Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides

Article abstract of DOI:10.1021/co500067c

Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several analogues showed diverse and interesting biological activities.

Full text of DOI:10.1021/co500067c

Research Article
pubs.acs.org/acscombsci
Solution-Phase Parallel Synthesis of Acyclic Nucleoside Libraries
of Purine, Pyrimidine, and Triazole Acetamides
Ashish K. Pathak,* Vibha Pathak, and Robert C. Reynolds*,†
Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
S
* Supporting Information
ABSTRACT: Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets
using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap
Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues
which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with
several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide
analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under
inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading
prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were
analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial
screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several
analogues showed diverse and interesting biological activities.
KEYWORDS: solution-phase, parallel synthesis, nucleoside libraries, acyclic nucleosides, high-throughput screening, drug discovery
INTRODUCTION
■
The introduction of rapid DNA sequencing and the genomic
sciences, combinatorial chemistry, and cell- and protein-based
assays, under automated high throughput screening (HTS) has
led to a new paradigm in drug discovery.1 The ultimate goal is
to translate the massive output from these higher throughput
technologies faster than historical approaches and to more
rapidly establish the roles of new biological targets in human
disease. The use of novel libraries of chemical probes in the
MLSMR is allowing a long-term vision to be realized through
new government initiatives for developing highly selective drug-
like candidates that will swiftly translate to benefits in public
health. In this approach, small molecule chemical probes are
used to study specific enzymatic processes, protein−protein
interactions, or even whole-cell metabolic pathways in a high
throughput chemical biology approach.2 As such, high quality,
diverse and unique small molecules are constantly in demand in
order to probe a wider range of new biological space. In
response, over the last several decades, special attention has
been directed at providing diverse and well-characterized sets of
small molecule probes for numerous HTS screens against an
Figure 1. General representation of library structures.
ever-growing platform of new biological targets in both
phenotypic and enzyme-based assays. For example, a major
goal in the field of diversity-oriented synthesis has been the
Received: April 24, 2014
Revised: June 4, 2014
© XXXX American Chemical Society
A
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emphasis has been given to chemical reactions in parallel and
combinatorial formats using solution-phase and solid supported
approaches on these diverse chemical scaffolds.5 Solid-phase
synthesis is used extensively as it has provided ease of purifica-
tion. On the other hand, certain benefits naturally accrue from
solution-phase approaches including good yields of higher
quantities of targets based on reaction homogeneity. Both of
these techniques are crucial to produce the required numbers of
diverse new small molecules at reasonable cost.
Table 1. Predicted Values of Physicochemical Properties
of Library Members
entry
parameter
range
av
1
2
3
4
5
6
7
molecular weight (MW)
LogP
239−504
371.5
−1.88−4.29
−3.13−4.28
0−4
3−10
1.21
LogD at pH 7.40
0.58
2.0
number of H-bond donor
number of H-bond acceptors
total polar surface area (TPSA) (Å2) 66.90−194.76
6.5
130.83
187.62
Natural nucleic acids and synthetic analogues are compo-
nents of numerous clinically used drugs, particularly antiviral,
and anticancer agents.6 Typical nucleoside drugs function as
antimetabolites, and act through direct incorporation into
nucleoside metabolic pathways interfering in downstream
enzyme-mediated reactions or the general processes of RNA
or DNA structure and function. Drugs based on these natural
scaffolds show diverse activities including anticancer, antipar-
asitic, antifungal and antiviral action. For example, a number of
nucleoside-based antimetabolites are used for cancer treatment
such as, cytarabine (cytosine arabinoside, Ara-C), an antileukemic
agent used for the treatment of acute myeloid leukemia and
non-Hodgkin’s lymphoma; Purinethol (6-mercaptopurine, 6-
MP) used for the acute lymphoblastic leukemia, 5-fluorouracil
(Efudex; 5-FU, a thymidylate synthase inhibitor used for the
treatment of colon, rectal, stomach, skin, breast, and pancreatic
cancer; antileukemic agents Vidaza (5-azacytidine) and
Dacogene (2′-deoxy-5-azacytidine, decitabine) currently the
most successful agents approved for therapy of myelodysplastic
syndrome. Acyclovir [Zovirax, 9-(2-hydroxyethoxymethyl)guanine]
is an acyclic guanine analogue that selectively misincorporates
into DNA in infected cells via the herpesvirus thymidine kinase
and is active against HSV-1 and HSV-2 infections.7 Acyclovir,
