U.S. patent application number 13/373513 was filed with the patent office on 2013-05-16 for photogenerated reagents.
The applicant listed for this patent is Xiaolian GAO. Invention is credited to Xiaolian GAO.
Application Number | 20130123486 13/373513 |
Document ID | / |
Family ID | 35266349 |
Filed Date | 2013-05-16 |
United States Patent
Application |
20130123486 |
Kind Code |
A1 |
GAO; Xiaolian |
May 16, 2013 |
Photogenerated reagents
Abstract
This invention describes reagent precursors and methods for
chemical and biochemical reactions. These reagent precursors that
can be activated in solution upon irradiation to generate reagents
required for the subsequent chemical reactions. Specifically,
photogenerated reagents (PGR) are useful for controlling parallel
combinatorial synthesis and various chemical and biochemical
reactions.
Inventors: |
GAO; Xiaolian; (Houston,
TX) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
GAO; Xiaolian |
Houston |
TX |
US |
|
|
Family ID: |
35266349 |
Appl. No.: |
13/373513 |
Filed: |
November 16, 2011 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
12454471 |
May 18, 2009 |
8076501 |
|
|
13373513 |
|
|
|
|
11648717 |
Dec 29, 2006 |
7544829 |
|
|
12454471 |
|
|
|
|
11242622 |
Oct 3, 2005 |
7235670 |
|
|
11648717 |
|
|
|
|
10701135 |
Nov 4, 2003 |
6965040 |
|
|
11242622 |
|
|
|
|
60423680 |
Nov 4, 2002 |
|
|
|
Current U.S.
Class: |
536/25.31 |
Current CPC
Class: |
C07C 243/34 20130101;
C07C 2603/18 20170501; C07C 329/10 20130101; C07C 229/36 20130101;
C07C 227/20 20130101; C07F 9/2429 20130101; C07F 9/2408 20130101;
C07C 205/42 20130101; C07C 227/20 20130101; C07D 257/04 20130101;
C07D 295/205 20130101; C07D 317/62 20130101; C07D 317/52 20130101;
C07B 2200/11 20130101; C07H 21/00 20130101 |
Class at
Publication: |
536/25.31 |
International
Class: |
C07H 21/00 20060101
C07H021/00 |
Goverment Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
[0002] Rights to inventions in part made under the sponsored
research by National Institutes of Health (R01 GM49957).
Claims
1-64. (canceled)
65. A method for forming a nucleic acid polymer comprising: (a)
derivatizing a solid surface with a protected moiety containing at
least one protective group; (b) contacting the solid surface with
solution comprising at least one photogenerated reagent precursor
and at least one co-reagent; (c) irradiating the solution thereby
generating a photogenerated reagent in at least a portion of the
solution such that the protective group is removed from the
protected moiety; and (d) coupling a nucleic acid monomer to the
deprotected moiety.
66. The method of claim 1 wherein the photogenerated reagent
precursor is a photogenerated reagent acid precursor.
67. The method of claim 1 wherein the co-reagent is a base.
68. The method of claim 1 wherein the protected moiety is a
protected nucleotide.
69. The method of claim 1 wherein the photogenerated reagent
precursor is a photogenerated reagent base precursor.
70. The method of claim 1 wherein the co-reagent is an acid.
71. The method of claim 1 wherein the protected moiety is a
protected nucleic acid.
72. The method of claim 1 wherein the co-reagent is a sensitizer or
supersensitizer.
73. A method of deprotecting protected nucleic acids attached to a
solid surface and wherein the nucleic acids have one or more
protecting group(s) comprising a) contacting the protecting group
moieties with a solution comprising one or more PGR-P(s) and one or
more co-reagent(s) and b) irradiating the solution to produce one
or more PGR(s) wherein the PGR(s) remove the protecting group(s)
from the protected nucleic acids.
74. The method of claim 9 wherein the photogenerated reagent
precursor is a photogenerated reagent acid precursor.
75. The method of claim 9 wherein the co-reagent is a base.
76. The method of claim 9 wherein the protected moiety is a
protected nucleotide.
77. The method of claim 9 wherein the photogenerated reagent
precursor is a photogenerated reagent base precursor.
78. The method of claim 9 wherein the co-reagent is an acid.
79. The method of claim 9 wherein the protected moiety is a
protected amino acid.
80. The method of claim 9 wherein the co-reagent is a sensitizer or
supersensitizer.
Description
RELATED U.S. APPLICATION DATA
[0001] This is a continuation application of Ser. No. 12/454,471
filed May 18, 2009 which is a divisional application of U.S.
application Ser. No. 11/648,717 filed on Dec. 29, 2006 now U.S.
Pat. No. 7,544,829, which is a continuation of Ser. No. 11/242,622
filed Oct. 3, 2005 now U.S. Pat. No. 7,235,670 which is a
continuation U.S. application Ser. No. 10/701,135 filed Nov. 4,
2003 now U.S. Pat. No. 6,965,040 which claims priority to U.S.
Provisional Application No. 60/423,680 filed Nov. 4, 2002.
BACKGROUND OF THE INVENTION
[0003] The present invention relates to the field of chemical and
biochemical reactions. More specifically, the present invention
relates to the use of photogenerated reagents (PGR) for use in
parallel synthesis and assay of a plurality of organic and
bio-organic molecules on a substrate surface in accordance with a
predetermined spatial distribution pattern. Methods and apparatus
of the present invention are useful for preparing and assaying
very-large-scale arrays of DNA and RNA oligonucleotides, peptides,
oligosacchrides, phospholipids and other biopolymers and biological
samples on a substrate surface.
[0004] Development of modern medicine, agriculture, and materials
imposes enormous demands on technological and methodological
progress to accelerate sample screening in chemical and biological
analysis. Development of parallel processes on a micro-scale is
critical to the progress. Many advances have been made in this area
using parallel synthesis, robotic spotting, inkjet printing, and
microfluidics (Marshall et al., Nature Biotechnol. 16, 27-31
(1998)). Continued efforts are sought for more reliable, flexible,
faster, and inexpensive technologies.
[0005] For high-throughput screening applications, a promising
approach is the use of molecular microarray (MMA) chips,
specifically biochips containing high-density arrays of biopolymers
immobilized on solid surfaces. These biochips are becoming powerful
tools for exploring molecular genetic and sequence information
(Marshall et al., Nature Biotechnol. 16, 27-31 (1998) and Ramsay,
Nature Biotechnol. 16, 40-44 (1998)). Target molecules have been
hybridized to DNA oligonucleotides and cDNA probes on biochips for
determining nucleotide sequences, probing multiplex interactions of
nucleic acids, identifying gene mutations, monitoring gene
expression, and detecting pathogens (Schena, et al., Science 270,
467-460 (1995); Lockhart et al., Nature Biotechnol. 14, 1675-1680;
Weiler, Nucleic Acids Res. 25, 2792-2799 (1997); de Saizieu et al.,
Nature Biotechnol. 16, 45-48 (1998); Drmanc et al., Nature
Biotechnol. 16, 54-58 (1998)). The continued development of biochip
technology will have a significant impact on the fields of biology,
medicine, and clinical diagnosis.
[0006] Light-directed on-chip parallel synthesis has been used in
the fabrication of very-large-scale oligonucleotide arrays with up
to one million sequences on a single chip. Two major methods have
been disclosed: synthesis using photolabile-group protected
monomers (Pirrung et al., U.S. Pat. No. 5,143,854 (1992); Fodor et
al., U.S. Pat. No. 5,424,186 (1995)) and synthesis using chemical
amplification chemistry (Beecher et al., PCT Publication No. WO
98/20967 (1997)). Both methods involve repetitive steps of
deprotection, monomer coupling, oxidation, and capping. Photomasks
are used to achieve selective light exposure in predetermined areas
of a solid substrate surface, on which oligonucleotide arrays are
synthesized.
[0007] For the synthesis process involving photolabile-protecting
groups, the photolabile-protecting groups are cleaved from the
reactant, i.e., the 5'-O of the growing oligonucleotide molecules
in illuminated surface areas while in non-illuminated surface areas
the protecting groups on oligonucleotide molecules are not
affected. The substrate surface is subsequently contacted with a
solution containing monomers having an unprotected first reactive
center and a second reactive center protected by a
photolabile-protecting group. In the illuminated surface areas,
monomers couple via the unprotected first reactive center with the
deprotected oligonucleotide molecules. However, in the
non-illuminated surface areas oligonucleotides remain protected
with the photolabile-protecting groups and, therefore, no coupling
reaction takes place. The resulting oligonucleotide molecules after
the coupling are protected by photolabile protecting groups on the
second reactive center of the monomer. Therefore, one can continue
the above photo-activated chain propagation reaction until all
desired oligonucleotides are synthesized.
[0008] There are significant drawbacks in the method involving
photolabile-protecting groups: (a) the chemistry used is
non-conventional and the availability of building blocks is limited
(only DNA oligonucleotides are now routinely made); (b) the method
is not applicable to the synthesis of other types of organic
molecules due to the unavailability of the photolabile protected
building blocks; (c) the method suffers from low sequence fidelity
due to inherent low efficiency of the photoreaction used and
requirement of 100% deprotection efficiency.
[0009] The method of using chemical amplification chemistry has its
limitations as well: (a) The method requires application of a
polymer/photoresist layer and is not suitable for routine solution
reactions since there is no measure provided for separating sites
of reaction on a solid surface; (b) in certain circumstances,
destructive chemical conditions required for pre- and post-heating
and stripping the polymer/photoresist layer cause the decomposition
of oligonucleotides on solid surfaces; (c) the entire process is
labor intensive and difficult to automate due to the requirement
for many cycles (up to 80 cycles if 20-mers are synthesized) of
photoresist coating, heating, alignment, light exposure and
stripping; (d) the method is not applicable to a broad range of
biochemical reactions or biological samples to which chemical
amplification reagents are applied since embedding of biological
samples in such a polymer/photoresist layer may be prohibitive.
[0010] Additional limitations are linked to the use of photomasks
in the above two methods: (a) Setup for making a new chip is
expensive and time consuming due to a large number of photomasks
that have to be made; (b) photolithography equipment is expensive
and complicated, and thus, can not be accessed by many interested
users; (c) photolithography processes have to be conducted in an
expensive cleanroom facility and require trained technical
personnel. These limitations undermine the applications of
oligonucleotide chips and the development of the various
MMA-chips.
[0011] Recently a new method for producing biopolymers on biochips
and microarrays has been developed. U.S. Pat. No. 6,426,184
describes an apparatus and methods for synthesizing and assays of
arrays of biopolymers utilizing PGRs. These PGRs are useful in the
synthesis and assays of arrays of biopolymers by virtue of the fact
that the precursors of these reagents can be used in conventional
synthesis reactions to produce biopolymers with high yield or that
the precursors of these reagents can be used in conventional
reaction conditions to induce changes in reaction conditions. The
production of the PGRs is accomplished by the irradiation of these
PGR precursors, which undergo photolytic reaction upon irradiation
to produce product or intermediate that can be utilized in
synthesis and other chemical reactions.
[0012] While not intended for solution reactions, there are ample
examples of PGR-P compounds, which are used as polymerization
initiators and as reagents used in chemical amplification reactions
of photoresists (a polymer matrix). These processes are fundamental
to microelectronic fabrication of semiconductor industries.
Examples of PGR-P compounds are photogenerated acid precursors
(PGA-P) that yield H.sup.+ in the form of carboxylic acids,
phosphate acids, sulfate acids, and hydrohalogen acids. PGA-P may
also be Lewis acids, forming complexes, such as M.sub.mX.sub.n (m
and n are number of atoms). Examples of PGR-P compounds also
include photogenerated base precursors (PGB-P) that yield a base,
such as an amine, a hydroxide or the like, upon irradiation.
References for such compounds may be found in Sus et al., Liebigs
Ann. Chem. 556, 65-84 (1944); Hisashi Sugiyama et al., U.S. Pat.
No. 5,158,855 (1997); Cameron et al., J. Am. Chem. Soc. 113,
4303-4313 (1991); Frechet, Pure & Appl. Chem. 64, 1239-1248
(1992); Patchornik et al., J. Am. Chem. Soc. 92, 6333-6335 (1970).
