Synthesis, docking, and biological studies of phenanthrene β-diketo acids as novel HIV-1 integrase inhibitors

Article abstract of DOI:10.1016/j.bmcl.2013.09.009

In the present study we report the synthesis of halogen-substituted phenanthrene β-diketo acids as new HIV-1 integrase inhibitors. The target phenanthrenes were obtained using both standard thermal- and microwave-assisted synthesis. 4-(6-Chlorophenanthren-2-yl)-2,4-dioxobutanoic acid (18) was the most active compound of the series, inhibiting both 3′-end processing (3′-P) and strand transfer (ST) with IC₅₀ values of 5 and 1.3 μM, respectively. Docking studies revealed two predominant binding modes that were distinct from the binding modes of raltegravir and elvitegravir, and suggest a novel binding region in the IN active site. Moreover, these compounds are predicted not to interact significantly with some of the key amino acids (Q148 and N155) implicated in viral resistance. Therefore, this series of compounds can further be investigated for a possible chemotype to circumvent resistance to clinical HIV-1 IN inhibitors.

Full text of DOI:10.1016/j.bmcl.2013.09.009

Accepted Manuscript
Synthesis, docking, and biological studies of phenanthrene β-diketo acids as
novel HIV-1 integrase inhibitors
Horrick Sharma, Tino W. Sanchez, Nouri Neamati, Mervi Detorio, Raymond
F. Schinazi, Xiaolin Cheng, John K. Buolamwini
PII:
S0960-894X(13)01072-X
http://dx.doi.org/10.1016/j.bmcl.2013.09.009
BMCL 20861
DOI:
Reference:
To appear in:
Bioorganic & Medicinal Chemistry Letters
Received Date:
Revised Date:
Accepted Date:
26 July 2013
29 August 2013
3 September 2013
Please cite this article as: Sharma, H., Sanchez, T.W., Neamati, N., Detorio, M., Schinazi, R.F., Cheng, X.,
Buolamwini, J.K., Synthesis, docking, and biological studies of phenanthrene β-diketo acids as novel HIV-1
integrase inhibitors, Bioorganic & Medicinal Chemistry Letters (2013), doi: http://dx.doi.org/10.1016/j.bmcl.
2
013.09.009
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com
Synthesis, docking, and biological studies of phenanthrene β-diketo acids as
novel HIV-1 integrase inhibitors
a
b
b
c
c
Horrick Sharma , Tino W. Sanchez , Nouri Neamati , Mervi Detorio , Raymond F. Schinazi , Xiaolin
d
a,∗
Cheng , and John K. Buolamwini
a
Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee health Science Center, 847 Monroe Avenue, Suite 327, Memphis,
3
8163, USA,
b
Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA
9
0089, USA
c
Emory University School of Medicine/VA Medical Center, Medical Research 151H, 1670 Clairmont Road, Decatur, GA 30033, USA
d
UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
ARTICLE INFO
ABSTRACT
Article history:
Received
Revised
Accepted
Available online
In the present study we report the synthesis of halogen-substituted phenanthrene β-diketo acids
as new HIV-1 integrase inhibitors. The target phenanthrenes were obtained using both standard
thermal- and microwave-assisted synthesis. 4-(6-Chlorophenanthren-2-yl)-2,4-dioxobutanoic
acid (18) was the most active compound of the series that inhibited both 3′-end processing (3′-
P) and strand transfer (ST) with IC50 values of 5 and 1.3 µM, respectively. Docking studies
revealed two predominant binding modes that were distinct from the binding modes of
raltegravir and elvitegravir, and suggest a novel binding region in the IN active site. Moreover,
these compounds do not interact significantly with some of the key amino acids (Q148 and
N155) implicated in viral resistance. Therefore, this series of compounds can further be
investigated for a possible chemotype to circumvent resistance to clinical HIV-1 IN inhibitors.
Keywords:
HIV-1
HIV-1 Integrase
Phenanthrene β-diketo acids
ST inhibitors
Docking
2009 Elsevier Ltd. All rights reserved.
and also ADD Mervi Detorio from my group.
∗
Corresponding author. Tel.: +1-901-448-7533; fax: +1-901-448-6828; e-mail: jbuolamwini@uthsc.edu