similar to the many other antiherpetic agents (penciclovir,
ganciclovir, and their pro-drug forms), belongs to the group of
acyclic nucleoside analogues, compounds having the sugar
furanose ring substituted in a nucleoside with a polyhydroxylic
polar solvent accessible surface area
76.38−298.86
(polar SASA) (Å2)
efficient production of small-molecule libraries in biologically
relevant chemical space.3 Subsequently, screening across a wide
range of newly developed biological HTS assays provides direct
biological validation of the functional capabilities of these
libraries. Toward this end, diverse varieties of natural product-
based or inspired libraries have been synthesized, and early
results are promising.4
The Pilot Scale Library (PSL) Program was implemented
to specifically produce libraries based on biologically relevant
scaffolds with greater chemical diversity than provided by
commercial chemical library space. Furthermore, successful
approaches used to generate these libraries should be robust,
leading to easily purified samples in high enough yields to allow
deposition of sufficient material to supply the NIH Roadmap
screening centers. Ideally, a funded grant would produce small
diverse sets (∼15−30 members) from highly biologically
relevant scaffolds. Sample acceptance into the MLSMR requires
compounds with >90% purity by HPLC and fully characterized
by NMR and MS spectral techniques. These small diverse sets
would possess, in theory, broader biological relevance, and
would more likely lead to hits against the numerous new targets
deriving from genomics and disease pathway and metabolism
analyses. For the purpose of chemical library generation, special
Figure 2. Graphical representations of physicochemical properties distribution of library members.
B
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Scheme 1. Synthesis of 6-Benzylhypoxanthine-9-acetamides and 6-Benzyladenine-9-acetamides
carbon chain.8 These compounds represent the so-called
second generation of nucleoside antimetabolites where the
structural resemblance to a natural metabolite is only present in
the nucleic acid. Typically, acyclic nucleosides are less toxic
because of preferential metabolism by pathogens such as viruses
(e.g., acyclovir and gancyclovir). Our initial interest based
on PSL requirements were to use these scaffolds to produce
libraries that could not enter standard eukaryotic metabolism
but would appear as routine and diverse three-dimensional
pharmacophores filling alternative 3D chemical space. Pursuant
to these interests, our nucleoside-like libraries did not contain a
5′-hydroxyl function that might be phosphorylated allowing
further progression into crucial nucleoside metabolic pathways.9
Rather, they were designed around the class of nucleoside
antibiotics that have interesting and alternative modes of action.
We were interested in acyclic nucleoside structures since many
of these acylic nucleoside scaffolds with an amide bond10 were not
well represented in commercial chemical space, including the
MLSMR (http://www.ncbi.nlm.nih.gov/pcsubstance) (Figure 1).
Furthermore, the chemistry was well established in the preparation
C
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Scheme 2. Synthesis of 6-Methylthioguanine-9-acetamides and Structures of Analogues 69−93
Scheme 3. Synthesis of Thymine-3-acetamides and Structures of Analogues 94−128
of the peptide nucleic acids, or PNAs, that have been studied
as alternative DNA scaffolds, and, considering the ease of this
chemistry, it is notable that there are very few examples of using
the starting reagents for the PNAs to generate chemical diver-
sity.11 Hence, we have designed and prepared acyclic
nucleoside antibiotic12 like small molecule libraries under the
Pilot Scale Library Program of the NIH Roadmap Initiative
to probe specific or general biological activities. We report,
herein, the initial phase of this program, the high throughput
automated parallel preparation of a small library of 181
compounds comprising 6-benzylhypoxanthine, 6-benzylade-
nine, 6-thiomethylguanine, thymine, Cbz-cytosine, cytosine,
and 3-(3,4-dimethylphenylcarbamoyl)-1H-1,2,4-triazole acet-
amides (Figure 1 and Schemes 1−6). A set of diverse amines
were chosen after a computational diversity analysis using
Pipeline Pilot program with the proprietary functional class
fingerprints.13 The predicted ranges of physicochemical proper-
ties such as LogD at pH 7.0, LogP, range of masses in amu,
D
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Scheme 4. Synthesis of Benzaloxycytosine-3-acetamides and Structures of Analogues 129−151
Scheme 5. Synthesis of 2-(3-(3,4-Dimethylphenylcarbamoyl)-1H-1,2,4-triazol-1-yl)acetamides and Structures of Analogues
152−173
hydrogen bond acceptor (HBA), hydrogen bond donor (HBD),
total polar surface area (TPSA in Å2), and total polar sol-
vent accessible surface area (SASA) (Polar SASA in Å2) of
library members are represented in Table 1 and graphical
representations of physicochemical properties distribution of
library members are shown in Figure 2. The predicted values
of physicochemical properties for these library members are,
for the most part, well within accepted parameters for small
molecule libraries.
