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DEVELOPMENT OF MICROPLATE SCREENING SYSTEM
AND CONSTRUCTION OF FLUORESCEIN-BASED
LIBRARY
FENG SUIHAN
A THESIS SUMBITTED
FOR THE DEGREE OF MASTER OF SCIENCE
DEPARTMENT OF CHEMISTRY
NATIONAL UNIVERSITY OF SINGAPORE
2010
Acknowledgements
First of all, I would like to express my deep gratitude to my supervisor, Associate Professor
Young-Tae Chang for his profound knowledge, invaluable guidance, constant support and
inspiration throughout my graduate studies. The knowledge, both scientific and otherwise,
that I accumulated under his supervision, will aid me greatly throughout my life.
Next, I would like to give my sincere thanks to Dr. Marc Vendrell and Dr. Hyung-Ho Ha, for
their warm support during my entire graduate studies.
Besides, my sincere thinks goes to Miss Siqiang Yang, who helped me to set up the
microplate screening platform.
Also, I would like to thank all the graduate students of Chang lab, Animesh, Duanting, Ghosh,
Jun-Seok, Yun-Kyung, Raj, for their cordiality and friendship. We had a great time together.
I also benefited from all other lab members, particularly but not limited to, Siti, Yee Ling,
Chew Yan, Xubin, Jeffrey, Shin Hui, Dr. Bi, Dr. Cho, Dr. Jun Li, Dr. Lees, Dr. Kang, Dr.
Kim, Dr. Park, and etc. Thanks for making the working place an enjoyable one.
I am grateful to Dr. Tan for recruiting me into NUS Medicinal Chemistry graduate program
and I am also thankful to NUS for awarding me the research scholarship.
At last, I would like to express greatest thanks to my family, particularly my wife, Bai Yang,
whose encourage and understanding help me to finish my graduate study in NUS.
i
Table of Contents
Chapter One
1.1
1.2
1.3
1.4
1.5
Introduction
1
Chemical Genetics
1
1.1.1
1
Overview
Chemical Toolboxes
3
1.2.1 Diversity Oriented Synthesis
3
1.2.2
Tagged Library Approach
5
1.2.2.1 PNA Tagged Library
5
1.2.2.2 Click Chemistry Library Approach
6
1.2.2.3 Activity-Based Protein Profiling
8
1.2.2.4 Dynamic Combinatorial Library
9
Diversity Oriented Fluorescence Library Approach
10
1.3.1
Styryl Library
10
1.3.2 Hemicyanine Library
12
1.3.3 Rosamine Library
14
1.3.4
15
BODIPY library
Screening System
16
1.4.1
16
In vitro screening
1.4.2 Cell based screening
17
Conclusion and Perspectives
18
Reference
19
ii
Chapter Two
Development of microplate screening system and
discovery of a green DNA probe
27
2.1
Introduction
27
2.2
Development of the microplate screening system
28
2.3
Discovery of a Green DNA Probe for Live-Cell Imaging
31
2.4
Experimental Section
39
2.4.1
Development of the microplate screening system
39
2.4.1.1
Preliminary Test
39
2.4.1.2
Analytes Information
40
2.4.2 Discovery of a Green DNA Probe for Live-Cell Imaging
41
2.4.2.1
General Information
41
2.4.2.2
C61 Characterization
41
2.5 Conclusion
42
Reference
43
Chapter Three
Synthesis of fluorescein-based library
46
3.1 Introduction
46
3.2 Results and discussion
47
3.2.1 Synthesis of CF library
47
3.2.2 Cell screening of CF library
51
3.3 Experimental Section
52
3.4 Conclusion
54
Reference
55
iii
Summary
Chemical genetics studies the structures and functions of genes at the molecular level using
small molecules. Probe development is thus of great interests in molecular biology,
particularly in cell imaging study. Due to the simplicity and straight forwardness,
fluorescence techniques are emerging recently to help elucidate and explain complicated
biological phenomena in cells and animals. Furthermore, the green fluorescein protein (GFP)
also facilitated the progress of fluorescence imaging research.
However, novel fluorescent sensor design is still difficult and time consuming, as little
knowledge is well understood in this field. There is a pressing need to development new
approaches to design fluorescent sensors. Diversity Oriented Fluorescence Library Approach
(DOFLA) provided an alternative strategy to generate large number of fluorescent
compounds by combining solid phase chemistry and combinatorial chemistry. Although the
obstacle of generating diversified fluorophores could be achieved, it is crucial to design a
practical platform to select fluorescent sensors.
Chapter 2 describes a novel biological screening system to find potential sensors. Besides,
one green DNA probe, C61, to stain live and dead cells is presented. Compare with available
green fluorescent sensors, C61 showed dramatic DNA selectivity over RNA. Chapter 3
presents one chloro-fluorescein library synthesis and its biological exploration in melanoma
and skill cancer cells.
iv
List of abbreviation
CDCl3
Deuterated chloroform
DCM
Dichloromethane
DIC
N,N'-Diisopropylcarbodiimide
DMF
N, N-Dimethylformamide
DMSO
Dimethyl sulfoxide
DMSO-d6
Deuterated Dimethyl Sulfoxide
EA
Ethyl acetate
Et2O
Diethyl ether
EtOH
Ethanol
HATU
2-(1H-7-Azabenzotriazol-1-yl)--1,1,3,3-tetramethyl uronium
hexafluorophosphate Methanaminium
HEPES
4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid
HOBt
Hydroxybenzotriazole
KOH
Potassium hydroxide
MeOH
Methanol
NMR
Nuclear Magnetic Resonance
RBF
Round bottom flask
p-TsOH
p-Toluenesulfonic acid
v
List of Figures
Figure 1.1
Forward genetics and reverse genetics
1
Figure 1.2
Forward chemical genetics and reverse chemical genetics
2
Figure 1.3
Diversity Oriented Synthesis (DOS)
4
Figure 1.4
The chemical structure of Peptide Nucleic Acid (PNA)
6
Figure 1.5
Activity-Based Protein Profiling (ABPP) probes
7
Figure 1.6
target identification using ABPP probes
8
Figure 1.7
Dynamic combinatorial libraries
9
Figure 1.8
Application of styryl library; (a) Images of representative localizations
(bar = 10 mm), (b) localization distribution of styryl sensors
11
Figure 1.9
Confocal images and chemical structures of amyloid sensors
12
Figure 1.10
Constructuion of hemicyanine library
13
Figure 1.11
Fluorescence spectra and CCD images of GTP Green
13
Figure 1.12
Chemical structures of heparin sensors and the corresponding
CCD images
Figure 1.13
Confocal images (A) and fluorescence emission spectra
(B) of Glucagon Yellow
Figure 2.1
13
16
The hydrogen peroxide sensor designed by cleavage
of carbon-arylboronate bond
27
Figure 2.2
Analyte map for high throughput screening
28
Figure 2.3
Liquid handling automated system
29
Figure 2.4
DOFL screening database
30
Figure 2.5
Absorbance and emission spectra of C61 in ethanol
32
Figure 2.6
(a) Fluorescence response of C61 (5 µM) with dsDNA (green line)
vi
and total RNA (red line) at different concentrations.