ACCEPTED MANUSCRIPT
Acquired immunodeficiency syndrome (AIDS) caused by the
human immunodeficiency virus (HIV) has resulted in the deaths
(PPh ) with triethyl amine as a base in a dioxane-ethanol solvent
3 4
23
under an inert atmosphere. Conditions varied from ice-cold (0
°C) to reflux, and the reaction was stirred from 6 to 48 h
depending upon the starting materials used. The aldehyde
intermediates were converted to the corresponding alkynes by
Seyferth-Gilbert homologation under which, a mixture of
1
,2
of about 30 million people since it was first reported in 1981.
Most of the approved anti-retroviral drugs target mainly viral
reverse transcriptase or protease, two essential enzymes involved
3,4
in viral replication. To circumvent viral resistance, which is a
major bottleneck in anti-HIV therapy, the currently available
regimens include cocktails of drugs from two or more classes.
Although, highly active antiretroviral therapy (HAART) has been
successful in reducing morbidity and mortality, the emergence of
multi-drug resistant viral strains, along with the issues of toxicity,
intermediates
5a-5h,
dimethyl-(1-diazo-2-oxopropyl)
phosphonate, and K
2
CO in methanol was stirred in ice for 7-17
3
24
h. The alkyne intermediates 6a-6h were then subjected to a 6-
endo dig cyclization using PtCl as catalyst and refluxing in
2
toluene for 24 h under inert conditions to yield acetyl
phenanthrenes intermediates 9a-9h. An alternative efficient
5
-12
25
and dosing have rendered the current therapy ineffective.
Thus, there is an urgent need to target other essential enzymes
involved in viral survival and replication. Towards this end, IN
has been shown to be a promising target with the entry of
raltegravir (MK-0518), elvitegravir (GS-9137) and dolutegravir
microwave synthesis shown in Scheme 2 was used to synthesize
the acetyl phenanthrene derivatives 9i and 9j. This one-pot
synthesis of phenanthrenes was accomplished by a step-wise
Suzuki-Miyaura coupling reaction followed by an intramolecular
aldol condensation. Thus, 7a and 7b phenyl propanone starting
materials were coupled with (2-formyl-4-methoxyphenyl)
26
(
GSK-1349572) into the clinic, in clinical trials for the
13,14
management of AIDS.
boronic acid (8) using Pd (PPh
Phos as catalyst. The reaction was performed in
toluene/ethanol (2:1) mixture and irradiated at 60-80 W and 150
C for 10 min. The acetyl phenanthrene intermediates 9i-9j were
3 4 2 3
) with Cs CO as a base and S-
IN, a 32 kDa 288 amino acid protein is an important enzyme
involved in viral replication. Since IN has no homologue in
human cells, it offers a promising strategy for anti-retroviral drug
development. β-Diketo acids and isosteres are the most advanced
a
a
°
15
then subjected to oxalylation reaction. Our initial attempt with
diethyl oxalate did not yield the desired product. A literature
class to have shown promising HIV-1 IN inhibitory activity.
S1360 was the first IN inhibitor to enter clinical trials followed
27
16
report suggests that tert-butyl methyl oxalate is an efficient
by a naphthyridine carboxamide L-870, 810. Although, over the
last two decades promising IN inhibitors (Fig. 1) were designed
based on the diketo acid functionality, raltegravir (MK-0518),
elvitegravir (GS-9137) and dolutegravir are the only IN
oxalylating agent for halogen-substituted acetophenones. Thus,
we used of tert-butyl methyl oxalate (11), which was prepared
28
according to a previously reported method, by the reaction of
17
methyl chlorooxo acetate, tert-butanol and pyridine in anhydrous
ether. This resulted successful formation of the corresponding
diketo esters 12i-12j. The ester derivatives were then hydrolyzed
with aq NaOH to their corresponding desired diketo acid final
