Synthesis, conformational study and antiviral activity of L-like neplanocin derivatives

Article abstract of DOI:10.1016/j.bmcl.2017.08.009

The L-like enantiomer of 9-(trans-2′, trans-3′-dihydroxycyclopent-4′-enyl)-3-deazaadenine (DHCDA) (1), its 3-deaza-3-bromo derivative (3), and the conformational restricted methanocarba (MC) nucleoside analogues (2 and 4) were synthesized. X-ray crystal structures showed the L isomer MC analogue 4 adopts a similar North-like locked conformation as conventional D-MC nucleosides, while the DHCDA analogue 3 preferred south-like conformer. Compounds 1 and 4 showed potent antiviral activity against norovirus, while compound 2 and 3 were less potent or inactive. The conformational behavior of “sugar” puckering (north/south) and nucleobase orientation (syn /anti) may contribute to the antiviral activity differences. For compound 3, antiviral activity was also found against Ebola virus.

Full text of DOI:10.1016/j.bmcl.2017.08.009

Bioorganic & Medicinal Chemistry Letters xxx (2017) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis, conformational study and antiviral activity of L-like
neplanocin derivatives
⇑
Qi Chen , Amber Davidson
Department of Chemistry, Slippery Rock University, Slippery Rock, PA 16057, United States
a r t i c l e i n f o
a b s t r a c t
0
0
0
Article history:
The L-like enantiomer of 9-(trans-2 , trans-3 -dihydroxycyclopent-4 -enyl)-3-deazaadenine (DHCDA) (1),
Received 13 June 2017
Revised 31 July 2017
Accepted 5 August 2017
Available online xxxx
its 3-deaza-3-bromo derivative (3), and the conformational restricted methanocarba (MC) nucleoside
analogues (2 and 4) were synthesized. X-ray crystal structures showed the L isomer MC analogue 4
adopts a similar North-like locked conformation as conventional D-MC nucleosides, while the DHCDA
analogue 3 preferred south-like conformer. Compounds 1 and 4 showed potent antiviral activity against
norovirus, while compound 2 and 3 were less potent or inactive. The conformational behavior of ‘‘sugar”
puckering (north/south) and nucleobase orientation (syn /anti) may contribute to the antiviral activity
differences. For compound 3, antiviral activity was also found against Ebola virus.
Keywords:
Carbocyclic nucleosides
L
-like nucleosides
Ó 2017 Elsevier Ltd. All rights reserved.
Nucleoside conformation
Neplanocin
Antiviral
Introduction
To further investigate L-like carbocyclic nucleosides, based on
compound 6, we sought the analogues of DHCDA (that is 1 and
9
Nucleoside analogues play a vital role in chemotherapy of viral
3). DHCDA is a neplanocin derivative whose broad spectrum
1
2
infectious diseases.
cavir and entecavir (Fig. 1) with the similar configuration as nat-
urally occurring nucleosides, effectively interact with target
D
-like carbocyclic nucleosides, such as aba-
antiviral activities were attributed to the inhibition of AdoHcy
hydrolase, and reduced cytotoxicity due to lacking the 5 hydroxyl
group necessary for the 5 -phosphorylation and circumventing
antiviral activity through polymerase inhibition.
3
4
0
0
3
,4
enzymes and, thus, possess interesting biological activities.
Despite acting as conventional polymerase inhibitors, the antiviral
properties of adenine-derived carbocyclic nucleosides can act by
the inhibition of S-adenosylhomocysteine (AdoHcy) hydrolase, a
cellular enzyme involved in controlling viral transcription by regu-
lating the mRNA cap structures.2 However, the development of
such carbocyclic nucleosides as therapeutics is limited by cytotox-
It has been well recognized that the conformational behavior of
ribonucleosides and modified nucleosides, including those in the
category carbocyclic, owe their biological properties to sugar puck-
ering and the orientation of the heterocyclic base. Among these
properties are their metabolic pathways, enzyme binding affinity,
,5
1
0
and therapeutic effects and toxicity. The sugar puckering of ribo-
furanosyl nucleosides is known to exist in dynamic equilibrium
0
icity that commonly arises from its C-5 phosphate metabolites
5
0
0
arising from various cellular enzymes. In order to seek ways to cir-
between north (3 -endo) and south (2 -endo) conformations. In
most the cases, binding affinity to a pharmacological target favors
one conformer over the other. Furthermore, nucleosides adopt
either an anti or a syn nucleobase orientation. It has been
cumvent this metabolic pathway, and, hence decrease unwanted
toxicity, the uncommon
sides arose.