(b) Fluorescence emission spectra (excitation: 420nm, cutoff: 495 nm)
of C61 (5 µM) with dsDNA at different concentrations
in HEPES buffer (20mM, pH 7.4)
33
Figure 2.7
DNA/RNA responses in vitro
34
Figure 2.8
Live and fixed cell staining of C61 in A549 and HeLa cell lines
35
Figure 2.9
The DNase and RNase digest experiments
36
Figure 2.10
DNA cell cycle analysis of C61
37
Figure 2.11
Cytotoxicity measurement
38
vii
List of Schemes
Scheme 1.1
Click chemistry reaction
6
Scheme 1.2
Synthesis of styryl library
10
Scheme 1.3
Synthetic routine of rosamine library
14
Scheme 1.4
Synthetic routine of BODIPY library
15
Scheme 1.5
The chemical structure of pluripotin
17
Scheme 2.1
The chemical structure of C61
31
Scheme 3.1
The chemical structure of modified fluorescein derivatives
46
Scheme 3.2
Synthetic routine of dichlorofluorsecein
47
Scheme 3.3
Synthesis routine of fluorescein-based library (CF)
48
Scheme 3.4
Chemical structures of amine build blocks
49
viii
List of Tables
Table 2.1
Fluorescence properties of C61
32
Table 3.1
Maximum absorbance and fluorescence wavelength of CF library 50
50
ix
Chapter One
Introduction
1.1 Chemical Genetics
1.1.1 Overview
In molecular biology and cell biology, genetic study stresses on the structures and functions
of genes at the molecular level. Based on the difference of investigative directions, genetic
research can be divided into two approaches1: forward genetic and reverse genetics (Figure
1.1). Typically, forward genetic research starts from choosing the specific mutant, and then
identifying the specific genes that are responsible for a particular phenotype of interest, which
can be termed as ‘from phenotype to genotype’, while reverse genetics follows the opposite
direction, i.e. from genotype to phenotype. Specifically, a target gene is first selected, and the
consequences of the mutation are investigated after modification or deletion of this gene.
Figure 1.1 Forward genetics and reverse genetics1
1
Chemical genetics, first proposed by Schrieber et al2., was defined as genetic study using
small molecules to elucidate the biological processes. Similarly, chemical genetics is divided
into two major research fields: forward chemical genetics, and reverse chemical genetics
(Figure 1.2)2-3. In forward chemical genetics, typically the study starts from the phenotypes
selection. With one specific phenotype, small molecules are screened under biological assays.
Once the compounds demonstrated interested results or phenomena, the next step work is to
identify the target that the small molecule binds inside the phenotype. Due to the complicity
of the biological system, identification of the binding site always takes more time, and is
tedious sometimes. On the other hand, reverse chemical genetics study starts from the
interested proteins or other biological component, then the ligands were screened with small
molecule libraries to find the hit compounds. Phenotype assay is the next step to test the
feasibility of this compound with the ligand in vivo. But unlike classical genetics, chemical
genetics focuses on analyzing of proteins instead of genes.
Figure 1.2 Forward chemical genetics and reverse chemical genetics3a
2
In classical genetics, genetic techniques are relatively difficult to proceed and is time
consuming. But chemical genetics, by using libraries of compounds, avoids the shortcomings
of genetic techniques, and it can be conducted on the cellular, tissue, and animal models in a
relative short time. More importantly, small molecules that bind to proteins and affect their
activities could mimic the random mutations used in classical genetic screens. This is
particularly useful when the gene is crucial to the organism’s survival, since altering the gene
(knockout) may cause the organism to die quickly, and the chemical genetic approach, as an
alternative way, enables researchers to investigate the target protein without killing the
organisms.
1.2 Chemical Toolboxes
To facilitate the development of chemical genetics, it is necessary to generate a large number
of diversified small molecules. Nature has accumulated numerous of bioactive compounds
from long periods of evolution, and some of them, such as colchicines, have been used for
medical treatment over 2000 years.1a, 4 Nowadays, many new drugs are still designed based
on natural resources like terrestrial and marine organisms5. However, natural products are
always coexisted with other component in the mixture, and it is difficult to isolate and purify
the single component from the extract. Therefore, the role of bioactive natural products is
more similar as the template rather than the library itself. Indeed, libraries are often built up
based on the target natural products by keeping the active sites and modifying the nonreactive
motifs.
1.2.1 Diversity Oriented Synthesis
Proposed by Schreiber et al. in 1990s, diversity oriented synthesis (DOS)6 has recently
emerged as a power tool in chemical genetics (Figure 1.3). DOS is a strategy which allows
3
quick access to molecule libraries with an emphasis on skeletal diversity and unexplored
regions of chemical spaces. Using this approach and small-molecule screening, Schreiber
helped illuminate the nutrient-response signaling network involving TOR proteins in yeast
and mTOR in mammalian cells. Besides, Schreiber and co-workers has demonstrated the
utility of using a densely functionalized β-amino alcohol to generate multiple scaffolds 2–8
via pairing reactions.7 In another example, Shair et al. demonstrated the power of DOS
combined with phenotypic screening in their synthesis of a library of compounds based upon
the natural product galanthamine.8 From this library, they discovered a compound, secramine,
which blocked protein trafficking from the Golgi apparatus to the plasma membrane.
Figure 1.3 Diversity Oriented Synthesis (DOS) 6
4
1.2.2 Tagged Library Approach
Diversity oriented synthesis (DOS) approach improved both the number and diversity of the
small molecule libraries. After high throughput screening, bioactive compounds are selected
for structure-activity relationship (SAR) study and further optimization. In forward chemical
genetics, the next step is protein identification of the ‘hit’ compound, which may bring more
synthetic modification if the compound cannot form covalent bond with the target protein or
macromolecules. One solution is tagged library approach, which has been designed to
overcome the problems of target identification. A tag here referred to a small moiety that
adds to the molecule scaffold for additional functions, which help to visualize, purify, and
identify the target macromolecules.3a
1.2.2.1 PNA Tagged Library
Peptide Nucleic Acids (PNA) are synthetic oligonucleotides with modified backbones
(Figure 1.4).9 In PNAs, the sugar backbone is replaced by peptide-like backbones. Since
PNAs can bind to both DNA and RNA targets to form stable double helical structure, PNA
tagged libraries have been developed for the spatially addressable localization and
identification of probes on the microarray surfaces. In the early work, Schultz and co-workers
demonstrated10 that PNA-encoded libraries of protein ligands can be screened against several
targets simultaneously by incubating the library with the various targets containing different
fluorophores. Also, based on PNA tagged libraries, Bradley et al. identified specific peptides
targeting different enzymes, including proteases11, Abelson tyrosine kinase12, and so on.
5
O
B
HN
O
B
N
O
O P O
O
O
O
B
HN
B
O
N
O
O
O
O P O
O
HN
B
B
O
N
O
O
O
O P O
HN
O
DNA
PNA
Figure 1.4 The chemical structure of Peptide Nucleic Acid (PNA)
1.2.2.2 Click Chemistry Library Approach
Another typical example of the tag approach is the azide - alkyne cycloaddition reaction
(click chemistry, Scheme 1.1). Sharpless et al. developed click chemistry13 to generate
substances quickly and reliably by joining small units together. So far, azide-alkyne
cycloaddition reaction (Huisgen reaction) is the most successful application of this concept.
Either azide or alkyne can be added into the scaffold as a tag, and this tagged molecule can be
identified by the counterpart in vivo under suitable conditions, and verse versa. Approaches
based on this reaction have been extensively used drug discovery, proteomics, cell imaging,
and so on.
R N3
+
R'
Cu+
R'
N N
Click Chemistry
N R
Scheme 1.1 Click chemistry reaction
6
In 2002, a femtomolar inhibitor of acetylcholinesterase (Kd = 77 fM) has been successfully
identified14 from an array of building blocks containing an azide group which undergo an
click chemistry reaction as a result of binding to the enzyme. Later on, many potential
enzyme inhibitors were reported based on the in situ click chemistry. For example, Omura et
al. reported one new and potential inhibitor (syn-7)15 against Serratia marcescens chitinase
(SmChi) B by click chemistry after rapid screening; Herczegh et al. discovered several
teicoplanin derivatives16 that showed good anti-bacteria or anti-influenza virus activity.
Furthermore, Bertozzi lab17 extended the application of the clycoaddition reaction by
avoiding copper catalyst, which is harmful for the living organisms. To date, Bertozzi and coworkers successfully developed series of bioorthogonal probes based copper-free click
chemistry, and applied into the detection and modification of glycans18, glycoproteins19 and
fatty acids20. In 2008, this Cu-free click chemistry method even applied into the in vivo
imaging of zebrafish21 by adding one fluorescent probe on the membrane associate glycans.