products 13-22.
inhibitors approved by the FDA. Unfortunately, clinical studies
have reported viral mutants particularly G148H, N155H, and
double mutant G148H G140S, that are resistant to both
1
8,19
raltegravir and elvitegravir.
Thus, it is highly imperative to
design new chemical classes as new generation HIV-1 IN
inhibitors that not only have potent inhibitory activities, but also
have the potential to circumvent the viral resistance to present IN
inhibitors.
Scheme 1.
Scheme 2.
Scheme 3.
Figure 1.
In our previous study, we reported 5(H)-phenanthridin-6-one
diketo acids and their phenanthrene DKA analogs as a novel
class of HIV-1 IN inhibitors that also showed cell culture
2
0
antiviral activity. Herein, we report the synthesis of a new series
of phenanthrene β-diketo acids incorporating halogen
substituents to provide better metabolic stability than the parent
The synthesized target compounds 13-22 (Table 1) were then
tested for their ability to inhibit strand transfer (ST) and 3′-end
processing (3′-P) according to the assay we have previously
20
29
non-halogenated compounds. These also turned out to have
substantial IN inhibitory activities. Selected compounds were
then tested for their abilities to inhibit HIV-1 replication in cell
culture. Furthermore, to gain understanding of their binding
modes at the IN active site, docking studies were conducted
using our recently reported homology model of full-length HIV-1
reported. The structure activity relationship around these
halogen-substituted phenanthrene derivatives suggests that the β-
1
2
diketo acid functionality is well tolerated at R and R positions.
Thus, compounds 17, 18, and 20 have potent and similar ST IC50
values of 1.4, 1.3, and 1.2 µM, respectively. Moreover,
compound 18 showed potent activities against both 3′-P and ST
reactions with IC50s of 5.0 µM and 1.3 µM, respectively.
Comparison of 20 vs. 19 and 13 vs. 14 indicates that the β-diketo
21
IN in complex with DNA, which was built using the foamy IN-
2
2
20
DNA structure as a template. In the previous docking studies
2
we used the structures of IN that was not bound to DNA, and
therefore was less biologically relevant.
acid functionality is slightly more favorable at the R position
1
than the R position. In particular, compound 20 was found to be
about four times more active than compound 19 against ST
The synthesis of target halogenated phenanthrene β-diketo
acids was accomplished by first synthesizing the halogenated
acetyl phenanthrene intermediates 9a-9h using Scheme 1. On the
basis of commercial availability, two different sets of starting
materials were used to perform the Suzuki coupling reaction.
Thus, either the acetyl boronic acid derivatives (1a-1d) were
reacted with the aldehyde containing halogen partners (2a-2d) to
synthesize intermediates 5a-5d, or alternatively, the formyl
boronic acid derivatives (3e-3h) were coupled with iodo acetyl
starting materials (4e-4h) to synthesize intermediates 5e–5h. The
coupling reaction was optimized by using a polymer bound Pd
reaction. Our laboratory has previously reported unsubstituted
2
phenanthrene derivative 23 with diketo acid at the R position
20
which had an ST IC50 value of 2.7 µM. With respect to
6
compound 23, while substitution of a chlorine atom at R position
(compound 20) improved activity, a fluoro substituent at this
position (compound 13) resulted in a slight loss of potency; also
implying that the choloro substituent did better than the fluoro
counterpart (compare compounds 20 and 13) at this position.
6
That fluorine may not be an optimal substituent at the R position
is also evident when one considers that compound 22 (ST IC50
=
3
µM) was two-folds more active than compound 21 (ST IC50 = 6

