Design, synthesis, and antibacterial evaluation of PFK-158 derivatives as potent agents against drug-resistant bacteria

Article abstract of DOI:10.1016/j.bmcl.2021.127980

Infections caused by antibiotic resistant bacteria are a major health concern throughout the world. It is well known that PFK-158 can enhance the antibacterial effect of polymyxin, but its own anti-bactericidal effect is rarely discussed. In order to inve

Full text of DOI:10.1016/j.bmcl.2021.127980

Bioorg. Med. Chem. Lett. 41 (2021) 127980
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design, synthesis, and antibacterial evaluation of PFK-158 derivatives as
potent agents against drug-resistant bacteria
Wei Wanga, You-Wen Zhangb, Shang-Jiu Hub, Wei-Ping Niub, Guo-Ning Zhangb, Mei Zhub,
,
,
,*
Ming-Hua Wangb, Fan Zhanga *, Xue-Mei Lic *, Ju-Xian Wangb
a School of Pharmacy, Jinzhou Medical University, Jinzhou 121001, PR China
b Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
c Center for Drug Evaluation, National Medical Products Administration, Beijing 100022, PR China
A R T I C L E I N F O
A B S T R A C T
Keywords:
Infections caused by antibiotic resistant bacteria are a major health concern throughout the world. It is well
known that PFK-158 can enhance the antibacterial effect of polymyxin, but its own anti-bactericidal effect is
rarely discussed. In order to investigate the anti-bactericidal effect of PFK-158 and its derivatives, PFK-158 and
35 derivatives were designed, synthesized, and evaluated for their antibacterial activities. Compounds A1, A3,
A14, A15 and B6 exhibited potent antibacterial effect against both clinical drug sensitive and resistant Gram-
positive bacteria, and they are 2–8 folds more potent than levofloxacin against Methicillin-resistant staphylo-
coccus epidermidis (MRSE). A significant synergistic effect of these compounds and polymyxin against drug-
resistant Gram-negative bacteria, which is similar to PFK-158 was also observed. The result can provided a
new and broader prospect for the development of new medicine against drug-resistant bacteria.
PFK-158 derivatives
Synthesized
Antibacterial effect
Drug-resistant bacteria
Since the 1950 s, research on antibiotics progressed rapidly and
dozens of drugs have been developed.1–2 However, due to the abuse of
antibiotics, many bacteria have developed resistance to most of the
antibiotics including vancomycin. And the rapid emergence of antibiotic
resistance makes infectious diseases become a worldwide medical
challenge.3–5 It is estimated that by 2050, at least 10 million people will
die each year from antibiotic resistance.6–7 Therefore, it is urgent to
explore and develop novel antibiotics to overcome this problem.
PFK-158 is a small molecule inhibitor of PFKFB3, which inhibits the
up-regulation of glycolysis in most cancer cells and shows anti-tumor
activity.8–14 PFK-158 can also enhance the effect of polymyxin against
carbapenem resistant Enterobacteriaceae, but itself shows no antibacte-
rial effect on this Gram-negative bacteria.15
of Gram-negative bacteria16–20. So the quaternary ammonium salt (se-
ries C) was also designed and synthesized to enhance the antibacterial
activity against Gram-negative bacteria by increasing membrane
permeability.(see in Fig. 1)
R: -CF3 or -H. M: M-ring of quinoline. P: P-ring of quinoline. X1: CH or
N at different positions on the quinoline ring, When X1 is in M ring, it
may be at the position of m1 or m2. X2: CH or N
The synthetic schemes of the target product A-C are summarized in
Scheme 1. Briefly, the α,β-unsaturated carbonyl in PFK-158 series A and
B were constructed by a aldol condensation of the corresponding alde-
hydes and ketones. If not specified, the aldehydes and ketones were
purchased commercially. Some of them were synthesized from the
commercial available substituted aniline and the specific process can be
find in the experiment section. The quaternary ammonium salt (series C)
were obtained by the methylation of the corresponding compounds A
and B using methyl iodide. The structure of target products were shown
in figure 2 and they were fully characterized by both NMR and high
resolution mass spectrometry.
In order to investigate whether PFK-158 and its derivatives have
antibacterial effect, 36 derivatives (including PFK-158) were designed
and synthesized by changing the position of trifluoromethyl on quino-
line ring, position of N-atom on pyridine ring, removing N-atom from the
quinoline ring or the pyridine ring(series A) and reversing the
α
,β-unsaturated carbonyl group in PFK-158 structure(series B). Litera-
MIC agar method was used to evaluate their antibacterial activities of
PFK-158 and its derivatives in vitro. Levofloxacin was used as a positive
control. As shown in table 1, most of the compounds in series A and B
ture reports have shown that quaternary ammonium salts can increase
the permeability of small molecule compounds to the outer membrane
* Corresponding authors.
E-mail addresses: zhangfan720@jzmu.edu.cn (F. Zhang), lixm@cde.org.cn (X.-M. Li), wangjuxian@imb.pumc.edu.cn (J.-X. Wang).
https://doi.org/10.1016/j.bmcl.2021.127980
Received 7 November 2020; Received in revised form 6 March 2021; Accepted 16 March 2021
Available online 22 March 2021
0960-894X/© 2021 Published by Elsevier Ltd.