Figure 1.5 Activity-Based Protein Profiling (ABPP) probes 22
7
1.2.2.3 Activity-Based Protein Profiling
As an emerging chemical proteomic method, ABPP uses probes to monitor and visualize
changes in protein functions or levels in the cell, which makes it particularly useful in the
investigation of enzymes activity and proteomics. Although overlapped with click chemistry
in many cases, ABPP should be stressed independently due to its promising future.
As shown in Figure1.5, an ABPP probe22 consists of three elements: one probe with reactive
electrophilic group, one spacer, and one tag. But not limited into click chemistry reaction, the
tags vary from fluorophores to biotin, alkyne, azide, etc. Compare with traditional proteomic
profiling, ABPP enables to monitor the availability of the enzyme active site directly (Figure
1.6). By expanding the ABPP libraries, probes have been developed for more than a dozen
enzyme classes, including proteases23, kinases24, phosphatases25, glycosidases26, and
oxidoreductases27. In one example, Cravatt et al. reported that they could target glutathione
S-transferases (GST)28 both in vitro and in vivo in whole proteomes.
Figure 1.6 target identification using ABPP probes 22
8
1.2.2.4 Dynamic Combinatorial Library
Since Dynamic Combinatorial Chemistry (DCC, Figure 1.7) was independently reported by
the groups of Sanders29 and Lehn30 in the mid-1990s, it has become a powerful tool to
develop compounds with significant molecular recognition properties. In contrast to the
traditional combinatorial libraries which are synthesized primarily by parallel or split-pool
techniques, dynamic combinatorial libraries (DCLs) require only one step library
construction. DCC bases on the generation of a mixture of compounds by connecting simple
building blocks using a reversible reaction. Since the constituents are mixed by reversible
reactions, the thermodynamic stability of DCLs is not only influenced by constituents
themselves, but also by the external chemical and physical environments (e.g. temperature,
pH, solvents, substrates, etc). The reversible characteristic of DCL makes it particularly
useful in molecular recognition, and sensor development, although DCL has been used to
identify protein ligands. For example, Lehn et al. has identified one potent HPr
kinase/phosphatase inhibitor from the DCLs which contain up to 440 different constituents.31
Figure 1.7 Dynamic combinatorial libraries
9
1.3 Diversity Oriented Fluorescence Library Approach
The technical advances in imaging instruments promoted not only the development of cell
biology and neurobiology, but also the progress of fluorescent small molecules. Fluorescent
sensors, molecules that undergo changes in fluorescence upon recognition of the specific
target, have drawn considerable attention for its application in analytical chemistry and
macromolecules labeling. For example, DAPI and Hoechst are known to be the most popular
dyes to label DNA in nucleus; Rhodamine and derivatives32 are extensively used as probes in
mitochondria. Nevertheless, the design of fluorescent sensors is largely rely on the research
experience rather than systematic study. Furthermore, the difficult of purification in
synthesizing fluorophores, together with the limited class of fluorophores, hindered the
development of novel fluorescent molecules. Thus, the fluorescent sensors are reported
separately in a relative low speed.
To accelerate the development of fluorescent sensors, Chang and co-workers proposed the
concept of diversity oriented fluorescence library approach (DOFLA).33 Using this approach,
thousands of fluorescent small molecules, which cover all the visible colors, have been
synthesized by combinatorial chemistry and solid-phase chemistry. Moreover importantly,
fluorescent probes have an extra advantage over conventional probes in chemical genetics, as
they are visible by fluorescence microscopy. Here, I list the representative libraries designed
by the diversity oriented fluorescence library approach.
1.3.1 Styryl Library
R'
H3 C
Microwave or heating
R
N
+
R'
CHO
R
DMSO-EtOH, pyrrolidine
N
I
I
Scheme 1.2 Synthesis of styryl library
10
Styryl compounds have been investigated as plasma membrane and mitochondrial labeling
probes. Since styryl dyes are compounds that connecting pyridinium or quinolinium moiety
with one or more aromatic groups via a double bond bridge, thus styryl libraries can be easily
synthesized by knoevenagel condensation reaction. As shown in Scheme 1.2, Rosania et al.
constructed the first styryl library34 by condensing 14 pyridinium and 41 commercial
aldehydes in the 96-well plate. This library has a broad color range good fluorescence
properties, and especially the potential to stain different cellular organelles, such as nucleus,
mitochondria, reticulum, vesicles, etc (Figure 1.8).
Figure 1.8 Application of styryl library; (a) Images of representative localizations (bar = 10
mm), (b) localization distribution of styryl sensors 35
Following modification of styryl library36 by Li et al. induced the solid-phase chemistry into
the styryl library, and the size was enlarged. In addition, this library found its application in
the detection of amyloid aggregation (Figure 1.9). Amyloid has been associated with a large
number of protein-misfolding diseases, including Alzheimer’s Parkinson’s, Huntington’s and
others. But the decomposition of β-amyloid (Aβ) aggregates in brain tissue cannot be
11
accurately detected by conventional methods. Thus, the discoveries of several amyloid
sensors, and following reports, provided novel idea to detect Alzheimer’s disease (AD).
Figure 1.9 Confocal images and chemical structures of amyloid sensors 33
1.3.2 Hemicyanine Library
As one of the heimicyanine dyes, benzimidazolium dyes are widely used as sensitizers and
additives in photographic industry. Wang and Chang reported37 the benzimidazolium library
through both solution phase and solid phrase chemistry (Figure 1.10). With positively
charged benzimidazolium scaffold, 96 derivatives were designed to specifically interact with
negatively charged molecules. After screening, one GTP sensor (GTP Green, Figure 1.11)
with green fluorescence emission color was discovered to selectively stain GTP over
nucleotide analogues. Besides, due to the low quantum yield, GTP green was reported as a
turn-on senor for the detection of GTP.
12
Figure 1.10 Constructuion of hemicyanine library 37
Figure 1.11 Fluorescence spectra and CCD images of GTP Green 37
As a negatively charged glycosaminoglycan, heparin has vital functions in physiological
research38, but only few assays have been established to monitor the heparin concentration in
physiological conditions39. The screening of benzimidazolium library also led to the
discovery of two heparin sensors40 (Figure 1.12), which demonstrated potential clinical
applicability through further validation experiment which detected heparin using
concentrations within the therapeutic range.
Figure 1.12 Chemical structures of heparin sensors and the corresponding CCD images40
13
1.3.3 Rosamine Library
Whereas low quantum yields of fluorescence dyes are preferable to develop turn-on sensors,
brightness is one of the criteria to select fluorophores which suitable for fluorescence
microscopy. In addition, other photophysical properties, such as extinction coefficient,
photostability, pH-insensitivity and relative longer emission, are also need to be considered.
Rhodamine derivatives are one of the highly favorable dyes in bioimaging because they
satisfy all of the criteria addressed above. However, the synthesis of rhodamine dyes is one of
the most challenging tasks, as the low yield and difficulty of purification. To overcome this
limitation, Ahn and Chang41 developed a novel solid-phase approach (Scheme 1.3). In this
method, the xanthone moiety was first synthesized, and then loaded onto the resin. The final
product was obtained by condensing the xanthone moiety with Grignard reagents on the resin.
Since the last step was performed in the resin, the purification problem was largely
circumvented. To date, more than 300 compounds were reported, and several probes to detect
different targets, including glutathione41, human serum albumin42, zebrafish neural system43,
myogenic44, and etc have been reported.
Scheme 1.3 Synthetic routine of rosamine library 41
14
1.3.4 BODIPY library
4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
(BODIPY)
has
outstanding
photophysical
properties as a fluorescent scaffold, and the chemical modification of it has been well
studied45. But a library based on BODIPY has not been thoroughly studied due to the
synthetic challenges46. Recently, Lee et al. reported the first BODIPY library47, which
contains 160 members, based on dimethyl BODIPY scaffold using solution phase chemistry
(Scheme 1.4). The dimethyl scaffold was coupled with different commercial aldehydes using
the Knoevenagel reaction. After that, the purification step was completed with the help of
preparative HPLC.
