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14d): Yellow
solid, 35% yield, m.p. 198.2–199.7 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ: 12.64 (s, 1H), 11.16 (s, 1H),
10.42 (s,1H), 9.76 (s, 1H), 8.31 (d, J = 9.1 Hz, 1H), 8.10 (d, J = 8.9 Hz, 2H),7.31 (d, J = 15.7 Hz, 1H), 7.19
(t, J = 7.8 Hz, 1H), 6.97 (s, 2H), 6.95 (s,1H), 6.92 (s, 1H), 6.80 (d, J = 7.6 Hz, 1H), 6.59 (d, J = 15.8 Hz, 1H),
6.51 (d, J = 1.9 Hz, 1H), 6.25 (d, J = 1.9 Hz, 1H), 5.68 (d, J = 8.4 Hz, 1H), 5.19 (dd, J = 11.8, 5.3 Hz, 2H),
4.39 (t, J = 5.6 Hz, 1H), 3.88 (dd, J = 18.7, 9.2Hz, 1H), 3.55 (d, J = 5.1 Hz, 1H), 3.49–3.41 (m, 2H), 3.10
(s, 2H). HRMS (ESI): calcd. for [M + H]+ C30H28NO12+: 594.1612, found 594.1576.
3-O-(2-deoxy-2-((3-(4-trifluoromethylphenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14e):
Yellow solid, 35% yield, m.p. 178.8–180.1 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ: 12.66 (s, 1H), 10.28 (s, 2H),
8.31 (d, J = 9.2 Hz, 1H), 8.12 (d, J = 8.9 Hz, 2H), 7.91 (s, 1H), 7.88 (d, J = 7.8 Hz, 1H), 7.73 (d, J = 8.1 Hz,
1H), 7.67 (d, J = 7.8 Hz, 1H), 7.51 (d, J = 15.8 Hz, 1H), 6.90 (d, J = 8.9 Hz, 2H), 6.80 (d, J = 15.9 Hz, 1H),
6.41 (d, J = 1.9 Hz,1H), 6.16 (d, J = 1.9 Hz, 1H), 5.71 (d, J = 8.4 Hz, 1H), 5.12 (dd, J = 11.1, 3.7Hz, 2H), 4.34
(t, J = 5.2 Hz, 1H), 3.89 (dd, J = 18.6, 9.3 Hz, 1H), 3.58 (dd, J = 11.2,4.5 Hz, 1H), 3.45 (m, 2H), 3.12 (s, 2H).
HRMS (ESI): calcd. for [M + H]+ C31H27F3NO11+: 646.1536, found 646.1522.
3-O-(2-deoxy-2-((3-(4-methoxylphenyl)-1-oxo-2-propenyl)amino)-
β
-d-glucopyranosyl)-kaempferol (14f): Yellow
solid, 35% yield, m.p. 177.9–179.6 ◦C; 1H-NMR (600 MHz, DMSO-d6)
δ: 12.67 (s, 1H), 10.86 (s, 1H),
10.22 (s, 1H), 8.16 (d, J = 9.4 Hz, 1H), 8.12 (d, J = 8.7 Hz, 2H), 7.51 (d, J = 8.5 Hz, 2H), 7.36 (d, J = 15.7 Hz,
1H), 6.97 (d, J = 8.5 Hz, 2H), 6.90 (d, J = 8.7 Hz, 2H), 6.51 (d, J = 15.9 Hz, 1H), 6.43 (s, 1H), 6.18 (s, 1H),
5.70 (d, J = 8.4 Hz, 1H), 5.09 (d, J = 5.9 Hz, 2H), 4.32 (t, J = 5.0 Hz, 1H), 3.89 (dd, J = 18.5, 9.3 Hz, 1H),
3.78 (s, 3H), 3.58 (dd, J = 10.9, 4.8 Hz), 3.45–3.38 (m, 2H), 3.11 (s, 2H). HRMS (ESI): calcd. for [M + H]+
C31H30NO12+: 608.1768, found 608.1823.
