To optimize the biological activity of pyrrole-imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were found to form measurable particles 50-500 nm in size under biologically relevant conditions, while HPLC-based analyses revealed solubility trends in both core sequences and peripheral substituents that did not correlate with overall ionic charge. The solubility of both hairpin and cyclic polyamides was increased upon addition of carbohydrate solubilizing agents, in particular, 2-hydroxypropyl-β-cyclodextrin (HpβCD). In mice, the use of HpβCD allowed for improved injection conditions and subsequent investigations of the availability of polyamides in mouse plasma to human cells. The results of these studies will influence the further design of Py-Im polyamides and facilitate their study in animal models.
To optimize the biological activity of pyrrole-imidazole polyamide DNA-binding molecules, we characterized the aggregation propensity of these compounds through dynamic light scattering and fractional solubility analysis. Nearly all studied polyamides were found to form measurable particles 50-500 nm in size under biologically relevant conditions, while HPLC-based analyses revealed solubility trends in both core sequences and peripheral substituents that did not correlate with overall ionic charge. The solubility of both hairpin and cyclic polyamides was increased upon addition of carbohydrate solubilizing agents, in particular, 2-hydroxypropyl-β-cyclodextrin (HpβCD). In mice, the use of HpβCD allowed for improved injection conditions and subsequent investigations of the availability of polyamides in mouse plasma to human cells. The results of these studies will influence the further design of Py-Im polyamides and facilitate their study in animal models.
N-Methylpyrrole (Py)
and N-methylimidazole
(Im) polyamides are heterocycle-based oligomers that bind the minor
groove of DNA in a sequence-specific manner.[1−3] Investigations
of Py-Impolyamide biological properties have demonstrated that these
compounds are cell permeable,[3−5] localize to the nucleus,[3−5] and display transcriptional inhibition, likely through an allosteric
mechanism by disrupting the transcription factor–DNA interface.[6,7] This compression may be responsible for the observed reduction in
transcription factor occupancy upon polyamide–DNA complexation.[8−10] Gene regulation properties have been illustrated in cell culture
models targeting transcription factors androgen receptor (AR),[8] glucocorticoid receptor (GR),[10] hypoxia inducible factor (HIF),[9,11] nuclear
factor kappaB (NF-κB),[12] AURKA/AURKB,[13] and TGF-β.[14,15] We have investigated
the utility of Py-Im polyamides in organismal models through in vitro
ADMET studies,[16] real-time biodistribution
monitoring methods,[17] and, most recently,
the development of mouse pharmacokinetic and toxicity profiles.[18] Recent efforts to develop more potent polyamides,
however, have been hindered by poor solubility.[19] These observations raise concerns about the likely aggregation
of Py-Im polyamides. If aggregation is an issue, how does particle
size correlate with structural features such as size, charge, shape,
turn substitution, and Py/Im composition of the oligomer?Recent
studies of the aggregation of small-molecule drug candidates
through dynamic light scattering (DLS) and detergent-based assays
have highlighted the importance of such considerations in drug design.[20−23] Indeed, a screen of over 70000 potential drug candidates by Shoichet
and co-workers found that 95% of the initial hits acted as aggregate-based
inhibitors.[24] At the same time, several
currently approved drugs can be classified as aggregate-based inhibitors[25] and in some cases aggregate particle size may
be linked to pharmaceutical efficacy.[23,26,27] We thus decided to investigate this important pharmacokinetic
parameter and its relationship to the biological activity of Py-Impolyamides. As our laboratory explores the efficacy of polyamides
in animal disease models, there becomes a pressing need to characterize
the aggregation and solubility properties of these compounds as well
as to investigate the use of formulating reagents to solubilize polyamides
at the high concentrations required for animal injections.