Scheme 1.4 Synthetic routine of BODIPY library 47
After the image-based screening, one glucagon sensor was identified as it selectively stained
glucagon in AlphaTC1 cells. Following experiments confirmed the selectivity both in vitro
and in vivo (Figure 1.13).
15
Figure 1.13 Confocal images (A) and fluorescence emission spectra (B) of Glucagon
Yellow47
1.4 Screening System
In chemical genetics, whereas target oriented synthesis is usually designed for one specific
target, diversity oriented synthesis attempts to generate a large number of diverse compounds,
which may suitable for multi-targets. Therefore, numerous screening systems have been
developed in the last decades to maximize the opportunities to discover ‘hit’ compounds.
According to different purposes, the systems vary from in vitro screening, cell-based
screening, yeast-based screening, to zebrafish and mouse model screens.
1.4.1 In vitro screening
To target one macromolecule of interest, in vitro screening is the simplest option to select.
Using purified proteins, especially enzymes, these assays aim to find inhibitors or binders
with high affinity. This screening approach, due to the simplicity, is utilized as a standard tool
to identify effective inhibitors. For instance, Saltiel reported48 the discovery of one selective
inhibitor of the upstream kinase MEK that is orally active after the screening; after
16
synthesized a diverse purine combinatorial library, Schultz and co-workers49 screened them
for inhibition of cyclin-dependent kinase (CDK) activity, and identified two potent inhibitors.
In addition, Navre used a fluorescence-based assay to find potent and selective inhibitors of
collagenase-1 from a diketopiperazine combinatorial library.50
1.4.2 Cell based screening
In vitro screening provides a straightforward approach for identifying ligands for proteins,
but other factors that affected the real biological activity are not considered. Cell-based
assays, on the other hand, offer a more complex and more biological-friendly environment.
Furthermore, as a standard protocol in forward chemical genetics, cell-based assay are easier
to perform compare with more complicated model systems like zebrafish, elegan and mouse
systems.
H 3C
N
N
N
N
H
N
H
N
O
N
H
CF 3
N
O
CH 3
Scheme 1.5 The chemical structure of pluripotin
Equipped with high throughput screening platform and large arrayed chemical libraries, Ding
lab has been developing and integrating new chemical and functional genomic tools51 to
study stem cell biology and regeneration. In 2006, Ding et al. carried out a high-throughput
screen of 50,000 synthetic small molecules using a transgenic reporter mouse ES cell line
expressing green fluorescent protein (GFP) under control of the Oct4 gene (a gene
specifically expressed in pluripotent stem cells) regulatory elements. Following confirmation
and structure activity relationship (SAR) studies led to the discovery of pluripotin (Scheme
17
1.5),52 a small molecule activator of stem cell renewal that allows the propagation of OG2
mES cells for at least 10 passages in an undifferentiated state.
1.5 Conclusion and Perspectives
As an interdisciplinary research field, chemical genetics closely connects synthetic chemistry
and biological research. Using combinatorial chemistry approach, large numbers of libraries
have been synthesized to target specific biological challenges. On the other hand, probes,
inhibitors, and substrates have been identified and evaluated by the in vivo system after
screening. In this rapid moving field, many methodologies, such as protein microarray, have
been established and become standard tools for researchers. Besides, novel ideas and
technologies are emerging to optimize or replace existing approaches, to promote the
development of this field. Undoubtedly, chemical genetics becomes the frontier and one of
the most important research branches in chemical biology.
Fluorescent dyes have been extensively used in industrial and academic research due to the
unique characteristics. But recent progress in cell biology53, medicine54, and fluorescence
microscopy techniques55, proposed more challenges and opportunities for researchers
working in fluorescence chemistry. Fluorescent library approach, which has been used for
probe development in chemical genetics, would be one of the solutions to resolve the new
challenges.
18
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26
Chapter Two
Development of microplate screening system and discovery of a
green DNA probe
2.1 Introduction
While different assay systems are widely used to select and identify inhibitors and probes1 in
chemical genetics, fluorescent chemosensor development is heavily rely on specific binding
modes. Particularly, reactions which could trigger the turn-on fluorescence are preferable in
designing novel sensors. For instance, Chang et al. developed series of probes to detect the
hydrogen peroxide and applied into the living cells.2 The hydrogen peroxide probes all shared
one arylboronate motif (Figure 2.1), which breaks the bond with quenched fluorophore in the
existence of hydrogen peroxide, and emits fluorescence.
Figure 2.1 the hydrogen peroxide sensor designed by cleavage of carbon-arylboronate bond.
As this strategy dominates the fluorescent sensor development, most of the sensors, including
metal sensors,3 pH sensors,4 and reactive oxygen species (ROS) sensors,5 are generated using
this approach. Due to the challenges of synthesis, however, sensors are reported individually
with a relative low efficiency. To facilitate the sensor development, Chang et al. proposed the
concept of diversity oriented fluorescence library approach (DOFLA),6 combing sensor
27
development with combinatorial chemistry. So far, series of sensors are identified after the
target-specific screening, and some of them are successfully applied in the in vivo biological
system. However, different in vitro screening systems are utilized to evaluate different
libraries, which restrict the comparison between libraries. Also, the number of analytes is
limited, which reduces the opportunities to identify potential sensors. Therefore, designing of
novel in vitro screening system is of great concerns.
2.2 Development of the microplate screening system
To design a better high throughput screening method, more analytes were incorporated into
the screening. Since 96-well plate is widely used in the academic laboratories, we developed
a screening system containing 96 different analytes (Figure 2.2), which includes nucleosides
& nucleotides, proteins, peptides, DNAs & RNAs, pesticides, oxido-redox molecules, metal
ions, pH buffers, and other bioactive analytes, all of which were put according to this map in
the screening system.
Figure 2.2 Analyte map for high throughput screening
28
At the beginning of screening, all analytes solution are prepared in a 96 deep well plate, and
used within one day. Then, the mother plate is diluted and distributed into three different
concentrations in three deep well plates respectively. By using an automated liquid handling
system (Figure 2.3), analytes of four concentrations are distributed in a 384 well plate
accordingly. Once the 384-well plates are prepared, the dye in HEPES buffer is added into
plates; and the fluorescence emission spectra is measured by a fluorescent reader.
Figure 2.3 Liquid handling automated system
The raw data are collected and uploaded onto the online database, and compare with the
control. The fluorescence variation reflects the binding between analytes and fluorescent
compounds. Selectivity, fluorescence variation, and fluorescence properties are criteria to
select the potential sensors. To reflect the information of criteria, fluorescence foldchange is
labeled by different colors in the database. Specifically, green color indicates fluorescence
enhancement; red color indicates fluorescence quenching. Besides, corresponding color
variation bar is shown in the database as the log2 value for comparison. With the color
change of each compound, good sensor candidates are easily selected from the screening
results. Furthermore, structure information, such as structure, molecule weight, formula,
compound code, absorbance, and emission is also included in the database (Figure 2.4).
29
Figure 2.4 DOFL screening database
The BD library7 was first screened; in the next step we screened styryl library8, amyloid
library9, JC library10 and some Rosamine compounds11.
30
2.3 Discovery of a Green DNA Probe for Live-Cell Imaging
Nucleic acid-staining fluorophores are extensively used in biological assays including cellular
imaging and DNA quantification. Though many such probes are available,12 only limited
dyes such as Hoechst13 and DRAQ514, are suitable for live-cell imaging. Hoechst is the most
commonly used probe, but it requires UV illumination, which is known to damage cellular
DNA. DRAQ5 emits fluorescence in the deep red region, maybe with low phototoxicity, but
shows high chemical cytotoxicity. Recently, BENA43515 was reported to stain the nucleus in
live cells, but still with emission located at the cyan region (lem = 485 nm). Thus, discovery
of DNA-selective probes with both low toxicity and various emission-colors are of interest.