RESULTS AND DISCUSSION
■
Synthesis of the required starting acetic acid analogues of
nucleobases (6-benzylhypoxanthine, 6-benzyladenine, 6-
(methylthio)guanine, thymine, Cbz-cytosine and cytosine)
E
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Scheme 6. Synthesis of Cytosine-3-acetamides and Structures of Analogues 174-192
and 1,2,4-triazole base A(i−vii) in sufficient quantities was the
first task to achieve the synthesis of the desired libraries
B(i−vii) represented in Figure 1. Purine bases A(i and ii),
2-(6-(benzyloxy)-9H-purin-9-yl)acetic acid (3A),14 and 2-(6-
(benzylamino)-9H-purin-9-yl)acetic acid (3B),15 were synthe-
sized as represented in Scheme 1 by reported methods. In
short, alkylation with the 2-bromoacetate of commercially
available 6-benzylhypoxanthine and 6-benzyladenine in the
presence of K2CO3 produced methyl esters 2A and 2B in
excellent yields. Further, saponification of 2A and 2B with 1N
NaOH in methanol gave the desired acetic acid analogues 3A
and 3B respectively. Synthesis of purine base A(iii), 2-(2-
amino-6-(methylthio)-9H-purin-9-yl)acetic acid (5), was ac-
complished as shown in Scheme 2. Starting from commercially
available 6-chloroguanine which was N-alkylated with methyl
2-bromoacetate in the presence of K2CO3 in DMF for 24 h
provided 4 in good yield after column purification. Reaction
of precursor compound 4 with NaSCH3 in MeOH not only
installed the thiomethyl group on 4, but saponified the methyl
ester to provide final product 6-(methylthio)guanine acetic acid
(5). Pyrimidine bases A(iv and v), (thymin-1-yl)acetic acid
(7),16 and Cbz-cytosine acetic acid (9)17 were synthesized from
thymine and Cbz-cytosine respectively as reported, and the
chemistry is shown in Schemes 3 and 4 respectively. Base
A(vi), 2-(3-(3,4-dimethylphenylcarbamoyl)-1H-1,2,4-triazol-1-yl)-
acetic acid (11), was synthesized starting from commercially
available 1,2,4-triazole-3-carboxylic acid as shown in Scheme 5.
In the first step, 1,2,4-triazole-3-carboxylic acid was reacted
overnight with 3,4-diemethylaniline with coupling reagent
HATU [(2-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethy-
luronium hexafluorophosphate] and base N,N-diisoproplyethyl
amine (DIPEA) in DMF at room temperature to give amide 10
in 75% yield. Next, 10 was suspended in DMF and reacted
overnight at room temperature with methyl bromoacetate and
K2CO3. After standard work-up and purification by column
chromatography, the methyl ester of the target acetic acid 11
was obtained as a white powder in 70% yield. Finally, saponification
of the methyl ester with 1 N NaOH in MeOH at room
temperature produced the desired acetic acid analogue 11 in
excellent yield after purification.
Once all the starting materials were in hand, we employed
several peptide coupling reagents and various solution-phase
conditions in several model amide forming reactions. A number
of different nucleobase carboxylic acids and various amines
were reacted using alternative coupling reagents such as HBTU
[2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexa-
fluorophosphate], DCC [N,N′-dicyclohexylcarbodiimide] or
HATU to achieve our targeted acyclic amide-linked compounds
B(i−viii) given in Figure 1. These reagents are reported to
rapidly provide the peptide linkage in high yield with little or no
racemization. In our hands, the best results in terms of yield
and reaction purity were obtained with HATU (1.0 equiv) and
DIEA (1.5 equiv) in CH3CN for 180 min at room temperature.