PGA-P compounds have been widely used for many years in printing
and microelectronics industries as a component in photoresist
formulations (Willson, in "Introduction to microlithography",
Thompson et al. Eds., Am. Chem. Soc.: Washington D.C., (1994)). A
specific example of a PGA-P is triarylsulfonium
hexafluoroantimonate derivatives (Dektar et al., J. Org. Chem. 53,
1835-1837 (1988); Welsh et al., J. Org. Chem. 57, 4179-4184 (1992);
DeVoe et al., Advances in Photochemistry 17, 313-355 (1992)). This
compound belongs to a family of onium salts, which undergo
photodecompositions, either directly or sensitized, to form free
radical species and finally produce diarylsulfides and H.sup.+.
[0013] The PGA chemical amplification reaction has recently been
modified and applied to an imaging process (acid amplified imaging
or AAI, Marshall et al. Science 297, 1516 (2002)). In these solid
phase reactions, sensitizer dyes, super sensitizer, iodonium
photo-acid generator, and amplifier reagents are present in thin
layers with or without the presence of a polymer matrix, such as
polystyrene (the binder). It is believed that the AAI reagents are
not dissolved in the polymer. Light irradiation activates
sensitizers which react with iodonium photo acid generator to
produce primary H.sup.+. The light activated reaction is
accelerated under after heating the thin layers of the AAI reagents
to high temperature (140.degree. C.). The system can be stabilized
after the AAI reactions by light bleaching the sensitizers,
reducing the iodonium salts using hydroquinone reducing agents
(fixer), and base neutralizing the acid generated.
[0014] The PGA compounds have been shown in solution reactions to
be effective for parallel synthesis of microarrays of
oligonucleotides and peptides (Gao et al. Nucleic Acids Res. 29,
4744-4750 (2001); Pellois et al., Nature Biotechnol. 20, 922-926
(2002)).
BRIEF SUMMARY OF THE INVENTION
[0015] The present invention provides novel compounds and methods
of synthesizing novel compounds which can be used for performing
chemical and biochemical reactions in solution using irradiation
generated products as reagents or co-reagents. The present
invention also provides examples for novel uses of these compounds.
These compounds when irradiated produce acids, bases or other
chemical species that can be used in chemical synthesis or
biochemical assays. These novel compounds are of particular use in
the parallel synthesis of libraries of bio-organic compounds and
biopolymers, such as DNA, RNA, peptides, carbohydrates and
combinatorial pharmaceutical organic compounds. These compounds are
soluble in solutions of one or more common solvent(s) employed in
the chemical reaction, including but not limited to such solvents
as CH.sub.2Cl.sub.2, CH.sub.3CN, toluene, hexane, CH.sub.3OH,
H.sub.2O, DMF (HC(O)N(CH.sub.3).sub.2), and/or an aqueous solution
containing at least one added solute, such as NaCl, MgCl.sub.2,
phosphate salts, etc. In a preferred embodiment of the present
invention the compounds can be used as reagent precursors (PGR-P,
compounds that form at least one intermediate or product upon
irradiation) for chemical synthesis on solid surface, utilizing
projected light patterns to initiate reactions. The illuminated
PGR-P forms PGR (photogenerated reagent) at illuminated sites; no
reaction occurs at dark (i.e., non-illuminated) sites. The PGR-P
and PGR of the present invention may be modified by reaction
conditions and may undergo further reactions in its confined area
as desired. Therefore, in the presence of at least one PGR-P, at
least one step of a multi-step reaction at a specific site on the
solid surface may be controlled by radiation, such as light,
irradiation. Hence, the compounds of the present invention have
great potential in the applications of parallel reactions, wherein
at each step of the reaction only selected sites in a matrix or
array of sites are allowed to react. The compounds of the present
invention are of particular use in the methods described in U.S.
Pat. No. 6,426,184, which is herein incorporated by reference.
[0016] Some of the compounds of the present invention include PGR-P
compounds as shown in Table 1. The photoactivable components of
these compounds are derived from nitrobenzyl and nitrophenylethyl
moieties and undergo photolytic reaction to generate XH. X groups
in Table 1 are leaving groups representing piperidine, hydrazine,
tetrazole, and other nucleophiles. Different X groups gave
different photoreaction yields. For instance, for NBOC
(2-nitrobenzyloxycarbony) protected carboxyl groups of amino acids,
leucine formed in 70% yield versus leu-gly in 84% yield. Piperidine
is the deprotecting reagent for the Fmoc-NH-amino acids. Hydrazine
deprotects side chain protecting group such as N-levulinyl and
N-ivDde (4,4-dimethyl-2,6-dioxocyclohexylidene-)3-methyl-butyl).
Tetrazole is a test case of a very weak base, allowing examination
of the leaving group effect when compared with the photoreaction
properties of the corresponding piperidine and hydrazine
derivatives. The substituents, R, exert steric, electronic, and
hydrophilic/hydrophobic effects, and thereby cause changes in the
chemical and physiochemical properties of the PGR-P compounds. The
substituents on the C.sub..alpha. position have been shown to have
profound effects on the reactivity and overall efficiency of
photolytic reactions by suppressing the formation of secondary
photoreaction products. Methyl, phenyl, 2-nitrophenyl, and
substituted phenyl or 2-nitrophenyl groups are some examples of
C.sub..alpha. substituents. The substituents of the aromatic rings
are used to tune the excitation wavelength (Table 2), thermal
stability, efficiency of photolytic reactions, solubility, and
other properties affecting the reactions. For instance, the methoxy
group substituted aromatic systems such as MeNPOC have been used in
several photolabile protection systems which shorten the t.sub.1/2
(half life of the photolytic compound) by 4-fold from that of NVOC
(NVOC is .alpha.-methyl NBOC); bromo- and nitro-aromatic
substitutions will increase the wavelength of the photolytic
chromophore group to give quantitative reaction yields via the
activation of the 2-nitro group. The trifluoromethyl group is
strongly electron withdrawing and also bulky in size. These
substituents, when incorporated into the ortho-, para-, or
meta-position, will provide PGB-P of vastly different chemical
properties.
TABLE-US-00001 TABLE 1 List of PGR-P Compounds
Representative/Aromatic 2.sup.nd Ring Substitution Generation of
Core Structure Derivatives C.sub..alpha.-Substitution Derivatives
Derivatives ##STR00001## ##STR00002## ##STR00003## ##STR00004##
##STR00005## ##STR00006## see C.sub..alpha. substitution in NBOC
examples see C.sub..alpha. substitution in NBOC examples
##STR00007## ##STR00008## see C.sub..alpha. substitution in NBOC
examples see C.sub..alpha. substitution in NBOC examples
Substitution Examples Br, NO.sub.2, CF.sub.3, OMe, OCH.sub.2O
##STR00009## ##STR00010## ##STR00011##
TABLE-US-00002 TABLE 2 UV Absorption of Mono-substitute Benzene. No
Substituent K and B Band Shifted (nm) 1 H 204 (3.90), 256 (2.30) 2
OCH3 217 (3.81), 269 (3.17) 3 --Br 2.10 (3.90), 261 (2.28) 4 --CN
224 (4.11), 2.71 (3.00) 5 --NO.sub.2 252 (4.00), 280 (3.00)
Numbers in parenthases are log(.epsilon.), .epsilon. is molar
extinction coefficient at the indicated wavelength.
[0017] The compounds of the present invention include PGR-P
compounds as shown in FIGS. 1A and 1B. PGR-Ps are comprised of a
photo-activatable group, such as a chromophore, and a
photogenerated reagent component. Suitable photo-activatable groups
include but are not limited to those listed in FIG. 2. The PGR
component may be any chemical entity that can be associated with,
preferably covalently linked to the phtoactivatable group and
released from the phtoactivatable group upon irradiation of the
PGR-P. Preferred photo-activatable groups of the present invention
include UV-Vis absorption moieties, such as a large family of
.pi.-conjugated systems, polyaromatic and polyheterocyclic
chromophores, aryl and polyaryl sulfonium and iodinium, aryl
diazoquinones, sulfonates, arylamines, nitrobenzyl, and aryl or
benzocarbonates and carbamates. Many photolabile groups have been
used as protecting groups and they are also suitable for use as
photo-activable group in PGR-P for generation of PGR (Green and
Wuts, Protective groups in organic synthesis. Wiley-Interscience,
1999).
[0018] PGR groups of the present invention include common chemical
reagents such as amines, alcohols, thiols, and carboxylic acids.
Preferred PGR groups of the present invention include piperidine,
hydrazine, tetrazole, thiophenol, trifluoroacetic acid (TFA),
sulfonic acids, and reagents for phosphorylation.
[0019] The preferred PGR-Ps of the present invention include but
not limited to 2-(2-nitrophenyl)propoxycarbonyl piperidine
(NPPOC-pip), 2-(2-nitrophenyl)propoxycarbonyl hydrazine (NPPOC-Hz),
2-(2-nitrophenyl)propoxycarbonyl tetrazole (NPPOC-tet),
2-(2-nitrophenyl)propoxycarbonyl thiophenol (NNPOC-SPh),
2-(2-nitrophenyl)propyltrifluoroacetate (NPP-TFA),
2-(2-nitrophenyl)propoxyl .beta.-cyanoethyl diisopropyl
phosphoramidite (NPPO-ppa),
2-(3,4-methylenedioxy-6-nitrophenyl)-propoxycarbonyl piperidine,
and N-methylsulfonyloxynaphthalimide. The preferred PGR-Ps of the
present invention are drawn schematically in FIG. 1A. The PGR-P
compounds are not limited to these shown in FIG. 1A. Derivatives of
NBOC, MeNPOC, DNBOC (Table 1) and 2-(2-nitrophenyl)propoxysulfonyl
(NPPOS) chromophore are also photolabile and their photoreaction
products include alcohol compounds ROH, which are potentially
useful reagents for organic reactions (Wolfgang Pfleiderer, U.S.
Pat. No. 6,153,744).
[0020] The applications of the PGR-P compounds of the present
invention provide a means for generation of chemical/biochemical
reagents that are used in the subsequent chemical and biochemical
reactions in selected sites among the many possible sites present.
One aspect of the invention is to change solution pH by
photogeneration of acids or bases in a controlled fashion. The pH
conditions of selected samples can be controlled by the amount of
photogenerated acids or bases present. The changes in pH conditions
effect chemical or biochemical reactions, such as by activating
enzymes and inducing couplings and cross-linking through covalent
or non-covalent bond formation between ligand molecules and their
corresponding receptors. In other aspects of the present invention,
PGRs themselves act as binding molecules that can interact with
other molecules in solution. The concentration of PGR for a given
PGR-P is determined by light irradiation and by the dose of light
irradiation, and thus, the reactivity and the ligand binding
affinity and specificity in more than one system can be examined in
parallel.
[0021] Another important aspect of the compounds of the present
invention is parallel synthesis of biopolymers, such as
oligonucleotides and peptides, wherein the compounds of the present
invention can be used to generate PGRs that are used for selective
deprotection or coupling reactions. These reactions permit
controlled fabrication of diverse biopolymers on solid surfaces.
These molecular microarrays are used in a wide range of fields,
such as functional genomics, diagnosis, therapeutics, genetic
agriculture, and for detecting and analyzing gene sequences and
their interactions with other molecules, such as antibiotics,
antitumor agents, oligosacchrides, and proteins.
[0022] The use of PGR-P in parallel synthesis of combinatorial
library of molecules, especially, of individually addressable
microarrays has been demonstrated. According to the articles by Gao
et al. (2001, Nucleic Acids Res. 29, 4744-4750) and Pellois et al.
(2002, Nature Biotechnol. 20, 922-926), biopolymers are synthesized
in high fidelity using PGA. There is a clear need in creating more
PGR-P and expanding their applications to a broad range of chemical
reactions since the method is particularly suited for
miniaturization, automation, and parallelization of combinatorial
synthesis. One objective of the present invention is to develop new
PGR-P compounds and the applications of PGRs.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING
[0023] FIG. 1A shows examples of the preferred PGR-Ps of the
present invention.
[0024] FIG. 1B shows examples of two-photon sulfonium and iodium
compounds.
[0025] FIG. 1C shows to examples of other O-nitrophenylethyl
compounds.
[0026] FIG. 2 shows examples of chromophoric photo-active groups as
a component of PGR-P
[0027] FIG. 3 shows examples of photosensitizers.