After analyzing the in microplate screening data, dyes with distinct preference to dsDNA
over RNA were selected and subjected to cellular imaging to confirm their DNA-selectivity
in cells. As a result, C61 (Scheme 2.1) was selected as the best DNA selective dye in terms of
selectivity, vivid cellular image and low cytotoxicity at reasonably low concentration.
S
I
S
N+
C61
Scheme 2.1 The chemical structure of C61
The detailed properties of C61 with and without DNA are summarized in Table 2.1 and
Figure 2.5. The maximum wavelength of absorbance was red-shifted from 399 nm to 425 nm,
and fluorescence emission was shifted to a slightly shorter wavelength. The fluorescence
quantum yield was increased 19.9 fold upon binding to dsDNA.
31
Table 2.1 Fluorescence properties of C61
λabs(nm)
λem(nm)
Ф
ε
Buffer
399
547
0.0034
6.8 × 103
DNA
425
540
0.0675
6.9 × 103
* The dye concentration of C61 was 5µM in HEPES buffer (20mM, pH 7.4). Acridine
Orange was used as the reference for quantum yield.
Figure 2.5 Absorbance and emission spectra of C61 in ethanol
32
In addition, the selectivity of C61 to DNA over RNA was about 10times (Figure 2.6). This
selectivity is much higher than DRAQ5, and is comparable to Hoechst and DAPI (Figure
2.7). Although several nucleic acid dyes, such as PicoGreen, YOYO, and SYBR dyes, show
higher DNA selectivity, they are restricted to in vitro DNA quantification, and are not
suitable for live-cell imaging due to their limited cell permeability.
Figure 2.6 (a) Fluorescence response of C61 (5 µM) with dsDNA (green line) and total RNA
(red line) at different concentrations. (b) Fluorescence emission spectra (excitation: 420nm,
cutoff: 495 nm) of C61 (5 µM) with dsDNA at different concentrations in HEPES buffer
(20mM, pH 7.4).
33
Figure 2.7 DNA/RNA response in vitro. For the measurement, all analytes (0.5 mg/ml) were
dissolved in HEPES buffer and mixed with 10 µM of each dye. Hoechst 33342 and DAPI
were excited at 350 nm and cutoff at 420 nm; C61 was excited at 420 nm and cutoff at 475
nm; DRAQ5 was excited at 640 nm and cutoff at 665nm.
34
The following cell-image staining experiments also confirmed that C61 stains nucleus clearly
in both live and fixed cells, as shown in Figure 2.8.
Figure 2.8 Live and fixed cell staining of C61 in A549 and HeLa cell lines. The final
concentration of C61 was 5 µM. The images were taken under FITC channel. The scale bar
represented 10µm.
35
With this distinctive selectivity to dsDNA in vitro, other important biological properties of
C61 were further investigated in live cells. The in vivo selectivity of DNA over RNA was
evaluated by deoxyribonuclease (DNase) and ribonuclease (RNase) digest experiments. The
fluorescence signal of C61 diminished dramatically after the DNase digestion, but was not
influenced by RNase digestion (Figure 2.9). A similar pattern of fluorescence signal was
observed with Hoechst, the conventional blue color DNA-selective probe. These results
supported that C61 has prominent selectivity to DNA over RNA inside cells.
Figure 2.9 The DNase and RNase digest experiments. A549 cell line was used in this
experiment. The final concentration of Hoechst was 10 µM, and the images were taken under
DAPI channel; the concentration of C61 was 50 µM, and the images were taken under FITC
channel. The scale bar represented 10um.
36
Next, C61 was applied to quantitate DNA contents in the cells, since one of the most
common usages of DNA-specific dyes was the cell cycle analysis using flow cytometry. To
examine DNA quantification of C61, we prepared two distinct cell populations: (i) normal
cells (ii) G2-M arrested cells by nocodazole treatment. Flow cytometry results showed clear
discrimination between two different cell cycle populations, and G2-M arrested cells showed
a doubled fluorescence signal that verified the suitability of C61 for flow cytometric analysis
of the cell cycle. (Figure 2.10)
Figure 2.10 DNA cell cycle analysis of C61, A549 cell line was used in this experiment. The
final concentration of C61 was 25um. The cells were compared between (a) normal cells, and
(b) Nocodazole-treated G2-M arrested cells.
37
Lastly, we assessed cytotoxicity of C61 with other DNA probes. Low cytotoxicity is one of
the key criteria for DNA probes, since most DNA probes cause damage to the cells. Using a
MTS assay, we compared the cytotoxicity of C61 (GI50 16.0 µM), Hoechst, DAPI, and
DRAQ5 with different concentrations in A549 and Hela cells. The result showed that
DRAQ5 is most cytotoxic as reported previously, and the other three dyes had similar ranges
of cytotoxicity (Figure 2.11). When we test the phototoxicity of those dyes, we observed a
similar toxicity pattern as a chemical toxicity result. These results indicated that our green
DNA probe, C61, is comparable to conventional blue color DNA probes in terms of toxicity.
Figure 2.11 Cytotoxicity measurement. To compare cytotoxic effects of DNA-selective dyes,
compounds were treated to cells at various concentrations covering their working
concentration. After 6 hours of incubation cytotoxicity was measured by MTS assay
(Promega). Blue bar represented C61; orange bar represented Hoechst 33342, green bar
represented DAPI, and red bar represented DRAQ5. Y axis indicates percentage of cell
proliferation. The GI50 of C61 was 16.0um.
38
2.4 Experimental Section
Unless otherwise noted, all chemicals and solvents were purchased from Sigma-Aldrich and
used without further purification. HEPES buffer (20mM, pH 7.4) was used in all solution
experiments.
2.4.1 Development of the microplate screening system
The Precision pH meter (Fisher Scientific, Singapore) was used to measure pH values; the
Microplate Pipetting System (Biotek, USA) was used to distribute prepared 384 well plate
from 96 deep well plate; the Microplate Spectrophotometer (SpectraPlus from Molecualr
Devices, USA) was used to collect absorbance data; the Microplate Spectrofluorometer
(Gemini XS from Molecualr Devices, USA) was used to collect fluorescence data.
2.4.1.1 Preliminary Test
As the aim of this screening system is designed to identify sensor which is compatible with
aqueous solution in terms of fluorescence, not all library compound is suitable for screening
due to poor solubility, low fluorescence, and low stability. Therefore, all compounds are
tested in this step.
Weigh 1mg of the testing fluorescent compound to make 10mM DMSO solution; if the
sample is not fully dissolved, add more DMSO to make 1mM DMSO dye solution. If the
sample is still not fully dissolved, then this sample is not suitable for the screening system.
For the qualified samples, take 1µl to make 10µM dye solutionin HEPES (20mM, pH = 7.4),
check for any precipitant.
39
For the prepared sample in DMSO, dilute with HEPES buffer (20mM, pH = 7.4) to make
100µM, 10µM, and 1µM solution respectively. Measure the absorbance spectra and
fluorescence spectra, only the compound with clear spectra are selected for the screening.
2.4.1.2 Analytes Information
The 96 analytes are classified into ten types, and the classification details are as follow.
1. Control:
Distilled water, HEPES (20mM, pH = 7.4);
2. Viscosity: Glycerol;
3. pH: pH = 2, 3, 4, 5, 6, 7, 8, 9, 10, 11;
4. Nucleotide & Nucleoside: Adenosine, AMP, ADP, ATP, Cytidine, CMP, CDP, CTP
Guanosine, GMP, GDP, GTP, Uridine, µMP, UDP, UTP, Sodium Phosphate, SodiµM
Pyrophosphate, Sodium Triphosphate, cAMP, cGMP;
5. DNA & RNA:
6. Peptide:
ssDNA; dsDNA; tRNA; total RNA
HA tag; HA12CA5 tag; His tag; HisG tag, VSV-G tag; V5 tag; IQ tag; AP tag;
Flag tag; cMyc tag,
7. Protein:
IgG(human),
IgG(bovine
serµM),
HSA,
BSA,
Transferrin
(holo),
Transferrin(apo), Insulin, Histone, Hemoglobin, Ubiquitin, Myoglobin, Fibrinogen,
Cytochrome C
8. Metal Ion: NaCl, KCl, MgCl2, ZnCl2, FeCl2, CaCl2
9. Oxido-Redox:
GSH, GSSG, NAD, NADH, Ascorbic acid, DTT, NaOCl, ROO, KO2,
Peroxide, Iron (II) with Peroxide, Pesticides Bitertanol, Buprofezin, Carbaryl, Diazinon,
Dimethoate, Ethoprophos, Hexythiazox, Phosalone;
10. Etc.:
Histamine, Dopamine, Heparin, Caffeine, GABA, MSG, Glucose, Glucose
phosphate, Fructose, Fructose phosphate.