W. Wang et al.
Bioorganic & Medicinal Chemistry Letters 41 (2021) 127980
R: -CF3 or -H. M: M-ring of quinoline. P: P-ring of quinoline. X1: CH or N at different positions
on the quinoline ring, When X1 is in M ring, it may be at the position of m1 or m2. X2: CH or N
Fig. 1. Chemical structure of target products.
Scheme 1. General synthetic scheme of target compounds. Reagents and conditions. a. (2E)-but-2-enal, 6 N
HCl, reflux, 2 h. b. Argon, 1,4-dioxane, SeO2, 80 ℃, 2 h. c. pyridine-2/3/4-carbaldehyde or benzaldehyde, TEA,
isopropanol, rt, 4 h, reflux, 16 h. c′. pyridine-2/3/4-carbaldehyde or benzaldehyde, methanol/water (v/v =
1:1), Na2CO3, reflux, 2 h. c′′. pyridine-2/3/4-carbaldehyde or benzaldehyde, Microwave irradiation, molecular
sieve, 135℃, 2 h. d. CH3MgBr, THF, Argon, 0℃, 1 h. e. CH3I, acetone, reflux, 8 h.
exhibit moderate to potent inhibition to the Gram-positive bacteria,
including methicillin-sensitive and resistant staphylococcus epidermidis,
staphylococcus aureus, and vancomycin-sensitive and resistant Entero-
coccus. The derivatives in series C show weaker inhibitory activity than
that of series A and B. And all of the target compounds show no inhib-
itory effect on Gram-negative bacteria. Interestingly, the MIC values of
these derivatives were similar against the methicillin and vancomycin
sensitive and the corresponding resistant Gram-positive bacteria. This
means that the resistance mechanism currently existing in bacteria to
methicillin and vancomycin does not affect PFK-158 and its derivatives.
MSSE: Methicillin-sensitive Staphylococcus epidermidis ATCC12228;
MRSE: Methicillin-resistant Staphylococcus epidermidis 16-5; MSSA:
Methicillin-sensitive Staphylococcus aureus ATCC 29213; MRSA:
Methicillin-resistant Staphylococcus aureus ATCC33591; VSE:
Vancomycin-sensitive Enterococcus ATCC 29212; VRE: Vancomycin-
resistant Enterococcus ATCC 51299; ESBLs(-): Extended-spectrum beta-
2

