Light-directed radial combinatorial chemistry: Orthogonal safety-catch protecting groups for the synthesis of small molecule microarrays

Article abstract of DOI:10.1021/ja044702q

We describe the development of photolabile protecting groups based on the 3,4,5-trimethoxyphenacyl group (TMP). Orthogonal safety-catches were created by introducing an acid-activatible dimethyl ketal (AA-TMP) and an oxidatively activatible 1,3-dithiane (

Full text of DOI:10.1021/ja044702q

Published on Web 12/04/2004
Light-Directed Radial Combinatorial Chemistry: Orthogonal Safety-Catch
Protecting Groups for the Synthesis of Small Molecule Microarrays
Alex Shaginian,† Madhusudan Patel,†,§ Mo-Huang Li,‡ Shane T. Flickinger,† Changhan Kim,‡
Franco Cerrina,‡ and Peter J. Belshaw*,†,|
Departments of Chemistry, Biochemistry, Electrical and Computer Engineering, and
Center for Nanotechnology, UniVersity of Wisconsin, Madison, Wisconsin 53706
Received September 2, 2004; E-mail: belshaw@chem.wisc.edu
Scheme 1. Orthogonal Safety-Catch Protecting Groups Based on
the Trimethoxyphenacyl Group
Methods for in situ light-directed synthesis have enabled the
production of linear polymers in spatial arrays, including peptides,1,2
oligocarbamates,3 oligonucleotides,4,5 and peptoids.6 The polymers
are assembled through iterative unmasking of reactive groups1,5 and
monomer coupling cycles. The locations of products in the array
are controlled by photolithography using physical masks, or more
flexibly, by light reflected from a digital micromirror device to
produce arrays with up to 786 432 features.7 The creation of small
molecule microarrays, by in situ synthesis8 or through the robotic
spotting of compound libraries, allows binding assays to be
conducted simultaneously on all members of the small molecule
array, greatly reducing the time and cost of high throughput screens.9
Although chemistries for the synthesis of linear polymers are well
developed, the synthesis of small molecule microarrays with radial
diversity requires chemistries that allow light-directed chemistry
to occur at multiple independent sites on a scaffold. The independent
orthogonal deprotection of photolabile protecting groups (PLPG)
has been achieved through the use of PLPGs that respond selectively
to light of differing wavelengths,10 although the reported selectivity
is not absolute and the number of independent groups that can be
developed may be limited by the broad absorption spectra of
photolabile protecting groups.
Scheme 2. Solution-Phase Derivatization of a Protected
Hydroxyproline Scaffold
Safety-catch (SC) PLPGs11 and linkers12 based on the benzoin13
PLPG have previously been developed to reduce light sensitivity
and improve the chemical stability of PLPGs used in syntheses.
Here we report the development of orthogonal safety-catch photo-
labile protecting groups allowing multiple reactive sites on a scaffold
to be independently photodeprotected. We chose to develop safety-
catches based on the phenacyl14 PLPG since masking the carbonyl
renders these groups photoinert. Two SC-PLPGs were developed.
In the first, the ketone of a 3,4,5-trimethoxyphenacyl group (TMP)
is masked as a dimethyl ketal, producing an acid activatible
safety-catch (AA-TMP); in the second, the ketone is masked as a
1,3-dithiane, producing an oxidatively activatible safety-catch
(OA-TMP). These can be sequentially activated upon conversion
of the dimethyl ketal or the dithiane to a photolabile ketone with
aqueous acid or periodic acid, respectively (Scheme 1). These two
SC-PLPGs, together with the directly photolabile TMP protecting
group, provide three independent protecting groups that can be used
for light-directed radial combinatorial chemistry.
To determine optimal activation and photolysis conditions for
these protecting groups, we synthesized several TMP esters,
carbonates, and carbamates and investigated conditions for activa-
tion and photolysis in solution (data not shown). These experiments
revealed that the photolysis of TMP protecting groups in the
presence of 15% 1,4-cyclohexadiene (CHD) to scavenge free
radicals gave near quantitative yields in MeCN. Additionally, 0.1%
thioxanthone could be added as a triplet sensitizer to allow
deprotection at long wavelengths (350-420 nm) in identical yield.15
Triplet sensitization by thioxanthone required the presence of the
3,4,5-trimethoxy substituents on the phenacyl group presumably
† Department of Chemistry.
| Department of Biochemistry.
‡ Department of Electrical and Computer Engineering.
§ Center for Nanotechnology.
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J. AM. CHEM. SOC. 2004, 126, 16704-16705
10.1021/ja044702q CCC: $27.50 © 2004 American Chemical Society

C O M M U N I C A T I O N S
2, and acetylated with acetic anhydride. Array elements 3 and 4
were then photolyzed and derivatized with Alexa-Fluor (488) NHS
ester (Molecular Probes) to generate amides. The slide was
incubated with the streptavidin-Texas Red conjugate (Amersham
Biosciences) and scanned to reveal the positions of biotin and
Alexa-Fluor functionalities (Figure 1). The image reveals the
anticipated pattern of fluorescence from the intended array elements.
We have demonstrated the utility of SC-PLPGs to enable the
light-directed synthesis of a small molecule microarray with radial
diversity elements. The incorporation of diversity elements at
branching points on scaffold molecules will greatly expand the
scope of materials that can be synthesized in a light-directed manner.
We expect that the synthesis of small molecule microarrays using
the maskless array synthesizer will significantly reduce the costs
of library construction and screening and enable the identification
of small molecules with useful biological activities. Additionally,
this chemistry could be applied to the in situ synthesis of sensor
arrays.
Acknowledgment. We thank the Burroughs Wellcome Fund,
the W. M. Keck Foundation, DARPA (DAAD 19-02-2-0026), and
the NIH (NIHGR 1R01HG003275) for financial support of this
work.
Figure 1. Loading protected hydroxyproline onto glass slide (top),
structures of intended array elements (bottom), and fluorescence image of
the microarray (inset with 500 µm scalebar).
Supporting Information Available: Synthetic protocols and
characterization of compounds 1-9. This material is available free of
charge via the Internet at http://pubs.acs.org.
to sufficiently lower the energy of the triplet state. The dimethyl
ketal was hydrolyzed in quantitative yield by 5% trifluoroacetic
acid (TFA) in 50% aqueous MeCN, and the dithiane was oxidatively
cleaved in near quantitative yield by H5IO6 in THF.
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