[0028] FIG. 4A shows examples of the reactions for preparation of
PGR-Ps based on 2-(2-nitrophenyl)propoxycarbonyl chromophore.
[0029] FIG. 4B shows examples of the reactions for preparation of
PGR-Ps based on naphthalimide chromophore
[0030] FIG. 5 shows examples of the photolytic reactions of PGR-Ps
to form photogenerated reagents (PGRs)
[0031] FIG. 6 shows the mechanism of the photolytic reaction of
NPPOC-pip.
[0032] FIG. 7 shows time dependence of the concentration of
2-(2-nitrophenyl)propoxycarbonyl piperidine (NPPOC-pip) (diamond, 1
in FIG. 6), 2-(2-nitrophenyl)propene (square, 2 in FIG. 6), and
piperidine (circle, 3 in FIG. 6) upon irradiation in DMF.
[0033] FIG. 8 shows the mechanism of the photolytic reaction of
NPPOC-Hz.
[0034] FIG. 9 shows the time dependence of the formation of
photogenerated hydrazine. NPPOC-Hz (triangle, 1 in FIG. 8),
2-(2-nitrophenyl)propene (square, 2 in FIG. 8), and
2-methyl-N-hydroxyoxindole (circle, 3 in FIG. 8) upon irradiation
in DMF
[0035] FIG. 10 shows schematics of the formation of the products
using various PGR reactions.
[0036] FIG. 11 shows HPLC and Mass characterization for the
deprotection reaction using photogenerated hydrazine on the side
chain group in
Phe-Lys(1-(4,4-dimethyl-2,6-dioxocyclohexylidene-)3-methyl-butyl)
(ivDde). Fmoc-Phe-Lys(ivDde) dipeptide was synthesized using
photogenerated piperidine.
[0037] FIG. 12A shows the HPLC profile of pentapeptides
Tyr-Gly-Gly-Phe-Leu synthesized using piperidine.
[0038] FIG. 12B shows the HPLC profile of pentapeptides
Tyr-Gly-Gly-Phe-Leu synthesized using photogenerated
piperidine.
DETAILED DESCRIPTION OF THE INVENTION
[0039] The present invention provides compounds that can be
utilized in methods for solution based photochemical reactions
involving reagents generated by irradiation. A conventional
chemical/biochemical reaction occurs between at least one reactant
(generically denoted as "A") and at least one reagent (generically
denoted as "R") to give at least one product as depicted below:
A+R.fwdarw.A'+R'
[0040] The compounds of the present invention can be utilized in
reactions that are controlled by irradiation with light. The
compounds of the present invention, PGR-Ps, produce PGRs upon
irradiation. The PGR then functions the same as a reagent
conventionally used in a chemical reaction, and, thus, the reaction
proceeds in an otherwise conventional way. The overall
photo-controlled reaction is depicted below.
##STR00012##
[0041] The use of PGR in the present invention permits
chemical/biochemical reactions under conventional conditions. The
occurrence of the reaction is controlled, however, by formation of
at least one reagent upon irradiation. In some embodiments,
irradiation is from a light source emitting UV and visible light.
Heat, IR and X-ray irradiation are also sources of irradiation. A
PGR is produced by irradiation of a PGR-P or a PGR-P in combination
with a photosensitizer (FIG. 3) which in turn transfers its energy
to a PGR-P or affects the excitation energy of PGR-P. The
sensitization effect can be enhanced by a supersensitizer which
further improves the efficiency of photoreaction conversions. PGR
may be an intermediate or a stable compound. The PGR is derived
from a portion of the PGR-P molecule which has dissociated from the
parent structure or which has been rearranged in structure from the
PGR-P. PGR may be an acid, a base, a nucleophile, an electrophile,
or other reagents of specific reactivities.
[0042] Typically, a PGR-P contains one or more photo-activable
chromophoric groups, such as substituted aryls or thiolaryls in
onium salt sulfonium hexafluoroantimonate. This family compounds
are acid generators and can abstract hydrogen from reaction media
to produce strong protic acids. According to the present invention,
nitrobenzyl or O-nitrophenylethyl moieties are examples of
photo-activable chromophoric groups (FIG. 2). The photo-activable
chromophoric groups may be represented by a large family of
polyaromatic or polyheterocyclic ring moieties and they undergo
reactions via different mechanisms. The photo-activable
chromophoric groups useful in the present invention include but are
not limited to those shown in FIG. 2. The chromophore portion of
the PGR-P serves to absorb radiation, either directly or by energy
transfer from a sensitizer. The absorbed energy induces one or more
chemical reactions that ultimately result in cleavage of one or
more chemical bond in PGR-P, and thus, irradiation leads to the
formation of PGR in solution. One embodiment of the invention
defines a PGR-P molecule containing one or more chromophoric
moieties and one or more chemical moieties, which are precursor of
the resulting reagents formed upon irradiation.
[0043] The photo-activable group would have the suitable excitation
energy and thus at a given wavelength photolytic reaction would
occur. It is most desirable that the photolytic reaction is
associated with high photochemical quantum yield and produces no
harmful side products. The nitrobenzyl derivatives have been used
in the last few decades as photo-activable group for protection of
functional groups. Examples can be found in the photolabile
protection of the amino group of amino acids and hydroxyl group of
nucleotides. Recently, photolytic generation of acids from
nitrobenzyl derivatives have been used to remove DMT group from
nucleotides (Pawel J. Serafinowski and Peter B. Garland PCT WO
03/000644). However, the photolytic reactions of these carbamate
and carbonate derivatives in such applications did not provide
satisfactory results, which could be due to inefficient photolytic
reaction because of low quantum yield of photo-deprotection or
other unfavorable reaction conditions required by the photolytic
reaction. The ortho-nitrophenylethyl carbonyl group was introduced
to offer improved stability, several fold enhancement in quantum
yield, and shorter deprotection times (Wolfgang Pfleiderer, U.S.
Pat. Nos. 5,763,599 and 6,153,744). The ortho-methylenedioxy
substitution was introduced to the nitrophenylethyl group in
2-(3,4-methylenedioxy-6-nitrophenyl)-propoxycarbonyl to cause the
UV absorption of the molecule red shifted (Berroy et al. Sensors
and Actuators B: Chemical, 74, 186 (2001)). In one preferred
embodiment of the present invention, useful photo-activable
chromophoric group include N--O-substituted 1,8-naphthalimides
(NAI) and 1,4,5,8-naphthaldiimides (NDI) derivatives, such as
N-sulfonates, N-carbonates, or N-carbamates, which undergo
photolytic reaction upon irradiation, resulting in cleavage of the
N--O bond to give PGR. The present invention also makes use of, but
is not limited to, PGR-P containing conjugated .pi.-molecular
structures (FIG. 1). A particular group of these compounds are
photogenerated reagents reacting through a two photon photolytic
mechanism, based on sulfonium moieties attached to a
bis[(diarylamino)styryl]benzene (BDASB) core (Zhou, et al.,
Science, 296, 1106-1109 (2002); Albota, et al., Science, 281,
1653-1656 (1998)) (FIG. 1B). The photo-activable groups in these
molecules are bridged through a D-.pi.-D conjugation system, i.e.,
BDASB. As a result, the excitation wavelength is shifted to longer
than 650 nm and the quantum yield of photochemical reactions is
improved by 80% as compared to classic arylsulfonium compounds.
[0044] An important aspect of the application of PGRs is the
selection of a PGR-P that would produce a PGR at a suitable
wavelength. Electromagnetic radiation, in the form of ultraviolet
light, visible light, or infrared can be used to generate the
reagents. Obviously, the wavelength that maximizes the reaction of
the PGR-P to form the reagent will depend on the specific precursor
and sensitizer, if any, that are employed, and a wavelength that
penetrates the solvent and does not damage other compounds in the
reaction solution will be preferred. The duration of irradiation is
also dependent on several factors including concentration of the
specific precursor employed, the radiance of the light source, and
whether a photosensitizer (with or without other co-reagent, such
as a stabilizer or H-donor) is present. For organic synthesis, it
is desirable to use irradiation at wavelengths longer than 365 nm,
since shorter wavelengths may induce undesirable photoreactions
among the reactants. The choice of wavelengths is also limited by
the compatibility of the photoreaction apparatus. The use of
digital photolithography through a micromirror devices to produce
PGRs from PGR-Ps is facilitated if the reflected light has
wavelength is or above 365 nm. At different wavelengths, there are
also various laser light sources and organic light emitting diode
devices available as the choices of photoreaction devices using the
digital photolithographic approach.
[0045] A desirable property of the application of PGRs is the
behavior of the PGR induced reactions follows a non-linear
correlation of the reaction efficiency with the light strength
provided (irradiation time and/or intensity). Examples have been
reported in using PGA deprotection of the 5'-DMT group in
oligonucleotide synthesis (Gao et al. Nucleic Acids Res. 29, 4744,
2001) or PGA deprotection of the N-t-Boc group in peptide synthesis
(Pellois, Ph.D. Dissertation, 2002). This non-linear correlation
reduces the side reactions in nonilluminated areas due to the
presence of trace PGR generated by stray light or diffusion. In
contrast, direct cleavage of a photolabile group such as
((.alpha.-methyl-2-nitropiperonyl)-oxy)carbonyl (MeNPOC) often
follows a linear correlation (McGall et al. J. Am. Chem. Soc. 119,
5081, 1997), which is more sensitive to the boundary conditions of
light irradiation.
[0046] In some embodiments of the present invention, PGR-P
compounds are used in combination with co-reagents to enhance the
reaction. One specific example is the use of photosensitizers and
supersensitizer, which are compounds that can lower excitation
energies of PGR-P either by direct energy transfer to or through
complex formation with PGR-P in the ground or excited state. The
sensitizers useful in the present invention include but are not
limited to those, the derivatives of thiofluorene, fluorine,
quinoline, thioxanthanone, anthraquinone, pyrene, perylene,
dipyrromethene boron complex, shown in FIG. 3. Other sensitizers
also include benzophenone, acetophenone, benzoinyl C1-C12 alkyl
ethers, benzoyl triphenylphosphine oxide, anthracene, Ru.sup.2+
complexes, or other polyaromatic or polyheterocyclic compounds;
optionally substituted on the ring systems with nitro, halogen,
alkyl, alkenyl, alkynyl, aryl, alkoxyl, heterocyclic, CN,
N(alkyl)2, sulfonyl, alkylsulfonyl, or other aromatic substitution
groups. One effect of photosensitizers is to shift the excitation
wavelength used in photochemical reaction, and thus, allows the
formation of PGR at a wavelength at which the PGR-P alone would not
react or would not react efficiently thereby enhancing the
efficiency of the formation of photogenerated reagents.
Accordingly, in one embodiment, the present invention makes use of,
but is not limited to, thioxanthones or perylene, as co-reagents in
PGR reactions. The PGR-P photolytic quantum efficiency can be
further improved by species that can function as electron transfer
intermediates between the primary sensitizer and the PGR-P. In the
presence of these co-sensitizers, the generation of PGR proceeds at
a faster rate.
[0047] Further examples of using co-reagents include the reactions
of 2-nitrobenzyl and 2-nitrophenylproxy compounds which are
affected by other reagents added to the reaction system. For
instance, the side products were significantly suppressed in the
reactions of NBOC and NVOC compounds when auxiliary reagents, such
as acids mixed with aldehyde reacting reagents (such as hydrazine,
hydroxylamine hydrochloride, semicarbazide hydrochloride) were
added, and quantitative deprotection yields were obtained for
N-protected amino acids (Patchornik et al., J. Am. Chem. Soc. 92,
6333, 1970). A second example is that the cleavage of the
2-nitrophenylproxy group from 5'-O position of nucleotides was
inhibited at low pH but enhanced by the presence of co-reagent such
as DBU (0.05 M, 1,8-diazabicyclo[5.4.0]undec-7-en) (Walbert et al.,
Helv. Chim. Acta 84, 1601, 2001). Side reactions due to DBU were
not detected. The third example is the usefulness of added acid and
base function as buffer to counter the actions of the PGR
generated. A desirable condition is that PGR forms in a confined
area and there is a high contrast ratio of reacted and unreacted
molecules in the peripheral around the reaction site.
