Design and synthesis of hybrids of diarylpyrimidines and diketo acids as HIV-1 inhibitors

Article abstract of DOI:10.1016/j.bmcl.2017.03.009

Based on the strategy of molecular hybridization, diketo acid fragment as a classical phamacophore of integrase inhibitors was introduced to reverse transcriptase inhibitors diarylpyrimidines to design a series of diarylpyrimidine-diketo acid hybrids (DAPY-DKAs). The target molecules 10b and 11b showed inhibitory activities against WT HIV-1 with EC₅₀ values of 0.18?μM and 0.14?μM, respectively. And the results of molecular docking demonstrated the potential binding mode and revealed that the DKA moiety and its ester could both be tolerated in the nonnucleoside binding site (NNBS) of HIV-1 RT.

Full text of DOI:10.1016/j.bmcl.2017.03.009

Accepted Manuscript
Design and synthesis of hybrids of diarylpyrimidines and diketo acids as HIV-1
inhibitors
Ping Xue, Huan-Huan Lu, Yuan-Yuan Zhu, Xiu-Lian Ju, Christophe
Pannecouque, Xiao-Jiao Zheng, Gen-Yan Liu, Xiu-Lan Zhang, Shuang-Xi Gu
PII:
S0960-894X(17)30244-5
DOI:
http://dx.doi.org/10.1016/j.bmcl.2017.03.009
BMCL 24761
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
4 February 2017
22 February 2017
6 March 2017
Please cite this article as: Xue, P., Lu, H-H., Zhu, Y-Y., Ju, X-L., Pannecouque, C., Zheng, X-J., Liu, G-Y., Zhang,
X-L., Gu, S-X., Design and synthesis of hybrids of diarylpyrimidines and diketo acids as HIV-1 inhibitors,
Bioorganic & Medicinal Chemistry Letters (2017), doi: http://dx.doi.org/10.1016/j.bmcl.2017.03.009
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Design and synthesis of hybrids of diarylpyrimidines and diketo acids
as HIV-1 inhibitors
Ping Xue a, Huan-Huan Lua, Yuan-Yuan Zhu b,*, Xiu-Lian Ju a, Christophe Pannecouque c, Xiao-Jiao Zheng a,
Gen-Yan Liu a, Xiu-Lan Zhang a, Shuang-Xi Gu a,*
a
Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering &
Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
b School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China
c
KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega
Institute for Medical Research, B-3000 Leuven, Belgium
*Corresponding Authors:
E-mail: yyzhu531@163.com (Y.-Y. Zhu); shuangxigu@163.com (S.-X. Gu).
Abstract: Based on the strategy of molecular hybridization, diketo acid fragment as a classical
phamacophore of integrase inhibitors was introduced to reverse transcriptase inhibitors
diarylpyrimidines to design a series of diarylpyrimidine-diketo acid hybrids (DAPY-DKAs). The
target molecules 10b and 11b showed inhibitory activities against WT HIV-1 with EC50 values of
0.18 µM and 0.14 µM, respectively. And the results of molecular docking demonstrated the
potential binding mode and revealed that the DKA moiety and its ester could both be tolerated in
the nonnucleoside binding site (NNBS) of HIV-1 RT.
Key word: HIV-1 inhibitors; AIDS; reverse transcriptase; integrase; molecular hybridization;
diarylpyrimidines; diketo acids
Reverse transcriptase (RT) and integrase (IN) both play vital roles in the process of HIV-1
replication.1 NNRTIs has become a mainstay of highly active antiretroviral therapy (HAART)2
and been used as the first-line drugs against HIV-1 due to their unique antiviral potency, high
specificity and low cytotoxicity.3, 4, 5 Among them, TMC125 and TMC278 (Fig. 1) as NNRTIs
characterized by their DAPY structures, have been paid extensive attention for their excellent
activities against both WT HIV-1 and mutant strains.6, 7, 8 And in recent years, some compounds
were discovered to exhibit potent activities against a recombinant IN, however, the majority of
these compounds did not show antiviral activity in cellular level, and the remaining compounds
10
generally exhibited high cytotoxicity.9,
Among them, β-diketo acid derivatives (DKAs)
displayed excellent inhibitory activities against both recombinant IN and HIV-1 strains.11 The
three FDA-approved INIs, raltegravir, dolutegravir and elvitegravir, are all derived from classical
diketo acids.9 So, it is rational to design a series of diarylpyrimidine-diketo acids hybrids to get the
better HIV-1 inhibitions.
13
In this work, we adopted molecular hybridization strategy12,
to design a series of