Results
We selected two libraries of Py-Im hairpin
polyamides, 1–6 and 7–11,
targeting the AR/GR consensus sequence 5′-WGWWCW-3′
(W = A/T)[8,28] or the NF-κB consensus sequence 5′-WGGWWW-3′,
respectively (Figure 1).[12] These two different heterocyclic cores were diversified
with a variety of substituents at the 4-aminobutyric acid (GABA) turn
positions (R1, R2) and at the C-terminus (R3). Substituents at these positions are known to affect DNA
binding and biological activities.[4,5,19,29,30] For example, the first-generation modification at the C-terminus,
β-alanine-3-(dimethylamino)-propylamine, was shown to be a negative
determinant of cell uptake.[4,5] This study focuses on
the second-generation modification of the C-terminus without a β-alanine
linker and with incorporation of isophthalic acid used in our cell
culture studies.[30] In addition, the employment
of cyclic polyamide architectures has resulted in increased DNA binding
affinities and selectivities[31] as well
as improved efficacy against AR-regulated genes.[28] Taken in context with our recent finding of increased murinetoxicity of cyclic polyamides,[18] we decided
to also investigate the properties of cycles 12–14 (Figure 2). All Py-Im polyamides
were synthesized according to previously published solid-phase procedures.[12,18,19,32]
Figure 1
Chemical
structures of hairpin polyamide library along with the
corresponding circle–stick models and target DNA sequences.
Legend: black circle = Im; white circle = Py; semicircle = γ-aminobutyric
acid unit with dashed (R, β) or wedge (R, α) substituents;
hexagon = isophthalic acid/IPA; rectangle = fluorescein/FITC; W =
A/T bases.
Figure 2
Chemical structures of cyclic polyamide library along
with the
corresponding circle–stick model and target DNA sequence. Legend:
black circle = Im; white circle = Py; semicircle = γ-aminobutyric
acid unit with dashed (R, β) substituents; W = A/T bases.
Chemical
structures of hairpin polyamide library along with the
corresponding circle–stick models and target DNA sequences.
Legend: black circle = Im; white circle = Py; semicircle = γ-aminobutyric
acid unit with dashed (R, β) or wedge (R, α) substituents;
hexagon = isophthalic acid/IPA; rectangle = fluorescein/FITC; W =
A/T bases.Chemical structures of cyclic polyamide library along
with the
corresponding circle–stick model and target DNA sequence. Legend:
black circle = Im; white circle = Py; semicircle = γ-aminobutyric
acid unit with dashed (R, β) substituents; W = A/T bases.The aggregation propensity of Py-Im polyamides
was investigated
through dynamic light scattering (DLS). Compounds 1–14 were studied at 1, 4, and 10 μM concentrations in
a 0.1% DMSO/PBS solution in order to approximate the DMSO concentration
and salt content present in cell culture experiments. Stock solutions
(1000×) of each polyamide in DMSO were rapidly mixed with PBS,
and the scattered light intensity was measured over the course of
10 min. The minimum concentration at which each compound was found
to give a significant signal intensity (3× the buffer signal
as per manufacturer guidelines), along with the respective particle
sizes derived from a cumulant fit of the autocorrelation functions,
are listed in Table 1.[33] Hairpin polyamides generally formed particles with radii of 70–200
nm at 4 μM concentration. One notable trend is that the benzamide
substituted compounds (4 and 10) formed
measurable particles at lower concentrations (1 vs 4 μM) than
their free amine counterparts (2 and 8).
Py-Im polyamides containing fluorescein substituents (5 and 6) formed significantly larger particles when compared
to the isophthalic acid conjugates (2 and 4), and compound 11 precipitated from the solution before
particle size could be determined. Interestingly, cyclic polyamides 12–14 formed larger particles than the
hairpin polyamides, with the bis-β-amino substituted cycle 13 forming the largest particles in this data set. Similar
results were observed for a number of additional polyamides (see Supporting Information, Table S1), except for
compounds containing three or four consecutive imidazole rings (17, 18), which formed particles too large to
be accurately measured (radii >1 μM).
Table 1
Estimated Radii of Polyamide Aggregate
Particles at the Concentration of Minimum Signal in 0.1% DMSO/PBS
at 25 °C
Radii derived from a cumulant fit
of the average autocorrelation functions collected over 10 min. Errors
represent standard deviation of at least three independent measurements.
Radius could not be determined
due
to rapid precipitation of the compound at 1 μM concentration.