ACCEPTED
4
MANUSCRIPT
µM). Chlorine was also found to improve activity at positions R
DNA complex structure is a major improvement over our
5
and R . Compounds 18 and 17 were about four times more potent
than their unsubstituted counterpart (compound 24, ST IC50 of
.8 µM). Chlorine substitution at R position in compound 17
also improved selectivity (nine-folds) for the ST step. The reason
for the dramatic loss of potency for both ST and 3′-P with
compound 15 is not apparent. It might be due to ineffective metal
chelation by the β-diketo acid functionality considering, the
electron withdrawing effect of the adjacent fluorine substituent.
The improvement of activity of compound 16 (ST IC50 = 8.0
µM), relative to compound 15, implies a favorable effect of the
fluoro substituent at the R position. This may be one of the
reasons why compound 17, having a more hydrophobic Cl at the
position, had improved activity over compound 16; also
implying that hydrophobic interaction at this position may be an
important contributing factor to activity. Compound 22, with an
electron donating methoxy group at the R position, and the
diketo acid moiety at R showed an IC50 of 3 µM against ST.
This is a significant loss of activity when compared to its parent
previous studies on partial IN structure without DNA and provide
more detailed insights into the binding modes of the target
phenanthrene β-diketo acids. More importantly, there were no
significant interactions with Gln148 and Asn155, key residues
implicated in viral resistance.
20
5
4
The novel binding mode of these compounds could be
exploited to develop agents active against the current drug-
resistant strains of HIV. Since, compound 15 exhibited a
significant loss of activity (ST IC50 of 63 µM), its binding pose
was also evaluated. It was observed that compound 15
5
predominantly docked in
a
different binding mode
5
(Supplementary material, Figure S1). In this orientation, while
the phenanthrene ring interacted with Thr66, His67, and Leu68,
only the acid and the enolic oxygen of the β-diketo acid motif
R
2+
1
chelated the two Mg ions. The loss of potency may be
7
attributed to a disruption of chelation by an adjacent electron
withdrawing fluorine substituent. The structurally similar
derivative 16 had a similar binding pose as compound 15
(Supplementary material, Figure S2). However, the improved
activity of compound 16 might result from a favorable contact
unsubstituted diketo acid analog 25 (ST IC50 of 0.38 µM) that our1
20
laboratory has previously reported. This suggests that the R
position is sensitive to modifications and could be further
exploited to determine the structure activity relationship around
this novel class of IN inhibitors.
5
that the R position fluoro makes with the side chain of Leu68.
Figure 2.
Table 1.
In summary, a series of new phenanthrene-β-diketo acid
derivatives bearing mostly halogen substituents were synthesized
and evaluated as HIV-1 integrase inhibitors. In general,
compounds were active against the ST catalytic step but some
also showed good activities against 3′-P as well. Selected
compounds were also found to moderately inhibit HIV-1
replication. Docking studies with a more refined structure than
we previously used to dock earlier parent phenanthrene DKAs
suggest that these derivatives bind to a potential novel region in
the IN active site. In particular, the bulky phenanthrene ring
system does not dock into the cavity characteristically occupied
by the halobenzyl groups of IN inhibitors in clinical use, and
does not appear to interact with Gln146 and viral DNA.
Furthermore, no contacts with two of the most critical residues
implicated in viral resistance, Asn155 and Gln148, were
observed. This series of compounds could be further optimized to
develop agents to overcome viral resistance against currently
used HIV-1 IN inhibitors.
Next, to determine their potential as anti-HIV agents, potent
analogs of the series, compounds 18, and 17 were tested for their
ability to inhibit HIV-1 replication in primary human peripheral
blood mononuclear cells (PBMC) according to the previously
30
reported procedure.
Both compounds showed moderate
inhibition of HIV replication with IC50s of 20.7 and 27.5 µM,
respectively (Table 2). The reduced antiviral potency might be
because of poor solubility, binding to serum proteins and/or
31,32
cellular distribution factors. Cytotoxicity assays
showed that
the selected compounds, 17 and 18, have toxicities when tested
against PBMC, human CEM lymphoblastic leukemia cells and
African green monkey Vero cells. However, the non-halogenated
compound 23, had an EC50 of 8.0 µM for inhibition of HIV
replication in cell culture and a selectivity index of 10 against
PBMCs in our previous study suggesting that there is potential
for optimization to improve selectivity index along with their
anti-viral activities.
2
0
Acknowledgments
Table 2.
Financial support from the National Institute of Allergy and
Infectious Diseases (NIAID), NIH Grant No. AI084710, the
Department of Pharmaceutical Sciences, and Department of
Veterans Affairs is gratefully acknowledged.
After synthesis and biological evaluation, a homology model
of the structure of full HIV-1 integrase bound to DNA that we
recently constructed based on the foamy virus crystal structure,
21
was used to determine binding modes of the compounds. The
docking studies revealed two distinct poses. The docked
conformations of compound 18, active against both ST and 3′-P,
are shown in Fig. 2. In both orientations, the β-diketo acid
Supplementary data
Supplementary data (Docking poses of compounds 15 and 16
and Chemistry experimental data) associated with this article can
be found, in the online version, at
2
+
chelating pharmacophore interacted with the two Mg ions in the
IN active site, thus contributing to IN inhibition in accordance
with the proposed mechanism of action of ST inhibitors. The
phenanthrene ring in one binding mode interacted with residues
Glu92, Ser119, Asn120, and Phe121 in a possible novel binding
region in the IN active site. In the other mode, the phenanthrene
ring made contacts with Pro142, Tyr143, Asn117, and Gly118. It
is important to note that because of steric hindrance, the
phenanthrene ring does not dock into the DNA-IN interface
References and notes
1. Curran, J. W. N. Engl. J. Med. 1983, 309, 609.
2.
3.
4.
5.
Curran, J. W. R. I. Dent. J. 1984, 16, 19, 21.
Von Hentig, N. Drugs Today 2008, 44, 103.
MacArthur, R. D.; Novak, R. M. Clin. Infect. Dis. 2008, 47, 236.
Clavel, F.; Hance, A. J. N. Engl. J. Med. 2004, 350, 1023.
21
cavity into which the characteristic halobenzyl moieties of
clinically used IN inhibitors insert; thus making no contacts with
Gln146 or viral DNA. The present docking simulation on HIV-
6. Moyle, G.; Gatell, J.; Perno, C. F.; Ratanasuwan, W.; Schechter,
M.; Tsoukas, C. AIDS Patient Care STDs 2008, 22, 459.