40
2.4.2 Discovery of a Green DNA Probe for Live-Cell Imaging
2.4.2.1 General Information
A SpectraMax M2 microplate reader (Molecular Devices) was used to collect absorbance and
fluorescence spectra of JN-C61. DNA cell cycle assay experiment was analyzed by BD LSR
II Bioanalyzer (BD). Greiner 96- or 384 well polypropylene plates were used in the
experiments.
A549 and HeLa cells were grown on cell culture BD Falcon dishes in RPMI medium
supplemented
with
10%
fetal
bovine
serum
(FBS)
and
antibiotics
(100ug/ml
penicillin/streptomycin mixture) in a humidified atmosphere at 37ºC with 5% CO2.
All cell staining followed similar procedures as previous reported. Specifically, after adding
dyes, cells were incubated at 37ºC with 5% CO2 for 30min. Then the medium were removed
and changed with fresh medium. ImageXpress automated acquisition and analysis system
(Molecular Devices) was used in all the fluorescence image experiments. Cells were cultured
12-24 hours in the Greiner 96-well polystyrene cell culture plates before the fluorescence
image experiments. Image brightness and contrast were adjusted to improve picture quality.
For the cell cycle assay experiment, A549 were cultured 48 hours in the dishes before
fixation, Nocodazole was treated into the dish 24h before fixation with 1um final
concentration. The cells were fixed by 10% formaldehyde in 20min, and then the dye was
added, and incubated in 30min for flow cytometry experiment.
2.4.2.2 C61 Characterization
1
H-NMR (300 MHz, DMSO-d6): 8.38 (t, 1H, J=8.2Hz), 8.24 (d, 2H, J=8.0Hz), 7.78 (d, 2H,
J=8.4Hz), 7.70 (d, 4H, J=15.9Hz), 7.63 (d, 2H, J=15.9Hz), 7.35 (d, 4H, J=8.5Hz), 4.25 (s,
3H), 2.52 (s, 6H). ESI-MS(m/z) calcd (found): 390.1 (390.0) for [M]+.
41
2.5 Conclusion
In summary, one practical in vitro screening system has been built up. Besides, we
discovered a green color DNA-selective probe, C61, capable of cell imaging, and also DNA
quantification in flow cytometry. It is noteworthy that C61 works both in live and fixed cells,
which allows various experimental options for biological imaging by a simple chemical
method.
42
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Stockwell, B. R., Frontiers in chemical genetics. Trends Biotechnol 2000, 18 (11),
449-55.
2.
(a) Dickinson, B. C.; Chang, C. J., A targetable fluorescent probe for imaging
hydrogen peroxide in the mitochondria of living cells. J Am Chem Soc 2008, 130 (30), 96389; (b) Chang, M. C.; Pralle, A.; Isacoff, E. Y.; Chang, C. J., A selective, cell-permeable
optical probe for hydrogen peroxide in living cells. J Am Chem Soc 2004, 126 (47), 15392-3.
3.
Que, E. L.; Domaille, D. W.; Chang, C. J., Metals in neurobiology: probing their
chemistry and biology with molecular imaging. Chem Rev 2008, 108 (5), 1517-49.
4.
Han, J.; Burgess, K., Fluorescent indicators for intracellular pH. Chem Rev 2010, 110
(5), 2709-28.
5.
Nagano, T., Bioimaging probes for reactive oxygen species and reactive nitrogen
species. J Clin Biochem Nutr 2009, 45 (2), 111-24.
6.
Lee, J. S.; Kim, Y. K.; Vendrell, M.; Chang, Y. T., Diversity-oriented fluorescence
library approach for the discovery of sensors and probes. Mol Biosyst 2009, 5 (5), 411-21.
7.
Lee, J. S.; Kang, N. Y.; Kim, Y. K.; Samanta, A.; Feng, S.; Kim, H. K.; Vendrell, M.;
Park, J. H.; Chang, Y. T., Synthesis of a BODIPY library and its application to the
development of live cell glucagon imaging probe. J Am Chem Soc 2009, 131 (29), 10077-82.
8.
(a) Li, Q.; Kim, Y.; Namm, J.; Kulkarni, A.; Rosania, G. R.; Ahn, Y. H.; Chang, Y. T.,
RNA-selective, live cell imaging probes for studying nuclear structure and function. Chem
Biol 2006, 13 (6), 615-23; (b) Lee, J. W.; Jung, M.; Rosania, G. R.; Chang, Y. T.,
Development of novel cell-permeable DNA sensitive dyes using combinatorial synthesis and
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cell-based screening. Chem Commun (Camb) 2003, (15), 1852-3; (c) Rosania, G. R.; Lee, J.
W.; Ding, L.; Yoon, H. S.; Chang, Y. T., Combinatorial approach to organelle-targeted
fluorescent library based on the styryl scaffold. J Am Chem Soc 2003, 125 (5), 1130-1.
9.
(a) Lee, L. L.; Ha, H.; Chang, Y. T.; DeLisa, M. P., Discovery of amyloid-beta
aggregation inhibitors using an engineered assay for intracellular protein folding and
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E. M.; Lui, R.; Kim, H. Y.; Ji, Y.; Wu, H.; Wisniewski, T.; Chang, Y. T., Styryl-based
compounds as potential in vivo imaging agents for beta-amyloid plaques. Chembiochem 2007,
8 (14), 1679-87; (c) Li, Q.; Lee, J. S.; Ha, C.; Park, C. B.; Yang, G.; Gan, W. B.; Chang, Y.
T., Solid-phase synthesis of styryl dyes and their application as amyloid sensors. Angew
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(a) Wang, S.; Chang, Y. T., Discovery of heparin chemosensors through diversity
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Wang, S.; Kim, Y. K.; Chang, Y. T., Diversity-oriented fluorescence library approach
(DOFLA) to the discovery of chymotrypsin sensor. J Comb Chem 2008, 10 (3), 460-5.
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(a) Ahn, Y. H.; Lee, J. S.; Chang, Y. T., Selective human serum albumin sensor from
the screening of a fluorescent rosamine library. J Comb Chem 2008, 10 (3), 376-80; (b) Ahn,
Y. H.; Lee, J. S.; Chang, Y. T., Combinatorial rosamine library and application to in vivo
glutathione probe. J Am Chem Soc 2007, 129 (15), 4510-1.
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Crissman, H. A.; Hirons, G. T., Staining of DNA in live and fixed cells. Methods Cell
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45
Chapter Three
Synthesis of fluorescein-based library
3.1 Introduction
Fluorescein is characterized by large extinction coefficients (90 000 M-1cm-1), high quantum
yields (0.95), water solubility, biological tolerance, and the ability to be excited by the widely
used 488 nm line of the argon ion laser as applied in confocal fluorescence microscopy.1
Therefore, large number of fluorescein derivatives has been developed to detect metal ions,2
pH,3 NO,4 and label organelles5 inside cells and tissues, and so on.
However, the application of fluorescein dyes is restricted as fluorescein-based fluorophores
are pH sensitivity, and susceptible to photobleaching. To address the above problems,
different strategies have been used to modify the core structure of fluorescein (Scheme 3.1).