[0048] In some embodiment of the present invention, the selection
of solvent is important. An example is that a PGR-P, such as
triarylsulfonium hexafluoroantimonate, undergoes radical reaction
to produce a proton, H.sup.+. The source of the proton is likely
from a H-donor or the surrounding solvent. To facilitate the
reaction, a co-reagent called stabilizer of H-donor reagent may be
used. The stabilizer or H-donor compounds useful in the present
invention include but are not limited to ether solvents, propylene
glycol ethers, t-butane, t-butanol, thiols, cyclohexene,
chloroform, methylene chloride, and toluene as well as derivatives
thereof. One example is to provide at least one reagent to reduce
the lifetime of the reactive reaction intermediates, such as a free
radical species, generated during irradiation, and to provide a low
energy source of hydrogen. The reactions of stabilizer may be uni-
or bimolecular or by multistep mechanisms, well-known in
photoresist chemistry as acid amplification using acid amplifier
reagents.
[0049] In some embodiments of the present invention, improved
reaction yields and/or suppression of side reactions are achieved
by pre-irradiation activation of at least one PGR before mixing
with other reactants. Pre-irradiation activation allows
time-resolved reaction so that there is sufficient time for
potential harmful reaction intermediates, such as free radical
species generated during irradiation, to diminish and for products,
such as H.sup.+, to reach a stable concentration.
[0050] In some embodiments of the present invention, the reactions
at different reaction sites are modulated by providing irradiation
of different strength using a programmable photoreaction optical
device, such as Texas Instruments' digital light projector (DLP) or
digital micromirror device (DMD). The controlled light irradiation
allows control of the reactions to proceed at a desirable rate.
Further, the PGR reaction can be controlled or terminated using
conventional chemical approaches, such as base neutralization of
excess acids or base generated from PGA-P or PGB-P, respectively,
and chemically destroy excess PGR-P present in the reaction media
to prevent further reactions. Specific examples include using
hydroquione to reduce the PGA-P iodonium salt and using over dose
light to bleach the chromophore that is responsible for activating
PGR-P.
[0051] PGR-P compounds within the scope of the present invention
include any compound that produces a product, which potentially is
a reagent for a different reaction upon irradiation. Examples of
such precursor compounds include but not limited to arylazide
derivatives, benzocarbonates or carbamates, dimethoxybeonzoinyl
carbonates or carbamates, o-nitrobenzyloxycarbonates or carbamates,
nitrobenzenesulphenyl derivatives, and o-nitrobenzyloxyanilines,
onium salt of bis[(diarylamino)styryl]benzene,
2-(2-nitrophenyl)propoxycarbonyl or 2-(2-nitrophenyl)propoxyl
derivatives, and N-naphthlimide derivatives. Although the examples
and discussion herein refer to PGR-Ps that yield a nucleophilic
Lewis base, such as an amine, hydrazine, thiol, tetrazole, or the
like, upon irradiation, it should be understood that the methods of
the invention are applicable to a general scheme which a portion of
the molecule is activated upon irradiation and a portion of the
molecule is thus chemically converted into a reagent that is
required by the subsequent reaction. The examples provided below
are exemplification of the specific PGR-P compounds and methods of
making these compounds.
[0052] According to one embodiment of the present invention PGR-P
compounds are derived from 2-nitroethylbenzene derivatives (FIG.
4A), by condensation with formaldehyde in the presence of base to
form 2-(2-nitrophenyl)propanols. In an alternate embodiment the
reaction can begin with nitrotoluene and formaldehyde, which
produce compounds containing 2-nitrophenylethyloxylcarbonyl
(NPEOC). The 2-nitrophenylethyloxy and 2-(2-nitrophenyl)propyloxy,
or the 2-nitrophenylethyl moieties, are photo-activable
chromophores. These compounds are reacted with phosgene or
diphosgene to produce the corresponding chloroformates. Reaction of
the chloroformate with a nucleophile or a base, such as piperidine,
or hydrazine, or thiophenyl, or tetrazole, readily provides the
corresponding PGR-P compounds. One example of PGR-Ps is
2-(2-nitrophenyl)propoxycarbonyl (NPPOC) PGR-P compounds, where
NPPOC-pip is a PGB-P (base precursor). 2-(2-nitrophenyl)propanols
can directly react as a nucleophile with electron deficient
centers, such as a carbonyl or a phosphite (FIG. 4B) to produce the
corresponding PGR-P compounds. One example of PGR-P is
2-(2-nitrophenyl)propyltrifluoroacetate (NPP-TFA), where NPP-TFA is
a PGA-P (acid precursor). The triphosphite containing
2-(2-nitrophenyl)propyloxyl is a phosphilating agent (FIG. 4B). One
application of this compound is to react it with an alcohol and the
reaction is followed by oxidation to give a phosphate trimester,
which would be converted into a phosphate triester upon light
irradiation. Each PGR-P compound is not limited to contain one
irradiation or light irradiation activatable center and one PGR
moiety. An example is a PGR-P containing two photolytic centers and
being able to produce two molecules of photogenerated reagents.
[0053] The synthesis of the PGR-P compounds disclosed in the
present invention are known to those skilled in the art.
N-substitutednaphthalimide compounds can be prepared by
estserification of N-hydroxynaphthalimide in its salt form with
acyl chlorides, acyl anhydrids, sulfonyl chlorides, or sulfonic
acid anhydrids. N-carbamates (N--OC(O)NHR) of naphalimides can be
prepared by treating N-hydroxysuccinimide with RNCO.
2-(2-nitrophenyl)propoxysulfonyl derivatives of amines or thiols
can be prepared by reacting 2-(2-nitrophenyl)propoxysulfonyl
chloride with the corresponding nucleophile.
[0054] The PGR-P compounds of the present invention become reactive
under light irradiation (FIG. 5). The PGR-P compounds are
precursors of among others, photogenerated piperidine, or
photogenerated trifluoroacetic acid, or photogenerated thiophenol,
or photogenerated tetrazole, or photogenerated hydrazine. The
reactions occur in solutions of one or more solvents. Such solvents
include but are not limited to CH.sub.2Cl.sub.2, CH.sub.3CN,
toluene, hexane, CH.sub.3OH, DMF, DMSO, H.sub.2O, or mixtures of
more than one solvents. The concentration of PGR-P reagent in the
solvent can range from 0.1 to 1000 mM, but preferably is in the
range between 1 and 200 mM. A range of light sources can be applied
to the reaction solution to produce the reagent. Irradiation
wavelengths may be from about 254 nm to about 1000 nm, preferably
from about 365 nm to about 1000 nm, more preferably from about 405
nm to about 1000 nm.
[0055] The photolytic reaction of NPPOC leads to the formation of
piperidine, a secondary amine, and 2-(2-nitrophenyl)propene
(Wallbert et al. Helvetica Chimica Acta, 84, 1601 (2001), Pellois,
J. P. Ph. D. Dissertation, 2002) (FIG. 6), which was detectable by
proton NMR based on the presence of two terminal propene protons
resonating at 5.19 ppm. Continued light irradiation of the reaction
mixture caused 2-(2-nitrophenyl)propene to decompose to give
2-methyl-N-hydroxyoxindole (FIG. 6). This reaction followed a first
order kinetics with a rate constant in order of 3.0.times.10.sup.-3
s.sup.-1 and the formation of piperidine was quantitative (FIG. 7).
In a similar fashion, the photoreaction of NPPOC-hydrazine
(NPPOC-Hz) produces hydrazine, a nucleophile,
2-(2-nitrophenyl)propene, and 2-methyl-N-hydroxyoxindole (FIGS. 8
and 9).
[0056] In one embodiment of the present invention, the
photogenerated piperidine, a PGB, from PGR-P NPPOC-pip is a
deprotection reagent for removing 9-fluorenylmethyloxycarbonyl
(Fmoc) group from the protected amino group (FIG. 10). Examples of
the reactions (FIG. 10) using PGR include deprotection of the
levulinyl group from the protected hydroxyl group using
photogenerated hydrazine from PGR-P NPPOC-Hz; deprotection of the
1-(4,4-Dimethyl-2,6-dioxocyclohexylidene-)3-methyl-butyl (ivDde)
group from protected amino or carboxylic groups using
photogenerated hydrazine; deprotection of the dithiasuccinoyl or
the thiolcarbamate group from the protected thiol or amino groups
from photogenerated thiols; deprotection of the acid labile
protected hydroxyl or amino groups using photogenerated TFA from
NPP-TFA. Photogenerated piperidine or TFA are common reagents for
deprotection of amino acids and are wildly used in peptide
synthesis. The photogenerated tetrazole is a weak acid and
activates the coupling of a phosphoramidite with an alkyl OH group
by protonation of the amino group on the phosphite phosphorous. The
protonated amino group becomes a good leaving group under
nucleophilic attacking conditions, such as coupling of the 5'-OH
group with the nucleophosphoramidite monomer. Tetrazole is commonly
used as an activating agent in oligonucleotide coupling reactions.
These examples demonstrate that photogenerated reagents are
convenient ways of control of a wide range of solution reactions by
irradiations without significantly changing reaction
conditions.
[0057] One embodiment of the present invention illustrates the
orthogonal application of the PGR-P compounds, NPPOC-pip and
NPPOC-Hz, for peptide synthesis. The reaction began with coupling
Fmoc-Lys(ivDde)-OH to solid support, followed by deprotection of
Fmoc using the PGB, piperidine, from NPPOC-pip, and coupling to a
second amino acid monomer, Fmoc-Phe-OH. The terminal Fmoc of the
Phe-Lys(ivDde) dimer on solid support was deprotected using
photogenerated piperidine from NPPOC-pip and the deprotected
terminal amino group was capped with acetyl (Ac) group to give
Ac-Phe-Lys(ivDde) on solid support. NPPOC-Hz was then applied to a
portion of the dipeptide and light irradiation produced hydrazine
that removed ivDde on the Lys side chain amino group. Finally,
dipeptides, Ac-Phe-Lys(ivDde) and Ac-Phe-Lys, were cleaved from
solid support. The characterization of the resultant products using
HPLC and MALDI mass analysis indicates that the products obtained
are as expected (FIG. 11).
[0058] One embodiment of the present invention illustrates the
application of PGB-P in the preparation of a pentapeptide, leucine
enkephalin (SEQ ID 1: Tyr-Gly-Gly-Phe-Leu), using photogenerated
piperidine derived from NPPOC-pip as the Fmoc deprotection agent to
free the terminal amino group on the growing peptide chain on solid
support. The comparison experiment using regular piperidine was run
in parallel. The syntheses were performed on resin and all
procedures except the deprotection step using NPPOC-pip followed
those typical for peptide synthesis. HPLC and MALDI mass analysis
demonstrated that the correct sequence was obtained in high quality
using PGB-P NPPOC-pip and light irradiation to deprotect the Fmoc
amino protecting group (FIG. 12).
[0059] The present invention is not limited to the parallel
synthesis of individually addressable microarrays of
oligonucleotides or peptides. The method is of general use in solid
phase synthesis of molecular microarrays where complex synthesis
patterns are required at each step of chain extension synthesis.
One specific example is synthesis of oligosaccharide arrays
containing sequences of diverse carbohydrate units and branched
chains. According to the present invention, a PGA-P is applied to a
solid surface containing protected carbohydrates. Each carbohydrate
molecule contains several reactive OH groups, each of which is
protected by a protecting group. Each of these protecting groups
requires different deprotection conditions. A predetermined light
pattern is then projected onto the substrate surface. At the
illuminated sites, acid is produced and the protection groups
labile under this particular set of conditions are cleaved.
Deprotected OH groups are free to react with an incoming molecule.
At the dark sites, no acid is produced and, therefore, the acid
labile protecting groups of the carbohydrate molecules remain
intact. The substrate surface is then washed and subsequently
supplied with a monomer (a carbohydrate or oligosaccharide), which
adds only to the deprotected OH under conventional reaction
conditions to afford a glycosidic linkage (Wong et al., J. Am.
Chem. Soc. 120, 7137-7138 (1998)). These steps are repeated to give
oligosacchrides containing various glycosidic linkages at the first
deprotected OH position. Next, a PGB-P is applied to the substrate.