The reaction conditions were easily translated to a 24-well
reaction block at a 100 mg scale to ensure production of
sufficient pure product as per requirement of the PSL program.
These reactions were performed once and the yields are not
further optimized. In certain cases, efficient coupling did not
result based on TLC, and these reactions were discarded
and are not reported. After removal of the reaction solvent,
DMF, under centrifugal evaporation using a 24-vessel rack,
automated purification produced the expected pure targets.
The structures of these analogues are shown in Schemes 1-5.
However, synthesis of a 19-member cytosine library as shown
in Scheme 6 was carried out in two steps starting from Cbz-
cytosine acetic acid 9 in one pot. In step 1, the standard amide
coupling was achieved and solvent was evaporated from the
reaction block under centrifugal evaporation. In step 2, the
Cbz-protecting group was removed by reduction. To each
vessel in the block was added 20 mg of Pd/C and 2 equiv
of ammonium formate followed by 5 mL of MeOH. The
reaction block was shaken overnight at room temperature. The
reaction mixtures were aspirated via syringe, and were further
filtered through micrometer filter adapters onto RediSep
F
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Table 2. Representative Active Analogues in 12 Bioassays
PubChem
Bioassay
a
ID
assay title
active analogues (activity conc.)
686979
qHTS for Inhibitors of human tyrosyl-DNA phosphodiesterase
1 (TDP1): qHTS in cells in presence of CPT.
39 (8.2 μM), 43 (4.1 μM), 44 (10.3 μM), 45 (6.5 μM), 48 (18.4 μM), 52 (18.4 μM), 67
(5.8 μM), 69 (13.0 μM), 72 (16.4 μM), 74 (23.1 μM), 79 (14.6 μM), 91 (14.6 μM), 92
(1.4 μM), 150 (5.2 μM), 173 (18.4 μM)
686978
qHTS for Inhibitors of human tyrosyl-DNA phosphodiesterase
1 (TDP1): qHTS in cells in absence of CPT.
14 (16.4 μM), 21 (16.4 μM), 39 (2.6 μM), 43 (2.9 μM), 44 (5.8 μM), 45 (13.0 μM), 48
(8.2 μM), 67 (1.8 μM), 69 (14.6 μM), 72 (8.2 μM), 79 (20.6 μM), 83 (14.6 μM), 91
(20.6 μM), 92 (0.8 μM)
651820
602438
qHTS Assay for Inhibitors of Hepatitis C Virus (HCV)
29 (0.6 μM), 39 (0.6 μM), 69 (3.5 μM), 72 (8.9 μM), 91 (4.5 μM), 92 (1.4 μM), 108
(2.8 μM), 109 (2.8 μM), 118 (0.5 μM), 139 (2.8 μM), 150 (4.5 μM)
qHTS identification of modulators of interaction between CendR 132, 139, 140, 143, 175, 177, 178, 188
and NRP-1 using Fluorescence Polarization assay.
652048
652051
652115
651640
qHTS of D3 Dopamine Receptor Agonist: qHTS
qHTS of D3 Dopamine Receptor Potentiators: qHTS
MLPCN SirT-5 Measured in Biochemical System
55, 58, 67, 77, 185, 188
55, 58, 67, 77, 185, 186
45, 73, 76, 94, 110
DENV2 CPE-Based HTS Measured in Cell-Based and
Microorganism Combination System Using Plate Reader
33, 49, 138, 144, 149
651610
720504
493131
504467
HIV entry: Env-mediated Cell Fusion Measured in Cell-Based
System Using Plate Reader
67, 150, 169
qHTS for Inhibitors of PLK1-PDB (polo-like kinase 1 - polo-box 14 (23.8 μM), 22 (21.2 μM), 108 (21.2 μM), 125 (26.7 μM)
domain)
Activator for delta FosB/delta FosB homodimer Measured in
Biochemical System Using Plate Reader
23, 52, 73, 178
qHTS screen for small molecules that inhibit ELG1-dependent
DNA repair in human embryonic kidney (HEK293T) cells
expressing luciferase-tagged ELG1
67 (1.0 μM), 69 (6.5 μM), 77 (23.1 μM), 92 (2.3 μM)
504444
Nrf2 qHTS screen for inhibitors
28 (3.6 μM), 67 (3.6 μM), 74 (23.1 μM)
a
Concentration at which compound exhibits half-maximal efficacy, AC50. Extrapolated AC50’s also include the highest efficacy observed and the
concentration of compound at which it was observed.