3.2. Biological Activity
3.2.1. Telomerase Activity Assays
Compounds 5c, 6a–6c and 14a–14f were tested to search for inhibitors based on the structural
framework of natural products with telomerase activity by using the TRAP-PCR assay. The idea is
that if the compound does not inhibit telomerase activity at the labeled concentration, the number
and intensity of ladders of the lane should be comparable to the positive control lane (as there is no
inhibition, full-strength telomerase within cell lysate will lead to maximum number and intensity of
ladders). If there is no lysate added, only the internal control band will be visible. A lane with potent
inhibition will appear like the negative control lane. In detail, HeLa cells were first maintained in RPMI
1640 buffer, in which 10% fetal bovine serum was supplemented at 37 ◦C in a humidified atmosphere
containing 5% CO2. After trypsinization, 2
counted with a hemocytometer and collected in a tube, followed by incubation with baicalin and the
drugs at a series of concentrations. After 24 h, 200 L of CHAPS lysis buffer was added to resuspend the
×
105 HeLa cells in the logarithmic growth phase were
µ
cell pellet followed by incubation on ice for 30 min. The cell suspension was centrifuged at 14,000 rpm
for 20 min at 4 ◦C, and the cell lysate (supernatant) was transferred to a new tube. The TRAP reaction
was set up on ice in a 0.1 mL PCR tube. The reaction tube was incubated in 2720 Thermocycler (BioTek
Instruments, Winooski, VT, USA) (Applied Biosystem) at 30 ◦C for 30 min to undergo TS extension
followed by the 95 ◦C heat inactivation of telomerase for 5 min. Another reaction mix for the PCR was
set up and subsequently added to the reaction tube. PCR was then initiated at 94 ◦C for 30 s, 60 ◦C for
30 s, and 72 ◦C for 30 s. The PCR products were analyzed by 12.5% nondenaturing gel electrophoresis
in 0.5X TBE running buffer. The gel was stained with SYBR Green I Nuclei A (Invitrogen, Carlsbad, CA,
USA) according to the manufacturer’s instructions, and the results were obtained by autoradiography.
3.2.2. Cell Proliferation Assays
The antiproliferative activity of title compounds 5c
, 6c, 14b and 14e against the five tumor cell lines
(A549, HepG2, HeLa, MGC-803 and SGC-7901) as well as compound 5c against human normal cell

Molecules 2019, 24, 3180
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lines (Hacat and BEAS-2B) were evaluated using a standard CCK-8-based colorimetric assay. All the
above cell lines were provided by Jiangsu Keygen Biotech Co., Ltd. (Nanjing, China). In detail, target
tumor cells were grown to the log phase in RPMI 1640 buffer, in which 10% fetal bovine serum was
supplemented, and dilution to 5.5
Then each well of 96-well culture plates added 100
37 ◦C in a 5% CO2 atmosphere for 24 h for incubation before being subjected to the antiproliferation
assessment. Then, 100 L of a series of concentrations of drug-containing medium were dispensed
into wells to maintain final concentrations of 200, 100, 50, 25, 12.5, 6.25, 3.13, 1.56, and 0.78 M. Each
×
105 cells mL-1 (A549, 4
×
104 cells mL−1) with complete medium.