W. Wang et al.
Bioorganic & Medicinal Chemistry Letters 41 (2021) 127980
Fig. 2. Structure of target products A-C.
Table 1
In vitro antibacterial activity of 36 compounds.
Target
MIC (μg/mL)
Products
A1
MSSE
2
MRSE
4
MSSA
1
MRSA
1
VSE
>128
32
VRE
>128
32
ESBLs(+)
>128
>128
>128
>128
>128
>128
>128
>128
>128
>32
ESBLs(-)
>128
>128
>128
>128
>128
>128
>128
>128
>128
>32
NDM-1(+)
>128
>128
>128
>128
>128
>128
>128
>128
>128
>32
CRAB
128
A2
2
2
2
2
128
A3
2
2
1
1
>128
32
>128
16
128
A4
8
8
8
8
128
A5
16
32
16
32
8
32
32
128
A6
8
8
8
32
32
128
A7
16
16
8
8
32
32
128
A8
8
8
16
16
8
32
32
128
A9
8
8
8
32
32
128
A10
A11
A12
A13
A14
A15
A16
A17
A18
A19
A20
A21
A22
A23
A24
A25
A26
B1
32
32
32
32
2
32
32
>32
>32
>32
>32
>32
128
2
4
2
2
8
>32
>32
>32
1
1
2
1
4
4
>32
>32
>32
1
2
2
2
4
4
>32
>32
>32
1
2
1
1
4
4
>32
>32
>32
4
4
1
2
>128
>128
128
>128
>128
>128
>128
>128
>64
>128
>128
>64
>32
>32
32
128
>128
128
>128
>128
>128
>128
>128
>64
>128
>128
>64
>32
>32
>32
>128
>128
8
>128
>128
>128
>128
>128
>128
>128
>128
>64
>128
>128
>128
>128
>128
>128
>128
>128
>64
>128
>128
>128
>128
>128
>128
>128
>128
>64
>128
2
>128
4
>128
2
>128
2
>128
>128
>128
>128
>128
>128
>128
>64
>128
>128
>64
>32
>32
>32
>128
>128
>128
>128
>128
>128
>128
2
>128
>128
>128
>128
>128
>64
4
>128
>128
>128
>128
>128
>64
8
>128
>128
>128
>128
>128
>64
8
>128
>128
>128
>128
>128
>64
8
>128
>128
>64
>128
>128
>64
>128
>128
>64
16
16
32
32
32
16
32
2
16
32
32
>32
>32
2
>32
>32
4
>32
>32
4
>32
>32
>32
B2
>32
>32
>32
B3
>32
>32
>32
B4
4
8
8
4
>128
>128
8
>128
>128
>128
>128
>128
>128
>128
0.03
>128
>128
>128
>128
>128
>128
>128
0.12
>128
>128
>128
>128
>128
>128
>128
16
B5
4
16
8
8
B6
1
2
1
1
C1
>128
64
>128
64
>128
64
>128
32
64
128
0.12
>128
128
>128
>128
1
>128
128
>128
>128
0.5
C2
C3
128
64
128
>128
8
128
128
0.12
C4
Levofloxacin
0.12
3

W. Wang et al.
Bioorganic & Medicinal Chemistry Letters 41 (2021) 127980
Fig. 3. A selected compounds with antimicrobial activity against staphylococcus.
Table 2
Cytotoxicity of 9 target compounds.
Compd
A1
A2
A3
A11
21.1
A12
18.5
A13(PFK-158)
15.0
A14
9.8
A15
10.2
B3
IC50 M)
(
μ
45.4
>50
43.1
11.2
lactamase bacteria Escherichia coli-negative bacteria ATCC 25922; ESBLs
(+): Extended-spectrum beta-lactamase bacteria Escherichia coli-positive
bacteria ATCC 35218; NDM-1(+): New Delhi metallo- beta-lactamase 1-
positive Escherichia col ATCC 2469; CRAB: Carbapenem-resistant A.
baumannii Acinetobacter 16–33.
negative isolate Enterobacter cloacae D01, these compounds could
decreased their MIC values to a susceptible level by 128-fold.
The structure–activity relationship studies show that the nitrogen
atoms in PFK-158 derivatives have made a great contribution to their
antibacterial activity. The nitrogen atom in the quinoline ring is neces-
sary for antibacterial activity and when it is replaced with –CH– lead to
the completely loss of the activity (A20-21 vs A4-12). When the nitrogen
atom in the pyridine ring it is replaced with –CH–, activity also
decreased (A16 vs A13-15, A17 vs A11-12). After the replacement of
quinoline ring with naphthalene, A20-21 completely loss of the activity,
Among all the target compounds, 11 compounds showed effective
antibacterial activity against Gram-positive bacteria in vitro, especially
A1, A3, A14, A15, and B6 exhibited the most potent activity against
Methicillin-sensitive staphylococcus aureus (MSSA) with a MIC value of 1
μ
g/mL.
The antibacterial activity of compounds A2, A11-A13, A17 and B3 is
but when the α,β-unsaturated carbonyl group was reversed subsequently
2–8 folds superior to the control drug, levofloxacin, against Methicillin-
resistant Staphylococcus epidermidis (MRSE) (Fig. 3) which may provide a
new structures for the discovery of drug against resistant bacteria.
Besides, 9 derivatives of PFK-158 with good anti-bacterial activity
were selected for the test of their cytotocity. The results was shown in
Table 2. It can be seen that the IC50 values of A1, A2, A3, A11, and A12
compounds B4-6 exhibit potent Gram-positive bacteria inhibitory effect
again. However, for compounds A13-15, the reversal of the
α
,β-unsaturated carbonyl group lead to a decreased activity (A13-15 vs
B1-3). The trifluoromethyl on quinoline P ring also contributes to its
anti-bacteria effect, but the position is not so important (A1-A3 vs A13-
A15). The reason may be that the conjugation effect between quinoline
N-atom and its phenyl ring weakens the electron absorption-inductive
effect of trifluoromethyl. The position of the nitrogen atom of the
quinoline ring affects its antibacterial activity: compounds with a ni-
trogen atom at position m1 show more potent activity than that of at
position m2 (A4-A6 vs A10-A12); compounds with a nitrogen atom in
ring M show more potent activity than that of in ring P (A7-A9 vs A10-
A12). The position of nitrogen atom in the pyridine ring also effect on
the activity of the target compound, for example compounds with ni-
were all greater than that of A13 (PFK-158) (IC50 = 15.0 μM), indicating
that these 5 compounds were more promising for the development as
antibacterial drugs. Among them, compounds A1, A2, A3 showed little
cytotoxicity, especially compound A2, whose IC50 values is>50 μM.
The cells used in the experiment are A549; A549:Adenocarcinoma
human alveolar basal epithelial cells
To explore whether these PFK-158 derivatives can enhance the
antibacterial effect of polymyxin against carbapenem-resistant entero-
bacteriaceae bacteria when combined with polymyxin. PFK-158 de-
rivatives A11, A12, A13(PFK158), and B6 were selected to conduct a
checkerboard assay. Encouragingly, the results (Table 3) showed that all
these four compounds had a significant synergistic effect when com-
bined with polymyxin, and their fractional inhibitory concentration
indices (FICIs) of the polymyxin-based combination were all below 0.5.
The synergistic effect of A11, A12, B6 and polymyxin was equivalent to
that of A13 (PFK-158) and polymyxin. The MIC values against all
colistin-resistant bacteria, regardless of whether they were mcr-1 posi-
trogen atom in the ortho position of the
exhibit better activity than that of in the meta or para position, which
may be due to the formation of conjugation with the ,β- unsaturated
α,β- unsaturated carbonyl group
α
carbonyl group in the ortho position (B4-B5 vs B6). In addition, qua-
ternization has no or even negative contribution to the anti-bacteria
activity in the PFK-158 derivatives (C1-4 vs A21, 14, 20 and B5).
In conclusion, we have designed and synthesized a series of PFK-158
derivatives and evaluated their antibacterial activities in vitro. The re-
sults shows that most of the compounds in series A and B exhibit mod-
erate to potent inhibition to the Gram-positive bacteria, Among these
tive or negative isolate, could be decreased to 2 μg/ml. For the mcr-1
4