A second predetermined light pattern is then projected for the
second time onto the substrate surface. At the illuminated sites,
base is produced and the protection groups labile under this
condition are cleaved. Deprotected OH groups of the second batch
are free to react with an incoming molecule. At the dark sites, no
base is produced and, therefore, the base labile protecting groups
of the carbohydrate molecules remain intact. The substrate surface
is then washed and subsequently supplied with a second monomer,
which adds only to the second deprotected OH of the second time
under conventional reaction conditions to afford a glycosidic
linkage. These steps are repeated to give oligosacchrides
containing various glycosidic linkages at the second deprotected OH
position. Branched oligosacchrides are formed. In continued
synthesis, various PGR are used to achieve selective deprotection
of the OH protecting groups until desired oligosaccharide
microarrays are synthesized.
[0060] The present invention is not limited to the parallel
synthesis of individually addressable microarrays of
oligonucleotides, peptides, or oligosacchrides. In one embodiment
of the present invention, the selective deprotection of the amino
groups of the growing peptide chain using PGR at selected locations
is following by coupling of nucleotide phosphoramidite. The
microarray thus synthesized contains peptides and
peptide-oligonucleotide conjugates, which are library molecules
useful for many biochemical and biomedical assays. The syntheses of
molecular microarrays containing conjugates of
oligonucleotide-peptide, oligonucleotide-carbohydrate,
peptide-carbohydrate are possible to those skilled in the art.
[0061] The present invention is not limited to the parallel
synthesis of individually addressable microarrays of
oligonucleotides, peptides, oligosacchrides, or their conjugates.
In one embodiment of the present invention, the reaction surface is
derivatized with organic scaffold molecules, which share common
structures but each of which contain several protected functional
groups. Using a similar orthogonal, stepwise deprotection strategy,
different substituent groups are attached to the scaffold molecules
through multi-step reactions. These reactions result in molecular
libraries of combinatorial organic molecules, which are located in
a known address in the microarray and thus can be quickly assayed.
Examples of useful organic libraries include purine derivatives as
kinase inhibitors and triazine derivatives as factor Xa
inhibitors.
[0062] The present invention enables use of photogenerated reagents
in more cases than just deprotection reactions to achieve selective
reaction in accordance with a predetermined pattern without
changing the course of well-developed conventional chemistry.
Furthermore, the present invention is not limited to deprotection
reactions, photogenerated reactive compounds, such as alcohols
(ROH, R=alkyl, aryl and their substituted derivatives), can be used
as reagents for a variety of chemical conversions, such as
esterification, nucleophilic substitution and elimination
reactions. These reactions are important steps for fabrication of
molecular microarrays containing a variety of organic and
bioorganic molecules.
[0063] The applications of PGR-P in chemical reactions rely on
efficient generation and availability of the reagent required for
intended reactions, the compatibility of the photo-products forms
with the on-going reactions, and the availability of the PGR-P
compounds. One of skill in the art can apply the PGR reactions
described herein to other types of chemical conversions using
suitable PGR-P and reaction conditions. As important considerations
as in conventional chemical reactions, the chemical properties of
the PGR, such as chemical reactivity, solubility, acidity,
basicity, nucleophilicity, polarity, and molecular size, are also
determination factors for the success of chemical reactions using
PGR reagents.
EXAMPLES
Example I
Synthesis of 2-(2-nitrophenyl)propoxycarbonyl piperidine
(NPPOC-pip)
2-(2-nitrophenyl)propoxyl chloroformate (FIG. 4A, eq. 1)
[0064] 1-Ethyl-2-nitrobenzene (13.5 mL, 100 mmol) was dissolved in
dimethylsulfoxide (100 mL). Paraformaldehyde (4.50 g, 150 mmol) and
KOtBu (2.81 g, 25 mmol) in t-butyl alcohol (30 mL) were added and
the mixture was stirred at room temperature for 3 h. The solution
was washed with a molar solution of HCl (25 mL), followed by brine
(3.times.100 mL). All the aqueous layers were combined and
extracted with ethyl acetate (3.times.100 mL). The organic portion
was dried (MgSO.sub.4), filtered and the solvent was removed in
vacuo. The crude product was purified on a silica gel column.
Elution of the column with 20-30% ethyl acetate in hexanes gave
16.12 g (89 mmol, 89% yield) of 2-(2-nitrophenyl)propanol.
.sup.1H-NMR (600 MHz, DMSO-d.sub.6): .delta. 7.75 (d, J=8.10 Hz,
1H, Ar--H), 7.63 (t, J=7.62 Hz, 1H, Ar--H), 7.58 (d, J=7.80 Hz, 1H,
Ar--H), 7.42 (t, J=7.50, 1H, Ar--H), 4.73 (t, J=5.30 Hz, 1H, OH),
3.50 (m, 2H, CH.sub.2), 3.19 (m, 1H, CH), 1.21 (d, J=6.90 Hz, 3H,
CH.sub.3). TLC: 20% ethyl acetate in hexane, Rf=0.3.
[0065] A solution of 2-(2-nitrophenyl)propanol (16.12 g, 89 mmol)
and triethylamine (12.4 mL, 89 mmol) in anhydrous tetrahydrofuran
(THF) (96 mL) was added to a cold solution (0.degree. C.) of
diphosgene (10.7 mL, 89 mmol) in anhydrous THF (40 mL) over a
period of 15 min with stirring and under nitrogen. After 30 min the
cooling bath was removed and stirring was continued at room
temperature for 3 h. The mixture was filtered and washed with THF.
The solvent was removed in vacuo to give 28.20 g of
2-(2-nitrophenyl)propyl chloroformate as light brown oil that was
directly used for the next reaction step. TLC: 20% ethyl acetate in
hexanes, Rf=0.66.
2-(2-nitrophenyl)propoxycarbonyl piperidine (FIG. 4A, eq. 3,
R=101)
[0066] A solution of piperidine (22.8 mL, 230 mmol) in anhydrous
THF (50 mL) was added dropwise to a solution of
2-(2-nitrophenyl)propyl chloroformate (28.20 g) in anhydrous THF
(100 mL). The reaction mixture was then brought to reflux for 3 h
and stirred at room temperature overnight. The solvent was
evaporated to afford light brown oil. The mixture was diluted with
ether (100 mL) and water (100 mL) was added. The organic phase was
separated and the aqueous phase was re-extracted with ether
(3.times.50 mL). The organic extracts were combined and dried over
MgSO.sub.4, filtered, and the solvent was removed in vacuo. The
residue was purified on a silica gel column. Elution of the column
with 20% ethyl acetate in hexanes gave 16.54 g (56.6 mmol, 63.6%
yield, 56.6% total yield) of 2-(2-nitrophenyl)propoxycarbonyl
piperidine. .sup.1H-NMR (600 MHz, DMF-d.sub.7): .delta. 7.88 (d,
J=8.1 Hz, 1H, Ar--H), 7.74 (m, 2H, Ar--H), 7.53 (t, J=7.1 Hz, 1H,
Ar--H), 4.23 (m, 2H, CH.sub.2), 3.54 (m, 1H, CH), 3.24 (m, 4H,
CH.sub.2), 1.50 (m, 2H, CH.sub.2), 1.35 (m, 7H, CH.sub.2 and
CH.sub.3). .sup.13C-NMR (150 MHz, DMF-d.sub.7): .delta. 155.09
(OCOR), 151.50 (C ipso to NO.sub.2), 137.90 (C ipso to
CH(CH.sub.3)CH.sub.2OCOR), 133.49 (C para to NO.sub.2), 129.31 (C
para to CH(CH.sub.3)CH.sub.2OCOR), 128.44 (C ortho to
CH(CH.sub.3)CH.sub.2OCOR), 124.35 (C ortho to NO.sub.2), 69.45
(CH.sub.2OCOR), 45.08 (C.alpha. to ring N), 34.26 (CH), 26.08
(C.beta. to ring N), 24.69 (C.gamma. to ring N), 17.91 (CH.sub.3).
TLC: 20% ethyl acetate in hexanes, R.sub.f=0.4. Mass analysis
(MALDI-TOF): calculated for C.sub.15H.sub.21N.sub.2O.sub.4 293.34,
found 293.24.
Example II
2-(2-nitrophenyl)propoxycarbonyl hydrazine (FIG. 4A, eq. 3, R=102)
(NPPOC-Hz)
[0067] A solution of 2-(2-nitrophenyl)propyl chloroformate (6.0 g,
24.6 mmol) in methylene chloride (20 mL) was added dropwise to a
solution of hydrazine (3.0 mL, 98 mmol) in methylene chloride (50
mL) over a period of 30 min. The reaction mixture was stirred at
room temperature for an additional 15 min. The solvent was
evaporated to afford light brown oil. The residue was purified on a
silica gel column. Elution of the column with 20% ethyl acetate in
hexanes gave 3.35 g (14 mmol, 57% yield) of
2-(2-nitrophenyl)propoxycarbonyl hydrazine. .sup.1H-NMR (600 MHz,
DMSO-d.sub.6): .delta. 8.10 (s, 2H, CONH), 7.82 (d, J=7.5 Hz, 1H,
Ar--H), 7.67 (m, 2H, Ar--H), 7.47 (m, 1H, Ar--H), 4.15 (d, J=7.2
Hz, 2H, CH.sub.2), 3.9 (s, 2H, NH.sub.2), 3.39 (m, 1H, CH), 1.25
(d, J=6.9 Hz, 3H, CH.sub.3). .sup.13C-NMR (150 MHz, DMSO-d.sub.6):
.delta. 157.99 (OCOR), 150.00 (C ipso to NO.sub.2), 136.72 (C ipso
to CH(CH.sub.3)CH.sub.2OCOR), 132.86 (C para to NO.sub.2), 128.55
(C para to CH(CH.sub.3)CH.sub.2OCOR), 127.69 (C ortho to
CH(CH.sub.3)CH.sub.2OCOR), 123.68 (C ortho to NO.sub.2), 67.49
(CH.sub.2OCOR), 33.36 (CH), 17.93 (CH.sub.3). Mass analysis
(MALDI-TOF): calculated for C.sub.10H.sub.13N.sub.3O.sub.4 239.23,
found 239.20 (C.sub.10H.sub.13N.sub.3O.sub.4Na 262.18 is the major
peak). TLC: 5% methanol in chloroform, R.sub.f=0.5.
Example III
Di-(2-(2-nitrophenyl)propoxycarbonyl)hydrazine
[0068] A solution of hydrazine (0.32 mL, 10.25 mmol) in DCM (20 mL)
was added dropwise to a solution of 2-(2-nitrophenyl)propyl
chloroformate (5.0 g, 20 mmol) in methylene chloride (25 mL) over a
period of 30 min. The reaction mixture was stirred at room
temperature for an additional 15 min. The solvent was evaporated
and the residue was purified on a silica gel column. Elution of the
column with 20% ethyl acetate in hexanes gave 1.46 g (3.26 mmol,
32% yield) of di-(2-(2-nitrophenyl)propoxycarbonyl) hydrazine.
.sup.1H-NMR (300 MHz, DMSO-d.sub.6): .delta. 9.06-8.73 (d, 1H,
CONH), 7.84 (d, J=7.8 Hz, 1H, Ar--H), 7.63 (m, 2H, Ar--H), 7.48 (m,
1H, Ar--H), 4.20 (m, 2H, CH.sub.2), 3.39 (m, 1H, CH), 1.26 (d,
J=6.9 Hz, 3H, CH.sub.3). .sup.13C-NMR (75 MHz, DMSO-d.sub.6):
.delta. 156.19 (OCOR), 149.85 (C ipso to NO.sub.2), 136.53 (C ipso
to CH(CH.sub.3)CH.sub.2OCOR), 132.91 (C para to NO.sub.2), 128.52
(C para to CH(CH.sub.3)CH.sub.2OCOR), 127.76 (C ortho to
CH(CH.sub.3)CH.sub.2OCOR), 123.77 (C ortho to NO.sub.2), 67.86
(CH.sub.2OCOR), 33.30 (CH), 17.99 (CH.sub.3). Mass analysis
(MALDI-TOF): calculated for C.sub.20H.sub.22N.sub.4O.sub.8 446.42,
found 446.24 (C.sub.20H.sub.22N.sub.4O.sub.8Na 469.38 is the major
peak). TLC: 5% methanol in chloroform, R.sub.f=0.7.