µL of the obtained cell suspension and placed in at
µ
µ
concentration was tested in triplicate, and 5-fluorouracil (5-FU) (Sigma–Aldrich, St. Louis, USA) was
used as the positive control. After 48 h of incubation, cell survival was determined by the addition of
10 µ
L of CCK-8 (BIOSHARP, 35002) working solution. After postincubation at 37 ◦C for 3 h, the plates
were vortexed for 10 min to remove the air bubbles. The optical absorbance was measured at 450 nm
with a microplate reader (BioTek Instruments, Winooski, VT, USA, EL-x800). The data represented
the mean of three independent experiments in triplicate and were expressed as mean
±
SD. The IC50
value was defined as the concentration at which 50% of the cells could survive. The IC50 values were
calculated by fitting with the three-parameter Hill equation, with SPSS Statistics 19 where y is percent
inhibition, x is inhibitor concentration, n is the slope of the concentration–response curve (Hill slope),
and Vmax is maximal inhibition from three independent assays.
xn
y = Vmax
(
)
n
IC50 +xn
3.3. Molecular Simulation Assays
3.3.1. Molecular Docking
All ligand structures were prepared by Maestro 9.0 within the Schrödinger package. The 3D
structures of all the studied compounds were created with Marvin sketch, and the initial lowest
energy conformations were calculated with LigPrep. For protein preparation, the crystal structure
coordinates of the human telomerase holoenzyme were obtained from the reference and then prepared
with the Protein Preparation Wizard. All hydrogen atoms were added. The protein structure was then
aligned with a similar protein discovered from another species to confirm the binding site (PDB:5CQG).
Subsequently, the OPLS_2005 force field was used to optimize the protein energy and eliminate steric
hindrance. For all dockings, the grid center was placed at the centroid of the ligand-binding site, and a
24
×
24
×
24 Å grid box size was used. All dockings were performed with Glide using the XP protocol.
The docking poses were analyzed by PyMOL [28].
3.3.2. MD Simulations
Compounds 5c, 6c and BIBR1532 were used to form three complexes with the protein refer to
the molecular docking results. By using the Desmond 2014.2 software (Schrodinger, Harrison, NYC,
USA) suite (D. E. Shaw Research), all-atom (OPLS3 force field) explicit water MD simulations for each
researched compound were performed via Maestro MD systems and were built with the use of the
highest-scoring docking pose. Specifically, the coordinate files of the human telomerase holoenzyme
were obtained from the reference. An orthorhombic box with a boundary distance of 10 Å was
generated to define the binding pocket. During the simulation, the Desmond default OPLS3 force field
was used. All the 100 ns simulations were run on our servers [29,30]. Moreover, the RMSD, RMSF and
ligand–protein interaction were monitored to determine the stability of the docking complexes.
4. Conclusions
In this study, twelve novel flavonoid derivatives were designed and synthesized, and ten were
evaluated as potential telomerase inhibitors. It was surprising that compound 5c showed high

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inhibitory activity against telomerase with an IC50 < 50
µM. Moreover, compound 5c exhibited potent
broad-spectrum anticancer activity against the A549, HepG2, HeLa, MGC-803 and SGC-7901 cell lines
in vitro. The binding modes of BIBR1532 and compound 5c to telomerase indicated that the conserved
residues Lys 437 and Asn 421 were important for ligand binding via hydrogen bonding interactions,
which could explain the SAR of these compounds and match the active in vitro data. These results
help the reasonable design of the more potent telomerase inhibitors based on the structural scaffolds of
natural products for cancer therapy.
Supplementary Materials: The 1H-NMR spectra of compounds 5a
–5c, 6a–6c and 14a–14f are available online at
Figures S1–S12.
Author Contributions: M.-S.C, Y.L. and P.-C.S. supervised the whole experiment and provided technical guidance.
Z.-F.F. designed and synthesized all of the novel compounds. S.-T.H. and C.H. assisted in biology research. Y.F.
and L.Z. assisted in the synthesis. R.W. and J.W. supervised and carried out molecular modeling experiments.
Funding: The authors gratefully acknowledge the National Natural Science Foundation of China (No. 81473087),
the Program for Liaoning Innovative Talents in University (LR2017043), and the Career Development Support
Plan for Young and Middle-aged Teachers in Shenyang Pharmaceutical University (ZQN2016005) for the
financial support.
Conflicts of Interest: The authors declare no conflict of interest.
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2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
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