Radii derived from a cumulant fit
of the average autocorrelation functions collected over 10 min. Errors
represent standard deviation of at least three independent measurements.Radius could not be determined
due
to rapid precipitation of the compound at 1 μM concentration.Next, the macroscopic solubility properties of these
compounds
were investigated by measuring the concentration of selected Py-Impolyamides in the soluble fraction of solutions with similar maximum
concentrations (4 μM, Figure 3). Each
compound was added as a 1000× (4 mM) stock in DMSO to PBS in
accord with the light scattering experiments. Solutions were sonicated
and then allowed to equilibrate for 2 h at room temperature before
aggregates were removed through centrifugation. To measure the concentration
of polyamide in the supernatant, a plot of HPLC peak area vs concentration
was generated using polyamide 7 with detection at 310
nm, the wavelength at which each compound was quantified (see Supporting Information, Figure S1). In general,
the 5′-WGWWCW-3′-targeted hairpin polyamides (1–4) were found to be more soluble than
their 5′-WGGWWW-3′-targeted counterparts (7–10). Within each set of polyamide hairpin cores,
a relationship between turn substituents and solubility was observed.
Polyamides with β-amine-substituted turns (2, 8)[29] were found
to be more soluble than those compounds with α-amine-substituted
turns (1, 7),[34] and the former compounds were further solubilized upon acetylation
(3, 9). Increased solubility upon incorporation
of acetylated turn units was also observed in the cyclic architecture
(13 vs 14). The benzamide-substituted compounds
(4, 10)[19] and
the bis-β-amine substituted cycle 14(18,28) were found to be the least soluble, in good agreement with the light
scattering measurements. Interestingly, none of the studied polyamides
were fully soluble under these conditions.
Figure 3
Calculated soluble concentration
of select polyamides in 0.1% DMSO/PBS
at 25 °C. Maximum concentration estimated at 4 μM (dotted
line) based on quantitation of starting material in 0.1% DMSO/water.
Resultant concentrations determined by HPLC peak area at 310 nm detection
after comparison with a standard curve (see Supporting
Information). Error bars represent standard deviation of at
least three independent measurements.
Calculated soluble concentration
of select polyamides in 0.1% DMSO/PBS
at 25 °C. Maximum concentration estimated at 4 μM (dotted
line) based on quantitation of starting material in 0.1% DMSO/water.
Resultant concentrations determined by HPLC peak area at 310 nm detection
after comparison with a standard curve (see Supporting
Information). Error bars represent standard deviation of at
least three independent measurements.We thus decided to investigate the ability of known
formulating
reagents, in particular cyclodextrins (CDs),[35] to decrease aggregation and/or precipitation among the less soluble
hairpin polyamides 7–10 (Figure 4). 2-Hydroxypropyl-β-cyclodextrin (HpβCD)
was chosen initially due to its high water solubility and low animal
toxicity.[36] Using procedures identical
to the solubility analyses, peak areas of Py-Im polyamides in the
presence of 0, 5, or 50 mM HpβCD were measured. A cyclodextrin-dependent
increase of soluble polyamide concentration was observed for all compounds
studied, with compounds 7 and 8 near the
maximum expected concentration in solutions of 50 mM HpβCD (Figure 4A). Impressively, 50 mM HpβCD increased the
concentration of the least soluble derivative (benzamide-substituted
polyamide 10) over 50-fold. Surprisingly, the soluble
concentration observed for polyamide 9 was significantly
higher than expected based on the quantitation of the corresponding
DMSO stock solution. This result likely derives from aggregation and/or
precipitation of compound 9 upon dilution of the polyamide
in water before the absorbance is measured, resulting in an underestimation
of the stock concentration. We further probed the specificity of these
effects by studying the solubilization of polyamide 7 by other carbohydrate formulating reagents, namely α-CD, γ-CD,
hydroxypropyl methylcellulose (hypromellose), and dextrose (see Supporting Information, Figure S2). The three
cyclodextrin derivatives were studied at 5 mM concentrations, while
hypromellose, a linear substituted glucose polymer, and dextrose,
the glucose monomer, were normalized for total sugar content against
5 mM HpβCD. In addition to HpβCD, polyamide 7 was solubilized by γ-CD and hypromellose (Figure 4B). Polyamide 12, which would seem less likely
to form an inclusion complex with cyclodextrin due to its cyclic form,
was screened against the same formulating agents. HpβCD and
hypromellose also solubilized cyclic compound 12. Notably,
neither polyamide displayed an increased solubility in the monomer
(dextrose) solution.