Example IV
2-(2-nitrophenyl)propoxycarbonyl thiophenol (FIG. 4A, eq. 3,
R=104)
[0069] A solution of thiophenol (2.5 mL, 24.6 mmol) in anhydrous
THF (10 mL) was added dropwise to a solution of 2 (4 g) in
anhydrous THF (20 mL). The reaction mixture was then brought to
reflux for 6 h and stirred at room temperature overnight. The
solvent was evaporated to afford light yellow oil. The mixture was
diluted with ether (20 mL) and water (20 mL) was added. The organic
phase was separated and the aqueous phase was re-extracted with
ether (3.times.10 mL). The organic extracts were combined and dried
over MgSO.sub.4, filtered, and the solvent was removed in vacuo.
The residue was purified on a silica gel column. Elution of the
column with 20% ethyl acetate in hexanes gave 3.2 g (10.3 mmol,
42.0% yield,) of 2-(2-nitrophenyl)propoxycarbonyl thiophenol.
.sup.1H-NMR (300 MHz, CDCl.sub.3): .delta. 7.80 (d, J=6.9 Hz, 1H,
Ar--H), 7.47 (m, 8H, Ar--H), 4.41 (d, J=6.0 Hz, 2H, CH.sub.2), 3.72
(m, 1H, CH), 1.35 (d, 6.3 Hz, 3H, CH.sub.3). .sup.13C-NMR (75 MHz,
CDCl.sub.3): .delta. 169.71 (OCOR), 150.27 (C ipso to NO.sub.2),
136.88 (C ipso to CH(CH.sub.3)CH.sub.2OCOR), 135.04 (C para to
NO.sub.2), 132.88, 129.80, 129.33, 128.54, 128.18, 127.63, 124.49,
71.25 (CH.sub.2OCOR), 33.42 (CH), 17.72 (CH.sub.3).
Example V
Photometric Analysis of the Photoreaction of NPPOC-pip
[0070] This experiment demonstrates efficient generation of the
base piperidine upon light irradiation of a PGB-P as monitored by
increased UV absorbance value of the dye and pH indicator
fluorescein as a function of light irradiation time.
[0071] Fluorescein was purified in the lactone form as follows: the
dye was dissolved in dilute aqueous NaOH, filtered, precipitated by
adding dilute HCl, and dried under vacuum overnight. A stock
solution of fluorescein (12 .mu.M) in distilled DMF was prepared.
To calibrate the absorption of fluorescein, different amounts of
piperidine in DMF were added to 0.5 mL of the fluorescein solution
in a 1 cm quartz cuvette. After mixing, the UV-Vis absorption
spectra of the mixture were recorded. The increase of absorbance at
521 nm was correlated to the amount of piperidine added (after
volume correction calculations). 2-(2-nitrophenyl)propoxycarbonyl
piperidine (5.84 mg, 20 mM) in 1 mL DMF was prepared and irradiated
at 365 nm using a collimated light source (20 mW, Oriel, Stanford,
Calif.). Aliquots (10 to 20 .mu.L) of the irradiated sample were
added to fresh fluorescein solution (0.5 mL, 12 .mu.M) and to DMF
(0.5 mL). Absorbance at 521 nm was recorded (aliquots of the
non-irradiated photogenerated base mixture in DMF was used to
verify that absorbance of the photoproducts at 521 nm was
negligible) and correlated to the amount of piperidine produced
upon irradiation. Measurements for calibration and irradiated
samples were carried out the same day and repeated three times.
[0072] In FIG. 7 (curve 3), the estimated concentration of
piperidine produced upon increasing irradiation time is plotted.
The formation of piperidine under the conditions used follows a
first order kinetics relationship and the apparent rate constant
for formation of piperidine derived is 3.0.times.10.sup.-3.+-.0.1
s.sup.-1.
Example VI
NMR Experiments of the Photoreaction of NPPOC-Hz
[0073] A Bruker Avance 600 MHz NMR instrument was used for data
acquisition. Samples of 2-(2-nitrophenyl)propoxycarbonyl hydrazine
(23.9 mg, 100 (mot, 200 mM) (FIG. 1A) were prepared in 0.5 mL of
N,N-dimethylformamide-d.sub.7, transferred into 5 mm NMR tubes, and
protected from light. Typically, at the beginning of an experiment,
a sample was placed in the detection probe in the NMR instrument
and a spectrum was immediately recorded. The sample was removed
from the instrument and irradiated carried directly with a light
beam (350-450 nm) covering the entire surface of the sample for a
fixed duration of time. After irradiation, the sample was quickly
placed into the NMR detection probe again and one-dimensional
proton NMR spectrum was immediately recorded within 1 min following
the end of irradiation. A single scan was recorded with a time
domain data size of 16,384 points and a spectral width of 5495 Hz.
Chemical shifts were from the calibration of DMF-d.sub.7 for the
residual HC peak at 8.01 ppm (.sup.1H). The rest of the NMR peaks
were integrated used 8.01 ppm peak as the reference. The following
set of peaks were assigned to 2-(2-nitrophenyl)propene (FIG. 6, 2),
appearing progressively upon light irradiation. .sup.1H-NMR (300
MHz, DMF-d.sub.7): .delta. 7.95 (d, J=7.10 Hz, 1H, Ar--H), 7.72 (t,
J=7.45 Hz, 1H, Ar--H), 7.59 (t, J=7.80 Hz, 1H, Ar--H), 7.50 (d,
J=7.81 Hz, 1H, Ar--H), 5.20 (s, 1H, CH), 4.92 (s, 1H, CH), 2.08 (s,
3H, CH.sub.3). The appearance of 2-methyl N-hydroxyoxindole (FIG.
6, 4) was discernible. The markers used for the detection were
.delta. 1.32 (CH.sub.3) for 2-(2-nitrophenyl)propoxycarbonyl
hydrazine .delta. 4.92 (terminal ethylene CH.sub.2) for
2-(2-nitrophenyl)propene, and .delta. 2.29 (CH.sub.3) for 2-methyl
N-hydroxyoxindole. These results were plotted in FIG. 9, suggesting
NPPOC-Hz photolysis undergoes a mechanism similar to that of
NPPOC-pip with intramolecular hydrogen abstraction, followed by
.beta.-elimination and decarboxylation to give hydrazine and
2-(2-nitrophenyl)propene.
Example VII
Stability Test of Fmoc and ivDde Protected Amino Acid
[0074] Light Irradiation without the Presence of PGR-P.
[0075] A sample of Fmoc-Lys(ivDde)-OH (5.74 mg, 10 .mu.mol) in 0.5
mL DMF-d.sub.7 was placed in the reaction vessel usually used for
peptide synthesis using PGR deprotection. The sample was then
irradiated for 30 min (350-450 nm, 80 mW/cm.sup.2 measured at 400
nm, or 365 nm, 20 mW/cm.sup.2 measured at 365 nm). The solution was
transferred to a NMR tube and analyzed. HPLC, mass NMR analysis
showed that the recovered compound was identical to the starting
material Fmoc-Lys(ivDde)-OH. HPLC: 1 peak Rt=13.06 min. .sup.1H NMR
(300 MHz, DMF-d.sub.7): .delta. 13.81 (s, 1H, .epsilon.NH),
(7.94-7.32 (m, 8H, Fmoc ArH), 7.63 (d, 1H, .alpha.NH), 4.28 (m, 3H,
Lys .alpha.CH, Fmoc CH.sub.2), 4.18 (m, 1H, Fmoc CH), 3.57 (q,
J.sub.1=5.4 Hz, J.sub.2=6.6 Hz, 2H, .epsilon.CH.sub.2), 3.07 (m,
2H, ivDde CH.sub.2CH), 2.29 (s, 4H, ivDde CH.sub.2), 1.92 (m, 2H,
.beta.CH.sub.2), 1.83 (m, 1H, ivDde CH), 1.71 (m, 2H,
.delta.CH.sub.2), 1.62 (m, 2H, .gamma.CH.sub.2), 0.96-0.94 (s, 12H,
CH.sub.3). Mass analysis (MALDI-TOF): calculated for
Fmoc-Lys(ivDde)-OH 574.70, found 575.00.
NPPOC-Hz Mixing with Lys(ivDde) but without Light Irradiation.
[0076] To Fmoc-Lys(ivDde)-OH (28.7 mg, 50 .mu.mol) was added
2-(2-nitrophenyl)propoxycarbonyl hydrazine (35.8 mg, 150 .mu.mol)
in 0.5 mL DMF-d.sub.7. The mixture was agitated for 3 h in dark.
The and .sup.13C NMR spectra of the reaction solution recorded
before and after the treatment did not show any change in chemical
shifts.
NPPOC-Hz Mixing with Lys(ivDde)-Resin but without Light
Irradiation.
[0077] To Fmoc-Lys(ivDde)-resin (10 mg) was added
2-(2-nitrophenyl)propoxycarbonyl hydrazine (95.6 mg, 400 .mu.mol,
200 mM) in 2 mL of DMF. The mixture was shaken for 3 h in a dark
room. The resin was washed with DMF (5.times.1 mL), 10% DIPEA in
DMF (5.times.1 mL), and DCM (5.times.1 mL). The peptide was then
cleaved from the resin. HPLC: 1 peak Rt=12.98 min (reference
compound, Rt=13.06 min), NMR identical to Fmoc-Lys(ivDde). Mass
analysis (MALDI-TOF): calculated for Fmoc-Lys(ivDde)-OH 574.70,
found 575.07.
NPPOC-Hz Mixing with Phe-Lys(ivDde) but without Light
Irradiation.
[0078] To Ac-Phe-Lys(ivDde)-resin (10 mg) was added
2-(2-nitrophenyl)propoxycarbonyl hydrazine (95.6 mg, 400 .mu.mol,
200 mM) in 2 mL DMF. The mixture was shaken for 3 h in a dark room.
The resin was washed with DMF (5.times.1 mL), 10% DIPEA in DMF
(5.times.1 mL), and DCM (5.times.1 mL). The peptide was then
cleaved from the resin as described. HPLC, mass NMR analysis showed
that the recovered compound was identical to Ac-Phe-Lys(ivDde)-OH.
HPLC: 1 peak Rt=8.53 min, identical to the reference
Ac-Phe-Lys(ivDde)-OH. NMR identical to Ac-Phe-Lys(ivDde)-OH. Mass
analysis (MALDI-TOF): calculated for Ac-Phe-Lys(ivDde)-OH 541.7,
found 541.6.
Example VIII
Deprotection of Amino Acids Using PGB
[0079] To Fmoc-Tyr(tBu)-Wang resin (5 mg, 5 .mu.mol) was added
2-(2-nitrophenyl)propoxycarbonyl piperidine in 2 mL DMF (58.4 mg,
200 .mu.mol, 100 mM). In one reaction set, the solution was left in
the dark for at least 30 min and washed with DMF. In a second set,
the resin was washed with DMF, immersed in 2 mL DMF, and UV
irradiated (365 nm) for 15 min. Both reaction products gave a
negative ninhydrin test. For both reactions, after washing with DMF
and DCM, the resin was treated with TFA/water (95:5) for 3 h for
deprotection of tBu and the molecule was cleaved from resin. The
products were analyzed by HPLC.
[0080] In a third set, the reaction solution was UV illuminated
(365 nm) for 15 min. The amino acid on resin was washed with DMF,
dioxane/water (2:1), DMF, and DCM. Positive ninhydrin test was
observed. The resin was then treated with Fmoc-Leu-OH (14.1 mg, 40
.mu.mol) using coupling reagents DIC (6.2 .mu.L, 40 .mu.mol) and
HOBt (6.1 mg, 40 mop in DMF/DCM for 1 h or repeated until a
negative ninhydrin test was observed. After washing with DMF and
DCM, the resin was treated with TFA/water (95:5) for 3 h for
deprotection of tBu and the peptide was cleaved from resin. The
product was examined using HPLC.