ACCEPTED MANUSCRIPT
7
.
Johnson, V. A.; Brun-Vezinet, F.; Clotet, B.; Gunthard, H. F.;
Kuritzkes, D. R.; Pillay, D.; Schapiro, J. M.; Richman, D. D. Top
HIV Med. 2010, 18, 156.
8
9
.
.
Emini, E. A.; Graham, D. J.; Gotlib, L.; Condra, J. H.; Byrnes, V.
W.; Schleif, W. A. Nature 1993, 364.
Calmy, A.; Hirschel, B.; Cooper, D. A.; Carr, A. Antivir. Ther.
2
009, 14, 165.
10. Marcello, A. Retrovirology 2006, 3, 7
11. Geeraert, L.; Kraus, G.; Pomerantz, R. J. Annu. Rev. Med. 2008,
5
9, 487.
12. Malta, M.; Magnanini, M. M.; Strathdee, S. A.; Bastos, F. I. AIDS
Behav. 2010, 14, 731.
1
3. Summa, V.; Petrocchi, A.; Bonelli, F.; Crescenzi, B.; Donghi, M.;
Ferrara, M.; Fiore, F.; Gardelli, C.; Gonzalez Paz, O.; Hazuda, D.
J.; Jones, P.; Kinzel, O.; Laufer, R.; Monteagudo, E.; Muraglia, E.;
Nizi, E.; Orvieto, F.; Pace, P.; Pescatore, G.; Scarpelli, R.;
Stillmock, K.; Witmer, M. V.; Rowley, M. J. Med. Chem. 2008,
5
1, 5843.
1
4. Sato, M.; Motomura, T.; Aramaki, H.; Matsuda, T.; Yamashita,
M.; Ito, Y.; Kawakami, H.; Matsuzaki, Y.; Watanabe, W.;
Yamataka, K.; Ikeda, S.; Kodama, E.; Matsuoka, M.; Shinkai, H.
J. Med. Chem. 2006, 49, 1506.
1
5. Hazuda, D. J.; Felock, P.; Witmer, M.; Wolfe, A.; Stillmock, K.;
Grobler, J. A.; Espeseth, A.; Gabryelski, L.; Schleif, W.; Blau, C.;
Miller, M. D. Science 2000, 287, 646.
1
6. Hazuda, D. J.; Anthony, N. J.; Gomez, R. P.; Jolly, S. M.; Wai, J.
S.; Zhuang, L.; Fisher, T. E.; Embrey, M.; Guare, J. P., Jr.;
Egbertson, M. S.;Vacca, J. P.; Huff, J. R.; Felock, P. J.; Witmer,
M.V.; Stillmock, K.A.; Danovich, R.; Grobler, J.; Miller, M. D.;
Espeseth, A. S.; Jin, L.; Chen, I. W.; Lin, J. H.; Kassahun, K.;
Ellis, J. D.; Wong, B. K.; Xu, W.; Pearson, P. G.; Schleif, W. A.;
Cortese, R.; Emini, E.; Summa, V.; Holloway, M. K.; Young, S.
D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 11233.
1
7. U.S. Food and Drug Administration.
http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?f
useaction=Search.DrugDetails Accessed Aug 29 2013
18. Marinello, J.; Marchand, C.; Mott, B. T.; Bain, A.; Thomas, C. J.;
Pommier, Y. Biochemistry 2008, 47, 9345.
1
9. Goethals, O.; Clayton, R.; Van Ginderen, M.; Vereycken, I.;
Wagemans, E.; Geluykens, P.; Dockx, K.; Strijbos, R.; Smits, V.;
Vos, A.; Meersseman, G.; Jochmans, D.; Vermeire, K.; Schols,
D.; Hallenberger, S.; Hertogs, K. J. Virol. 2008, 82, 10366.
0. Patil, S.; Kamath, S.; Sanchez, T.; Neamati, N.; Schinazi, R. F.;
Buolamwini, J. K. Bioorg. Med. Chem. 2007, 15, 1212.
1. Sharma, H.; Cheng, X.; Buolamwini, J. K.. J. Chem. Inf. Model.
2
2
2
2
012, 52, 515.
2. Hare, S.; Gupta, S. S.; Valkov, E.; Engelman, A.; Cherepanov, P.
Nature 2010, 464, 232.
2
2
3. Jang, S. B. Tetrahedron Lett. 1997, 38, 1793.
4. Roidl, G.; Enkelmann, V.; Adams, R. D.; Bunz, U. H. J.
Organomet. Chem. 1999, 578, 144.
2
2
5. Furstner, A.; Mamane, V. J. Org. Chem. 2002, 67, 6264.
6. Kim, Y. H.; Lee, H.; Kim, Y. J.; Kim, B. T.; Heo, J. N. J. Org.
Chem. 2008, 73, 495.
2
2
2
3
7. Jiang, X. H.; Song, L. D.; Long, Y. Q. J. Org. Chem. 2003, 68,
7
555.
8. Bucher, G.; Halupka, M.; Kolano, C.; Schade, O.; Sander, W.
Eur. J. Org. Chem. 2001, 3, 545-552.
9. Sharma, H.; Patil, S.; Sanchez, T. W.; Neamati, N.; Schinazi, R.
F.; Buolamwini, J. K. Bioorg. Med. Chem. 2011, 19, 2030.
0. Stuyver, L. J.; Lostia, S.; Adams, M.; Mathew, J. S.; Pai, B. S.;
Grier, J.; Tharnish, P. M.; Choi, Y.; Chong, Y.; Choo, H.; Chu, C.
K.; Otto, M. J.; Schinazi, R. F. Antimicrob. Agents Chemother.
2
002, 46, 3854.
3
1. Schinazi, R. F.; Sommadossi, J. P.; Saalmann, V.; Cannon, D. L.;
Xie, M. Y.; Hart, G. C.; Smith, G. A.; Hahn, E. F. Antimicrob.
Agents Chemother. 1990, 34, 1061.
32. Sommadossi, J. P.; Carlisle, R.; Schinazi, R. F.; Zhou, Z.
Antimicrob. Agents Chemother. 1988, 32, 997.