W. Wang et al.
Bioorganic & Medicinal Chemistry Letters 41 (2021) 127980
compounds, 11 derivates have potent inhibitory effect on tested Gram-
positive bacteria, especially A1, A3, A14, A15, and B6, and their MIC
values were 1 μg/mL against Methicillin-sensitive staphylococcus aureus
(MSSA). Compounds A2, A11-A13, A17 and B3 show a 2–8 folds more
potent anti-bacteria effect Methicillin-resistant staphylococcus epi-
dermidis(MRSE) than levofloxacin. Besides, representative compounds
A1, A2, A3 show little toxicity in the cytotoxicity assay. A significant
synergistic effect of these compounds and polymyxin on against drug-
resistant Gram-negative bacteria, which is similar to PFK-158 was also
observed. These results can provide a new structures for the discovery of
drug against resistant bacteria.
Although literature reported the quaternization can help to broaden
the antibacterial spectrum to the Gram-negative bacteria through in-
crease the permeability of small molecule compounds to the outer
membrane, the quaternization of PFK-158 derivatives does not make
any contribution to their antibacterial effect.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Acknowledgements
The research was supported by the National Natural Science
Foundation of China (grant number 81703366), National Science &
Technology Major Project “Key New Drug Creation and
Manufacturing Program”, China(Numbers: 2019ZX09201001-003-
007, 2019ZX09721001-004-006), CAMS innovation fund for Medi-
cal Sciences (grant numbers 2016-I2M-1-011 WYC, and 2016-I2M-3-
014 WJX), and Natural Science Foundation of Liaoning Province
(2019-ZD-0834).
Appendix A. Supplementary data
Copies of 1H NMR, 13C NMR and HRMS, method details of the target
compounds described in this article were provided. Supplementary data
to this article can be found online at https://doi.org/10.1016/j.bmcl.20
21.127980.
References
1
Cui WP, An LH, Ma CC, et al. Novel azithoromycin derivatives with the C-4” bisamide
side chains: synthesis and biological evaluation against Gram-positive bacteria.
J Antibiot. 2012;65(7):383.
2
3
Singh SB, Young K, Silver LL. What is an “Ideal” Antibiotic? Discovery Challenges
and Path forward. Biochem Pharmacol. 2017;133:63–73.
Zhang E, Qin SS, Xu SM, Wang MM, Zhao E, Bai PG, Zhou MM, Wang P, Wang S,
Wang Y, Cui DY, Hua YG, Liu HM. Chalcone derivatives with antimicrobial activity.
CN105622492A, 2016-06-01.
4
5
Zhang E, Qin SS, Chu WC, Bai PP, Yang ZQ, Cui DY, Hua YG, Wang MM, Wang YN,
Liu HM. Quaternary ammonium chalcone derivatives with antimicrobial activity,
preparation method and application. CN107235894B, 2020-04-03.
Li Y-G, Wang J-X, Zhang G-N, et al. Design, synthesis, and biological activity
evaluation of a series of pleuromutilin derivatives with novel C14 side chains. Bioorg
Med Chem Lett. 2020;30(7):126969. https://doi.org/10.1016/j.bmcl.2020.126969.
De Kraker ME, Stewardson AJ, Harbarth S. Will 10 million people die a year due to
antimicrobial tence by 2050? PLoS Med. 2016;13(11), e1002184.
Guan DL. Design, synthesis and antimicrobial activity of new glycopeptide and
lipopeptide antibiotics. University of Chinese Academy of Sciences (Shanghai
Institute of Pharmaceutical Research, Chinese Academy of Sciences), 2019, 07:297.
Boutard N, Białas A, Sabiniarz A, et al. Synthesis of amide and sulfonamide
substituted N-aryl 6-aminoquinoxalines as PFKFB3 inhibitors with improved
physicochemical properties. Bioorgan Med Chem Lett. 2019;29(4):646–653.
Brooke DG, van Dam EM, Watts CKW, et al. Targeting the Warburg Effect in cancer;
relationships for 2-arylpyridazinones as inhibitors of the key glycolytic enzyme 6-
phosphofructo-2-kinase/2,6-bisphosphatase 3 (PFKFB3). Bioorgan Med Chem. 2014;
22(3):1029–1039.
6
7
8
9
¨
10 Staehler M, Haseke N, Schoppler G, et al. Carcinoma of the collecting ducts of Bellini
of the kidney: adjuvant chemotherapy followed by multikinase-inhibition with
sunitinib. Eur J Med Res. 2008;13(11):531–535.
5