L-like carbocyclic enantiomeric nucleo-
6
1
1
Recently, we reported the
of 3-deaza- and 3-deaza-3-bomo-1 , 6 -isoneplanocin (Fig. 2),
which have been found to possess potent and broad spectrum
D
-like (5) and -like (6) enantiomers
L
reported
that nucleoside analogues with a syn orientation
0
0
antiviral activities. Interestingly, the
or more potent than the -isomers against human cytomegalo-
virus, hepatitis B virus (HBV), norovirus, measles and Ebola virus.
L-isomers (6) were equally
D
7
,8
⇑
Corresponding author.
E-mail address: qi.chen@sru.edu (Q. Chen).
Fig. 1. Examples for carbocyclic nucleosides.
http://dx.doi.org/10.1016/j.bmcl.2017.08.009
960-894X/Ó 2017 Elsevier Ltd. All rights reserved.
0
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2
Q. Chen, A. Davidson / Bioorganic & Medicinal Chemistry Letters xxx (2017) xxx–xxx
0 0
D L-like 1 , 6 -isoneplanocin derivatives and designed targer compounds.
and
Fig. 2.
exhibited much lower binding affinities to adenosine based recep-
tors. Incorporating these parameters in our study, the 3-bromo
substitution in 2 is envisioned to increase the stereo hindrance sig-
nificantly and force the nucleobase to adopt an anti conformation
(Fig. 3). In that direction, methanocarba (MC) nucleoside analogues
(2 and 4, Fig. 2) were also included as target compounds in this
study. The bicyclic[3.1.0]hexane ring in 2 and 4 was expected to
Scheme 3. Synthesis of cyclopentenol derivatives. Reaction and conditions:
a. LiAIH , CeCl , THF, 95%; b. Diethylzinc, CH , DCM, 70%.
4
3
2 2
I
constrain the pseudo sugar component and result in locked
1
2
north-like conformers, which are expected to show the different
antiviral profile comparing with conformers 1 and 3. Further Struc-
ture-Activity Relationship (SAR) study can be expected to provide
valuable information for exploring the mechanism of carbocyclic
nucleosides as antiviral agents.
We envisioned a versatile retrosynthetic plan (Scheme 1) to the
proposed targets. The plan involved a coupling reaction between
two main components: a cyclopentenol pseudo-sugar potion and
a modified purine base. In the latter regard, synthesis of the 3-
deazapurine base 7 was accomplished by adapting known proce-
dures using 2-chloro-3,4-diaminopyridine (11) as the starting
1
3,14
material (Scheme 2).
Construction of the carbocyclic coupling
Fig. 4. Stereochemistry of bicycle[3.1.0]hexanol 9.
precursors 8 and 9 was achieved from
a Luche condition reduction (for 8), and a Simmons Smith reaction
L
-cyclopentenone 1015 via
1
6,17
18
(
for 9) (Scheme 3).
The stereo chemistry of compound 9 was
1
8
confirmed by ROSEY (Fig. 4 ) and X-ray crystallography of com-
pound 4.
Mitsunobu coupling reaction was preformed between 7 and
L
-form cyclopentenol 8 (Scheme 4) or 9 (Scheme 5) to provide cou-
Fig. 3. Syn and Anti conformers of compound 3.
19
pled products 15 and 16, which, upon deprotection, gave 1 and
2
2
0
21
22
.
3-Bromo functionalized targets 3 and 4 were accessible
from 1 and 2 via suitable bromination conditions.
In addition to NMR data, X-ray crystallography structures23 of 3
and 4 further confirmed the regiospecific bromination at the C-3
position of 1 and 2.
0
Crystal structures also showed 3 adopting a south (3 -exo) con-
formation when posed with similar orientation with D-nucleosides,
while more structural rigid bicyclo[3.1.0] hexane locked 4 into an
0
north (2 -exo) conformation in the solid state (Fig. 5). As expected,
the bromo group at the C-3 position forced both 3 and 4 to adopt
the less congested anti conformation.
Compounds 1–4 were assayed for their antiviral potential.2
4,25
Scheme 1. Retrosynthesis design for trager compounds.
Compounds 1 and 4 displayed activity against norovirus. Com-
Scheme 2. 13,14Synthesis of 3-deazapurine base. Reaction and conditions: a. CH(OMe)
3 2 2 2 2
, 85%; b. i)NH NH ii) Raney Ni, H O, 70%; c. (Boc) O, THF, 90%; d. TBAF, THF, 88%.