[0081] HPLC elution solvents were water and acetonitrile containing
0.1% and 0.08% TFA, respectively. The gradients used were 15 to 80%
of water in acetonitrile in 13 min. The Fmoc-Tyr-OH and
Fmoc-Leu-Tyr-OH synthesized on resin using conventional piperidine
deprotection (20% in DMF, 1.times.2 min, 1.times.15 min) were used
as the reference compounds. HPLC retention times were 9.2 min for
Fmoc-Tyr(tBu)-OH, 7.7 min for Fmoc-Leu-Tyr-OH, and 6.7 min for
Fmoc-Tyr-OH. The correct identity of the PGB deprotection products
was also confirmed by co-injection of an equal amount of the
product and the reference compound Fmoc-Leu-Tyr-OH, confirming
identical HPLC retention times and UV absorption profile. Upon
light irradiation, the observed deprotection efficiency (% of HPLC
peak integration) is 98%. In the absence of light, no deprotection
was detected.
Example IX
Peptide Synthesis Using NPPOC-pip and NPPOC-Hz
Fmoc-Lys(ivDde)-resin.
[0082] Fmoc-Lys(ivDde)-OH (29 mg, 50 .mu.mol) was attached to
2-chlorotrityl chloride on Wang resin (Novabiochem, La Jolla,
Calif.) (50 mg, 41 .mu.mol) by mixing the amino acid, the resin,
and diisopropylamine (DIPEA, 35 .mu.L, 200 .mu.mol) and stirring
for 30 min. The resin was then washed with DCM and treated with
CH.sub.3OH/DCM/DIPEA (8:1:1) for 10 min to cap the unreacted trityl
chloride sites.
Ac-Phe-Lys(ivDde)-resin.
[0083] To the Fmoc-Lys(ivDde)-resin (10 mg, .about.8 .mu.mol) was
added 2-(2-nitrophenyl)propoxycarbonyl piperidine (58.4 mg, 200
.mu.mol, 100 mM) in 2 mL DMF. A standard TLC visualization UV lamp
(350-450 nm) was pointed towards the reaction vessel and turned on
for 10 min. The resin was then extensively washed with DMF,
dioxane/water (2:1), DMF, and DCM. After washing, a ninhydrin test
was performed to confirm the presence of free amino groups.
[0084] To the deprotected Lys-resin sample was added Fmoc-Phe (8.8
mg, 33.2 .mu.mol) in DCM/DMF and 1,3-diisopropylcarbodiimide (DIC)
(3 .mu.L, 20 .mu.mol. The coupling reaction was continued for 2 h
and ninhydrin tests gave negative amino group readings. The
Fmoc-Phe-Lys(ivDde) on resin was then treated with photogenerated
piperidine as described above. Upon completion of the reaction, the
resin was washed with DCM/DMF. Capping of the
NH.sub.2-Phe-Lys(ivDde)-resin was carried out for 1 h with acetic
anhydride (470 .mu.L, 5 mmol) and TEA (700 .mu.L, 5 mmol) in 1.5 mL
DMF to give Ac-Phe-Lys(ivDde)-resin.
[0085] In a separate control experiment, regular piperidine
deprotection was used. To the Fmoc-Lys(ivDde)-resin (10 mg,
.about.8 .mu.mol) was added piperidine in DMF (20%, 2 mL). The
mixture was shaken for 1 min and drained. Another 2 mL of 20%
piperidine was added and the mixture was shaken for 15 min. The
resin was then washed, coupled with Fmoc-Phe as described above to
give Ac-Phe-Lys(ivDde)-resin.
Ac-Phe-Lys-resin.
[0086] To Ac-Phe-Lys(ivDde)-resin (10 mg) was added
2-(2-nitrophenyl)propoxycarbonyl hydrazine (95.6 mg, 400 .mu.mol,
200 mM) in 2 mL DMF. The UV lamp (350-450 nm) was directly pointed
towards the reaction vessel and turned on for 10 min. The resin was
then washed with DMF and the deprotection reaction was monitored by
ninhydrin test and repeated as necessary. Finally, the resin was
washed with DMF (5.times.1 mL), 10% DIPEA in DMF (5.times.1 mL),
and DCM (5.times.1 mL).
[0087] In a separate control experiment, to Ac-Phe-Lys(ivDde)-resin
(10 mg) was added hydrazine monohydrate (40 .mu.L, 824 .mu.mol, 412
mM) in 2 mL DMF. After 5 min agitation, the solution removed by
suction and a fresh 2% hydrazine monohydrate solution was added for
an additional 7 min. The resin was washed with DMF (5.times.1 mL),
10% DIPEA in DMF (5.times.1 mL), and DCM (5.times.1 mL).
Ac-Phe-Lys-OH and Ac-Phe-Lys(ivDde)-OH.
[0088] Cleavage of the synthesized peptides from resin was
accomplished using 1% TFA in DCM (twice resin bed volume) for
.about.2 min. For each sample, aliquots were dried on a speed-vac
and directly used for HPLC or MALDI-TOF analysis. HPLC Column was
reverse phase (Waters RP-C18, 8C1810.mu.). Elute solvents were
water and acetonitrile containing 0.1% or 0.08% TFA, respectively.
The gradient used was 15 to 95% of water in acetonitrile in 16 min
with a flow rate of 3 mL/min. Ac-Phe-Lys(ivDde)-OH by
photogenerated piperidine synthesis, Rt=8.55 min; piperidine
synthesis, Rt=8.57 min. Ac-Phe-Lys-OH, by photogenerated piperidine
and hydrazine synthesis, Rt=3.55 min; regular synthesis (piperidine
and hydrazine) Rt=3.54 min. .sup.1H NMR (300 MHz, DMSO d.sub.6):
Ac-Phe-Lys(ivDde)-OH synthesized using either photogenerated
piperidine or piperidine gave identical NMR spectra; .delta. 13.60
(s, 1H, NH), 12.62 (br s, COOH), 8.27 (d, J=8.1 Hz, 1H, CONH), 8.06
(d, J=7.8 Hz, 1H, CONH), 7.22 (m, 5H, ArH), 4.51 (m, 1H,
.alpha.CH), 4.18 (m, 1H, .alpha.CH), 3.38 (m, Phe .beta.CH.sub.2,
Lys .epsilon.CH.sub.2), 3.00 (m, 2H, ivDde CH.sub.2), 2.25 (s, 4H,
ivDde CH.sub.2), 1.80 (m, .beta.CH.sub.2), 1.72 (s, CH.sub.3), 1.58
(m, ivDde CH, Lys .delta.CH.sub.2), 1.40 (m, 2H, .gamma.CH.sub.2),
0.92 (s, 6H, CH.sub.3), 0.88 (s, 6H, CH.sub.3). Ac-Phe-Lys-OH (both
dipeptides synthesized using either photogenerated piperidine and
hydrazine versus piperidine and hydrazine gave identical NMR
spectra), .delta. 12.67 (br s, COOH), 8.31 (d, J=7.8 Hz, 1H, CONH),
8.09 (d, J=7.8 Hz, 1H, CONH), 7.65 (s, NH.sub.3.sup.+), 7.22 (m,
5H, ArH), 4.51 (m, 1H, .alpha.CH), 4.18 (m, 1H, .alpha.CH), 3.34
(m, 1H, Phe .beta.CH), 2.98 (m, 1H, Phe .beta.CH), 2.74 (m, 2H,
.epsilon.CH.sub.2), 1.72 (s, 3H, CH.sub.3), 1.58 (m,
.beta.CH.sub.2), 1.55 (m, .delta.CH.sub.2), 1.34 (m,
.gamma.CH.sub.2). Mass analysis (MALDI-TOF): calculated for
Ac-Phe-Lys(ivDde)-OH 541.7, found 541.9 for that by photogenerated
piperidine synthesis and found 541.8 for that by piperidine;
calculated for Ac-Phe-Lys-OH 335.4, found 335.5 for that by
photogenerated piperidine and hydrazine, found 335.5 for that by
piperidine and hydrazine.
Example X
Tyr-Gly-Gly-Phe-Leu-OH synthesis using PGB
[0089] Wang resin (30 mg, 30 .mu.mol) in DMF/DCM (v/v 1/1, unless
otherwise specified, 1 mL) was treated with Fmoc-Leu (180 .mu.mol)
in the presence of coupling reagents DIC (14 .mu.L, 90 .mu.mol) and
DMAP (0.37 mg, 3 .mu.mol) for 2 h. The Fmoc-Leu-resin was washed
thoroughly with DMF and DCM, dried under vacuum, and stored in a
dry place. To this resin (10 mg, 10 .mu.mol) was added
2-(2-nitrophenyl)propoxycarbonyl piperidine in 2 mL of DMF (58.4
mg, 200 .mu.mol, 100 mM). The UV lamp (365 nm) was directly pointed
towards the reaction vessel and turned on for 15 min. The resin was
extensively washed with DMF, dioxane/water (2:1), DMF, and DCM.
After washing, a ninhydrin test was performed to confirm the
presence of free amino groups.
[0090] In a separate experiment, to Fmoc-Leu-resin was added
piperidine in DCM (20%, 2 mL). The mixture was shaken for 1 min and
drained. Another 2 mL of 20% piperidine was added and this time the
mixture was shaken for 15 min. The resin was then washed as
described above.
[0091] To the Fmoc-Leu resin was added Fmoc-Phe (40 mop in DCM/DMF
(1 mL) and DIC (3 .mu.L, 20 .mu.mol). The coupling reaction was
continued for 2 h and repeated if a ninhydrin test gave positive
amino group reading. The resin was then washed with DCM/DMF. The
steps of coupling and deprotection using either photogenerated
piperidine or piperidine were repeated until the completion of the
pentapeptide synthesis. The coupling steps were carried out as
described using an appropriate Fmoc-amino acid.
Tyr(tBu)-Gly-Gly-Phe-Leu-resin synthesized using either
photogenerated piperidine or piperidine were treated with TFA/water
(95:5) for 3 h for removal of the tBu group and cleavage from
resin. The collected samples were injected on to HPLC and the
retention times for Tyr-Gly-Gly-Phe-Leu-OH were 9.19 or 9.15 min,
respectively (FIG. 12). Synthesis yields were calculated from the
integration of HPLC peaks monitored at 214 nm and were 89% and 74%
(stepwise yields were 93 and 97%) for the synthesis using either
photogenerated piperidine or piperidine, respectively. Mass
analysis (MALDI-TOF, external calibration on Angiotensin II 1046.54
g/mol): calculated for YGGFL C.sub.28H.sub.37N.sub.5O.sub.7 555.62,
found 555.65 (synthesized using photogenerated piperidine) and
556.11 (synthesized using piperidine). Mass analysis of the crude
product also indicates the presence of Phe-Leu-OH (278.37),
Gly-Gly-Phe-Leu-OH (392.44), and Tyr(tBu)-Gly-Gly-Phe-Leu-OH
(613.21) in both of the synthesis using either photogenerated
piperidine or piperidine.
Example XI
Synthesis of 2-(2-nitrophenyl)propyl trifluoroacetate (FIG. 4A; eq.
4, R=105a)
[0092] To a solution of 2-(2-nitrophenyl)propanol (0.219 g, 1.20
mmol) and triethylamine (0.33 mL, 2.4 mmol) in 3 mL THF,
trifluoroacetic anhydride (0.27 mL, 1.92 mmol) was added slowly in
drops. The reaction was monitored by TLC using 2:7 ethyl
acetate:hexane. After 3.5 h the reaction mixture was quenched with
water. It was then extracted with DCM and the organic layer was
washed with water and brine and then dried over anhydrous sodium
sulfate. On evaporating the organic layer 420 mg of crude product
was obtained. .sup.1H NMR (300 MHz, CDCl.sub.3) .delta. (ppm): 7.80
(d, 1H, Ar--H), 7.61 (t, 1H, Ar--H), 7.55-7.36 (m, 2H, Ar--H), 4.52
(d, 2H, CH.sub.2), 3.79 (q, 1H, CH), 1.41 (d, 3H, CH.sub.3).
.sup.1H NMR (300 MHz, DMF-d.sub.7): .delta. 7.85 (d, 1H, Ar--H),
7.68 (m, 2H, Ar--H), 7.47 (t, 1H, Ar--H), 4.62 (d, 2H, CH.sub.2),
3.63 (q, 1H, CH), 1.32 (d, 3H, CH.sub.3).