solid sample loading prepacked cartridges (2.5 g of silica)
followed by drying under vacuum before purification by column
chromatography on automated medium pressure liquid
chromatographic (MPLC) system. Each purified product
was checked for purity by HPLC and characterized by NMR
and mass analysis. General experiment procedures, detailed
analytical data and complete list of structures along with
their PubChem ID’s as hyperlinks to all library members are
provided in Supporting Information.
(29 μM), and 26 (43 μM). Also, these compounds were tested
via in house HTS screening in vitro against three human tumor
cell lines (HT29 colon, PC3 prostate, and MDA-MB-231
breast) as described.9a Only eight compounds showed cyto-
toxicity at less than 50 μM in one or more of these cells and
data are provided in Table 3.
Table 3. Effect of Analogues on Cancer Cell Growth
cancer cell line screen
a
a
a
analogues
HT29 (CC50)
PC3 (CC50)
MDA-MB-231 (CC50)
BIOLOGICAL EVALUATIONS
■
14
23
39
43
48
57
67
172
30
6
>50
>50
22
42
43
The prepared analogues were submitted (20 mg) to the MLSMR,
the Roadmap compound repository, for further quality assessment
and distribution to the various NIH screening centers as probes
against a wide range of biological assays. Each submitted
compound has a unique PubChem ID number (CID), and
these numbers are provided herein as a hyperlink with structure
in the Supporting Information section to allow the reader ready
access to all PubChem information. To date, the reported
libraries have been screened against 301 protein targets from
530 bioassays. Approximately 88 compounds out of 185
analogues and precursors reported in this article have shown
activity in one or more assays. Several library members were
active in 147 bioassays (details of the assays with assay ID’s of
hits are summarized in Supporting Information as a table).
Representative 12 bioassays data with active library members
are shown in Table 2.
All library members were also tested for inhibition of
Mycobacterium tuberculosis (Mtb H37Rv) growth in vitro. The
libraries were evaluated in a dose response (DR) format against
Mtb and in a cell cytotoxicity assay using a mammalian cell
line, VERO cells, as previously described.18 Certain analogues
showed Mtb growth inhibition (IC90 <50 μM) and these are
85 (2.0 μM), 186 (21 μM), 31 (26 μM), 39 (27 μM), 172
3
25
5
>50
>50
>50
32
26
2
17
7
>50
45
2
15
16
17
a
CC50 = Concentrations in μM of analogue required for 50% growth
inhibition of cancer cells.
CONCLUSIONS
■
Herein, we report the synthesis and preliminary biological
evaluation of a diverse library of 181 purine, pyrimidine, and
1,2,4-triazole acetamide analogues which were prepared in a
high throughput solution-phase parallel reaction format under
the Pilot Scale Library Program of the NIH Roadmap initiative.
These reactions were performed in 24-well reaction blocks with
automatic reagent dispensing under inert atmosphere. All com-
pounds were characterized by NMR and HRMS, and were
checked for purity by HPLC before submission to The Molec-
ular Libraries Small Molecule Repository (MLSMR) at NIH.
G
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(d) Dolle, R. E.; Nelson, K. H. Comprehensive survey of
combinatorial library synthesis. J. Comb. Chem. 1999, 1, 235−282.
(e) Geysen, H. M.; Schoenen, F.; Wagner, D.; Wagner, R.
Combinatorial compound libraries for drug discovery: an ongoing
challenge. Nat. Rev. Drug Discovery 2003, 2, 222−230. (f) Dolle, R. E.
Comprehensive survey of combinatorial library synthesis: 2003. J.
Comb. Chem. 2004, 6, 623−679. (g) Kaisera, M.; Wetzel, S.; Kumar,
K.; Waldmann, H. Biology-inspired synthesis of compound libraries.
Cell. Mol. Life Sci. 2008, 65, 1186−1201.
Preliminary screening was performed through the Molecular
Libraries Probe Production Centers Network (MLPCN)
program and further screening continues through this program
(for updates see http://www.ncbi.nlm.nih.gov/pcsubstance and
input search term Robert Reynolds).