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Q. Chen, A. Davidson / Bioorganic & Medicinal Chemistry Letters xxx (2017) xxx–xxx
3
3
Scheme 4. Synthesis of compound 3. Reaction and conditions: a. DIAD, PPh , THF, 77%; b. 1 M HCl/MeOH, 87%; c. NBS, DCM/DMF, 74%.
3
Scheme 5. Synthesis of compound 4. Reaction and conditions: a. DIAD, PPh , THF, 56%; b. 1 M HCl/MeOH, 81%; c. NBS, DCM/DMF, 71%.
Acknowledgments
We are grateful to the Slippery Rock University, Faculty/Student
Research Grants and to Stewart W. Schneller and Chong Liu at
Auburn University for support of this research. We are indebted
to the NIAID in vitro assay team for the viral data presented herein:
Don Smee, Utah State University; Brent Korba, Georgetown Univer-
sity; Mark Prichard, University of Alabama – Birmingham; Michael
Murray, Southern Research Institute and to We also appreciate the
assistance of Steven Cardinale and Terry Bowlin of Microbiotix, Inc.
for providing the S-adenosylhomocysteine hydrolase data and John
Gorden at Auburn University for X-ray crystallography analysis.
References
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Schneller SW. Rec Adv Nucleosides. 2002;291–297.
Fig. 5. North and South conformation for compound 3 and 4.
pound 1 (EC50 = 4.2
(EC50 = 33 M). On the other hand, the antiviral profile against
norovirus for MC nucleosides 2 and 4 were reversed. In contrast
to 1, compound 2 (EC50 > 100 M) lost anti-norovirus activity, the
bromo derivative 4 (EC50 = 3.0 M) showed stronger viral inhibi-
tion than 3. As evidenced in the crystal structures, 3 and 4 are
locked into the anti-conformation in solid state, while 1 and 2
are more flexible. The most active norovirus 4 represents the
l
M) was more potent than its bromo analogue
7. Liu C, Chen Q, Schneller SW. Bioorg Med Chem Lett. 2016;26:928.
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anti-north
is in order. In comparison with the
DHCDA (1) showed antiviral activity against vaccinia virus
L
-like nucleosides and suggests more extensive study
7. Choi MJ, Chandra G, Lee HW, et al. Org Biomol Chem. 2011;9:6955.
1
D
-like nucleosides, compound
18. Structural assignments for
9
were accomplished by
H COSY and the
stereochemistry was assigned by
a
ROSEY, which shows strong NOE
2
6
correlations between H-1 and H-5, H-3 and H-4, H4 and H-5 protons (Fig. 4).
(
l
EC50 = 0.7
lg/mL)
and vesicular stomatitis virus (EC50 = 0.2
9. Compound 1, white solid; 1H NMR (600 MHz, MeOD): d 8.07 (s, 1H), 7.68 (d, J =
1
2
6
g/mL) , but no anti-norovirus activity was reported to our
6.1 Hz, 1H), 6.90 (d, J = 6.1 Hz, 1H), 6.32 (dt, J = 6.2, 2.52 Hz, 1H), 6.20 (dd, J =
6
.2, 1.7 Hz, 1H), 5.41 (m, 1H), 4.66 (dd, J = 2.7, 1.3 Hz, 1H), 4.65 (dd, J = 2.6, 1.3
knowledge.
Additionally, 3 (EC50 = 8.3
against Ebola virus than 1 (EC50 = 29.5
and 4 were completely inactive. Compound 3 displayed toxicity
13
Hz, 1H); C NMR (150.9 MHz, MeOD): d153.5, 142.3, 141.0, 140.2, 137.9, 133.7,
1
l
g/mL) showed stronger activity
g/mL), while MC analogues
[M+H]+ 233.1039,
28.4, 99.5, 78.9, 74.5, 68.3; HRMS Calcd for C11
13 4 2
H N O
l
found 233.1035. Anal. Calcd for C11H12N O . 0.3H O: C, 55.60; H, 5.34; N, 23.58.
4
2
2
2
found: C, 55.83; H, 5.32; N, 23.34..
2
7
20. Compound 2, white solid; 1H NMR (600 MHz, MeOD): d 8.24 (s, 1H), 7.73 (d, J =
related mild active towards the flavivirus family in vero cell line.