diarylpyrimidine-diketo acids hybrids (Fig. 2), in which the introduction of DKA fragment was
expected to improve the anti-HIV-1 activities. The reported crystal structures of the HIV-1
RT/DAPY complexes 6 have verified the existence of π-π stacking interaction between the left aryl
ring and aromatic amino acid residues such as Tyr181, Tyr188, Phe227 and Trp229 in hydrophoic
pockets. Because strong electron withdrawing ability of the fragment of diketo acid will reduce
the left wing aromatic ring electron density and π-π stacking interaction between the left aryl ring
and aromatic amino acid residues. Therefore, the diketo acid esters 10a and 10b were designed in
order to better keep the hydrophobicity of target molecules.
Figure 1. The structure of DAPYs inhibitors (1 and 2) and DKAs inhibitor (3)
Figure 2. Design of diarylpyrimidine-diketo acid hybrids through molecular hybridization
The newly designed compounds were synthesized by an expeditious method as depicted in
Scheme 1. The intermediate 7 was synthesized through a three-step reaction according to our
previously reported steps.14, 15 And intermediates 9a-b were prepared from 8a-b and diethyl
oxalate in the presence of THF and NaH, and the 10a-b were obtained via a nucleophilic
substitution of 7 with 9a-b using Cs2CO3 as base in DMSO. Finally, 9a-b and 10a-b were subject
to a simple hydrolysis to get the corresponding compounds 11a-b and 12a-b.

Scheme 1. Synthesis of target molecules Reagents and conditions: (a) MeI, NaOH, H2O, rt, 24 h;
(b) 4-cyanoaniline, 180–190℃, 10 h; (c) POCl3, reflux, 0.5 h; (d) diethyl oxalate, NaH, THF,
reflux, 20 min; (e) Cs2CO3, DMSO, 110℃, 40 min; (f) THF, CH3OH, NaOH, rt, 2.5 h; (g) THF,
CH3OH, NaOH, rt, 2 h
Table 1. Activities against WT HIV-1 and mutants in MT-4 cell and HIV-1 RT inhibitory activities
HIV-1 EC50 (µM)
K103N RES056
CC50 (µM)
SI
IC50 (µM)
RT
Compd
HIV-1 WT HIV-1 WT
WT
>466
>356
0.19
-
-
-
466
356
18
<1
<1
-
9a
9b
-
-
10
>18
>14
>42
>9
-
95
5.864
6.059
25.208
5.930
-
10a
0.18
>14
>42
38
14
78
10b
0.23
42
183
71
11a
0.14
10
11b
>600
>528
0.084
0.0054
0.0033
0.0077
0.16
-
>600
528
>15
>9
1
12a
-
-
<1
-
12b
Nevirapine
Efavirenz
Etravirine
Azidothymidine
3b
>15
0.17
0.004
0.016
-
>15
0.17
0.03
0.01
-
>179
>1717
>1391
>971
>61
1.528a
0.022a
0.011a
-
>5
>7
>10
>100
a Ref. 15
b Ref. 16
The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) method was used
18
for biological evaluation.17,
Compounds 10a-b, 11a-b, 12a-b were evaluated for their