ASSOCIATED CONTENT
* Supporting Information
■
S
Additional materials as described in the text and detailed
analytical data for all new analogues. This material is available
free of charge via the Internet at http://pubs.acs.org.
(6) (a) Robins, R. K.; Revankar, G. R. Purine analogs and related
nucleosides and nucleotides as antitumor agents. Med. Res. Rev. 1985,
5, 273−296. (b) Cheson, B. D.; Keating, M. J.; Plunkett, W. Nucleoside
Analogues in Cancer Therapy; Marcel Dekker: New York, 1997; Vol.
12. (c) Scozzafava, A.; Owa, T.; Mastrolorenzo, A.; Supuran, C.
Anticancer and antiviral sulfonamides. Curr. Med. Chem. 2003, 10,
925−953. (d) Lee, W.; Martin, J. Perspectives on the development of
acyclic nucleoside analogs as antiviral drugs. Antiviral Res. 2006, 71,
254−259. (e) Srivastava, R.; Bhargava, A.; Singh, R. Synthesis and
antimicrobial activity of some novel nucleoside analogues of adenosine
and 1,3-dideazaadenosine. Bioorg. Med. Chem. Lett. 2007, 17, 6239−
6244. (f) Komiotis, D.; Manta, S.; Tsoukala, E.; Tzioumaki, N.
Antiviral unsaturated nucleosides. Curr. Med. Chem. 2008, 7, 219−244.
(g) Arts, E.; Hazuda, D. HIV-1 antiretroviral drug therapy. Cold Spring
Harbor Perspect. Med. 2012, 2, 1−23. (h) Sun, R.; Wang, L. Inhibition
of Mycoplasma pneumoniae growth by FDA-approved anticancer and
antiviral nucleoside and nucleobase analogs. BMC Microbiol. 2013, 13,
184−195.
AUTHOR INFORMATION
Corresponding Authors
*E-mail: pathaka@southernresearch.org.
*E-mail: rcr12lkt@uab.edu.
■
Present Address
†Robert C. Reynolds: Department of Chemistry, University of
Alabama at Birmingham, 901 14th Street South, Birmingham,
AL 35294, U.S.A.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
(7) Freeman, S.; Gardiner, J. M. Acyclic nucleosides as antiviral
compounds. Mol. Biotechnol. 1996, 5, 125−137.
This work was supported through NIH Grant 1P41 GM086163-01
to Robert C. Reynolds. We thank Mr. James M. Riordan, Ms.
Jackie Truss, Mr. Mark Richardson, and Mr. David Poon of the
Molecular and Spectroscopy Department at Southern Research
Institute for providing analytical and spectral data.
(8) (a) De Clercq, E.; Holy, A.; Rosenberg, I.; Sakuma, T.; Balzarini,
́
J.; Maudgal, P. C. A novel selective broad-spectrum anti-DNA virus
agent. Nature 1986, 323, 464−467. (b) Chu, C. K.; Culter, S. J.
Chemistry and antiviral activities of acyclonucleosides. J. Heterocyclic
Chem. 1986, 23, 289−319. (c) Ullas, G. V.; Chu, C. K.; Ahn, M. K.;
Kosugi, Y. Synthesis of C-nucleoside analog of (S)-9-(2,3-
dihydroxypropyl)adenine and related acyclonucleosides. J. Org.
Chem. 1988, 53, 2413−2418. (d) De Clercq, E. Towards an effective
chemotherapy of virus infections: Therapeutic potential of Cidofovir
[(S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl] cytosine, HPMPC]
for the treatment of DNA virus infections. Collect. Czech. Chem.
Commun. 1998, 63, 480−506. (e) Safrin, S. J.; Jaffe, H. S. Adv. Exp.
REFERENCES
■
(1) (a) Shoemaker, R. H.; Scudiero, D. A.; Melillo, G.; Currens, M. J.;
Monks, A. P.; Rabow, A. A.; Covell, D. G.; Sausville, E. A. Application
of high-throughput, molecular-targeted screening to anticancer drug
discovery. Curr. Top. Med. Chem. 2002, 2, 229−246. (b) Ramstrom,
̈
O.; Lehn, J.-M. Drug discovery by dynamic combinatorial libraries.