6
1
.0 Hz, 1H), 6.97 (d, J = 6.0 Hz, 1H), 4.68 (d, J = 1.2 Hz, 1H), 4.60 (t, J = 6.0 Hz,
H), 3.84 (d, J = 6.6 Hz, 1H), 2.02 (m, 1H), 1.77 (m, 1H), 1.84 (dd, J = 9.0, 4.2 Hz,
Compounds 1,2 and 4 showed no apparent toxicity towards the
testing cell lines.
13
1H), 0.83 (m, 1H); C NMR (150.9 MHz, MeOD): d 153.5, 141.5, 141.1, 140.0,
15 4 2
28.1, 98.8, 77.9, 72.9, 65.5, 24.7, 19.6, 8.43; HRMS Calcd for C12H N O
1
No effects were found for 1–4 towards AdoHcy hydrolase
+
[
M+H] 247.1195, found 247.1188.
5
(
IC50 > 10 mM for all compounds) which most likely correlated
1
2
1. Compound 3, white solid; H NMR (600 MHz, MeOD): d 8.11 (s, 1H), 7.78 (s,
-carbocyclic nucleosides.2
1H), 6.36 (m, 1H), 6.29 (m, 1H), 6.13 (m, 1H), 4.71 (m, 1H), 4,27 (m, 1H);
13
C
with the activity of
D
Please cite this article in press as: Chen Q., Davidson A. Bioorg. Med. Chem. Lett. (2017), http://dx.doi.org/10.1016/j.bmcl.2017.08.009

4
Q. Chen, A. Davidson / Bioorganic & Medicinal Chemistry Letters xxx (2017) xxx–xxx
NMR (150.9 MHz, MeOD):d 153.2, 143.6, 142.1, 138.4, 137.2, 133.6, 129.7, 90.9, 24. For the antiviral and hydrolase assay details: Chen Q, Liu C, Komazin G, Bowlin
+
7
3
4
9.8, 74.8, 67.2; HRMS Calcd for
C
11
H
12
N
4
O
2
Br [M+H] 311.0144, found
SW, Schneller SW. Bioorg Med Chem. 2014;22:6961.
25. No significant activities were found for 1–4 towards Adenovirus, Chikungunya
virus, Dengue virus, Poliovirus, Punta Toro virus, Rift Valley fever virus,
Tacaribe virus, Usutu virus, Venezuelan equine encephalitis virus, West Nile
virus, Yellow fever virus, Japanese encepahalitis virus, Zika virus and measles
virus.
11.0132. Anal. Calcd for C11
2.63; H, 3.63; N, 17.74.
11 4 2
H N O Br: C, 42.46; H, 3.56; N, 18.01. found: C,
2
2. Compound 4, white solid; 1H NMR (600 MHz, MeOD): d 8.32 (s, 1H), 7.77 (s,
1
H), 4.64 (d, J = 1.2 Hz, 1H), 4.58 (t, J = 5.4 Hz, 1H), 3.94 (d, J = 6.0 Hz, 1H), 2.0
13
(
m, 1H), 1.76 (m, 1H), 1.40 (dd, J = 9.0, 4.2 Hz, 1H), 0.79 (m, 1H); C NMR (150.9
MHz, MeOD): d 151.7, 141.9, 140.6, 135.0, 128.3, 89.3, 75.9, 71.4, 63.6, 22.9,
26. De Clercq E, Cools M, Balzarini J, et al. Antimicrob Agents Chemother.
1989;33:1291.
+
1
9.2, 6.69; HRMS Calcd for C12
H
14
N
4
O
2
Br [M+H] 325.0300, found 325.0313.
and has been
2
3. Crystallographic data (excluding structure factors) for
3
4
27. Compound 3 towards Dengue virus (Vero IC50=7.2
Valley fever virus (Vero IC50=31 g/mL, CC50=39
encephalitis virus (Vero IC50=27 g/mL, CC50=27
g/mL); Yellow fever virus (Vero IC50=32
g/mL); Japanese encepahalitis virus (Vero IC50=32 g/mL, CC50=32
l
l
g/mL, CC50=28
g/mL); Venezuelan equine
g/mL); West Nile virus (Vero
g/mL,
lg/mL); Rift
deposited with the Cambridge Crystallographic Data Centre with the following
deposition number CCDC 1544960 and CCDC 1544961 respectively. Copies of
the data can be obtained, free of charge, on application to CCDC, 12 Union Road,
Cambridge CB2 1EZ, UK, fax: +44 (0)1223 336033 or e-mail: deposit@ccdc.cam.
ac.uk.
l
l
l
IC50=32
CC50=32
l
l
g/mL, CC50=32
l
l
l
lg/mL).
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