For example, halogen-based fluorescein has been designed to increase the photostability.
Recently, Nagano and co-workers developed novel fluorescein dye, Tokyo Green,6 by
replacing carboxylic acid with methyl group, which reduced the pH sensitivity.
-
O
O
O
-
O
O
O
F
COO-
Fluorescein
-
O
O
F
O
-
O
O
F
O
F
COO-
Oregon Green
Tokyo Green
Pennsylvania Green
Scheme 3.1 The chemical structure of modified fluorescein derivatives
46
In addition, to enter the cells, fluorescein dyes need to be protected to form esters. After
entering the cells, the ester bonds are cleaved by esterase, and the fluorescence starts to emit.
Although effective, the protecting step brings extra work, and limits the application.
In this chapter, one fluorescein-based library (CF library, 80 compounds) was synthesized,
with the aim to identify fluorescein dyes which could selectively enter cell lines.
3.2 Results and discussion
3.2.1 Synthesis of CF library
HO
HO
O
OH
DCM / Et2 O
O
Cl
O
OH
OH
Cl
OH
Cl
MeSO 3H
95%
COOMe
1
HO
1. p-TsOH, toluene, reflux
O
Cl
O
Cl
2. KOH, 2-propanol / H2 O
28%
COOH
2
Scheme 3.2 Synthetic routine of dichlorofluorsecein
It is reported that1 the dichloro-fluorescein was more photostable and less pH sensitive. Thus
dichloro-fluorsecein (compound 2, Scheme 3.2) was chosen as the library scaffold. In
addition, the carboxylic acid group was removed based on our previous experience in
Rosamine library.7 As shown in Scheme 3.2, the fluorescein scaffold (compound 2) was
synthesized by following the reported approach.1, 8
47
HO
O
Cl
O
Cl
HO
O
O
O
NO2
N
H
OH
Cl
Cl
DMF, HATU
COOH
O
2
O
3
HO
R
N
H
O
O
R'
Cl
Cl
DMF
R'
N
R
O
4
Scheme 3.3 Synthesis routine of fluorescein-based library (CF)
In the next step, the dichlorofluorescein (compound 2) was loaded onto nitro phenol resin,9
forming the active ester resin (compound 3). After adding the amine in DMF, the final
product was obtained after simple workup (Scheme 3.3). Considering the poor solubility of
the final product in non-protic solvents, DMF was used during the reaction, and removed in
workup. In addition, since anilines were not reactive enough to form the amine bond,
aliphatic amines were selected as build blocks, which consist of 80 amines with various
chemical structures (Scheme 3.4). After synthesized the CF library, we also measured the
absorbance and fluorescence, which clearly showed that most of the compounds had
absorbance close to 535 nm, fluorescence close to 565 nm.
48
H
N
N
O
HN
NH2
11
NH
NH
NH 2
O
20
32
33
34
66
NH2
F
NH2
H
N
74
NH 2
NH 2
77
H2N
F
78
80
95
100
Cl
F
O
F
F
H2 N
NH2
H2 N
115
131
NH
H 2N
166
135
167
H 2N
O
157
H
N
O
NH 2
N
H
Cl
NH2
171
O
H2 N
175
164
NH 2
177
180
O
O
NH2
NH 2
N
H
H 2N
182
184
185
H
N
193
201
195
NH 2
NH
H
N
NH 2
199
HN
188
H 2N
206
215
219
222
O
O
NH 2
N
O
HN
N
H
NH
223
227
NH
NH
269
H 2N
O
230
O
H2 N
232
H 2N
271
O
N
266
273
274
277
292
NH 2
H
N
335
O
N
343
O
279
349
NH2
H2 N
NH 2
H2 N
357
373
377
H 2N
382
384
NH2
O
NH2
O
H
N
N
H
NH 2
311
NH 2
387
H2N
395
H
N
419
422
424
462
NH 2
NH 2
H 2N
428
H
N
NH 2
NH 2
429
H2 N
439
441
F
442
443
Cl
O
NH2
NH2
477
478
NH 2
NH2
NH2
480
599
N
H
O
426
H
N
N
H
602
307
582
H
N
H 2N
28
H 2N
H 2N
NH 2
O
657
H2 N
55
65
Scheme 3.4 Chemical structures of amine build blocks
49
Table 3.1 Maximum absorbance and fluorescence wavelength of CF library
Code
CF-28
CF-32
CF-55
CF-66
CF-77
CF-80
CF-115
CF-164
CF-166
CF-171
CF-175
CF-177
CF-188
CF-193
CF-195
CF-215
CF-222
CF-230
CF-266
CF-277
CF-349
CF-384
CF-387
CF-395
CF-428
CF-429
CF-442
CF-443
CF-478
CF-582
CF-11
CF-20
CF-33
CF-34
CF-65
CF-74
CF-78
CF-95
CF-100
CF-131
Abs(nm)
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
468
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
535
Em(nm)
568
569
568
566
567
570
568
567
568
568
568
567
566
569
568
566
569
568
569
568
569
569
569
568
564
568
568
568
568
563
567
565
565
565
565
565
568
568
568
568
Code
CF-135
CF-157
CF-554
CF-180
CF-182
CF-184
CF-185
CF-199
CF-201
CF-206
CF-219
CF-223
CF-227
CF-232
CF-269
CF-271
CF-273
CF-274
CF-279
CF-292
CF-307
CF-311
CF-335
CF-343
CF-357
CF-373
CF-377
CF-382
CF-419
CF-422
CF-424
CF-426
CF-439
CF-441
CF-462
CF-477
CF-480
CF-599
CF-602
CF-657
Abs(nm)
535
534
535
535
535
535
535
535
535
535
535
535
534
535
534
535
535
535
535
535
535
534
535
535
535
535
535
535
535
535
534
534
535
535
534
535
535
535
535
535
Em(nm)
567
564
568
566
567
567
564
564
568
564
566
566
563
565
563
565
569
567
569
569
563
562
566
567
566
569
566
567
568
567
566
563
566
567
563
567
566
568
567
562
50
3.2.2 Cell screening of CF library
The cell screening system was designed to evaluate the cell permeability of CF library. As a
preliminary test, five skin cancer and melanoma cell lines (H522, HeKaT, HEKa, M14, SKMEL-28) were selected; and normal human fibroblast (NHF) was used as control cells. After
the cell screening, two compounds, CF-311 and CF-582, were discovered to selectively stain
skin cancer cells, rather than NHF.
HO
O
Cl
O
N
CF311
O
HO
Cl
Cl
O
O
Cl
O
N
CF582
Scheme 3.5 Chemical Structure of CF-311 and CF-582
51
3.3 Experimental Section
Unless otherwise noted, all chemicals and solvents were purchased from Sigma-Aldrich,
Acros, Nova-biochem, and used without further purification.
4-(2,7-dichloro-6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid (Compound 2, Scheme
3.2)
Put the chlororesorcinol (1.44 g, 10 mmol, 2 equiv.), and methyl 4-formylbenzoate (0.82 g, 5
mmol, 1eqiv.) into 100ml RBF, and add 50 ml of DCM / Ether (1 : 1). Add 5 ml of
methanesulfonic acid into the reaction system and stir at ambient temperature under nitrogen
atmosphere. Monitor the reaction by TLC (DCM : MeOH = 10 : 1). After 2 h, the starting
material disappeared, quench the reaction by adding 20ml of water, and stir 5 min. After
adding 100 ml of Ethyl Acetate, separate by separation funnel. Wash by water (20 ml × 2),
saturated sodium bicarbonate solution (20 ml × 1), water (20 ml × 1). Dry by sodium sulfate,
concentrate. Further dry under vacuum pump. 2.1 g was obtained (yield 96%). The crude was
used directly for the next step without further purification.
Put compound 1 (440 mg, 1mmol, 1eqiv.), p-Toluenesulfonic acid (1.4 g, 8 equiv.), and 100
ml Toluene into a 250ml RBF. Reflux under nitrogen gas. Stop heating after 20 h. Remove
the solvent, add 200 ml of ethyl acetate and 50ml of brine, filter. Collect the red powder.