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Table 1. Structure and HIV-1 IN inhibitory activities of phenanthrene β-diketo acids
1
2
3
4
5
6
7
Comp.
R
R
R
R
R
R
R
Activity (IC50 µM)
a b
3′-P
ST
3 ± 2
c
13
14
15
16
17
18
19
20
H
DKA
H
DKA
H
DKA
DKA
H
H
H
F
H
H
H
H
H
Cl
H
H
H
H
F
Cl
H
H
H
F
F
H
11 ± 2
35 ± 13
83 ± 15
63 ± 12
12 ± 3
5 ± 3
H
H
H
H
H
H
H
4 ± 1
63 ± 16
8 ± 2
1.4
1.3 ± 0.1
4 ± 1
H
H
H
H
Cl
H
F
DKA
DKA
DKA
H
H
H
H
H
H
19 ± 2
11 ± 4
H
H
Cl
1.2 ± 0.3
DKA
H
H
DKA
H
H
2
2
2
2
2
1
2
3
4
5
OCH3
OCH3
H
DKA
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
F
DKA
DKA
H
H
DKA
44 ± 10
32 ± 12
25 ± 7
23 ± 6
9 ± 2
6 ± 2
3 ± 2
2.7 ± 2
4.8 ± 2
0.38 ±
0.11
H
H
H
H
d
d
d
e
S-1360
11 ± 2
0.6 ± 0.1
a
Represents 3′-processing.
b
Represents strand transfer.
c
Represents β-diketo acid.
d
Compounds synthesized previously.
e
Standard.
Table 2. Anti-HIV activity of selected novel potent derivatives
Comp.
Anti-HIV-1 Activity
Cytotoxicity (IC50, µM)
c
a
b
in PBMCs , EC (µM)
PBMC CEM VERO
5
0
1
7
8
20.9 ± 15.8
27.5 ± 10.2
0.005 ±
12.1
13.1
14.3
7.2
1
4.1
.0
1
4.5
4
AZT
56.0
(
control)
0.0009
>100
a
Human peripheral blood mononuclear cells.
b
Effective concentrations inhibiting 50 % HIV replication.