Figure 4
(A) Calculated soluble concentration of polyamides 7–10 in 0.1% DMSO/PBS containing 0, 5,
or 50 mM
HPβCD at 25 °C. (B) Calculated soluble concentration of
polyamides 7 and 12 in 0.1% DMSO/PBS containing:
5 mM α-, Hpβ-, γ-cyclodextrin (α, β,
γ, respectively), 6 mg/mL hypromellose (HM), 35 mM dextrose
(DX). Maximum concentration estimated at 4 μM (dotted line)
based on quantitation of starting material in 0.1% DMSO/water. Resultant
concentrations determined by HPLC peak area (λ = 310 nm) after
comparison with a standard curve (see Supporting
Information). Error bars represent standard deviation of at
least three independent measurements.
(A) Calculated soluble concentration of polyamides 7–10 in 0.1% DMSO/PBS containing 0, 5,
or 50 mM
HPβCD at 25 °C. (B) Calculated soluble concentration of
polyamides 7 and 12 in 0.1% DMSO/PBS containing:
5 mM α-, Hpβ-, γ-cyclodextrin (α, β,
γ, respectively), 6 mg/mL hypromellose (HM), 35 mM dextrose
(DX). Maximum concentration estimated at 4 μM (dotted line)
based on quantitation of starting material in 0.1% DMSO/water. Resultant
concentrations determined by HPLC peak area (λ = 310 nm) after
comparison with a standard curve (see Supporting
Information). Error bars represent standard deviation of at
least three independent measurements.The utility of these results was further probed
in an animal model
system. Our laboratory recently found that high blood levels of polyamide 7 can be achieved in mice following an intraperitoneal (IP)
injection of 120 nmol compound in a vehicle of 20% DMSO/PBS (600 μM
concentration, Figure 5A).[18] Using HpβCD, the DMSO content could be reduced to
1% with no loss in solubility. IP injections of 120 nmol polyamide 7 in a 1% DMSO/80 mM HpβCD/PBS vehicle and the subsequent
blood collection were performed under identical conditions to those
previously reported. After blood collection, the plasma was isolated
through centrifugation and the bulk proteins removed through methanol
precipitation. The supernatant was then mixed with dilute aqueous
trifluoroacetic acid (TFA), and a reference compound in acetonitrile
was added. The injection vehicle containing HpβCD yielded circulating
polyamide concentrations comparable to those previously reported (Figure 5B). In both cases, polyamide concentrations of 13–14
μM were detected in mouse plasma 1.5 h after injection, with
no polyamide detected after 24 h. Furthermore, FITC-labeled compound 11, which formed a precipitate in 20% DMSO/PBS solutions,
was fully solubilized upon addition of HpβCD (80 mM), allowing
the compound to be injected into mice. Slightly reduced plasma concentrations
of compound 11 were observed as compared to compound 7, which may indicate reduced bioavailability of the FITC-modified
polyamide (Figure 6A).
Figure 5
HPLC traces of mouse
plasma isolated from four mice at three time
points after injection with 120 nmol polyamide 7 in two
different vehicles: 20% PBS/DMSO (A) and 1% DMSO/80 mM HPβCD/PBS
(B).
Figure 6
(A) HPLC traces of mouse plasma isolated from four mice
at three
time points after injection with 120 nmol polyamide 11 in 20% DMSO/80 mM HPβCD/PBS. (B) Confocal image of A549 cells
after 16 h incubation with mouse plasma isolated 1.5 h after injection
with polyamide 11.
HPLC traces of mouse
plasma isolated from four mice at three time
points after injection with 120 nmol polyamide 7 in two
different vehicles: 20% PBS/DMSO (A) and 1% DMSO/80 mM HPβCD/PBS
(B).(A) HPLC traces of mouse plasma isolated from four mice
at three
time points after injection with 120 nmol polyamide 11 in 20% DMSO/80 mM HPβCD/PBS. (B) Confocal image of A549 cells
after 16 h incubation with mouse plasma isolated 1.5 h after injection
with polyamide 11.We then sought to investigate the availability
of the circulating
polyamide to human cells by taking advantage of the nuclear staining
generally observed with FITC–polyamide conjugates. Plasma samples
isolated from mice injected with compound 11 were added
to A549 (humanlung cancer) cells 16 h prior to imaging live cells
with confocal microscopy. In cells treated with plasma collected at
1.5 h postinjection, strong nuclear fluorescent signals were observed
(Figure 6B). Greatly reduced levels were observed
with plasma isolated 4.5 h postinjection, and no significant signal
was observed with the addition of the 24 h plasma sample (see Supporting Information, Figure S3).