Example XII
Synthesis of 2-(2-nitrophenyl)propoxyl .beta.-cyanoethyl
diisopropyl phosphoramidite (NPPO-ppa)
[0093] To a solution of 2-(2-nitrophenyl)propanol (0.530 g, 2.91
mmol) and triethylamine (1.63 mL, 11.6 mmol) in 9 mL DCM,
2-cyanoethyl diisopropyl-chlorophosphoramidite (0.98 mL, 4.37 mmol)
was added slowly in drops. The reaction was monitored by TLC using
2:7 ethyl acetate:hexane. After 2 h the reaction mixture was cooled
in an ice bath and 4 mL triethylamine and 12 mL saturated
NaHCO.sub.3 in cold water were added. It was then extracted with
DCM and the organic layer was dried over anhydrous sodium sulfate.
On evaporating this solution crude product was obtained, which was
purified on silica gel column eluting with ethyl acetate:hexane
(1:2, 0.2% TEA) to obtain 0.418 g (37%) of NPPOC-ppa. The purified
product was dried under vacuum. .sup.1H NMR (300 MHz, DMSO-d.sub.6)
.delta. (ppm): 7.76 (m, 1H), 7.63 (t, 2H), 7.34 (m, 1H), 3.74-3.36
(m, 6H), 2.69-2.62 (m, 2H), 1.26-1.23 (m, 3H), 1.06-0.92 (m, 9H);
.sup.31P NMR (CDCl.sub.3) .delta. (ppm): 148.48, 148.41.
Example XIII
Synthesis of N-methylsulfonyloxynaphthalimide (FIG. 4B, R=107)
[0094] The compound N-hydroxy-1,8-naphthalimide (300 mg, 1.40 mmol)
and t-BuOK (166 mg, 1.40 mmol) were dissolved in dry THF (10 mL)
under N.sub.2. After the reaction mixture was stirred for 1 h at
r.t., the solvent was removed in vacuo to give 323 mg (1.37 mmol,
98% yield) of a red solid that was directly used for next reaction
step.
[0095] A solution of methanesulfonic acid (30 .mu.L, 0.41 mmol) in
anhydrous dimethoxymethane (150 .mu.L) was added to a cold solution
(-15.degree. C., dry ice/ethylenediol) of sodium
N-hydroxynaphthalimide (100 mg, 0.42 mmol) in anhydrous
dimethoxymethane (5 mL) over a period of 4 min with stirring and
under N.sub.2. After 15 min, the reaction mixture was allowed to
warm up to room temperature and the stirring was continued for 1 h.
DCM (50 mL) was added to the reaction mixture and the resulting
solution was washed with 2% aqueous sodium bicarbonate and water.
The organic portion was dried over Na.sub.2SO.sub.4 and filtered.
The solvent was removed in vacuo and 90 mg of a yellow powder was
obtained. Recrystallization of the product from DCM/hexane yielded
80 mg (0.28 mmol, 67% yield) of N-methanesulfonyloxynaphthalimide.
.sup.1H-NMR (300 MHz, DMSO-d.sub.6) .delta. 8.53 (d, J=7.5 Hz, 2H,
Ar--H), 8.32 (d, J=8.7 Hz, 2H, Ar--H), 7.78 (t, J=8.4 Hz, 2H,
Ar--H), 3.54 (s, 3H, CH.sub.3). TLC: 20% ethyl acetate in hexanes,
R.sub.f.sup.=0.2.
Example XIV
Synthesis of 2-(3,4-methylenedioxy-6-nitrophenyl)-propoxycarbonyl
piperidine (FIG. 4A, eq. 4, R=101)
##STR00013##
[0096] Preparation of 3,4-(methylenedioxy)-6-nitroacetophenone
[0097] To 3,4-(methylenedioxy)-acetophenone (2.70 g, 17.5 mmol) in
30 mL CH.sub.3NO.sub.2 at r.t. was added HNO.sub.3 (6.9 mL, 105
mmol) dropwise in 30 min. The solution was stirred for additional 2
h. The reaction mixture was carefully neutralized by the addition
of saturated aqueous NaHCO.sub.3 solution and then extracted with
DCM. The combined organic phase was dried overnight over anhydrous
Na.sub.2SO.sub.4. The solvent was removed in vacuo and the residue
was purified by silica gel chromatography (eluant: AcOEt/Hex, 1/2,
v/v) to afford 3,4-(methylenedioxy)-6-nitroacetophenone (2.80 g,
82%) as light yellow solid. .sup.1H-NMR (300 MHz, CDCl.sub.3):
.delta. 7.56 (s, 1H, Ar--H), 6.76 (s, 1H, Ar--H), 6.19 (s, 2H,
CH.sub.2), 2.50 (s, 3H, CH.sub.3). TLC: 33% ethyl acetate in
hexane, Rf=0.5.
##STR00014##
Preparation of 2-(3,4-methylenedioxy-6-nitrophenyl)propyl enol
methyl ether
[0098] BuLi (2.0 M in cyclohexane, 10 mL, 20 mmol) was added to 20
mL THF. The solution was stirred under nitrogen atmosphere at
-10.degree. C. To this solution was added
methoxymethyltriphenylphosphonium chloride (6.80 g, 20 mmol) in
four portions. After 15 min stirring, the nitrated ketone,
3,4-(methylenedioxy)-6-nitroacetophenone (2.10 g, 10 mmol) in THF
(20 mL) was added in drops for 30 min. The reaction was nearly
complete in 2 h (monitored by TLC, eluant: AcOEt/Hex, 1/7, v/v).
The crude reaction mixture was poured onto ice/water and THP was
evaporated. The residue was dissolved in DCM, the organic phase was
collected and dried over anhydrous Na.sub.2SO.sub.4 overnight, and
the solvent was evaporated in vacuo. Purification by silica gel
chromatography (eluant:AcOEt/Hexane, 10/90, v/v) provided
2-(3,4-methylenedioxy-6-nitrophenyl)-propyl enol methyl ether
(mixture of E,Z isomer, 1.30 g, 60%). .sup.1H-NMR (300 MHz,
CDCl.sub.3): .delta. 7.40 (s, 0.4H, Ar--H), 7.37 (s, 0.6H, Ar--H),
6.70 (s, 0.4H, Ar--H), 6.68 (s, 0.6H, Ar--H), 6.08 (s, 2H,
CH.sub.2), 5.96 (d, J=1.8 Hz, 0.6H, CH), 5.93 (d, J=1.8 Hz, 0.4H,
CH), 3.67 (s, 1.8H, CH.sub.3), 3.50 (s, 1.2H, CH.sub.3), 1.87 (d,
J=1.2 Hz, 1.2H, CH.sub.3), 1.85 (d, J=1.2 Hz, 1.8H, CH.sub.3). TLC:
12% ethyl acetate in hexanes, Rf=0.3.
##STR00015##
Preparation of 2-(3,4-methylenedioxy-6-nitrophenyl)propyl
aldehyde
[0099] 2-(3,4-methylenedioxy-6-nitrophenyl)propyl enol methyl ether
(1.29 g, 6 mmol) was dissolved in CH.sub.3CN/HCl (6 N, 1/1, v/v, 50
mL) and the solution was stirred for 1.5 h at r.t., and the mixture
was slowly poured into a solution saturated with NaHCO.sub.3. After
extraction with DCM, the organic phase was dried over anhydrous
MgSO.sub.4. The solvent was removed in vacuo and
2-(3,4-methylenedioxy-6-nitrophenyl)propyl aldehyde was obtained as
a yellow oil (0.89 g, 74%). .sup.1H-NMR (300 MHz, CDCl.sub.3):
.delta. 9.74 (s, 1H, CH), 7.54 (s, 1H, Ar--H), 6.70 (s, 1H, Ar--H),
6.13 (s, 2H, CH.sub.2), 4.32 (q, J=7.2 Hz, 1H, CH), 2.50 (d, J=7.2
Hz, 3H, CH.sub.3). TLC: 12% ethyl acetate in hexanes, Rf=0.2.
##STR00016##
Preparation of 2-(3,4-methylenedioxy-6-nitrophenyl)propanol
[0100] To crude 2-(3,4-methylenedioxy-6-nitrophenyl)propyl aldehyde
(1.23 g, 5.5 mmol) in anhydrous methanol (20 mL) was added
NaBH.sub.4 (250 mg, 6.6 mmol). The reaction was monitored by TLC
(eluent: AcOEt/Hex, 1/2, v/v) and complete after 1 h. The mixture
was poured into a saturated NH.sub.4CL aqueous solution and
extracted with DCM. The organic phase was dried over anhydrous
MgSO.sub.4 and the solvent was removed in vacuo. The residue was
purified using silica gel chromatography (eluant:
AcOEt/CH.sub.2Cl.sub.2, 1/99, v/v) and provided
2-(3,4-methylenedioxy-6-nitrophenyl)propanol (0.99 g, yield 80%).
.sup.1H-NMR (300 MHz, CDCl.sub.3): .delta. 7.31 (s, 1H, Ar--H),
6.88 (s, 1H, Ar--H), 6.07 (m, 2H, CH.sub.2), 3.75 (m, 2H,
CH.sub.2), 3.64 (m, 1H, CH), 1.77 (s, 1H, OH), 1.27 (d, 3H,
CH.sub.3). TLC: 33% ethyl acetate in hexanes, Rf=0.3.
##STR00017##
Preparation of 2-(3,4-methylenedioxy-6-nitrophenyl)propoxyl
chloroformate
[0101] To 2-(3,4-methylenedioxy-6-nitrophenyl)propanol (0.97 g, 4.3
mmol) and DIPEA (750 .mu.L, 4.3 mmol) in dry THF (40 mL) was added
to a cold solution (0.degree. C.) of diphosgene (520 .mu.L, 4.3
mmol) in dry TI-IF (40 mL) over a period of 25 min with stirring
and under nitrogen. The reaction solution was stirred for
additional 30 min and was allowed to warm up to r.t. slowly and
continued stirring for 3 h. The solvent was removed in vacuo to
give product as light colored oil (0.67 g, 48%). This crude product
was directly used in the next step reaction. TLC: 33% ethyl acetate
in hexane, Rf=0.7
##STR00018##
Preparation of 2-(3,4-methylenedioxy-6-nitrophenyl)propoxycarbonyl
piperidine
[0102] To 2-(3,4-methylenedioxy-6-nitrophenyl)propoxyl
chloroformate (650 mg, 2.3 mmol) in dry THF (30 mL) was dropwisely
added piperidine (800 .mu.L, 8.1 mmol) in dry THF (20 mL). The
reaction mixture was refluxed for 3 h and then stirred at r. t.
overnight. The solvent was evaporated and the residue was dissolved
in water and washed with ether four times. The organic extracts
were combined and dried over anhydrous Na.sub.2SO.sub.4. The
solvent was removed in vacuo and the residue was purified by silica
gel chromatography (eluant: AcOEt/Hex, 1/4, v/v). The collected
fraction provided
2-(3,4-methylenedioxy-6-nitrophenyl)propoxycarbonyl piperidine
(0.61 g, yield 79%). .sup.1H-NMR (600 MHz, CDCl.sub.3): .delta.
7.21 (s, 1H, Ar--H), 6.79 (s, 1H, Ar--H), 6.01 (s, 2H, CH.sub.2),
4.12 (m, 2H, CH.sub.2), 3.71 (m, 1H, CH), 3.23 (s, 4H, CH.sub.2),
1.47 (m, 2H, CH.sub.2), 1.38 (s, 4H, CH.sub.2), 1.22 (d, 3H, J=6.6
Hz, CH.sub.3). .sup.13C-NMR (150 MHz, CDCl.sub.3): .delta. 154.86
(OCOR), 151.50 (C ipso to NO.sub.2), 146.13 (C para to NO.sub.2),
143.89 (C para to CH(CH.sub.3)CH.sub.2OCOR), 134.59 (C ipso to
CH(CH.sub.3)CH.sub.2OCOR), 106.75 (C ortho to
CH(CH.sub.3)CH.sub.2OCOR), 105.02 (C ortho to NO.sub.2), 102.75
(OCH.sub.2O), 68.96 (CH.sub.2OCOR), 44.63 (C.alpha. to ring N),
33.45 (CH), 25.47 (C.beta. to ring N), 24.21 (C.gamma. to ring N),
17.78 (CH.sub.3). TLC: 33% ethyl acetate in hexanes, Rf=0.5.
* * * * *