ACCEPTED MANUSCRIPT
c
Human CEM lymphoblastic leukemia cells.

ACCEPTED MANUSCRIPT
O
O
O
OH
F
OH
O
N
F
O
H
N
N
N
N
N
N
NH
O
S-1360
MK-0518
F
O
O
OH
O
Cl
OH
F
F
O
N
H
N
O
N
N
O
H
O
OH
GSK-1349572
GS-9137
Figure 1. Representative structures of potent HIV-1 integrase inhibitors.

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Figure 2. (a) Two-binding modes of compound 18 within the active site of IN-DNA homology model, (b) binding
interactions of one of the pose of compound 18. Ligand is colored by yellow carbons and represented by tubes, (c) binding
interactions of the second pose of compound 18. Ligand is colored with gray carbons and represented by ball and stick.
2
+
Residues are shown within 4 Å of the ligand in the IN active site. Mg ions are represented by magenta spheres. Active
site residues is represented by tubes and colored by element.

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3 4 3
Scheme 1. Reagent and Conditions: (a) Pd[P(Ph) ] (polymer bound) (1mol%), Et N, dioxane, EtOH ice/reflux , 6h-2
days (b) dimethyl- (1-diazo-2-oxopropyl) phosphonate, K
2
CO
3 2
, MeOH, ice, 7-17 h (c) PtCl , Toluene, reflux, 24 h.
o
Scheme 2. Reagent and Conditions: (a) Microwave: 10 min, 150 C, Pd[P(Ph)
3
]
4
(4 mol%), S-Phos (6 mol%), Cs
2
CO
3
,
Toluene:EtOH 2:1.

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°
Scheme 3. Reagent and Conditions: (a) t-butanol, pyridine, ether, rt, 2h (b) NaOMe, MeOH, 60 C, 4h (c) aq. NaOH,
MeOH, THF, 6h.

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Graphical Abstract
Synthesis, docking, and biological studies of
phenanthrene β-diketo acids as novel HIV-1
integrase inhibitors
Leave this area blank for abstract info.
a
b
b
c
d
a, ∗
Horrick Sharma , Tino W. Sanchez , Nouri Neamati , Raymond F. Schinazi , Xiaolin Cheng , and John K. Buolamwini