Separate the liquid, and wash the organic layer by water (50 ml × 2). Concentrate to remove
solvent, combine with the red powder, approximate 120 mg of crude is obtained. Add 20ml
of iso-propanol, 20 ml of 2 M potassium hydroxide solution, stir at ambient temperature,
leave it overnight. During this process, the solid is fully dissolved under basic conditions, and
the deep red color is expected to see. Pour the reaction into a 250 ml beaker, adjust pH by
adding concentrated HCl until the pH is less than 2. Then the red solid is generated. Filter,
52
wash by water, cold ether, and cold methanol. Dry under vacuum pump. 100 mg red solid
was obtained (Yield 25%). 1H NMR (300 MHz, DMSO-d6): 6.14-8.16 (d, 2H, J=8.4 Hz),
7.55-7.58 (d, 2H, J=8.2 Hz), 6.83 (s, 2H), 6.25 (s, 2H). ESI-MS (m/z) calcd (found): 401.0
(400.0) for [M] +
General procedures of synthesizing CF library
The nitro phenol active ester resin was prepared according to the reported method. Generally,
in a 50-mL polystyrene cartridge, to an amino polystyrene resin (1 g, 1.2 mmol) in DMF (15
mL) were added 4-hydroxy-3-nitrobenzoic acid (1a, 1 g, 5.5 mmol), HOBt (1 g, 7.4 mmol),
and DIC (1 ml, 6.4 mmol). After overnight shaking, the reaction mixture was washed with
DMF (20 ml, 5 times), DCM, and methanol (20 ml, 5 times alternatively). To remove any
undesirable side product, DMF (5 ml) and piperidine (0.5 ml) were added to the cartridge and
allowed to shake for 1.5 h. The resin was filtered and washed with DMF (20 ml, 5 times).
The resulting piperidine salt was removed via the addition of a 10% HCl solution (in DMF,
20 ml) and was allowed to shake for 1.5 h. The resin was then filtered; washed with DMF,
methanol, and DCM (20 ml, 5 times each); and dried by nitrogen gas flow.
Nitro phenol resin (250mg, 0.25 mmol), HATU (190 mg, 0.5 mmol), and fluorescein acid
(200 mg, 0.5mmol) were put into the 50 ml cartridge, shake overnight after adding 20 ml
DMF. The resin was filtered and washed with DMF, methanol, and DCM (20 ml, 5 times
each); and dried by nitrogen gas flow.
In the last step, generally 20 mg (0.02 mmol) fluorescein active ester resin was mixed with
amine (0.05 mmol, 2 equiv.) in 1 ml DMF, heating 10 minutes under 50 °C. Add Ethyl
Acetate (15 ml) and water (5 ml), wash to remove the excess amine. The amine was further
monitored under ninhydrin test. All the library compounds were characterized by LC-MS,
and the purity was all above 85%.
53
3.4 Conclusion
In Summary, one fluorescein library was synthesized based on solid phase chemistry, and the
biological screening identified two dyes, CF-311 and CF-582, which selectively penetrated
the cell membrane of skin cancer cells. The above results suggest that properly modified
fluorescein derivatives are able to enter cell directly without protection groups.
54
Reference
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7.
(a) Ahn, Y. H.; Lee, J. S.; Chang, Y. T., Selective human serum albumin sensor from
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Y. H.; Lee, J. S.; Chang, Y. T., Combinatorial rosamine library and application to in vivo
glutathione probe. J Am Chem Soc 2007, 129 (15), 4510-1.
55
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Mottram, L. F.; Maddox, E.; Schwab, M.; Beaufils, F.; Peterson, B. R., A concise
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[...]... generate a large number of diverse compounds, which may suitable for multi-targets Therefore, numerous screening systems have been developed in the last decades to maximize the opportunities to discover ‘hit’ compounds According to different purposes, the systems vary from in vitro screening, cell -based screening, yeast -based screening, to zebrafish and mouse model screens 1.4.1 In vitro screening To target... after the screening; after 16 synthesized a diverse purine combinatorial library, Schultz and co-workers49 screened them for inhibition of cyclin-dependent kinase (CDK) activity, and identified two potent inhibitors In addition, Navre used a fluorescence -based assay to find potent and selective inhibitors of collagenase-1 from a diketopiperazine combinatorial library. 50 1.4.2 Cell based screening. .. Bertozzi and coworkers successfully developed series of bioorthogonal probes based copper-free click chemistry, and applied into the detection and modification of glycans18, glycoproteins19 and fatty acids20 In 2008, this Cu-free click chemistry method even applied into the in vivo imaging of zebrafish21 by adding one fluorescent probe on the membrane associate glycans Figure 1.5 Activity -Based Protein Profiling... the help of preparative HPLC Scheme 1.4 Synthetic routine of BODIPY library 47 After the image -based screening, one glucagon sensor was identified as it selectively stained glucagon in AlphaTC1 cells Following experiments confirmed the selectivity both in vitro and in vivo (Figure 1.13) 15 Figure 1.13 Confocal images (A) and fluorescence emission spectra (B) of Glucagon Yellow47 1.4 Screening System. .. identified and evaluated by the in vivo system after screening In this rapid moving field, many methodologies, such as protein microarray, have been established and become standard tools for researchers Besides, novel ideas and technologies are emerging to optimize or replace existing approaches, to promote the development of this field Undoubtedly, chemical genetics becomes the frontier and one of the... rosamine library and application to in vivo glutathione probe J Am Chem Soc 2007, 129 (15), 4510-1 42 Ahn, Y H.; Lee, J S.; Chang, Y T., Selective human serum albumin sensor from the screening of a fluorescent rosamine library J Comb Chem 2008, 10 (3), 376-80 43 Li, J.; Ha, H H.; Guo, L.; Coomber, D.; Chang, Y T., Discovery of novel zebrafish neural tracers by organism -based screening of a rosamine library. .. reported separately in a relative low speed To accelerate the development of fluorescent sensors, Chang and co-workers proposed the concept of diversity oriented fluorescence library approach (DOFLA).33 Using this approach, thousands of fluorescent small molecules, which cover all the visible colors, have been synthesized by combinatorial chemistry and solid-phase chemistry Moreover importantly, fluorescent... distribution of styryl sensors 35 Following modification of styryl library3 6 by Li et al induced the solid-phase chemistry into the styryl library, and the size was enlarged In addition, this library found its application in the detection of amyloid aggregation (Figure 1.9) Amyloid has been associated with a large number of protein-misfolding diseases, including Alzheimer’s Parkinson’s, Huntington’s and others... compare with more complicated model systems like zebrafish, elegan and mouse systems H 3C N N N N H N H N O N H CF 3 N O CH 3 Scheme 1.5 The chemical structure of pluripotin Equipped with high throughput screening platform and large arrayed chemical libraries, Ding lab has been developing and integrating new chemical and functional genomic tools51 to study stem cell biology and regeneration In 2006, Ding... reported, and several probes to detect different targets, including glutathione41, human serum albumin42, zebrafish neural system4 3, myogenic44, and etc have been reported Scheme 1.3 Synthetic routine of rosamine library 41 14 1.3.4 BODIPY library 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) has outstanding photophysical properties as a fluorescent scaffold, and the chemical modification of it ... Conclusion and Perspectives 18 Reference 19 ii Chapter Two Development of microplate screening system and discovery of a green DNA probe 27 2.1 Introduction 27 2.2 Development of the microplate screening. .. Chapter Two Development of microplate screening system and discovery of a green DNA probe 2.1 Introduction While different assay systems are widely used to select and identify inhibitors and probes1... Fluorescence Library Approach 10 1.3.1 Styryl Library 10 1.3.2 Hemicyanine Library 12 1.3.3 Rosamine Library 14 1.3.4 15 BODIPY library Screening System 16 1.4.1 16 In vitro screening 1.4.2 Cell based screening