Discussion and Conclusions
Dynamic light scattering
measurements revealed that both hairpin
and cyclic polyamides form measurable particles between 50 and 500
nm in size at biologically relevant concentrations (Table 1). Interestingly, particles of similar size were
observed for all polyamides containing an isophthalic acid (IPA) at
the C-terminus despite the differing activities of these compounds
in cell culture. These results support a mechanism of polyamide activity
in which aggregation may not be a key factor.Another interesting
observation is that neither aggregation nor
solubility is affected by the overall ionic charge of the polyamide.
While organic compounds with ionizable groups are generally expected
to be more soluble in aqueous salt solutions, neither light scattering
nor solubility analyses revealed such a dependence. Indeed, hairpins
and cycles in which the GABA amino turn units were modified with acetyl
groups were found to be the most soluble.At first glance, the
lack of solubility observed for some polyamides
is surprising as similar concentrations are commonly used in cell
culture experiments, often without evidence of aggregation or precipitation.
However, the experimental conditions required for the solubility experiments
are a limited comparison to those in cell culture. For example, cell
media generally contain a variety of small molecule and protein nutrients,
and cell cultures are kept at higher temperatures (37 °C vs 25
°C). In addition, the soluble fraction isolated by centrifugation
is not necessarily representative of the available polyamide concentration
during a typical cell incubation period (48–72 h), particularly
if aggregation is a dynamic process. We note that similar solubility
issues have been reported by Sugiyama and co-workers, who enhanced
the biological activity of seco-CBIpolyamide conjugates
through PEGylation[37] or liposomal formulations.[38]We were able to mitigate the problem of
polyamide solubility through
the addition of carbohydrate formulating reagents, in particular HpβCD.
As cyclodextrins are generally thought to form discrete inclusion
complexes with small organic molecules,[36,39] we postulated
that the linear conformation of hairpin polyamides may be well-solubilized
by such additives. Indeed, the solubilization of polyamide 7 by the larger cyclodextrins (β and γ) is consistent
with the formation of possible cyclodextrin inclusion complexes,[40] which in this case may result from interactions
with the isophthalic acid unit at the C-terminus or the N-methylimidazole group at the N-terminus. Such interactions would
not be expected, however, between cyclodextrins and cyclic polyamide 12. Interestingly, solubilization of compound 12 was observed with HpβCD but not the other cyclodextrin derivatives.
The lack of solubilization with γCD would be consistent with
a model in which the interactions between HpβCD and cycle 12 rely more on the hydroxypropyl substituents unique to HpβCD,
perhaps through additional hydrogen bonding interactions, rather than
encapsulation. While both the linear 7 and cyclic 12 polyamide compounds were solubilized by hypromellose, presumably
through encapsulation within the polymer matrix, it is notable that
no significant solubilization was observed with the dextrose monomer.
This latter observation may indicate the importance of an ordered
carbohydrate structure, such as that available with cyclodextrins
and hypromellose, for efficient polyamide solubilization. Further
studies are necessary, however, before conclusions can be drawn regarding
the interactions between Py-Im polyamides and carbohydrate derivatives,
and such investigations fall outside the scope of this work.Further evidence of the utility of HpβCD as a formulating
reagent was gathered in mouse experiments. First, we demonstrated
that the HpβCD vehicle did not significantly affect circulating
levels of polyamide 7. On the other hand, the fluorescently
labeled derivative 11 was only sufficiently soluble in
HpβCD solutions. As a result, hairpin 11 could
be injected into mice using this vehicle. This tagged compound was
of particular interest due to the high plasma protein binding levels
(>99%) that had been previously reported for Py-Im polyamides during
ADMET studies.[28] Evidence of nuclear uptake
was observed in A549 cells following incubation with plasma from hairpin 11-treated mice, thus demonstrating the availability of circulating
polyamides to humancancer cells.In summary, these studies
have provided evidence that the aggregation
propensity of Py-Im polyamides likely does not contribute
to biological activity and may not be a critical concern in pharmacokinetic
analyses. Solubility experiments revealed important trends, such as
the increased solubility achieved by acetylation of the GABA amino
turn unit, which will impact the design of next generation polyamides.
Furthermore, the identification of an effective delivery vehicle will
allow for the in vivo study of otherwise inaccessible Py-Im polyamides.
These studies represent a contribution to the field of small molecule
transcriptional inhibitors and their ultimate utility as tools for
perturbing gene expression networks in vivo.