Nat. Rev. Drug Discovery 2002, 1, 26−36. (c) Mayr, L. M.; Bojanic, D.
Novel trends in high-throughput screening. Curr. Opin. Pharmacol.
Med. Biol. 1999, 458, 111−120. (f) De Clercq, E.; Holy, A. Acyclic
́
́
2009, 9, 580−588. (d) Rodríguez-Devora, J. I.; Shi, Z. D.; Xu, T.
Direct assembling methodologies for high-throughput bioscreening.
Biotechnol. J. 2011, 6, 1454−65.
nucleoside phosphonates: A key class of antiviral drugs. Nat. Rev. Drug
Discovery 2005, 4, 928−940. (g) Dolak
́
ova,
̌
́ ́ ̌ ̌
Masojídkova, M.; Solínova, V.; Kasicka, V.; Holy, A. Acyclic nucleoside
́ ̌
́
P.; Dracínsky, M.;
́
(2) (a) Crews, C. M. Deciphering isozyme function: Exploring cell
biology with chemistry in the post-genomic era. Chem. Biol. 1996, 3,
961−965. (b) Lenz, G. R.; Nash, H. M.; Jindal, S. Chemical ligands,
genomics and drug discovery. Drug Discovery Today 2000, 5, 145−156.
(c) Schreiber, S. L. Target-oriented and diversity-oriented organic
synthesis in drug discovery. Science 2000, 287, 1964−1969.
(3) (a) Thompson, L. A.; Ellman, J. A. Synthesis and applications of
small molecule libraries. Chem. Rev. 1996, 96, 555−600. (b) Tan, D. S.
Diversity-oriented synthesis: Exploring the intersections between
chemistry and biology. Nat. Chem. Biol. 2005, 1, 74−84.
(4) (a) Prabhat, A.; Joseph, R.; Chou, D. T. H. Toward high-
throughput synthesis of complex natural product-like compounds in
the genomics and proteomics age. Chem. Biol. 2002, 9, 145−156.
(b) Bauer, R. A.; Wurst, J. M.; Tan, D. S. Expanding the range of
“druggable” targets with natural product-based libraries: An academic
perspective. Curr. Opin. Chem. Biol. 2010, 14, 308−314.
(5) (a) Janda, K. D. Tagged versus untagged libraries: Methods for
the generation and screening of combinatorial chemical libraries. Proc.
Natl. Acad. Sci. U.S.A. 1994, 91, 10779−10785. (b) Andres, C. J.;
Denhart, D. J.; Deshpande, M. S.; Gillman, K. W. Recent advances in
the solid phase synthesis of druglike heterocyclic small molecules.
Comb. Chem. High Throughput Screening 1999, 2, 191−210. (c) Went-
worth, P., Jr.; Janda, K. D. Generating and analyzing combinatorial
chemistry libraries. Curr. Opin. Biotechnol. 1998, 9, 109−115.
bisphosphonates: synthesis and properties of chiral 2-amino-4,6-
bis[(phosphonomethoxy)alkoxy]pyrimidines. Eur. J. Med. Chem. 2009,
44, 2408−2424.
(9) (a) Moukha-chafiq, O.; Reynolds, R. C. Parallel solution-phase
synthesis of an adenosine antibiotic analog library. ACS Comb. Sci.
2013, 15, 147−152. (b) Moukha-Chafiq, O.; Reynolds, R. C. Synthesis
of novel peptidyl adenosine antibiotic analogs. Nucleos. Nucleot. Nucl.
2014, 33, 53−63. (c) Moukha-Chafiq, O.; Reynolds, R. C. Parallel
solution-phase synthesis and general biological activity of a uridine
antibiotic analog library. ACS Comb. Sci. 2014, DOI: 10.1021/
co4001452.
(10) (a) Efimtseva, E. V.; Mikhailov, S. N.; Jasko, M. V.; Malakhov,
D. V.; Semizarcv, D. G.; Fomicheva, M. V.; Kern, E. R. Acyclic
nucleoside and nucleotide analogues with amide bond. Nucleosides
Nucleotides 1995, 14, 373−375. (b) Kim, Y.-C.; Gallo-Rodriguez, C.;
Jang, S.-Y.; Nandanan, E.; Adams, M.; Harden, T. K.; Boyer, J. L.;
Jacobson, K. A. Acyclic analogues of deoxyadenosine 3′,5′-bi-
sphosphates as P2Y1 receptor antagonists. J. Med. Chem. 2000, 43,
746−755.