W. Wang et al.
Bioorganic & Medicinal Chemistry Letters 41 (2021) 127980
11 Clem BF, O’Neal J, Tapolsky G, et al. Targeting 6-phosphofructo-2-kinase (PFKFB3)
as a therapeutic strategy against cancer. Mol Cancer Ther. 2013;12(8):1461–1470.
12 Lu L, Chen Y, Zhu Yu. The molecular basis of targeting PFKFB3 as a therapeutic
strategy against cancer. Oncotarget. 2017;8(37):62793–62802.
16 Richter MF, Drown BS, Riley AP, et al. Predictive compound accumulation rules yield
a broad-spectrum antibiotic. Nature. 2017;545(7654):299–304.
17 Richter MF, Hergenrother PJ. The challenge of converting Gram-positive-only
compounds into broad-spectrum antibiotics. Ann N Y Acad Sci. 2019;1435(1):18–38.
18 Ho H, Miu A, Alexander MK, et al. Structural basis for dual-mode inhibition of the
ABC transporter MsbA. Nature. 2018;557(7704):196–201.
13 Zhu W, Ye L, Zhang J, et al. PFK15, a Small Molecule Inhibitor of PFKFB3, Induces
Cell Cycle Arrest, Apoptosis and Inhibits Invasion in Gastric Cancer. PLoS ONE. 2016;
11(9):e0163768.
19 Alexander MK, Miu A, Oh A, et al. Disrupting Gram-negative bacterial outer
membrane biosynthesis through inhibition of the lipopolysaccharide transporter
MsbA. Antimicrob Agents Chemother. 2018;62(11). https://doi.org/10.1128/
AAC.01142-18.
14 Boyd S, Brookfield JL, Critchlow SE, et al. Structure-Based Design of Potent and
Selective Inhibitors of the Metabolic Kinase PFKFB3. J Med Chem. 2015;58(8):
3611–3625.
15 Zhang Y, Wang X, Li X, et al. Synergistic effect of colistin combined with PFK-158
against colistin-resistant Enterobacteriaceae. Antimicrob Agents Chemother. 2019;63
(7). https://doi.org/10.1128/AAC.00271-19.
20 Imai Yu, Meyer KJ, Iinishi A, et al. A new antibiotic selectively kills Gram-negative
pathogens. Nature. 2019;576(7787):459–464.
6