Experimental Section
Synthesis of Hairpin Py-Im Polyamides (1–11, 15–32)
The synthesis
of Py-Im polyamides has been extensively described in previous work[5,12,19,29,32] and is summarized as follows: Reagents were
purchased from Sigma-Aldrich or Novabiochem. Py-Im cores were synthesized
on Kaiser oxime resin using Boc-based chemistry, cleaved using 3,3′-diamino-N-methyldipropylamine, and purified by reverse phase preparative
HPLC. The C-terminal amine was then derivatized with either isophthalic
acid (IPA) or fluorescein isothiocyanate (FITC) and the crude intermediate
isolated through ether precipitation. The GABA turn protecting groups
(α-NHBoc or β-NHCBz) were removed under acidic conditions.
If applicable, the crude intermediate was again isolated through ether
precipitation and further derivatized at the GABA turn amine with
either acetic anhydride or PyBOP-activated benzoic acid. Final products
were purified through reverse phase HPLC and the identity confirmed
through matrix-assisted laser desorption ionization–time-of-flight
(MALDI-TOF) mass spectrometry. The synthesis and characterization
of compounds 1;[10]2–6;[19]7, 11;[12]15, 25–32[19] were
in line with literature reports. Results from MALDI-TOF characterization
for compounds 8–10, 12–14, and 16–24 are available in the Supporting Information
(Table S2).
Synthesis of Cyclic Py-Im Polyamides (12–14)
The synthesis and characterization of polyamides 12 and 13 have been previously described.[18] In brief, the heterocyclic cores of these polyamides
were synthesized on Kaiser oxime resin as above, except that a terminal
GABA turn unit (Boc-GABA–OH or (R)-4-(Boc-amino)-3-(Z-amino)butyric acid) was added. Following deprotection
of the terminal Boc unit, the core was cleaved from the resin with
DBU/H2O and the resulting acid purified by reverse phase
HPLC. The precursor acid was then cyclized using diphenylphosphorylazide
under basic conditions. The crude intermediate was isolated through
ether precipitation and the CBz group(s) removed as above. Polyamides 12 and 13 were then isolated through reverse
phase preparative HPLC. Polyamide 14 was synthesized
by reaction of 13 with acetic anhydride under basic conditions
and then purified be reverse phase HPLC. Results from MALDI-TOF characterization
for compound 14 are available in the Supporting Information (Table S2).
Polyamide Quantification
Polyamide concentrations were
measured by UV-absorption analysis on an Agilent 8453 diode array
spectrophotometer in distilled and deionized water containing up to
0.1% DMSO using a molar extinction coefficient (ε) of 69500
M–1 cm–1 at 310 nm.
Dynamic Light Scattering
DMSO and PBS were passed through
a 0.02 μM syringe filter (Whatman) immediately prior to use.
Stock solutions of each polyamide in DMSO were quantified as above
and the purity determined by HPLC to be greater than 95%. Solutions
of 1, 4, and 10 mM in DMSO were prepared and then centrifuged for
15 min at 16g to remove particulates. Immediately
before measurement, 0.5 μL of the DMSO stock was added to 500
μL of PBS in a microcentrifuge tube. The solution was mixed
briefly with a pipet tip and transferred to a disposable plastic cuvette
(Fisher). Measurements were performed on a Wyatt Dynapro Nanostar
instrument using a 659 nm/100 mW laser at 100% power and a 90°
detection angle at 25 °C. Acquisition times of 10–15 s
were collected over 10 min and analyzed using the cumulant fit tool
in the Dynamics (6.11.1.3) software with PBS as the referenced solvent.
Acquisitions in which the baseline value of the fit was greater than
±0.1 were omitted and the remaining traces averaged. Measurements
in which the intensity (cts/s) was less than 3× the buffer signal
intensity were considered below the detection limit.
Solubility Analysis
Stock solutions of each polyamide
in DMSO were quantified as above and the purity checked by HPLC. Solutions
of 4 mM stock were prepared in DMSO. Polyamide (0.5 μL) was
added to 500 μL of PBS in a microcentrifuge tube, and the solution
was immediately vortexed and placed in a sonicating water bath at
25 °C for 20 min. The tubes were then removed from the bath and
allowed to equilibrate for 2 h at room temperature. Samples were centrifuged
for 20 min at 16g and 100 μL of the supernatant
removed for HPLC analysis. Analytical HPLC analysis was conducted
on a Beckman Gold instrument equipped with a Phenomenex Gemini analytical
column (250 mm × 4.6 mm, 5 μm) and a diode array detector
(Mobile phase: 10–80% CH3CN in 0.1% CF3CO2H (aqueous) over 17.5 min. Flow rate: 1.50 mL/min.