(11) (a) Shakeel, S.; Karim, S.; Ali, A. Peptide nucleic acid (PNA)
A review. J. Chem. Technol. Biot. 2006, 81, 892−899. (b) Corradini, R.;
Sforza, S.; Tedeschi, T.; Totsingan, F.; Manicardi, A.; Marchelli, R.
Peptide nucleic acids with a structurally biased backbone. Updated
H
dx.doi.org/10.1021/co500067c | ACS Comb. Sci. XXXX, XXX, XXX−XXX

ACS Combinatorial Science
Research Article
review and emerging challenges. Curr. Top. Med. Chem. 2011, 11,
1535−54.
(12) (a) Epple, R.; Kudirka, R.; Greenberg, W. A. Solid-phase
synthesis of nucleoside analogues. J. Comb. Chem. 2003, 5, 292−310.
(b) Isono, K. Nucleoside antibiotics: Structure, biological activity and
biosynthesis. J. Antibiot. 1988, 41, 1711−1739. (c) Isono, K. Current
progress on nucleoside antibiotics. Pharmacol. Ther. 1991, 52, 269−
286. (d) Knapp, S. Synthesis of complex nucleoside antibiotics. Chem.
Rev. 1995, 95, 1859−1876. (e) Rosemeyer, H. The chemodiversity of
purine as a constituent of natural products. Chem. Biodiversity 2004, 1,
361−401. (f) Lagoja, I. M. Pyrimidines as constituent of natural
biologically active compounds. Chem. Biodiversity 2005, 2, 1−50.
(13) (a) Hassan, M.; Bielawski, J. P.; Hempel, J. C.; Waldman, M.
Optimization and visualization of molecular diversity and combinato-
rial libraries. Mol. Diversity 1996, 2, 64−74. (b) Khanna, V.;
Ranganathan, S. Structural diversity of biologically interesting datasets:
A scaffold analysis approach. J. Cheminf. 2011, 3, 30.
(14) (a) Winther, L. Systems and methods for biological and
chemical detection, comprising automatic selection of reagent sets.
PCT Int. Appl. 2009007787, 15 Jan 2009. (b) Lohse, J. Monomeric
and polymeric linkers useful for conjugating biological molecules and
other substances. PCT Int. Appl. 2007015168, 08 Feb 2007.
(15) Zlatkov, A.; Danchev, N.; Nikolova, I.; Peikov, P. Synthesis,
kinetic study and brain antihypoxic activity of 6-benzylamino-9-
purineacetic acid. Farmatsiya (Sofia, Bulg.) 2006, 53, 6−12.
(16) (a) Liu, Xue-Jun; Chen, Ru-Yu. Synthesis of novel
phosphonotripeptides containing uracil or thymine group. Phosphorus,
Sulfur Silicon Relat. Elem. 2001, 176, 19−28. (b) Katritzky, A. R.;
Narindoshvili, T. Chiral peptide nucleic acid monomers (PNAM) with
modified backbones. Org. Biomol. Chem. 2008, 6, 3171−3176.
(17) Schwergold, C.; Depecker, G.; Di Giorgio, C.; Patino, N.;
Jossinet, F.; Ehresmann, B.; Terreux, R.; Cabrol-Bass, D.; Condom, R.
Cyclic PNA hexamer-based compound: modelling, synthesis and
inhibition of the HIV-1 RNA dimerization process. Tetrahedron 2002,
58, 5675−5687.
(18) Ananthan, S.; Faaleolea, E. R.; Goldman, R. C.; Hobrath, J. V.;
Kwong, C. D.; Laughon, B. E.; Maddry, J. A.; Mehta, A.; Rasmussen,
L.; Reynolds, R. C.; Secrist, J. A., 3rd; Shindo, N.; Showe, D. N.; Sosa,
M. I.; Suling, W. J.; White, E. L. High-throughput screening for
inhibitors of Mycobacterium tuberculosis H37Rv. Tuberculosis 2009, 89,
334−353.
I
dx.doi.org/10.1021/co500067c | ACS Comb. Sci. XXXX, XXX, XXX−XXX