cytotoxicity and anti-HIV activities in MT-4 cells infected with wild-type (WT) HIV-1 (strain
IIIB), common HIV-1 mutants [L100I, K103N, Y181C, Y188L, E138K, F227L+V106A,
K103N+Y181C (RES056)], as well as HIV-2 (strain ROD), along with four FDA-approved drugs:
nevirapine, efavirenz, etravirine (TMC125), azidothymidine as reference drugs. And also, the
activities of DKA inhibitor 3was also cited as reference16. The results were summarized in Table 1,
which was expressed by CC50 (cytotoxic concentration that reduces 50% normal cell), EC50
(concentration requires to attain 50% HIV-1 replication), SI (selectivity index, CC50/EC50 ratio)
and IC50 (concentration requires to inhibit 50% HIV-1 RT polymerase activity) values.
Intermediates 9a-b and their hydrolysis products 12a-b were inactive against WT and
drug-resistant mutant strains. All hybrid molecules showed activities against WT HIV-1 strain
closed to the activities of DKA inhibitor 3 with EC50 values ranged from 0.14 to 0.23 µM. Among
them, the most potent compound 11b displayed good activity with an EC50 of 0.14 µM. And the
trend of the potency seems to be as follows: meta-substitution > para-substitution (10b > 10a and
11b > 11a). Unfortunately, none of these inhibitors exhibited activities against double mutant
strain RES056 at a subtoxic concentration. And also, nearly all compounds are devoid of activities
against common HIV-1 mutants such as L100I, Y181C, Y188L, E138K, F227L+V106A (see
supporting information). Therefore, our further efforts are aimed at improving activities against
both WT HIV-1 and HIV-1 mutants. Moreover, expectedly, the compounds lack the HIV-2
inhibitory activities (see supporting information), demonstrating that non-nucleoside reverse
transcriptase inhibitors (NNRTIs) are specific for human immunodeficiency virus type 1 (HIV-1)
reverse transcriptase (RT) and do not inhibit HIV-2.19
HIV-1 RT inhibitory assay was also performed via an ELISA assay using a commercial kit
(using poly rA: Dt as the template/primer). All hybrid inhibitors displayed moderate inhibitory
activities against HIV-1 RT with EC50 values ranged from 5.864 µM to 25.208 µM. Although the
activities of all targets compounds were not as good as etravirine (IC50 = 0.011 µM). But it is
worth mention that DKAs inhibitor 3 showed no RT inhibitor activities16. It suggests that the
newly synthesized DAPY-DKAs bind to HIV-1 RT and belong to the NNRTIs. It is notable that
10a, 10b and 11b exhibited similar activity against HIV-1 RT, while the anti-HIV-1 activity of 11a
was distinctly inferior to them, which might be ascribed to that the para-substitution was not
conducive to binding between DKA and RT.
To investigate the potential binding mode, the molecular docking was performed using the
software SYBYL Surflex-Dock program and crystal structure of WT HIV-1 RT/TMC125 (PDB
code: 3MEC) to take the docking studies.6 Ester 10b and acid 11b were both docked into the
HIV-1 RT nonnucleoside binding site (NNBS) (Fig. 3). The docking studies showed that the
molecules could be well located in the NNBS and verified the existence the π-π stacking
interactions between the left wing of 10b (or 11b) and the aromatic amino acid residues Tyr188,
Trp229 as well as Phe227. It shows the fragment of diketo acid (ester) seems to have no
significant effect on π-π stacking interaction between the left aryl ring and aromatic amino acid

residues, which might be the carboxylic (ester) group has no obvious effect on the left wing
aromatic ring electron density because it far away from the benzene. It also account for that acid
11a (11b) displayed the similar WT HIV-1 inhibitory activity with correponding ester 10a (10b).
In conclusion, a series of DAPY-DKA hybrids were designed and synthesized as HIV-1
inhibitors. All target molecules showed activities against WT HIV-1 at submicromolar
conentrations and HIV-1 RT at micromolar concentrations. It illustrated that the introduction of
DKA or DKA ester fragment is tolerable in the modification of DAPYs. Compounds 10b and 11b
showed inhibitory activities against WT HIV-1 with EC50 values of 0.18 µM and 0.14 µM,
respectively. This work enriched the SAR of DAPYs, and provided a potential scaffold for the
development of new anti-HIV compounds.
Figure 3. Docking studies of 10b (purple) and 11b (organge) into NNBS
Acknowledgments
The financial support from the National Natural Science Foundation of China (No. 21402148, No.
21602164), the Hubei Provincial Department of Education of China (No. XD2014154, No.
Q20141510), Wuhan Institute of Technology Scientific Research Fund (No. K201441, No. K201304),
Wuhan Institute of Technology Teaching Research Project (No. X2015014), and Wuhan Institute of
Technology President Fund (No. 2016079), is gratefully acknowledged.
Supplementary data
Supplementary data (1H NMR, 13C NMR, and part of biological data) associated with this article
can be found, in the online version, at http://dx.doi.org/********.
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Graphical abstract