Injection volume: 40 μL.). Peaks were detected and integrated
at 310 nm absorbance using the Karat32 software. Sample concentrations
were determined through comparison to a standard curve of concentration
vs peak area that was generated using compound 7 (Supporting Information, Figure S1). Solubilization
by formulating agents proceeded similarly except that the DMSO stock
solutions were added to PBS containing 5 or 50 mM HpβCD, 5 mM
αCD, 5 mM γCD, 35 mM dextrose, or 6.00 mg/mL hypromellose
(approximately 35 mM relative glucose units based on reported substitution
for Aldrich lot no. 128k0214v).
Animal Experiments
Murine experiments were performed
as described previously.[18] In brief, C57bl/6
mice (8–12 weeks of age, Jackson Laboratory) were injected
intraperitoneally with 200 μL of a PBS solution containing:
(a) 120 nmol compound 7, 20% DMSO, (b) 120 nmol compound 7, 1% DMSO, 80 mM HpβCD, or (c) 120 nmol compound 11, 20% DMSO, 80 mM HpβCD. Blood was collected from
anesthetized animals (2–5% isoflurane) by retro-orbital withdrawal.
Immediately after the third blood draw, animals were euthanized by
asphyxiation in a CO2 chamber (2 atm).Plasma was
isolated by centrifugation of the collected blood. The samples from
the four replicate mice were combined at 5 μL/sample, yielding
20 μL combined plasma that was then treated with 40 μL
of CH3OH, vortexed, and centrifuged. Then 50 μL of
the supernatant were combined with 1 equiv of the HPLC loading solution
(4:1 water/CH3CN, 0.08% CF3CO2H)
containing Boc-Py-OMe (methyl 4-((tert-butoxycarbonyl)amino)-1-methyl-pyrrole-2-carboxylate)
as an internal spike-in control. Analytical HPLC analyses were conducted
with a Phenomenex Kinetex C18 analytical column (100 mm × 4.6
mm, 2.6 μm, 100 Å) and a diode array detector (Mobile phase:
5–60% CH3CN in 0.1% (v/v) aqueous CF3CO2H over 12.5 min. Flow rate: 2.0 mL/min. Injection volume:
40 μL.). Peaks were detected and integrated at 310 nm absorbance,
and sample concentrations were determined through comparison to the
previously published standard curve for this column.[18]
Confocal Microscopy
For confocal microscopy experiments,
A549 cells in F-12K medium supplemented with 10% FBS (1 mL, 100k cells/mL)
were applied to culture dishes equipped with glass bottoms for direct
imaging (MatTek). Cells were allowed to adhere for 18 h in a 5% CO2 atmosphere at 37 °C. The medium was then removed and
replaced with 200 μL of fresh medium supplemented with 20 μL
of plasma collected 1.5, 4.5, or 24 h after injection of compound 11. After an additional 16 h incubation period, 100 μL
of untreated medium was added to each slide prior to imaging. Imaging
was performed at the Caltech Beckman Imaging Center using a Zeiss
LSM 5 Pascal inverted laser scanning microscope equipped with a 63×
oil-immersion objective lens. Fluorescence and visible-light images
were obtained using standard filter sets for fluorescein and analyzed
using Zeiss LSM software.
Authors: Brian Y Feng; Anton Simeonov; Ajit Jadhav; Kerim Babaoglu; James Inglese; Brian K Shoichet; Christopher P Austin Journal: J Med Chem Date: 2007-04-21 Impact factor: 7.446
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Authors: David M Chenoweth; Daniel A Harki; John W Phillips; Christian Dose; Peter B Dervan Journal: J Am Chem Soc Date: 2009-05-27 Impact factor: 15.419
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Authors: Shuo Wang; Karl Aston; Kevin J Koeller; G Davis Harris; Nigam P Rath; James K Bashkin; W David Wilson Journal: Org Biomol Chem Date: 2014-10-14 Impact factor: 3.876
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